PLoS Computational Biology, Volume 18

Volume 18, Number 1, January 2022

Education Articles

• 
  Stevie A. Bain, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas R. Meagher, Michael G. Ritchie, Edward W. J. Wallace, Daniel Barker:
  Bringing bioinformatics to schools with the 4273pi project.
• 
  Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco:
  Project-based learning course on metabolic network modelling in computational systems biology.

Perspectives

• 
  Elizabeth Dupre, Chris Holdgraf, Agah Karakuzu, Loïc Tetrel, Pierre Bellec, Nikola Stikov, Jean-Baptiste Poline:
  Beyond advertising: New infrastructures for publishing integrated research objects.
• 
  Sheila M. Saia, Natalie G. Nelson, Sierra N. Young, Stanton Parham, Micah Vandegrift:
  Ten simple rules for researchers who want to develop web apps.

Research Articles

• 
  George Courcoubetis, Manasi S. Gangan, Sean Lim, Xiaokan Guo, Stephan Haas, James Q. Boedicker:
  Formation, collective motion, and merging of macroscopic bacterial aggregates.
• 
  István Z. Reguly, Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, Bence Keömley-Horváth, Tamás Kós, György Cserey, Kristóf Iván, Sándor Pongor, Gábor Szederkényi, Gergely Röst, Attila Csikász-Nagy:
  Microsimulation based quantitative analysis of COVID-19 management strategies.
• 
  He Li, Yixiang Deng, Konstantina Sampani, Shengze Cai, Zhen Li, Jennifer K. Sun, George E. Karniadakis:
  Computational investigation of blood cell transport in retinal microaneurysms.
• 
  Raga Krishnakumar, Anne M. Ruffing:
  OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.
• 
  Nathan C. L. Kong, Eshed Margalit, Justin L. Gardner, Anthony M. Norcia:
  Increasing neural network robustness improves match to macaque V1 eigenspectrum, spatial frequency preference and predictivity.
• 
  Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat, Claire Wyart:
  A lexical approach for identifying behavioural action sequences.
• 
  Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood, Andrew D. Rutenberg:
  Interpretable machine learning for high-dimensional trajectories of aging health.
• 
  Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Núria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco:
  Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.
• 
  Yan Wu, Lingfeng Xue, Wen Huang, Minghua Deng, Yihan Lin:
  Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data.
• 
  Eline R. Kupers, Noah C. Benson, Marisa Carrasco, Jonathan Winawer:
  Asymmetries around the visual field: From retina to cortex to behavior.
• 
  Marina Papadopoulou, Hanno Hildenbrandt, Daniel W. E. Sankey, Steven J. Portugal, Charlotte K. Hemelrijk:
  Self-organization of collective escape in pigeon flocks.
• 
  Jennifer Yihong Tan, Ana Claudia Marques:
  The activity of human enhancers is modulated by the splicing of their associated lncRNAs.
• 
  Arno Strouwen, Bart M. Nicolaï, Peter Goos:
  Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables.
• 
  Georgy Antonov, Christopher Gagne, Eran Eldar, Peter Dayan:
  Optimism and pessimism in optimised replay.
• 
  Le Khanh Ngan Nguyen, Itamar Megiddo, Susan Howick:
  Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff.
• 
  Yushi Yang, Francesco Turci, Erika Kague, Chrissy L. Hammond, John Russo, C. Patrick Royall:
  Dominating lengthscales of zebrafish collective behaviour.
• 
  Zhi Ming Xu, Sina Rüeger, Michaela Zwyer, Daniela Brites, Hellen Hiza, Miriam Reinhard, Liliana K. Rutaihwa, Sonia Borrell, Faima Isihaka, Hosiana Temba, Thomas Maroa, Rastard Naftari, Jerry Hella, Mohamed Sasamalo, Klaus Reither, Damien Portevin, Sebastien Gagneux, Jacques Fellay:
  Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.
• 
  William F. Turner, Daniel Feuerriegel, Robert Hester, Stefan Bode:
  An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind.
• 
  Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp, Tatsuya Akutsu:
  Identification of periodic attractors in Boolean networks using a priori information.
• 
  Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaïd Harchaoui, Francois Ribalet:
  A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series.
• 
  Xiangyu Kuang, Guoye Guan, Ming-Kin Wong, Lu-Yan Chan, Zhongying Zhao, Chao Tang, Lei Zhang:
  Computable early Caenorhabditis elegans embryo with a phase field model.
• 
  Joanna E. Handzlik, Manu:
  Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors.
• 
  Rory M. Donovan-Maiye, Eva Maxfield Brown, K. Caleb Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson:
  A deep generative model of 3D single-cell organization.
• 
  Winston Campeau, Andrew M. Simons, Brett Stevens:
  The evolutionary maintenance of Lévy flight foraging.
• 
  Md Zulfikar Ali, Robert C. Brewster:
  Controlling gene expression timing through gene regulatory architecture.
• 
  Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy, Zoltán Gáspári:
  Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach.
• 
  Chenfei Zhang, David Hofmann, Andreas Neef, Fred Wolf:
  Ultrafast population coding and axo-somatic compartmentalization.
• 
  Gorka Lasso, Saad Khan, Stephanie A. Allen, Margarette Mariano, Catalina Florez, Erika P. Orner, Jose A. Quiroz, Gregory Quevedo, Aldo Massimi, Aditi Hegde, Ariel S. Wirchnianski, Robert H. Bortz III, Ryan J. Malonis, George I. Georgiev, Karen Tong, Natalia G. Herrera, Nicholas C. Morano, Scott J. Garforth, Avinash Malaviya, Ahmed Khokhar, Ethan Laudermilch, M. Eugenia Dieterle, J. Maximilian Fels, Denise Haslwanter, Rohit K. Jangra, Jason Barnhill, Steven C. Almo, Kartik Chandran, Jonathan R. Lai, Libusha Kelly, Johanna P. Daily, Olivia Vergnolle:
  Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes.
• 
  Alexander J. Bryer, Tyler Reddy, Edward Lyman, Juan R. Perilla:
  Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.
• 
  Anton V. Chizhov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev:
  Ictal wavefront propagation in slices and simulations with conductance-based refractory density model.
• 
  Maggie Wisniewska, Ivan Puga-Gonzalez, Phyllis Lee, Cynthia Moss, Gareth Russell, Simon Garnier, Cédric Sueur:
  Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants - An exemplar of how human disturbance impacts group-living species.
• 
  Chen Jia, Abhyudai Singh, Ramon Grima:
  Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach.
• 
  Owen M. O'Connor, Razan N. Alnahhas, Jean-Baptiste Lugagne, Mary J. Dunlop:
  DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics.
• 
  Tadamune Kaneko, Macoto Kikuchi:
  Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution.
• 
  Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono:
  Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex.
• 
  Vladimír Palivec, Christian Johannessen, Jakub Kaminský, Hector Martinez-Seara:
  Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution.
• 
  Janet Ong, Stacy Soh, Soon Hoe Ho, Annabel Seah, Borame Sue Dickens, Ken Wei Tan, Joel Ruihan Koo, Alex R. Cook, Daniel Rex Richards, Leon Yan-Feng Gaw, Ng Lee Ching, Jue Tao Lim:
  Fine-scale estimation of effective reproduction numbers for dengue surveillance.
• 
  Mengting Niu, Quan Zou, Chen Lin:
  CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.
• 
  Arish Alreja, Ilya Nemenman, Christopher J. Rozell:
  Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices.
• 
  Priyan Bhattacharya, Karthik Raman, Arun K. Tangirala:
  Discovering adaptation-capable biological network structures using control-theoretic approaches.
• 
  Fabien Laporte, Alain Charcosset, Tristan Mary-Huard:
  Efficient ReML inference in variance component mixed models using a Min-Max algorithm.
• 
  André Bogdanowski, Thomas Banitz, Linea Katharina Muhsal, Christian Kost, Karin Frank:
  McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.
• 
  Ryan R. Wick, Kathryn E. Holt:
  Polypolish: Short-read polishing of long-read bacterial genome assemblies.
• 
  Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes:
  Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection.
• 
  Eduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia:
  The structural coverage of the human proteome before and after AlphaFold.
• 
  Qi Jiang, Shuo Zhang, Lin Wan:
  Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data.
• 
  Alexander Byers Brummer, Xin Yang, Eric Ma, Margarita Gutova, Christine E. Brown, Russell C. Rockne:
  Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy.
• 
  Elodie Goldwaser, Catherine Laurent, Nathalie Lagarde, Sylvie Fabrega, Laure Nay, Bruno O. Villoutreix, Christian Jelsch, Arnaud B. Nicot, Marie-Anne Loriot, Maria A. Miteva:
  Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9.
• 
  Tianwei Yu:
  AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments.
• 
  Quinn Dickinson, Jesse G. Meyer:
  Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences.
• 
  Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort, Arno Onken:
  Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships.
• 
  Alexander Nestor-Bergmann, Guy B. Blanchard, Nathan Hervieux, Alexander G. Fletcher, Jocelyn Étienne, Bénédicte Sanson:
  Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model.
• 
  Chloé Dequeker, Yasser Mohseni Behbahani, Laurent David, Elodie Laine, Alessandra Carbone:
  From complete cross-docking to partners identification and binding sites predictions.
• 
  Sayak Bhattacharya, Scott L. Brincat, Mikael Lundqvist, Earl K. Miller:
  Traveling waves in the prefrontal cortex during working memory.
• 
  Chunrui Xu, Henry Hollis, Michelle Dai, Xiangyu Yao, Layne T. Watson, Yang Cao, Minghan Chen:
  Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle.
• 
  Kaushik N. Shankar, Yiyuan Zhang, Talid Sinno, Scott L. Diamond:
  A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution.
• 
  Dave Osthus:
  Fast and accurate influenza forecasting in the United States with Inferno.
• 
  Tomiko Oskotsky, Ruchika Bajaj, Jillian Burchard, Taylor Cavazos, Ina Chen, William T. Connell, Stephanie Eaneff, Tianna Grant, Ishan Kanungo, Karla Lindquist, Douglas Myers-Turnbull, Zun Zar Chi Naing, Alice Tang, Bianca Vora, Jon Wang, Isha Karim, Claire Swadling, Janice Yang, AI4ALL Student Cohort, Bill Lindstaedt, Marina Sirota:
  Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.
• 
  Sina Tootoonian, Andreas T. Schaefer, Peter E. Latham:
  Sparse connectivity for MAP inference in linear models using sister mitral cells.
• 
  Vatsala Chauhan, Mohamed N. M. Bahrudeen, Cristina S. D. Palma, Ines S. C. Baptista, Bilena Almeida, Suchintak Dash, Vinodh Kandavalli, Andre S. Ribeiro:
  Analytical kinetic model of native tandem promoters in E. coli.
• 
  Richard M. Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander, Linda R. Petzold:
  Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.
• 
  Junhao Liang, Changsong Zhou:
  Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks.
• 
  Yuan Gao, Jeff Gaither, Julia Chifman, Laura Salter Kubatko:
  A phylogenetic approach to inferring the order in which mutations arise during cancer progression. 1010560

Corrections

• 
  Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin:
  Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data.
• 
  Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke, Nathan E. Lewis:
  Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models.

Volume 18, Number 2, February 2022

Editorials

• 
  Arkarachai Fungtammasan, Alexandra Lee, Jaclyn N. Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey S. Greene:
  Ten simple rules for large-scale data processing.
• 
  Nicole Contaxis, Jason A. Clark, Anthony Dellureficio, Sara Gonzales, Sara Mannheimer, Peter R. Oxley, Melissa A. Ratajeski, Alisa Surkis, Amy M. Yarnell, Michelle Yee, Kristi L. Holmes:
  Ten simple rules for improving research data discovery.
• 
  Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner:
  Ten simple rules for initial data analysis.

Education Articles

• 
  Camilo Fuentes-Beals, Alejandro Valdés-Jiménez, Gonzalo Riadi:
  Hidden Markov Modeling with HMMTeacher.
• 
  Greg Wilson:
  Twelve quick tips for software design.

Perspective

• 
  Jon Zelner, Nina B. Masters, Ramya Naraharisetti, Sanyu A. Mojola, Merlin Chowkwanyun, Ryan Malosh:
  There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.

Review

• 
  Mathieu Desroches, John Rinzel, Serafim Rodrigues:
  Classification of bursting patterns: A tale of two ducks.

Research Articles

• 
  Stefan Müller, Diana Széliová, Jürgen Zanghellini:
  Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth.
• 
  Myo T. Naung, Elijah Martin, Jacob E. Munro, Somya Mehra, Andrew J. Guy, Moses Laman, G. L. Abby Harrison, Livingstone Tavul, Manuel Hetzel, Dominic Kwiatkowski, Ivo Mueller, Melanie Bahlo, Alyssa E. Barry:
  Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens.
• 
  Ignacio Sanchez-Burgos, Jorge R. Espinosa, Jerelle A. Joseph, Rosana Collepardo-Guevara:
  RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins.
• 
  Gabriela Canto-Encalada, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga:
  Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.
• 
  Cristian Buc Calderon, Tom Verguts, Michael J. Frank:
  Thunderstruck: The ACDC model of flexible sequences and rhythms in recurrent neural circuits.
• 
  Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler, Julia Grajek, Katerina Stanková, Alexander T. Pearson, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling, Jan Poleszczuk, Jakob Nikolas Kather:
  Classical mathematical models for prediction of response to chemotherapy and immunotherapy.
• 
  Daniel Kaiser, Arthur M. Jacobs, Radoslaw Martin Cichy:
  Modelling brain representations of abstract concepts.
• 
  Anca R. Radulescu, Gabrielle C. Todd, Cassandra L. Williams, Benjamin A. Bennink, Alex A. Lemus, Haley E. Chesbro, Justin R. Bourgeois, Ashley M. Kopec, Damian G. Zuloaga, Annalisa Scimemi:
  Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes.
• 
  Benjamin J. Livesey, Joseph A. Marsh:
  The properties of human disease mutations at protein interfaces.
• 
  Aleksey V. Zimin, Steven L. Salzberg:
  The SAMBA tool uses long reads to improve the contiguity of genome assemblies.
• 
  Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani:
  INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation.
• 
  Thomas J. Moutinho Jr., Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin:
  Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.
• 
  Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud:
  Evaluating supervised and unsupervised background noise correction in human gut microbiome data.
• 
  David E. Chen Kersen, Gaia Tavoni, Vijay Balasubramanian:
  Connectivity and dynamics in the olfactory bulb.
• 
  Haiting Chai, Quan Gu, Joseph Hughes, David L. Robertson:
  In silico prediction of HIV-1-host molecular interactions and their directionality.
• 
  Lovemore Tenha, Mingzhou Song:
  Inference of trajectory presence by tree dimension and subset specificity by subtree cover.
• 
  Ramin Khajeh, Francesco Fumarola, L. F. Abbott:
  Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights.
• 
  György Abrusán, David B. Ascher, Michael Inouye:
  Known allosteric proteins have central roles in genetic disease.
• 
  Reza Yaesoubi, Ted Cohen, Katherine Hsu, Thomas L. Gift, Sancta B. St. Cyr, Joshua A. Salomon, Yonatan H. Grad:
  Evaluating spatially adaptive guidelines for the treatment of gonorrhea to reduce the incidence of gonococcal infection and increase the effective lifespan of antibiotics.
• 
  Qi Sun, Ali Nematbakhsh, Prashant Kumar Kuntala, Gretta Kellogg, B. Franklin Pugh, William K. M. Lai:
  STENCIL: A web templating engine for visualizing and sharing life science datasets.
• 
  Sevan K. Harootonian, Arne D. Ekstrom, Robert C. Wilson:
  Combination and competition between path integration and landmark navigation in the estimation of heading direction.
• 
  Anna Foix, Daniel López, Francisco Diez-Fuertes, Michael J. McConnell, Antonio J. Martin-Galiano:
  Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.
• 
  Robert C. Mines, Tomasz Lipniacki, Xiling Shen:
  Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts.
• 
  Júlia V. Gallinaro, Nebojsa Gasparovic, Stefan Rotter:
  Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams.
• 
  Samuel Goldman, Ria Das, Kevin K. Yang, Connor W. Coley:
  Machine learning modeling of family wide enzyme-substrate specificity screens.
• 
  Siyu Wang, Stephanie M. Reeve, Graham T. Holt, Adegoke A. Ojewole, Marcel S. Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G. Fowler, Dennis L. Wright, Bruce Randall Donald:
  Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.
• 
  Alexander Eugene Zarebski, Louis du Plessis, Kris V. Parag, Oliver George Pybus:
  A computationally tractable birth-death model that combines phylogenetic and epidemiological data.
• 
  Liron Sheintuch, Alon Rubin, Ziv Yaniv:
  Bias-free estimation of information content in temporally sparse neuronal activity.
• 
  Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K. Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine:
  A mechanistic modeling framework reveals the key principles underlying tumor metabolism.
• 
  Leonie van Steijn, Inge M. N. Wortel, Clément Sire, Loïc Dupré, Guy Theraulaz, Roeland M. H. Merks:
  Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics.
• 
  Juan Camilo Arboleda-Rivera, Gloria Machado-Rodríguez, Boris A. Rodríguez, Jayson Gutiérrez:
  Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns.
• 
  Liam M. Longo, Rachel Kolodny, Shawn E. McGlynn:
  Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich.
• 
  M. Eric Irrgang, Caroline Davis, Peter M. Kasson:
  gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
• 
  Nathaniel Diamant, Erik Reinertsen, Steven Song, Aaron D. Aguirre, Collin M. Stultz, Puneet Batra:
  Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling.
• 
  R. Krishnakumaran, Mohammed Raees, Supratim Ray:
  Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network.
• 
  Valeria d'Andrea, Riccardo Gallotti, Nicola Castaldo, Manlio De Domenico:
  Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks.
• 
  Nicholas J. Clark, Tatiana Proboste, Guyan Weerasinghe, Ricardo J. Soares Magalhães:
  Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model.
• 
  Ning Wang, Vladislav Lysenkov, Katri Orte, Veli Kairisto, Juhani Aakko, Sofia Khan, Laura L. Elo:
  Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data.
• 
  Alessandra Løchen, James Truscott, Nicholas J. Croucher:
  Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates.
• 
  Laura B. Ferguson, Amanda J. Roberts, R. Dayne Mayfield, Robert O. Messing:
  Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice.
• 
  Ana Carolina Leote, Xiaohui Wu, Andreas Beyer:
  Regulatory network-based imputation of dropouts in single-cell RNA sequencing data.
• 
  Nithya Ramakrishnan, Sibi Raj B. Pillai, Ranjith Padinhateeri:
  High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication.
• 
  Robert J. Wagner, Franck J. Vernerey:
  Computational exploration of treadmilling and protrusion growth observed in fire ant rafts.
• 
  Wilhelm Braun, Raoul-Martin Memmesheimer:
  High-frequency oscillations and sequence generation in two-population models of hippocampal region CA1.
• 
  Paul F. Zierep, Randi Vita, Nina Blazeska, Aurélien F. A. Moumbock, Jason A. Greenbaum, Bjoern Peters, Stefan Günther:
  Towards the prediction of non-peptidic epitopes.
• 
  Yufei Wu, Adrian F. Pegoraro, David A. Weitz, Paul A. Janmey, Sean X. Sun:
  The correlation between cell and nucleus size is explained by an eukaryotic cell growth model.
• 
  Paul Van Liedekerke, Lila Gannoun, Axelle Loriot, Tim Johann, Frédéric Lemaigre, Dirk Drasdo:
  Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation.
• 
  Emmanuel E. Moutoussamy, Qaiser Waheed, Greta J. Binford, Hanif M. Khan, Shane M. Moran, Anna R. Eitel, Matthew H. J. Cordes, Nathalie Reuter:
  Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage.
• 
  Galya V. Klink, Olga V. Kalinina, Georgii A. Bazykin:
  Phylogenetic inference of changes in amino acid propensities with single-position resolution.
• 
  Genelle F. Harrison, Laura Ann Leaton, Erica A. Harrison, Katherine M. Kichula, Marte K. Viken, Jonathan Shortt, Christopher R. Gignoux, Benedicte A. Lie, Damjan Vukcevic, Stephen Leslie, Paul J. Norman:
  Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1.
• 
  Jonathan S. Matthis, Karl S. Muller, Kathryn L. Bonnen, Mary M. Hayhoe:
  Retinal optic flow during natural locomotion.
• 
  Cedoljub Bundalovic-Torma, Darrell Desveaux, David S. Guttman:
  RecPD: A Recombination-aware measure of phylogenetic diversity.
• 
  Jannes Jegminat, Simone Carlo Surace, Jean-Pascal Pfister:
  Learning as filtering: Implications for spike-based plasticity.
• 
  Xian Yang, Shuo Wang, Yuting Xing, Ling Li, Richard Yi Da Xu, Karl J. Friston, Yike Guo:
  Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19.
• 
  Maureen A. Carey, Gregory L. Medlock, Michal Stolarczyk, William A. Petri Jr., Jennifer L. Guler, Jason A. Papin:
  Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.
• 
  Nicholas A. Bokulich, Pawel Laniewski, Anja Adamov, Dana M. Chase, J. Gregory Caporaso, Melissa M. Herbst-Kralovetz:
  Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment.
• 
  Rym Ben Boubaker, Asma Tiss, Daniel Henrion, Hajer Guissouma, Marie Chabbert:
  Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota.
• 
  Ying Liu, Ruihui Li, Jiawei Luo, Zhaolei Zhang:
  Inferring RNA-binding protein target preferences using adversarial domain adaptation.
• 
  Katherine E. Overman, Daniel M. Choi, Kawai Leung, Joshua W. Shaevitz, Gordon J. Berman:
  Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster.
• 
  Santhosh Sankar, Nagasuma Chandra:
  SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites.
• 
  Benedict Borer, Dani Or:
  Bacterial age distribution in soil - Generational gaps in adjacent hot and cold spots.
• 
  Nir Gavish, Guy Katriel:
  The role of childrens' vaccination for COVID-19 - Pareto-optimal allocations of vaccines.
• 
  Yuen Ler Chow, Shantanu Singh, Anne E. Carpenter, Gregory P. Way:
  Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic.
• 
  Sara Brin Rosenthal, Hao Wang, Da Shi, Cin Liu, Ruben Abagyan, Linda K. McEvoy, Chi-Hua Chen:
  Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics.
• 
  Tiam Heydari, Matthew A. Langley, Cynthia L. Fisher, Daniel Aguilar-Hidalgo, Shreya Shukla, Ayako Yachie-Kinoshita, Michael Hughes, Kelly M. McNagny, Peter W. Zandstra:
  IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.
• 
  Daniel Domingo-Fernández, Yojana Gadiya, Abhishek Patel, Sarah Mubeen, Daniel Rivas-Barragan, Chris W. Diana, Biswapriya B. Misra, David Healey, John C. Rokicki, Viswa Teja S. S. Colluru:
  Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery.
• 
  Nirmal Kumar Sampathkumar, Venkat Krishnan Sundaram, Prakroothi S. Danthi, Rasha Barakat, Shiden Solomon, Mrityunjoy Mondal, Ivo Carre, Tatiana El Jalkh, Aïda Padilla-Ferrer, Julien Grenier, Charbel Massaad, Jacqueline C. Mitchell:
  RNA-Seq is not required to determine stable reference genes for qPCR normalization.
• 
  Anil Yaman, Nicolas Bredèche, Onur Çaylak, Joel Z. Leibo, Sang Wan Lee:
  Meta-control of social learning strategies.
• 
  Indriani Puspitasari Astono, James S. Welsh, Christopher W. Rowe, Phillip Jobling:
  Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning.
• 
  Matteo D'Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Margaret K. R. Donovan, Agnieszka D'Antonio-Chronowska, Kelly A. Frazer:
  In heart failure reactivation of RNA-binding proteins is associated with the expression of 1, 523 fetal-specific isoforms.

Corrections

• 
  Christian Quirouette, Nada P. Younis, Micaela B. Reddy, Catherine A. A. Beauchemin:
  Correction: A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract.
• 
  Yashika Arora, Pushpinder Walia, Mitsuhiro Hayashibe, Makii Muthalib, Shubhajit Roy Chowdhury, Stéphane Perrey, Anirban Dutta:
  Correction: Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans.

Volume 18, Number 3, March 2022

Editorials

• 
  Luis Garcia Morales, Niek H. A. Savelkoul, Zoë Robaey, Nico J. Claassens, Raymond H. J. Staals, Robert W. Smith:
  Ten simple rules for building an enthusiastic iGEM team.
• 
  Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn A. Grüning, Ignacio Eguinoa, Philip Ewels, Carole A. Goble:
  Ten simple rules for making a software tool workflow-ready.

Education Articles

• 
  Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca:
  Ten quick tips for deep learning in biology.
• 
  Caroline J. Wendt, G. Brooke Anderson:
  Ten simple rules for finding and selecting R packages.
• 
  Laurel Fogarty, Madeleine Ammar, Thomas Holding, Adam Powell, Anne Kandler:
  Ten simple rules for principled simulation modelling.

Research Articles

• 
  Erich Hellemann, Jennifer L. Walker, Mitchell A. Lesko, Dakshayini G. Chandrashekarappa, Martin C. Schmidt, Allyson F. O'Donnell, Jacob D. Durrant:
  Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics.
• 
  Stuart A. MacGowan, Michael I. Barton, Mikhail Kutuzov, Omer Dushek, P. Anton van der Merwe, Geoffrey J. Barton:
  Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.
• 
  Christopher M. Wilson, Alex C. Soupir, Ram Thapa, Jordan H. Creed, Jonathan Nguyen, Carlos Moran Segura, Travis A. Gerke, Joellen M. Schildkraut, Lauren C. Peres, Brooke L. Fridley:
  Tumor immune cell clustering and its association with survival in African American women with ovarian cancer.
• 
  Weijia Wang, Ramón Escobedo, Stéphane Sanchez, Clément Sire, Zhangang Han, Guy Theraulaz:
  The impact of individual perceptual and cognitive factors on collective states in a data-driven fish school model.
• 
  Timos Papadopoulos, Emilia Vynnycky:
  Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches.
• 
  Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, David E. Shaw:
  How does a small molecule bind at a cryptic binding site?
• 
  Shanglin Zhou, Sotiris C. Masmanidis, Dean V. Buonomano:
  Encoding time in neural dynamic regimes with distinct computational tradeoffs.
• 
  Daniel R. Guest, Andrew J. Oxenham:
  Human discrimination and modeling of high-frequency complex tones shed light on the neural codes for pitch.
• 
  Philip Gerlee, Philipp M. Altrock, Adam Malik, Cecilia Krona, Sven Nelander:
  Autocrine signaling can explain the emergence of Allee effects in cancer cell populations.
• 
  Timothy O. West, Peter J. Magill, Andrew Sharott, Vladimir Litvak, Simon F. Farmer, Hayriye Cagnan:
  Stimulating at the right time to recover network states in a model of the cortico-basal ganglia-thalamic circuit.
• 
  Simon van Vliet, Christoph Hauert, Kyle Fridberg, Martin Ackermann, Alma Dal Co:
  Global dynamics of microbial communities emerge from local interaction rules.
• 
  He Li, Yixiang Deng, Zhen Li, Ander Dorken Gallastegi, Christos S. Mantzoros, Galit H. Frydman, George E. Karniadakis:
  Multiphysics and multiscale modeling of microthrombosis in COVID-19.
• 
  Vishal Kumar Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty:
  Model-based identification of conditionally-essential genes from transposon-insertion sequencing data.
• 
  Shin-ichi Koda, Shinji Saito:
  Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition.
• 
  Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres, Marco Oldiges:
  Bayesian calibration, process modeling and uncertainty quantification in biotechnology.
• 
  Samantha Petti, Sean R. Eddy:
  Constructing benchmark test sets for biological sequence analysis using independent set algorithms.
• 
  Richard D. Lange, Ralf M. Haefner:
  Task-induced neural covariability as a signature of approximate Bayesian learning and inference.
• 
  Jian K. Liu, Dimokratis Karamanlis, Tim Gollisch:
  Simple model for encoding natural images by retinal ganglion cells with nonlinear spatial integration.
• 
  Roei Zigelman, Ofri Eitan, Omer Mazar, Anthony J. Weiss, Yossi Yovel:
  A bio-mimetic miniature drone for real-time audio based short-range tracking.
• 
  Silas Kieser, Evgeny M. Zdobnov, Mirko Trajkovski:
  Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart.
• 
  M. A. Masud, Jae-Young Kim, Cheol-Ho Pan, Eunjung Kim:
  The impact of the spatial heterogeneity of resistant cells and fibroblasts on treatment response.
• 
  Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan, David J. Balding:
  Bayesian inference of ancestral recombination graphs.
• 
  Kaumadi Wijesooriya, Sameer A. Jadaan, Kaushalya L. Perera, Tanuveer Kaur, Mark Ziemann:
  Urgent need for consistent standards in functional enrichment analysis.
• 
  Qinhu Zhang, Ying He, Siguo Wang, Zhanheng Chen, Zhen-Hao Guo, Zhen Cui, Qi Liu, De-Shuang Huang:
  Base-resolution prediction of transcription factor binding signals by a deep learning framework.
• 
  Oscar Portoles, Manuel Blesa, Marieke K. van Vugt, Ming Cao, Jelmer P. Borst:
  Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task.
• 
  Kevin Yao, Evelien Schaafsma, Baoyi Zhang, Chao Cheng:
  Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer.
• 
  Snehalika Lall, Sumanta Ray, Sanghamitra Bandyopadhyay:
  A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data.
• 
  Ritabrata Dutta, Karim Zouaoui Boudjeltia, Christos Kotsalos, Alexandre Rousseau, Daniel Ribeiro de Sousa, Jean-Marc Desmet, Alain Van Meerhaeghe, Antonietta Mira, Bastien Chopard:
  Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning.
• 
  Stephen R. Piccolo, Avery Mecham, Nathan P. Golightly, Jérémie L. Johnson, Dustin B. Miller:
  The ability to classify patients based on gene-expression data varies by algorithm and performance metric.
• 
  Shehab S. Ahmed, Zaara T. Rifat, Ruchi Lohia, Arthur J. Campbell, A. Keith Dunker, M. Sohel Rahman, Sumaiya Iqbal:
  Characterization of intrinsically disordered regions in proteins informed by human genetic diversity.
• 
  Shibo Wang, Fangjie Xie, Shizhong Xu:
  Estimating genetic variance contributed by a quantitative trait locus: A random model approach.
• 
  Amédée Roy, Sophie Bertrand, Ronan Fablet:
  Deep inference of seabird dives from GPS-only records: Performance and generalization properties.
• 
  Héctor Carrión, Mohammad Jafari, Michelle Dawn Bagood, Hsin-Ya Yang, Roslyn Rivkah Isseroff, Marcella Gomez:
  Automatic wound detection and size estimation using deep learning algorithms.
• 
  Andrea Benucci:
  Motor-related signals support localization invariance for stable visual perception.
• 
  Iñigo Apaolaza, Edurne San José-Enériz, Luis Vitores Valcarcel, Xabier Agirre, Felipe Prósper, Francisco J. Planes:
  A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism.
• 
  Tong Liang, Braden A. W. Brinkman:
  Evolution of innate behavioral strategies through competitive population dynamics.
• 
  Jianle Sun, Ruiqi Lyu, Luojia Deng, Qianwen Li, Yang Zhao, Yue Zhang:
  SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included.
• 
  Noortje G. Godijk, Martin C. J. Bootsma, Henri C. van Werkhoven, Valentijn A. Schweitzer, Sabine C. de Greeff, Annelot F. Schoffelen, Marc J. M. Bonten:
  Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms.
• 
  Jonathan Fiorentino, Antonio Scialdone:
  The role of cell geometry and cell-cell communication in gradient sensing.
• 
  Thierry Pécot, Maria C. Cuitiño, Roger H. Johnson, Cynthia Timmers, Gustavo Leone:
  Deep learning tools and modeling to estimate the temporal expression of cell cycle proteins from 2D still images.
• 
  Romain Amyot, Arin Marchesi, Clemens M. Franz, Ignacio Casuso, Holger Flechsig:
  Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
• 
  Navid Mohammad Mirzaei, Navid Changizi, Alireza Asadpoure, Sumeyye Su, Dilruba Sofia, Zuzana Tatarova, Ioannis K. Zervantonakis, Young Hwan Chang, Leili Shahriyari:
  Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model.
• 
  Andreas Scheck, Stéphane Rosset, Michaël Defferrard, Andreas Loukas, Jaume Bonet, Pierre Vandergheynst, Bruno E. Correia:
  RosettaSurf - A surface-centric computational design approach.
• 
  Thomas W. Laver, Elisa De Franco, Matthew B. Johnson, Kashyap A. Patel, Sian Ellard, Michael N. Weedon, Sarah E. Flanagan, Matthew Wakeling:
  SavvyCNV: Genome-wide CNV calling from off-target reads.
• 
  George Courcoubetis, Chi Xu, Sergey V. Nuzhdin, Stephan Haas:
  Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model.
• 
  Moses Stamboulian, Jamie Canderan, Yuzhen Ye:
  Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species.
• 
  Andela Davidovic, Remy Chait, Grégory Batt, Jakob Ruess:
  Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level.
• 
  Alireza Naghizadeh, Wei-chung Tsao, Jong Hyun Cho, Hongye Xu, Mohab Mohamed, Dali Li, Wei Xiong, Dimitris N. Metaxas, Carlos A. Ramos, Dongfang Liu:
  In vitro machine learning-based CAR T immunological synapse quality measurements correlate with patient clinical outcomes.
• 
  Xiangyu Yao, Benjamin L. Heidebrecht, Jing Chen, John J. Tyson:
  Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock.
• 
  Soham Mukherjee, Darren Wethington, Tamal K. Dey, Jayajit Das:
  Determining clinically relevant features in cytometry data using persistent homology.
• 
  Yingjing Feng, Caroline H. Roney, Jason D. Bayer, Steven A. Niederer, Mélèze Hocini, Edward J. Vigmond:
  Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation.
• 
  Si-Kao Guo, Alexander J. Sodt, Margaret E. Johnson:
  Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins.
• 
  Suzan Farhang-Sardroodi, Michael A. La Croix, Kathleen P. Wilkie:
  Chemotherapy-induced cachexia and model-informed dosing to preserve lean mass in cancer treatment.
• 
  David Groenewoud, Avinoam Shye, Ran Elkon:
  Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool.
• 
  Philipp Wendering, Zoran Nikoloski:
  COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions.
• 
  Jonathan S. Tsay, Adrian M. Haith, Richard B. Ivry, Hyosub E. Kim:
  Interactions between sensory prediction error and task error during implicit motor learning.
• 
  Fei Xiao, Ziyun Zhou, Xingyu Song, Mi Gan, Jie Long, Gennady Verkhivker, Guang Hu:
  Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation.
• 
  Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen:
  Fast protein structure comparison through effective representation learning with contrastive graph neural networks.
• 
  Pablo E. García-Nieto, Ban Wang, Hunter B. Fraser:
  Transcriptome diversity is a systematic source of variation in RNA-sequencing data.
• 
  Takeru Matsuda, Fumitaka Homae, Hama Watanabe, Gentaro Taga, Fumiyasu Komaki:
  Oscillator decomposition of infant fNIRS data.
• 
  Agnes Korcsak-Gorzo, Michael G. Müller, Andreas Baumbach, Luziwei Leng, Oliver Julien Breitwieser, Sacha J. van Albada, Walter Senn, Karlheinz Meier, Robert Legenstein, Mihai A. Petrovici:
  Cortical oscillations support sampling-based computations in spiking neural networks.
• 
  Daniel James Lugar, Ganesh Sriram:
  Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness.
• 
  Charles Bayly-Jones, James C. Whisstock:
  Mining folded proteomes in the era of accurate structure prediction.
• 
  Zixin Peng, Alexandre Maciel-Guerra, Michelle Baker, Xibin Zhang, Yue Hu, Wei Wang, Jia Rong, Jing Zhang, Ning Xue, Paul Barrow, David Renney, Dov J. Stekel, Paul Williams, Longhai Liu, Junshi Chen, Fengqin Li, Tania Dottorini:
  Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming.
• 
  Mingyu Song, Yuji K. Takahash, Amanda C. Burton, Matthew R. Roesch, Geoffrey Schoenbaum, Yael Niv, Angela Langdon:
  Minimal cross-trial generalization in learning the representation of an odor-guided choice task.
• 
  Leonardo Souto Ferreira, Otavio Canton, Rafael Lopes Paixão da Silva, Silas Poloni, Vítor Sudbrack, Marcelo Eduardo Borges, Caroline Franco, Flavia Maria Darcie Marquitti, José Cássio de Moraes, Maria Amélia de Sousa Mascena Veras, Roberto André Kraenkel, Renato Mendes Coutinho:
  Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2.
• 
  John M. Brooke, Sebastian S. James, Alejandro Jiménez-Rodríguez, Stuart P. Wilson:
  Biological action at a distance: Correlated pattern formation in adjacent tessellation domains without communication.
• 
  Immanuel Meyer, Bnaya Steinmetz, Nadav M. Shnerb:
  How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments.
• 
  Stratis Tsirtsis, Abir De, Lars Lorch, Manuel Gomez-Rodriguez:
  Pooled testing of traced contacts under superspreading dynamics.
• 
  Gustavo S. Jeuken, Nicholas P. Tobin, Lukas Käll:
  Survival analysis of pathway activity as a prognostic determinant in breast cancer.
• 
  Junyi Zhou, Xiaoyu Lu, Wennan Chang, Changlin Wan, Xiongbin Lu, Chi Zhang, Sha Cao:
  PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning.
• 
  Daniele Proverbio, Françoise Kemp, Stefano Magni, Jorge M. Gonçalves:
  Performance of early warning signals for disease re-emergence: A case study on COVID-19 data.
• 
  Nicolas Franco, Pietro Coletti, Lander Willem, Leonardo Angeli, Adrien Lajot, Steven Abrams, Philippe Beutels, Christel Faes, Niel Hens:
  Inferring age-specific differences in susceptibility to and infectiousness upon SARS-CoV-2 infection based on Belgian social contact data.
• 
  João Pedro Fonseca, Elham Aslankoohi, Andrew H. Ng, Michael Chevalier:
  Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling.
• 
  Lei Wang, Jiangguo Zhang, Dali Wang, Chen Song:
  Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins.
• 
  Yi Wang, Stephanie C. Hicks, Kasper D. Hansen:
  Addressing the mean-correlation relationship in co-expression analysis.
• 
  Michael F. Staddon, Edwin M. Munro, Shiladitya Banerjee:
  Pulsatile contractions and pattern formation in excitable actomyosin cortex.
• 
  Elizabeth T. Bartom, Masha Kocherginsky, Bidur Paudel, Aparajitha Vaidyanathan, Ashley Haluck-Kangas, Monal Patel, Kaitlyn L. O'Shea, Andrea E. Murmann, Marcus E. Peter:
  SPOROS: A pipeline to analyze DISE/6mer seed toxicity.
• 
  Grant R. Howard, Tyler A. Jost, Thomas E. Yankeelov, Amy Brock:
  Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules.
• 
  Pablo M. De Salazar, Fred Lu, James A. Hay, Diana Gomez-Barroso, Pablo Fernández-Navarro, Elena V. Martínez, Jenaro Astray-Mochales, Rocío Amillategui, Ana García-Fulgueiras, Maria D. Chirlaque, Alonso Sánchez-Migallón, Amparo Larrauri, María J. Sierra, Marc Lipsitch, Fernando Simón, Mauricio Santillana, Miguel A. Hernán:
  Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data.

Correction

• 
  Jannes Jegminat, Maya A. Jastrzebowska, Matthew V. Pachai, Michael H. Herzog, Jean-Pascal Pfister:
  Correction: Bayesian regression explains how human participants handle parameter uncertainty.

Volume 18, Number 4, April 2022

Editorials

• 
  Tobias Reichmuth, Collin Y. Ewald:
  Ten simple rules for building a successful science start-up.
• 
  Matt Bawn, David Dent, Philip E. Bourne:
  Ten simple rules for using entrepreneurship skills to improve research careers and culture.
• 
  Rachel A. Zitomer, Jessica Karr, Mark Kerstens, Lindsey Perry, Kayla Ruth, Lindsay Adrean, Suzanne Austin, Jamie Cornelius, Jonathan Dachenhaus, Jonathan Dinkins, Alan Harrington, Hankyu Kim, Terrah Owens, Claire Revekant, Vanessa Schroeder, Chelsea Sink, Jonathon J. Valente, Ethan Woodis, James W. Rivers:
  Ten simple rules for getting started with statistics in graduate school.

Perspective

• 
  Carolyn J. Lawrence-Dill, Robyn L. Allscheid, Albert Boaitey, Todd Bauman, Edward S. Buckler IV, Jennifer L. Clarke, Christopher Cullis, Jack Dekkers, Cassandra J. Dorius, Shawn F. Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M. Reecy, Patrick S. Schnable, Nicole M. Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K. Tuggle, Alison Van Eenennaam, Rachael Voas:
  Ten simple rules to ruin a collaborative environment.

Review

• 
  Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutti, Christophe Godin, Jan Traas:
  Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets.

Research Articles

• 
  Haoyang Sun, Joel Ruihan Koo, Borame L. Dickens, Hannah E. Clapham, Alex R. Cook:
  Short-term and long-term epidemiological impacts of sustained vector control in various dengue endemic settings: A modelling study.
• 
  Damiano Fassina, Caroline Mendonça Costa, Stefano Longobardi, Elias Karabelas, Gernot Plank, Sian E. Harding, Steven A. Niederer:
  Modelling the interaction between stem cells derived cardiomyocytes patches and host myocardium to aid non-arrhythmic engineered heart tissue design.
• 
  Yuge Wang, Hongyu Zhao:
  Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders.
• 
  Silvia Zaoli, Jacopo Grilli:
  The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities.
• 
  Inbal Mizrahi, Robijn Bruinsma, Joseph Rudnick:
  Packaging contests between viral RNA molecules and kinetic selectivity.
• 
  Donghyuk Lee, Difei Wang, Xiaohong R. Yang, Jianxin Shi, Maria Teresa Landi, Bin Zhu:
  SUITOR: Selecting the number of mutational signatures through cross-validation.
• 
  Jacobo Ayensa-Jiménez, Mohamed Hamdy Doweidar, José Antonio Sanz-Herrera, Manuel Doblaré:
  Understanding glioblastoma invasion using physically-guided neural networks with internal variables.
• 
  Bastien Polizzi, Andrea Fanesi, Filipa Lopes, Magali Ribot, Olivier Bernard:
  Understanding photosynthetic biofilm productivity and structure through 2D simulation.
• 
  Katharina Ledebur, Michaela Kaleta, Jiaying Chen, Simon D. Lindner, Caspar Matzhold, Florian Weidle, Christoph Wittmann, Katharina Habimana, Linda Kerschbaumer, Sophie Stumpfl, Georg Heiler, Martin Bicher, Nikolas Popper, Florian Bachner, Peter Klimek:
  Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria.
• 
  Lynn K. A. Sörensen, Sander M. Bohté, Heleen A. Slagter, H. Steven Scholte:
  Arousal state affects perceptual decision-making by modulating hierarchical sensory processing in a large-scale visual system model.
• 
  Stefano Pascarelli, Paola Laurino:
  Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.
• 
  Wouter Schellekens, Carlijn Bakker, Nick F. Ramsey, Natalia Petridou:
  Moving in on human motor cortex. Characterizing the relationship between body parts with non-rigid population response fields.
• 
  Gautam Munglani, Hannes Vogler, Ueli Grossniklaus:
  Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit.
• 
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita:
  Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
• 
  Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia:
  Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction.
• 
  Simone Bruno, Ruth J. Williams, Domitilla Del Vecchio:
  Epigenetic cell memory: The gene's inner chromatin modification circuit.
• 
  Bryan T. Mayer, Allan C. deCamp, Yunda Huang, Joshua T. Schiffer, Raphael Gottardo, Peter B. Gilbert, Daniel B. Reeves:
  Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention.
• 
  Maria-Veronica Ciocanel, Aravind Chandrasekaran, Carli Mager, Qin Ni, Garegin A. Papoian, Adriana T. Dawes:
  Simulated actin reorganization mediated by motor proteins.
• 
  Nicholas J. Ose, Brandon M. Butler, Avishek Kumar, I. Can Kazan, Maxwell D. Sanderford, Sudhir Kumar, S. Banu Ozkan:
  Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants.
• 
  Jeta Molla, Alejandro Ponce-de-León-Chávez, Takayuki Hiraoka, Tapio Ala-Nissila, Mikko Kivelä, Lasse Leskelä:
  Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups.
• 
  Julia Jäger, Pintu Patra, Cecilia P. Sanchez, Michael Lanzer, Ulrich S. Schwarz:
  A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections.
• 
  Kathleen Bates, Kim N. Le, Hang Lu:
  Deep learning for robust and flexible tracking in behavioral studies for C. elegans.
• 
  Shuonan Chen, Jackson Loper, Pengcheng Zhou, Liam Paninski:
  Blind demixing methods for recovering dense neuronal morphology from barcode imaging data.
• 
  Alexandrina Pancheva, Helen Wheadon, Simon Rogers, Thomas D. Otto:
  Using topic modeling to detect cellular crosstalk in scRNA-seq.
• 
  Dominik Deffner, Anne Kandler, Laurel Fogarty:
  Effective population size for culturally evolving traits.
• 
  Mohamed A. Ghadie, Yu Xia:
  Are transient protein-protein interactions more dispensable?
• 
  Matteo Serafino, Higor S. Monteiro, Shaojun Luo, Saulo D. S. Reis, Carles Igual, Antonio S. Lima Neto, Matias Travizano, José S. Andrade Jr., Hernán A. Makse:
  Digital contact tracing and network theory to stop the spread of COVID-19 using big-data on human mobility geolocalization.
• 
  Kris V. Parag, Christl A. Donnelly:
  Fundamental limits on inferring epidemic resurgence in real time using effective reproduction numbers.
• 
  Szilvia Barsi, Henrietta Papp, Alberto Valdeolivas, Dániel J. Tóth, Anett Kuczmog, Mónika Madai, László Hunyady, Péter Várnai, Julio Saez-Rodriguez, Ferenc Jakab, Bence Szalai:
  Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.
• 
  Lijun Cheng, Pratik Karkhanis, Birkan Gokbag, Yueze Liu, Lang Li:
  DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data.
• 
  Filippo Grazioli, Raman Siarheyeu, Israa Alqassem, Andreas Henschel, Giampaolo Pileggi, Andrea Meiser:
  Microbiome-based disease prediction with multimodal variational information bottlenecks.
• 
  Nicolas Sundqvist, Nina Grankvist, Jeramie Watrous, Jain Mohit, Roland Nilsson, Gunnar Cedersund:
  Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors.
• 
  Tianyun Liu, Shiyin Wang, Michael Wornow, Russ B. Altman:
  Construction of disease-specific cytokine profiles by associating disease genes with immune responses.
• 
  Simone Di Leo, Stefano Marni, Carlos A. Plata, Tommaso P. Fraccia, Gregory P. Smith, Amos Maritan, Samir Suweis, Tommaso Bellini:
  Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.
• 
  Dillion M. Fox, Christopher M. MacDermaid, Andrea M. A. Schreij, Magdalena Zwierzyna, Ross C. Walker:
  RNA folding using quantum computers.
• 
  Noemi S. Araújo, Selvin Z. Reyes-Garcia, João Angelo Ferres Brogin, Douglas Domingues Bueno, Esper Abrão Cavalheiro, Fulvio Alexandre Scorza, Jean Faber:
  Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy.
• 
  Moustafa Abdalla, Mohamed Abdalla:
  A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules.
• 
  Arash Saeidpour, Shweta Bansal, Pejman Rohani:
  Dissecting recurrent waves of pertussis across the boroughs of London.
• 
  Rick Evertz, Damien G. Hicks, David T. J. Liley:
  Alpha blocking and 1/fβ spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes.
• 
  Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger:
  Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.
• 
  Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George Jr., Jens Meiler:
  Predicting the functional impact of KCNQ1 variants with artificial neural networks.
• 
  Vivekananda Sarangi, Yeongjun Jang, Milovan Suvakov, Taejeong Bae, Liana Fasching, Shobana Sekar, Livia Tomasini, Jessica Mariani, Flora Vaccarino, Alexej Abyzov:
  All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.
• 
  Meriem Mekedem, Patrice Ravel, Jacques Colinge:
  Application of modular response analysis to medium- to large-size biological systems.
• 
  William Poole, Ayush Pandey, Andrey Shur, Zoltán A. Tuza, Richard M. Murray:
  BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts.
• 
  Renato Giliberti, Sara Cavaliere, Italia Elisa Mauriello, Danilo Ercolini, Edoardo Pasolli:
  Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.
• 
  Amanda L. Peiffer, Julie M. Garlick, Stephen T. Joy, Anna K. Mapp, Charles L. Brooks III:
  Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states.
• 
  Daniele Linaro, Matthew J. Levy, David L. Hunt:
  Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons.
• 
  Chathika Krishan Weerasuriya, Rebecca Claire Harris, Christopher Finn McQuaid, Gabriela B. Gomez, Richard G. White:
  Updating age-specific contact structures to match evolving demography in a dynamic mathematical model of tuberculosis vaccination.
• 
  Hongyang Li, Ridvan Eksi, Daiyao Yi, Bradley Godfrey, Lisa R. Mathew, Christopher L. O'Connor, Markus Bitzer, Matthias Kretzler, Rajasree Menon, Yuanfang Guan:
  Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.
• 
  Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein:
  Phylogenetic analysis of migration, differentiation, and class switching in B cells.
• 
  Ryuichi Kumata, Shoya Iwanami, Katrina B. Mar, Yusuke Kakizoe, Naoko Misawa, Shinji Nakaoka, Yoshio Koyanagi, Alan S. Perelson, John W. Schoggins, Shingo Iwami, Kei Sato:
  Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection.
• 
  Vinita Periwal, Stefan Bassler, Sergej Andrejev, Natalia Gabrielli, Kaustubh Raosaheb Patil, Athanasios Typas, Kiran Raosaheb Patil:
  Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs.
• 
  Gergely Tibély, Dominik Schrempf, Imre Derényi, Gergely J. Szöllosi:
  Distinguishing excess mutations and increased cell death based on variant allele frequencies.
• 
  Luis Fernando Montaño-Gutierrez, Kevin Correia, Peter S. Swain:
  Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff.
• 
  James Rosado, Viet Duc Bui, Carola A. Haas, Jürgen Beck, Gillian Queisser, Andreas Vlachos:
  Calcium modeling of spine apparatus-containing human dendritic spines demonstrates an "all-or-nothing" communication switch between the spine head and dendrite.
• 
  Mansour Poorebrahim, Mohammad Foad Abazari, Leila Moradi, Behzad Shahbazi, Reza Mahmoudi, Hourieh Kalhor, Hassan Askari, Ladan Teimoori-Toolabi:
  Multi-targeting of K-Ras domains and mutations by peptide and small molecule inhibitors.
• 
  Cuiping Liang, Qince Li, Kuanquan Wang, Yimei Du, Wei Wang, Henggui Zhang:
  Mechanisms of ventricular arrhythmias elicited by coexistence of multiple electrophysiological remodeling in ischemia: A simulation study.
• 
  Julienne LaChance, Kevin Suh, Jens Clausen, Daniel J. Cohen:
  Learning the rules of collective cell migration using deep attention networks.
• 
  Tom W. Ouellette, Philip Awadalla:
  Inferring ongoing cancer evolution from single tumour biopsies using synthetic supervised learning.
• 
  Joram Keijser, Henning Sprekeler:
  Optimizing interneuron circuits for compartment-specific feedback inhibition.
• 
  Nicola De Maio, William R. Boulton, Lukas Weilguny, Conor R. Walker, Yatish Turakhia, Russell Corbett-Detig, Nick Goldman:
  phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.

Volume 18, Number 5, May 2022

Editorials

• 
  Anne M. Treasure, Siobhan Mackenzie Hall, Igor Lesko, Derek Moore, Malvika Sharan, Menno van Zaanen, Yo Yehudi, Anelda van der Walt:
  Ten simple rules for establishing a mentorship programme.
• 
  Courtney Peña, Latishya J. Steele, Debra S. Karhson, Judith T. Ned, Crystal M. Botham, Miranda B. Stratton:
  Ten simple rules for navigating the reference letter seeking process.

Research Articles

• 
  Wai-Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Timothy Sudijono, Kevin K. Yang, Sayan Mukherjee, Brenda M. Rubenstein, Lorin Crawford:
  A topological data analytic approach for discovering biophysical signatures in protein dynamics.
• 
  Ludovico Calabrese, Jacopo Grilli, Matteo Osella, Christopher P. Kempes, Marco Cosentino Lagomarsino, Luca Ciandrini:
  Protein degradation sets the fraction of active ribosomes at vanishing growth.
• 
  Bastien Blain, Joseph Marks, Philipp Czech, Tali Sharot:
  Observing others give & take: A computational account of bystanders' feelings and actions.
• 
  Rishikesh U. Kulkarni, Catherine L. Wang, Carolyn R. Bertozzi:
  Analyzing nested experimental designs - A user-friendly resampling method to determine experimental significance.
• 
  Jintao Gu, Sukbin Lim:
  Unsupervised learning for robust working memory.
• 
  Alessio Gravina, Jennifer L. Wilson, Davide Bacciu, Kevin Grimes, Corrado Priami:
  Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with deep graph networks.
• 
  Yuqing Lei, Alec Solway:
  Conflict and competition between model-based and model-free control.
• 
  Peter Uhl, John S. Lowengrub, Natalia L. Komarova, Dominik Wodarz:
  Spatial dynamics of feedback and feedforward regulation in cell lineages.
• 
  Roswitha Dolcemascolo, Lucas Goiriz, Roser Montagud-Martínez, Guillermo Rodrigo:
  Gene regulation by a protein translation factor at the single-cell level.
• 
  Carlos Bueno, James Liman, Nicholas P. Schafer, Margaret S. Cheung, Peter G. Wolynes:
  A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks.
• 
  Nomenjanahary Alexia Raharinirina, Esteban Acevedo-Trejos, Agostino Merico:
  Modelling the acclimation capacity of coral reefs to a warming ocean.
• 
  Daniel B. Amchin, Jenna A. Ott, Tapomoy Bhattacharjee, Sujit S. Datta:
  Influence of confinement on the spreading of bacterial populations.
• 
  Alice J. Sommer, Annette Peters, Martina Rommel, Josef Cyrys, Harald Grallert, Dirk Haller, Christian L. Müller, Marie-Abèle C. Bind:
  A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota.
• 
  Frank H. Hezemans, Noham Wolpe, Claire O'Callaghan, Rong Ye, Catarina Rua, P. Simon Jones, Alexander G. Murley, Negin Holland, Ralf Regenthal, Kamen A. Tsvetanov, Roger A. Barker, Caroline H. Williams-Gray, Trevor W. Robbins, Luca Passamonti, James B. Rowe:
  Noradrenergic deficits contribute to apathy in Parkinson's disease through the precision of expected outcomes.
• 
  Jonathan W. Garcia, Thomas M. Bartol, Terrence J. Sejnowski:
  Multiscale modeling of presynaptic dynamics from molecular to mesoscale.
• 
  Rakesh Krishnan, Srivastav Ranganathan, Samir K. Maji, Ranjith Padinhateeri:
  Role of non-specific interactions in the phase-separation and maturation of macromolecules.
• 
  Michael Hunter, Diana Fusco:
  Superinfection exclusion: A viral strategy with short-term benefits and long-term drawbacks.
• 
  Reyhaneh Abbasi, Peter Balazs, Maria Adelaide Marconi, Doris Nicolakis, Sarah M. Zala, Dustin J. Penn:
  Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap).
• 
  Helder Veras Ribeiro filho, Gabriel Ernesto Jara, Fernanda Aparecida Heleno Batista, Gabriel Ravanhani Schleder, Celisa Caldana Costa Tonoli, Adriana Santos Soprano, Samuel Leite Guimarães, Antonio Carlos Borges, Alexandre Cassago, Marcio Chaim Bajgelman, Rafael Elias Marques, Daniela Barretto Barbosa Trivella, Kleber Gomes Franchini, Ana Carolina Migliorini Figueira, Celso Eduardo Benedetti, Paulo Sérgio Lopes-de-Oliveira:
  Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding.
• 
  Etienne Baratchart, Chen Hao Lo, Conor C. Lynch, David Basanta:
  Integrated computational and in vivo models reveal Key Insights into macrophage behavior during bone healing.
• 
  Gaurav Malhotra, Marin Dujmovic, Jeffrey S. Bowers:
  Feature blindness: A challenge for understanding and modelling visual object recognition.
• 
  Maarten J. M. F. Reijnders, Robert M. Waterhouse:
  CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.
• 
  David O. Holland, Valer Gotea, Kevin Fedkenheuer, Sushil K. Jaiswal, Catherine Baugher, Hua Tan, Michael Fedkenheuer, Laura Elnitski:
  Characterization and clustering of kinase isoform expression in metastatic melanoma.
• 
  Brandon M. Invergo:
  Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data.
• 
  Boqiao Lai, Sheng Qian, Hanwei Zhang, Siwei Zhang, Anna A. Kozlova, Jubao Duan, Jinbo Xu, Xin He:
  Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning.
• 
  Nataliya Rokhmanova, Katherine J. Kuchenbecker, Peter B. Shull, Reed Ferber, Eni Halilaj:
  Predicting knee adduction moment response to gait retraining with minimal clinical data.
• 
  Wadim Koslow, Martin Joachim Kühn, Sebastian C. Binder, Margrit Klitz, Daniel Abele, Achim Basermann, Michael Meyer-Hermann:
  Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant.
• 
  Andonis Gerardos, Nicola Dietler, Anne-Florence Bitbol:
  Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.
• 
  Maria Bzówka, Karolina Mitusinska, Agata Raczynska, Tomasz Skalski, Aleksandra Samol, Weronika Bagrowska, Tomasz Magdziarz, Artur Góra:
  Evolution of tunnels in α/β-hydrolase fold proteins - What can we learn from studying epoxide hydrolases?
• 
  Andreagiovanni Reina, James A. R. Marshall:
  Negative feedback may suppress variation to improve collective foraging performance.
• 
  Peter Dieterich, Otto Lindemann, Mats Leif Moskopp, Sebastien Tauzin, Anna Huttenlocher, Rainer Klages, Aleksei V. Chechkin, Albrecht Schwab:
  Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis.
• 
  David Reyner-Parra, Gemma Huguet:
  Phase-locking patterns underlying effective communication in exact firing rate models of neural networks.
• 
  Quang P. Nguyen, Anne G. Hoen, H. Robert Frost:
  CBEA: Competitive balances for taxonomic enrichment analysis.
• 
  Thomas E. Valles, Hannah Shoenhard, Joseph Zinski, Sarah Trick, Mason A. Porter, Michael R. Lindstrom:
  Networks of necessity: Simulating COVID-19 mitigation strategies for disabled people and their caregivers.
• 
  Rajdeep Kaur Grewal, Jayajit Das:
  Spatially resolved in silico modeling of NKG2D signaling kinetics suggests a key role of NKG2D and Vav1 Co-clustering in generating natural killer cell activation.
• 
  Hazhir Rahmandad, Ran Xu, Navid Ghaffarzadegan:
  Enhancing long-term forecasting: Learning from COVID-19 models.
• 
  Gabrielle Bonnet, Francesco Pizzitutti, Eloy A. Gonzales-Gustavson, Sarah Gabriël, William K. Pan, Hector H. Garcia, Javier A. Bustos, Percy Vilchez, Seth E. O'Neal:
  CystiHuman: A model of human neurocysticercosis.
• 
  Lucas Cardoso Lázari, Ivan Rodrigo Wolf, Amanda Piveta Schnepper, Guilherme Targino Valente:
  LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress.
• 
  Sebastian Persson, Niek Welkenhuysen, Sviatlana Shashkova, Samuel Wiqvist, Patrick Reith, Gregor W. Schmidt, Umberto Picchini, Marija Cvijovic:
  Scalable and flexible inference framework for stochastic dynamic single-cell models.
• 
  James O'Keeffe, Sin Hui Yap, Ichasus Llamas-Cornejo, Vivek Nityananda, Jenny C. A. Read:
  A computational model of stereoscopic prey capture in praying mantises.
• 
  Sijie Tong, Navreeta K. Singh, Rastko Sknepnek, Andrej Kosmrlj:
  Linear viscoelastic properties of the vertex model for epithelial tissues.
• 
  Christopher I. Jarvis, Amy Gimma, Flavio Finger, Tim P. Morris, Jennifer A. Thompson, Olivier Le Polain de Waroux, W. John Edmunds, Sebastian Funk, Thibaut Jombart:
  Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics.
• 
  Nicole Pearcy, Marco Garavaglia, Thomas Millat, James P. Gilbert, Yoseb Song, Hassan Hartman, Craig Woods, Claudio Tomi-Andrino, Rajesh Reddy Bommareddy, Byung-Kwan Cho, David A. Fell, Mark Poolman, John R. King, Klaus Winzer, Jamie Twycross, Nigel P. Minton:
  A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications.
• 
  Nicolò Gozzi, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana L. Pastore y Piontti, Marco Ajelli, Nicola Perra, Alessandro Vespignani:
  Anatomy of the first six months of COVID-19 vaccination campaign in Italy.
• 
  Li Na Zhao, Philipp Kaldis:
  The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2).
• 
  Luis Fernando Montaño-Gutierrez, Nahuel Manzanaro Moreno, Iseabail L. Farquhar, Yu Huo, Lucia Bandiera, Peter S. Swain:
  Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.
• 
  Alberto Pérez de Alba Ortíz, Jocelyne Vreede, Bernd Ensing:
  Sequence dependence of transient Hoogsteen base pairing in DNA.
• 
  Maximilian Puelma Touzel, Paul Cisek, Guillaume Lajoie:
  Performance-gated deliberation: A context-adapted strategy in which urgency is opportunity cost.
• 
  Konstantin Röder, Amy M. Barker, Adrian Whitehouse, Samuela Pasquali:
  Investigating the structural changes due to adenosine methylation of the Kaposi's sarcoma-associated herpes virus ORF50 transcript.
• 
  Edward D. Lee, Xiaowen Chen, Bryan C. Daniels:
  Discovering sparse control strategies in neural activity.
• 
  Trystan Leng, Edward M. Hill, Robin N. Thompson, Michael J. Tildesley, Matt J. Keeling, Louise Dyson:
  Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study.
• 
  Justin Dean, Evan Goldberg, Franziska Michor:
  Designing optimal allocations for cancer screening using queuing network models.
• 
  Ángel Ramos-de-Miguel, José M. Escobar, David Greiner, Domingo Benitez, Eduardo Rodríguez, Albert Oliver, Marcos Hernández, Ángel Ramos-Macías:
  A phenomenological computational model of the evoked action potential fitted to human cochlear implant responses.
• 
  Moritz Möller, Sanjay G. Manohar, Rafal Bogacz:
  Uncertainty-guided learning with scaled prediction errors in the basal ganglia.
• 
  Laura Moody, Guanying Bianca Xu, Yuan-Xiang Pan, Hong Chen:
  Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors.
• 
  Luis Vitores Valcarcel, Edurne San José-Enériz, Xabier Cendoya, Ángel Rubio, Xabier Agirre, Felipe Prósper, Francisco J. Planes:
  BOSO: A novel feature selection algorithm for linear regression with high-dimensional data.
• 
  Emily K. Makowski, John S. Schardt, Matthew D. Smith, Peter M. Tessier:
  Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape.
• 
  Omer Acar, She Zhang, Ivet Bahar, Anne-Ruxandra Carvunis:
  Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.
• 
  Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen, Pjotr Prins:
  A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.

Corrections

• 
  Benjamin L. Moore, Patricia Carvajal López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, Nicola J. Mulder:
  Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.
• 
  Cristóbal Rodero, Marina Strocchi, Maciej Marciniak, Stefano Longobardi, John Whitaker, Mark D. O'Neill, Karli Gillette, Christoph M. Augustin, Gernot Plank, Edward J. Vigmond, Pablo Lamata, Steven A. Niederer:
  Correction: Linking statistical shape models and simulated function in the healthy adult human heart.

Volume 18, Number 6, June 2022

Editorials

• 
  Lauren Cadwallader, Feilim Mac Gabhann, Jason A. Papin, Virginia E. Pitzer:
  Advancing code sharing in the computational biology community.
• 
  Melanie Duc Bo Massey, Suchinta Arif, Shanukie Embuldeniya, Karma Nanglu, Joseph P. Bielawski:
  Ten simple rules for succeeding as an underrepresented STEM undergraduate.
• 
  Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia M. Palagi, Lars G. Hemkens, Meike Ramon, Nicolas Rothen, Stephen Senn, Eva Furrer, Leonhard Held:
  Ten simple rules for good research practice.

Education

• 
  Robert Muscarella, Lourens Poorter:
  Ten simple rules for managing communications with a large number of coauthors.

Perspectives

• 
  Philip E. Bourne:
  Ten simple rules for good leadership.
• 
  Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne:
  Ten simple rules for improving communication among scientists.

Research Articles

• 
  Hillary A. Raab, Careen Foord, Romain Ligneul, Catherine A. Hartley:
  Developmental shifts in computations used to detect environmental controllability.
• 
  Alaina Shumate, Brandon M. Wong, Geo Pertea, Mihaela Pertea:
  Improved transcriptome assembly using a hybrid of long and short reads with StringTie.
• 
  Nicholas J. Beeton, Andrew Wilkins, Adrien Ickowicz, Keith R. Hayes, Geoffrey R. Hosack:
  Spatial modelling for population replacement of mosquito vectors at continental scale.
• 
  Xingyue Guan, Cheng Tan, Wenfei Li, Wei Wang, D. Thirumalai:
  Role of water-bridged interactions in metal ion coupled protein allostery.
• 
  Nadezhda M. Belonogova, Gulnara R. Svishcheva, Anatoly V. Kirichenko, Irina V. Zorkoltseva, Yakov A. Tsepilov, Tatiana I. Axenovich:
  sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics.
• 
  Natalia Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak:
  fingeRNAt - A novel tool for high-throughput analysis of nucleic acid-ligand interactions.
• 
  Quan Wan, Jorge A. Menendez, Bradley R. Postle:
  Priority-based transformations of stimulus representation in visual working memory.
• 
  Aranyak Chakravarty, Mahesh V. Panchagnula, Alladi Mohan, Neelesh A. Patankar:
  Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model.
• 
  Rishabh Rishabh, Hadi Zadeh-Haghighi, Dennis R. Salahub, Christoph Simon:
  Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis.
• 
  Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak, Thierry Mora:
  Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies.
• 
  Anne Bertolini, Michael Prummer, Mustafa Anil Tuncel, Ulrike Menzel, María Lourdes Rosano-González, Jack Kuipers, Daniel J. Stekhoven, Tumor Profiler Consortium, Niko Beerenwinkel, Franziska Singer:
  scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.
• 
  Evgenii Kliuchnikov, Artem A. Zhmurov, Kenneth A. Marx, Alex Mogilner, Valeri Barsegov:
  CellDynaMo-stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly.
• 
  Lauren J. Beesley, Dave Osthus, Sara Y. Del Valle:
  Addressing delayed case reporting in infectious disease forecast modeling.
• 
  Danial Lashgari, Elena Merino Tejero, Michael Meyer-Hermann, Mathieu A. F. Claireaux, Marit J. van Gils, Huub C. J. Hoefsloot, Antoine H. C. van Kampen:
  From affinity selection to kinetic selection in Germinal Centre modelling.
• 
  Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen:
  A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait.
• 
  Maryam Sabzevari, Sándor Szedmák, Merja Penttilä, Paula Jouhten, Juho Rousu:
  Strain design optimization using reinforcement learning.
• 
  Moein Khalighi, Guilhem Sommeria-Klein, Didier Gonze, Karoline Faust, Leo Lahti:
  Quantifying the impact of ecological memory on the dynamics of interacting communities.
• 
  Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray:
  Induced fit with replica exchange improves protein complex structure prediction.
• 
  Adriana Gaia Cairelli, Renee Wei-Yan Chow, Julien Vermot, Choon Hwai Yap:
  Fluid mechanics of the zebrafish embryonic heart trabeculation.
• 
  Zhenhao Zhang, Fan Feng, Jie Liu:
  Characterizing collaborative transcription regulation with a graph-based deep learning approach.
• 
  Jasmin L. Walter, Lucas Essmann, Sabine U. König, Peter König:
  Finding landmarks - An investigation of viewing behavior during spatial navigation in VR using a graph-theoretical analysis approach.
• 
  Aghil Abed Zadeh, Brandon D. Turner, Nicole Calakos, Nicolas Brunel:
  Non-monotonic effects of GABAergic synaptic inputs on neuronal firing.
• 
  Hyun Kim, Cheolhong Min, Byeongha Jeong, Kyoung J. Lee:
  Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics.
• 
  María Hernández Mesa, Jonas van den Brink, William E. Louch, Kimberly J. McCabe, Padmini Rangamani:
  Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks.
• 
  Colin Thomas, Maximilien Cosme, Cédric Gaucherel, Franck Pommereau:
  Model-checking ecological state-transition graphs.
• 
  Colin Campbell, Laura Russo, Réka Albert, Angus Buckling, Katriona Shea:
  Whole community invasions and the integration of novel ecosystems.
• 
  Tinghua Huang, Hong Xiao, Qi Tian, Zhen He, Cheng Yuan, Zezhao Lin, Xuejun Gao, Min Yao:
  Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.
• 
  Tom Van Wouwe, Lena H. Ting, Friedl De Groote:
  An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise.
• 
  Florian Auer, Simone Mayer, Frank Kramer:
  Data-dependent visualization of biological networks in the web-browser with NDExEdit.
• 
  Yongze Yin, Huw A. Ogilvie, Luay Nakhleh:
  Annotation-free delineation of prokaryotic homology groups.
• 
  Niranjan Sarpangala, Ajay Gopinathan:
  Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors.
• 
  Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge:
  Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence.
• 
  Israel Ukawuba, Jeffrey Shaman:
  Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission.
• 
  Benjamin Gagl, Fabio Richlan, Philipp Ludersdorfer, Jona Sassenhagen, Susanne Eisenhauer, Klara Gregorova, Christian J. Fiebach:
  The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition.
• 
  Pratik Mullick, Sylvain Fontaine, Cécile Appert-Rolland, Anne-Hélène Olivier, William H. Warren, Julien Pettré:
  Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of 'stripe' formation in human data.
• 
  Justinas Cesonis, David W. Franklin:
  Contextual cues are not unique for motor learning: Task-dependant switching of feedback controllers.
• 
  Elke Smith, Jan Peters:
  Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice.
• 
  Maksim V. Zakhartsev, Filip Rotnes, Marie Gulla, Ove Øyås, Jesse C. J. van Dam, María Suárez-Diez, Fabian Grammes, Róbert Anton Hafþórsson, Wout van Helvoirt, Jasper J. Koehorst, Peter J. Schaap, Yang Jin, Liv Torunn Mydland, Arne B. Gjuvsland, Simen R. Sandve, Vítor A. P. Martins dos Santos, Jon Olav Vik:
  SALARECON connects the Atlantic salmon genome to growth and feed efficiency.
• 
  Anika Liu, Namshik Han, Jordi Muñoz-Muriedas, Andreas Bender:
  Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI).
• 
  Qing Xie, Chenggong Han, Victor Jin, Shili Lin:
  HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data.
• 
  Alfonso Santiago, Constantine Butakoff, Beatriz Eguzkitza, Richard A. Gray, Karen May-Newman, Pras Pathmanathan, Vi Vu, Mariano Vázquez:
  Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation.
• 
  Sang-Woo Lee, Yoshihiro Morishita:
  Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue.
• 
  Rachel Mester, Alfonso Landeros, Chris Rackauckas, Kenneth Lange:
  Differential methods for assessing sensitivity in biological models.
• 
  Arun S. Mahadevan, Byron L. Long, Chenyue W. Hu, David T. Ryan, Nicolas E. Grandel, George L. Britton, Marisol Bustos, Maria A. Gonzalez Porras, Katerina Stojkova, Andrew Ligeralde, Hyeonwi Son, John Shannonhouse, Jacob T. Robinson, Aryeh Warmflash, Eric M. Brey, Yu Shin Kim, Amina A. Qutub:
  cytoNet: Spatiotemporal network analysis of cell communities.
• 
  Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret:
  Discrete modeling for integration and analysis of large-scale signaling networks.
• 
  Thiago T. Varella, Yisi S. Zhang, Daniel Y. Takahashi, Asif A. Ghazanfar:
  A mechanism for punctuating equilibria during mammalian vocal development.
• 
  Erik J. Navarro, Wallace F. Marshall, Jennifer C. Fung:
  Modeling cell biological features of meiotic chromosome pairing to study interlock resolution.
• 
  Parvin Zarei Eskikand, Katerina Koussoulas, Rachel M. Gwynne, Joel C. Bornstein:
  Computational simulations and Ca2+ imaging reveal that slow synaptic depolarizations (slow EPSPs) inhibit fast EPSP evoked action potentials for most of their time course in enteric neurons.
• 
  Laura Schmid, Christian Hilbe, Krishnendu Chatterjee, Martin A. Nowak:
  Direct reciprocity between individuals that use different strategy spaces.
• 
  Beatriz Eymi Pimentel Mizusaki, Sally Si Ying Li, Rui Ponte Costa, Per Jesper Sjöström:
  Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning.
• 
  Jin Wang, Liang-Chih Yu, Xuejie Zhang:
  Explainable detection of adverse drug reaction with imbalanced data distribution.
• 
  Thao Vu, Julia Wrobel, Benjamin G. Bitler, Erin L. Schenk, Kimberly R. Jordan, Debashis Ghosh:
  SPF: A spatial and functional data analytic approach to cell imaging data.
• 
  Shuolun Wang, Kengo Saito, Hiroshi Kawasaki, Maria A. Holland:
  Orchestrated neuronal migration and cortical folding: A computational and experimental study.
• 
  Mahmudul Hasan Rifat, Jamil Ahmed, Milad Ahmed, Foeaz Ahmed, Airin Gulshan, Mahmudul Hasan:
  Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.
• 
  Yuxuan Li, James L. McClelland:
  A weighted constraint satisfaction approach to human goal-directed decision making.
• 
  Antonella Maselli, Pablo Lanillos, Giovanni Pezzulo:
  Active inference unifies intentional and conflict-resolution imperatives of motor control.
• 
  Shengbo Wang, David García-Seisdedos, Ananth Prakash, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Silvie Fexova, Pablo A. Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno:
  Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
• 
  Deb Sankar Banerjee, Shiladitya Banerjee:
  Size regulation of multiple organelles competing for a limiting subunit pool.
• 
  Luyan Yu, Thibaud O. Taillefumier:
  Metastable spiking networks in the replica-mean-field limit.
• 
  Kayson Fakhar, Claus C. Hilgetag:
  Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain.
• 
  Simon Martina Perez, Heba Sailem, Ruth E. Baker:
  Efficient Bayesian inference for mechanistic modelling with high-throughput data.
• 
  Toshitake Asabuki, Prajakta Kokate, Tomoki Fukai:
  Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data.
• 
  Brett W. Larsen, Shaul Druckmann:
  Towards a more general understanding of the algorithmic utility of recurrent connections.
• 
  Mikahl Banwarth-Kuhn, Kevin Rodriguez, Christian Michael, Calvin-Khang Ta, Alexander Plong, Eric Bourgain-Chang, Ali Nematbakhsh, Weitao Chen, Amit K. Roy-Chowdhury, G. Venugopala Reddy, Mark S. Alber:
  Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance.
• 
  Cristiano Capone, Paolo Muratore, Pier Stanislao Paolucci:
  Error-based or target-based? A unified framework for learning in recurrent spiking networks.
• 
  Christos Maniatis, Catalina A. Vallejos, Guido Sanguinetti:
  SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data.
• 
  Younes Bouhadjar, Dirk J. Wouters, Markus Diesmann, Tom Tetzlaff:
  Sequence learning, prediction, and replay in networks of spiking neurons.
• 
  Timon Wittenstein, Nava Leibovich, Andreas Hilfinger:
  Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks.
• 
  Joanneke E. Jansen, Dominik Aschenbrenner, Holm H. Uhlig, Mark C. Coles, Eamonn A. Gaffney:
  A method for the inference of cytokine interaction networks.
• 
  Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman:
  Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases.
• 
  Reem Khalil, Sadok Kallel, Ahmad Farhat, Pawel Dlotko:
  Topological Sholl descriptors for neuronal clustering and classification.
• 
  Balázs Török, David G. Nagy, Mariann Kiss, Karolina Janacsek, Dezso Németh, Gergo Orbán:
  Tracking the contribution of inductive bias to individualised internal models.
• 
  Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas Böttcher, Dmitry Burov, Alfredo Garbuno-Inigo, Gregory LeClaire Wagner, Sen Pei, Chiara Daraio, Raffaele Ferrari, Jeffrey Shaman:
  Epidemic management and control through risk-dependent individual contact interventions.
• 
  Goshi Ogita, Takefumi Kondo, Keisuke Ikawa, Tadashi Uemura, Shuji Ishihara, Kaoru Sugimura:
  Image-based parameter inference for epithelial mechanics.
• 
  Christoph Feinauer, Barthélémy Meynard-Piganeau, Carlo Lucibello:
  Interpretable pairwise distillations for generative protein sequence models.
• 
  Bolaji Eniwaye, Victoria Booth, Anthony G. Hudetz, Michal Zochowski:
  Modeling cortical synaptic effects of anesthesia and their cholinergic reversal.
• 
  Hasini R. Weerathunge, Gabriel A. Alzamendi, Gabriel J. Cler, Frank H. Guenther, Cara E. Stepp, Matías Zañartu:
  LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production.
• 
  Catalina Vich, Matthew Clapp, Jonathan E. Rubin, Timothy D. Verstynen:
  Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit.
• 
  Naomi R. Waterlow, Michiko Toizumi, Edwin van Leeuwen, Hien-Anh Thi Nguyen, Lay Myint-Yoshida, Rosalind M. Eggo, Stefan Flasche:
  Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study.
• 
  Hamid Alinejad-Rokny, Rassa Ghavami Modegh, Hamid R. Rabiee, Ehsan Ramezani Sarbandi, Narges Rezaie, Kin Tung Tam, Alistair R. R. Forrest:
  MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments.
• 
  Vítor Vieira, Jorge Ferreira, Miguel Rocha:
  A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale.
• 
  Jeremy Grignard, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval, François Fages:
  Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design.
• 
  Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Loewer, Mária Lukácová-Medvid'ová, Stefan Legewie:
  Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling.
• 
  Jair Andrade, Jim Duggan:
  Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data.
• 
  Yuliang Chen, Tao Liu, Xiaolin Yu, Qinghui Zeng, Zixi Cai, Haisheng Wu, Qingying Zhang, Jianpeng Xiao, Wenjun Ma, Sen Pei, Pi Guo:
  An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China.
• 
  Laurynas Kalesinskas, Sanjana Gupta, Purvesh Khatri:
  Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology.
• 
  Yili Zhang, Paul Smolen, Cristina M. Alberini, Douglas A. Baxter, John H. Byrne:
  Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIα and MeCP2.
• 
  Raphael R. Eguchi, Christian A. Choe, Po-Ssu Huang:
  Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation.
• 
  Gabriel Monteiro da Silva, Jordan Yang, Bunlong Leang, Jessie Huang, Daniel M. Weinreich, Brenda M. Rubenstein:
  Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase.
• 
  Shi Zhao, Marc K. C. Chong, Sukhyun Ryu, Zihao Guo, Mu He, Boqiang Chen, Salihu Sabiu Musa, Jingxuan Wang, Yushan Wu, Daihai He, Maggie Haitian Wang:
  Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility.
• 
  Verónica S. Martínez, Pedro A. Saa, Jason Jooste, Kanupriya Tiwari, Lake-Ee Quek, Lars Keld Nielsen:
  The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility.
• 
  Alex X. Lu, Amy X. Lu, Iva Pritisanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses:
  Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning.

Corrections

• 
  Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks:
  Correction: Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome.
• 
  Daniel A. Burbano L., Maurizio Porfiri:
  Correction: Modeling multi-sensory feedback control of zebrafish in a flow.
• 
  Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber:
  Correction: A probabilistic model for the ultradian timing of REM sleep in mice.
• 
  Richard F. Betzel, Katherine C. Wood, Christopher Angeloni, Maria N. Geffen, Danielle S. Bassett:
  Correction: Stability of spontaneous, correlated activity in mouse auditory cortex.
• 
  Ilya Plyusnin, Liisa Holm, Petri Törönen:
  Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
• 
  Huaming Yan, Daniel Ramirez-Guerrero, John S. Lowengrub, Min Wu:
  Correction: Stress generation, relaxation and size control in confined tumor growth.

Volume 18, Number 7, July 2022

Editorial

• 
  Rocío Joo, Andrea Sánchez-Tapia, Sara Mortara, Yanina Bellini Saibene, Heather L. Turner, Dorothea Hug Peter, Natalia Soledad Morandeira, Matt Bannert, Batool Almazrouq, Elizabeth Hare, Laura Ación, Juan Pablo Narváez-Gómez, Marcela Alfaro Cordoba, Federico Marini, Rita Giordano, Silvia Canelón, Anicet Ebou, Adithi R. Upadhya, Joselyn Chávez, Janani Ravi:
  Ten simple rules to host an inclusive conference.

Education

• 
  Rochelle-Jan Reyes, Nina Hosmane, Shasta Ihorn, Milo Johnson, Anagha Kulkarni, Jennifer Nelson, Michael Savvides, Duc Ta, Ilmi Yoon, Pleuni S. Pennings:
  Ten simple rules for designing and running a computing minor for bio/chem students.

Perspectives

• 
  Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L. Morgan:
  Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.
• 
  Sanne ten Oever, Karthikeya Ramesh Kaushik, Andrea E. Martin:
  Inferring the nature of linguistic computations in the brain.

Research Articles

• 
  Fabian Santiago, Suzanne S. Sindi:
  A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission.
• 
  Minh Son Phan, Katherine Matho, Emmanuel Beaurepaire, Jean Livet, Anatole Chessel:
  nAdder: A scale-space approach for the 3D analysis of neuronal traces.
• 
  Saleh Fayaz, Mohammad Amin Fakharian, Ali Ghazizadeh:
  Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions.
• 
  Bodhayan Prasad, Cathy M. McGeough, Amanda Eakin, Tan Ahmed, Dawn Small, Philip Gardiner, Adrian Pendleton, Gary Wright, Anthony J. Bjourson, David S. Gibson, Priyank Shukla:
  ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients.
• 
  Adrian Verster, Nicholas Petronella, Judy Green, Fernando Matias, Stephen P. J. Brooks:
  A Bayesian method for identifying associations between response variables and bacterial community composition.
• 
  Felix Molter, Armin W. Thomas, Scott A. Huettel, Hauke R. Heekeren, Peter N. C. Mohr:
  Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour.
• 
  Maxine T. Sherman, Zafeirios Fountas, Anil K. Seth, Warrick Roseboom:
  Trial-by-trial predictions of subjective time from human brain activity.
• 
  Vivian B. Brandenburg, Franz Narberhaus, Axel Mosig:
  Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators.
• 
  Barbara Schnitzer, Linnea Österberg, Iro Skopa, Marija Cvijovic:
  Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing.
• 
  Muriel M. Heldring, Lukas S. Wijaya, Marije Niemeijer, Huan Yang, Talel Lakhal, Sylvia Le Dévédec, Bob van de Water, Joost B. Beltman:
  Model-based translation of DNA damage signaling dynamics across cell types.
• 
  Alina A. Studenova, Arno Villringer, Vadim V. Nikulin:
  Non-zero mean alpha oscillations revealed with computational model and empirical data.
• 
  Joseph Chadi Lemaitre, Damiano Pasetto, Mario Zanon, Enrico Bertuzzo, Lorenzo Mari, Stefano Miccoli, Renato Casagrandi, Marino Gatto, Andrea Rinaldo:
  Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study.
• 
  Qilin Yu, Taeyoon Kim, Vijay Rajagopal:
  Role of actin filaments and cis binding in cadherin clustering and patterning.
• 
  Michelle J. Redinbaugh, Mohsen Afrasiabi, Jessica M. Phillips, Niranjan A. Kambi, Sounak Mohanta, Aeyal Raz, Yuri B. Saalmann:
  Thalamic deep brain stimulation paradigm to reduce consciousness: Cortico-striatal dynamics implicated in mechanisms of consciousness.
• 
  Hyojung Paik, Jimin Kim, Sangjae Seo:
  Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort.
• 
  Stav Marcus, Ari M. Turner, Guy Bunin:
  Local and collective transitions in sparsely-interacting ecological communities.
• 
  Kimberly Roche, Sayan Mukherjee:
  The accuracy of absolute differential abundance analysis from relative count data.
• 
  Hongli Ma, Han Wen, Zhiyuan Xue, Guojun Li, Zhaolei Zhang:
  RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.
• 
  Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang:
  AC-PCoA: Adjustment for confounding factors using principal coordinate analysis.
• 
  Fabian Fröhlich, Peter K. Sorger:
  Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models.
• 
  Chintan J. Joshi, Wenfan Ke, Anna Drangowska-Way, Eyleen J. O'Rourke, Nathan E. Lewis:
  What are housekeeping genes?
• 
  Edward M. Hill, Naomi S. Prosser, Eamonn Ferguson, Jasmeet Kaler, Martin J. Green, Matt J. Keeling, Michael J. Tildesley:
  Modelling livestock infectious disease control policy under differing social perspectives on vaccination behaviour.
• 
  Isaac Fradkin, Eran Eldar:
  If you don't let it in, you don't have to get it out: Thought preemption as a method to control unwanted thoughts.
• 
  Yuanhao Huang, Bingjiang Wang, Jie Liu:
  NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.
• 
  Long Liu, Qingyu Meng, Cherry Weng, Qing Lu, Tong Wang, Yalu Wen:
  Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data.
• 
  Tomoki Yoneyama, Mi-Sook Kim, Konstantin Piatkov, Haiqing Wang, Andy Z. X. Zhu:
  Leveraging a physiologically-based quantitative translational modeling platform for designing B cell maturation antigen-targeting bispecific T cell engagers for treatment of multiple myeloma.
• 
  Uria Mor, Yotam Cohen, Rafael Valdes-Mas, Denise Kviatcovsky, Eran Elinav, Haim Avron:
  Dimensionality reduction of longitudinal 'omics data using modern tensor factorizations.
• 
  Chirag Gupta, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, Daifeng Wang:
  Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease.
• 
  Jennifer Brennan, Lalit Jain, Sofia Garman, Ann E. Donnelly, Erik Scott Wright, Kevin G. Jamieson:
  Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design.
• 
  Eran Stark, Amir Levi, Horacio G. Rotstein:
  Network resonance can be generated independently at distinct levels of neuronal organization.
• 
  Jose M. Jimenez-Guardeño, Ana Maria Ortega-Prieto, Borja Menendez Moreno, Thomas J. A. Maguire, Adam Richardson, Juan Ignacio Diaz-Hernandez, Javier Díez-Pérez, Mark Zuckerman, Albert Mercadal Playa, Carlos Cordero Deline, Michael H. Malim, Rocio Teresa Martinez-Nunez:
  Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2.
• 
  Nicolai Pedersen, Torsten Dau, Lars Kai Hansen, Jens Hjortkjær:
  Modulation transfer functions for audiovisual speech.
• 
  Tahra L. Eissa, Joshua I. Gold, Kresimir Josic, Zachary P. Kilpatrick:
  Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence.
• 
  Seth Blumberg, Phoebe Lu, Ada T. Kwan, Christopher M. Hoover, James O. Lloyd-Smith, David Sears, Stefano M. Bertozzi, Lee Worden:
  Modeling scenarios for mitigating outbreaks in congregate settings.
• 
  Monika Richter-Laskowska, Paulina Trybek, Piotr Bednarczyk, Agata Wawrzkiewicz-Jalowiecka:
  To what extent naringenin binding and membrane depolarization shape mitoBK channel gating - A machine learning approach.
• 
  Madeline Galbraith, Federico Bocci, José N. Onuchic:
  Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.
• 
  Kevin Christopher VanHorn, Murat Can Çobanoglu:
  Haisu: Hierarchically supervised nonlinear dimensionality reduction.
• 
  Kenway Louie:
  Asymmetric and adaptive reward coding via normalized reinforcement learning.
• 
  Lisa Blum Moyse, Hugues Berry:
  Modelling the modulation of cortical Up-Down state switching by astrocytes.
• 
  Yu Hu, Haim Sompolinsky:
  The spectrum of covariance matrices of randomly connected recurrent neuronal networks with linear dynamics.
• 
  Victor Boutin, Angelo Franciosini, Frédéric Chavane, Laurent U. Perrinet:
  Pooling strategies in V1 can account for the functional and structural diversity across species.
• 
  Szymon Wisniewski, Paulina Dragan, Anna Makal, Dorota Latek:
  Helix 8 in chemotactic receptors of the complement system.
• 
  Alvaro Ruiz-Martinez, Chang Gong, Hanwen Wang, Richard J. Sové, Haoyang Mi, Holly Kimko, Aleksander S. Popel:
  Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model.
• 
  Hélène Cecilia, Roosmarie Vriens, Paul J. Wichgers Schreur, Mariken M. de Wit, Raphaëlle Métras, Pauline Ezanno, Quirine A. ten Bosch:
  Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection.
• 
  Changyoung Yuhn, Marie Oshima, Yan Chen, Motoharu Hayakawa, Shigeki Yamada:
  Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning.
• 
  Erin Angelini, Yue Wang, Joseph Xu Zhou, Hong Qian, Sui Huang:
  A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness.
• 
  Matthew S. Mietchen, Christopher T. Short, Matthew Samore, Eric T. Lofgren:
  Examining the impact of ICU population interaction structure on modeled colonization dynamics of Staphylococcus aureus.
• 
  Joseph M. Barnby, Mitul A. Mehta, Michael Moutoussis:
  The computational relationship between reinforcement learning, social inference, and paranoia.
• 
  Omer Karin, Uri Alon:
  The dopamine circuit as a reward-taxis navigation system.
• 
  Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee, Tim Regan, Barbara B. Shih, James G. D. Prendergast, David A. Hume, Tim Angus:
  Graphia: A platform for the graph-based visualisation and analysis of high dimensional data.
• 
  Takeshi Sugawara, Kunihiko Kaneko:
  Chemophoresis engine: A general mechanism of ATPase-driven cargo transport.
• 
  Hélène Chabas, Viktor Müller, Sebastian Bonhoeffer, Roland R. Regoes:
  Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.
• 
  Shannon M. Locke, Michael S. Landy, Pascal Mamassian:
  Suprathreshold perceptual decisions constrain models of confidence.
• 
  Alexander Kier Christensen, Matthew D. Piggott, Erik van Sebille, Maarten van Reeuwijk, Samraat Pawar:
  Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer.
• 
  Alexander S. Moffett, Peter J. Thomas, Michael Hinczewski, Andrew W. Eckford:
  Cheater suppression and stochastic clearance through quorum sensing.
• 
  Md. Rafiul Amin, Rose T. Faghih:
  Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference.
• 
  Jiaye Tao, Heping Wang, Wenjian Wang, Na Mi, Wei Zhang, Qiujia Wen, Jiajing Ouyang, Xinyun Liang, Min Chen, Wentao Guo, Guoming Li, Jun Liu, Hanning Zhao, Xin Wang, Xuemeng Li, Shengjun Feng, Xinguang Liu, Zhiwei He, Zuguo Zhao:
  Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs.

Volume 18, Number 8, August 2022

Editorial

• 
  Philipp Baumert, Francesco Cenni, Mikhail L. Antonkine:
  Ten simple rules for a successful EU Marie Skłodowska-Curie Actions Postdoctoral (MSCA) fellowship application.

Education Articles

• 
  Sara Gonzales, Matthew B. Carson, Kristi L. Holmes:
  Ten simple rules for maximizing the recommendations of the NIH data management and sharing plan.
• 
  Cristina A. Kita, Guillermo Florez-Montero, Sebastián Montoya-Bustamante, Renata L. Muylaert, Natalya Zapata-Mesa, Marco A. R. Mello:
  Ten simple rules for reporting information on species interactions.
• 
  Ramón Díaz-Uriarte, Elisa Gómez de Lope, Rosalba Giugno, Holger Fröhlich, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Armin Rauschenberger, Enrico Glaab:
  Ten quick tips for biomarker discovery and validation analyses using machine learning.
• 
  Davide Chicco, Giuseppe Agapito:
  Nine quick tips for pathway enrichment analysis.
• 
  Davide Chicco, Philip E. Bourne:
  Ten simple rules for organizing a special session at a scientific conference.

Research Articles

• 
  Nora Heitzman-Breen, Stanca M. Ciupe:
  Modeling within-host and aerosol dynamics of SARS-CoV-2: The relationship with infectiousness.
• 
  Anup Gopalakrishna Pillai, Suhita Nadkarni:
  Amyloid pathology disrupts gliotransmitter release in astrocytes.
• 
  Grégory Dumont, Alberto Pérez-Cervera, Boris S. Gutkin:
  A framework for macroscopic phase-resetting curves for generalised spiking neural networks.
• 
  Klara Elisabeth Burger, Peter Pfaffelhuber, Franz Baumdicker:
  Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown.
• 
  Rachit Dubey, Thomas L. Griffiths, Peter Dayan:
  The pursuit of happiness: A reinforcement learning perspective on habituation and comparisons.
• 
  Lu Li, Jiho Sohn, Robert J. Genco, Jean Wactawski-Wende, Steve Goodison, Patricia I. Diaz, Yijun Sun:
  Computational approach to modeling microbiome landscapes associated with chronic human disease progression.
• 
  Yidan Xue, Theodosia Georgakopoulou, Anne-Eva van der Wijk, Tamás I. Józsa, Ed van Bavel, Stephen J. Payne:
  Quantification of hypoxic regions distant from occlusions in cerebral penetrating arteriole trees.
• 
  Luca Manneschi, Guido Gigante, Eleni Vasilaki, Paolo Del Giudice:
  Signal neutrality, scalar property, and collapsing boundaries as consequences of a learned multi-timescale strategy.
• 
  Anastasios Marantos, Namiko Mitarai, Kim Sneppen:
  From kill the winner to eliminate the winner in open phage-bacteria systems.
• 
  Niklas Birth, Thomas Dencker, Burkhard Morgenstern:
  Insertions and deletions as phylogenetic signal in an alignment-free context.
• 
  Abdulwahab Alasfour, Paolo Gabriel, Xi Jiang, Isaac Shamie, Lucia Melloni, Thomas Thesen, Patricia Dugan, Daniel Friedman, Werner K. Doyle, Orrin Devinsky, David Gonda, Shifteh Sattar, Sonya Wang, Eric Halgren, Vikash Gilja:
  Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states.
• 
  Elizabeth Herbert, Srdjan Ostojic:
  The impact of sparsity in low-rank recurrent neural networks.
• 
  Oliver Ocsenas, Jüri Reimand:
  Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin.
• 
  Xiyun Zhang, Gabriela Lobinska, Michal Feldman, Eddie Dekel, Martin A. Nowak, Yitzhak Pilpel, Yonatan Pauzner, Baruch Barzel, Ady Pauzner:
  A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.
• 
  Ofra Amir, Liron Tyomkin, Yuval Hart:
  Adaptive search space pruning in complex strategic problems.
• 
  Jennifer A. Flegg, Georgina S. Humphreys, Brenda Montanez, Taryn Strickland, Zaira J. Jacome-Meza, Karen I. Barnes, Jaishree Raman, Philippe J. Guerin, Carol Hopkins Sibley, Sabina Dahlström Otienoburu:
  Spatiotemporal spread of Plasmodium falciparum mutations for resistance to sulfadoxine-pyrimethamine across Africa, 1990-2020.
• 
  Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice C. McHardy:
  Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.
• 
  Amit Singh, Congxin Li, Axel C. R. Diernfellner, Thomas Höfer, Michael Brunner:
  Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa.
• 
  You Wu, Qiao Liu, Yue Qiu, Lei Xie:
  Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's disease drug repurposing.
• 
  Espen Hagen, Steinn H. Magnusson, Torbjørn V. Ness, Geir Halnes, Pooja N. Babu, Charl A. P. Linssen, Abigail Morrison, Gaute T. Einevoll:
  Brain signal predictions from multi-scale networks using a linearized framework.
• 
  Sergio Marco Salas, Xiao Yuan, Christer Sylven, Mats F. Nilsson, Carolina Wählby, Gabriele Partel:
  De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.
• 
  Christopher Gagne, Sharon Agai, Christian Ramiro, Peter Dayan, Sonia J. Bishop:
  Biased belief priors versus biased belief updating: Differential correlates of depression and anxiety.
• 
  Georgia Christodoulou, Tim P. Vogels, Everton J. Agnes:
  Regimes and mechanisms of transient amplification in abstract and biological neural networks.
• 
  Michal Ben-Nun, Pete Riley, James Turtle, Steven Riley:
  Consistent pattern of epidemic slowing across many geographies led to longer, flatter initial waves of the COVID-19 pandemic.
• 
  Priyojit Das, Tongye Shen, Rachel Patton McCord:
  Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment.
• 
  Pau Casanova-Ferrer, Saúl Ares, Javier Muñoz-García:
  Terminal heterocyst differentiation in the Anabaena patA mutant as a result of post-transcriptional modifications and molecular leakage.
• 
  Wenxiang Zhang, Jialu Hou, Bin Liu:
  iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank.
• 
  Amir Akbari, Bernhard O. Palsson:
  Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.
• 
  Jian-Qiao Zhu, Pablo León-Villagrá, Nick Chater, Adam N. Sanborn:
  Understanding the structure of cognitive noise.
• 
  Shenglai Yin, Yanjie Xu, Mingshuai Xu, Mart C. M. de Jong, Mees R. S. Huisman, Andrea Contina, Herbert H. T. Prins, Zheng Y. X. Huang, Willem F. de Boer:
  Habitat loss exacerbates pathogen spread: An Agent-based model of avian influenza infection in migratory waterfowl.
• 
  Ximena G. Arceo, Elena F. Koslover, Brian M. Zid, Aidan I. Brown:
  Mitochondrial mRNA localization is governed by translation kinetics and spatial transport.
• 
  Alan Novaes Tump, Max Wolf, Pawel Romanczuk, Ralf H. J. M. Kurvers:
  Avoiding costly mistakes in groups: The evolution of error management in collective decision making.
• 
  Pierre Barrat-Charlaix, Timothy G. Vaughan, Richard A. Neher:
  TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
• 
  Fangfang Guo, Ignazio Carbone, David A. Rasmussen:
  Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination.
• 
  José L. Herrera-Diestra, Michael J. Tildesley, Katriona Shea, Matthew J. Ferrari:
  Cattle transport network predicts endemic and epidemic foot-and-mouth disease risk on farms in Turkey.
• 
  Adam Y. Li, Amber Mueller, Brad English, Anthony Arena, Daniel Vera, Alice E. Kane, David A. Sinclair:
  Novel feature selection methods for construction of accurate epigenetic clocks.
• 
  Enze Liu, Xue Wu, Lei Wang, Yang Huo, Huanmei Wu, Lang Li, Lijun Cheng:
  DSCN: Double-target selection guided by CRISPR screening and network.
• 
  Steffen Lange, Richard Mogwitz, Denis Hünniger, Anja Voss-Böhme:
  Modeling age-specific incidence of colon cancer via niche competition.
• 
  Rachel E. Murray-Watson, Frédéric M. Hamelin, Nik J. Cunniffe:
  How growers make decisions impacts plant disease control.
• 
  Elise J. Kuylen, Andrea Torneri, Lander Willem, Pieter J. K. Libin, Steven Abrams, Pietro Coletti, Nicolas Franco, Frederik Verelst, Philippe Beutels, Jori Liesenborgs, Niel Hens:
  Different forms of superspreading lead to different outcomes: Heterogeneity in infectiousness and contact behavior relevant for the case of SARS-CoV-2.
• 
  Alina Batzilla, Junyan Lu, Jarno Kivioja, Kerstin Putzker, Joe Lewis, Thorsten Zenz, Wolfgang Huber:
  Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling.
• 
  Richard A. Stein, Hassane S. Mchaourab:
  SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2.
• 
  Leonie Amstein, Jörg Ackermann, Jennifer Hannig, Ivan Dikic, Simone Fulda, Ina Koch:
  Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis.
• 
  Jana Schirmeyer, Thomas Eick, Eckhard Schulz, Sabine Hummert, Christian Sattler, Ralf Schmauder, Klaus Benndorf:
  Subunit promotion energies for channel opening in heterotetrameric olfactory CNG channels.
• 
  Pouyan Chamanian, Paul G. Higgs:
  Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures.
• 
  Vladimir Shchur, Vadim Spirin, Dmitry Sirotkin, Evgeni Burovski, Nicola De Maio, Russell Corbett-Detig:
  VGsim: Scalable viral genealogy simulator for global pandemic.
• 
  Stan Kerstjens, Gabriela Michel, Rodney J. Douglas:
  Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees.
• 
  Arturo Álvarez-Arenas, Wilfried Souleyreau, Andrea Emanuelli, Lindsay S. Cooley, Jean-Christophe Bernhard, Andreas Bikfalvi, Sébastien Benzekry:
  Practical identifiability analysis of a mechanistic model for the time to distant metastatic relapse and its application to renal cell carcinoma.
• 
  Julia Gimbernat-Mayol, Albert Dominguez Mantes, Carlos D. Bustamante, Daniel Mas Montserrat, Alexander G. Ioannidis:
  Archetypal Analysis for population genetics.
• 
  Emmet A. Francis, Volkmar Heinrich:
  Integrative experimental/computational approach establishes active cellular protrusion as the primary driving force of phagocytic spreading by immune cells.
• 
  Erik Lundgren, Ethan O. Romero-Severson, Jan Albert, Thomas Leitner:
  Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.
• 
  Vaitea Opuu, Nono S. C. Merleau, Vincent Messow, Matteo Smerlak:
  RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.
• 
  Tomas Gavenciak, Joshua Teperowski Monrad, Gavin Leech, Mrinank Sharma, Sören Mindermann, Samir Bhatt, Jan Markus Brauner, Jan Kulveit:
  Seasonal variation in SARS-CoV-2 transmission in temperate climates: A Bayesian modelling study in 143 European regions.
• 
  Claire Miller, Edmund J. Crampin, James M. Osborne:
  Multiscale modelling of desquamation in the interfollicular epidermis.
• 
  Nadav Amir, Naftali Tishby, Israel Nelken:
  A simple model of the attentional blink and its modulation by mental training.
• 
  Elena Piretto, Gianluca Selvaggio, Damiano Bragantini, Enrico Domenici, Luca Marchetti:
  A novel logical model of COVID-19 intracellular infection to support therapies development.
• 
  Naoto Kubota, Mikita Suyama:
  Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits.
• 
  Nika Abdollahi, Lucile Jeusset, Anne Langlois De Septenville, Hugues Ripoche, Frédéric Davi, Juliana S. Bernardes:
  A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data.
• 
  William R. P. Denault, Jon Bohlin, Christian M. Page, Stephen Burgess, Astanand Jugessur:
  Cross-fitted instrument: A blueprint for one-sample Mendelian randomization.
• 
  Marie Chion, Christine Carapito, Frédéric Bertrand:
  Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics.
• 
  Yosuke Tanigawa, Ethan Dyer, Gill Bejerano:
  WhichTF is functionally important in your open chromatin data?
• 
  Melanie H. Chitwood, Marcus Russi, Kenneth Gunasekera, Joshua Havumaki, Fayette Klaassen, Virginia E. Pitzer, Joshua A. Salomon, Nicole A. Swartwood, Joshua L. Warren, Daniel M. Weinberger, Ted Cohen, Nicolas A. Menzies:
  Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model.
• 
  Etienne Moullet, Agnès Roby-Brami, Emmanuel Guigon:
  What is the nature of motor adaptation to dynamic perturbations?

Correction

• 
  Manh Cuong Ngô, Mads Peter Heide-Jørgensen, Susanne Ditlevsen:
  Correction: Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence.

Volume 18, Number 9, September 2022

• 
  Lucie A. Huet, Hannah M. Emnett, Mitra J. Z. Hartmann:
  Demonstration of three-dimensional contact point determination and contour reconstruction during active whisking behavior of an awake rat. 1007763
• 
  Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel:
  Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. 1009767
• 
  Damianos P. Melidis, Christian Landgraf, Gunnar Schmidt, Anja Schöner-Heinisch, Sandra von Hardenberg, Anke Lesinski-Schiedat, Wolfgang Nejdl, Bernd Auber:
  GenOtoScope: Towards automating ACMG classification of variants associated with congenital hearing loss. 1009785
• 
  Yuncong Geng, Christopher Herrick Bohrer, Nicolás Yehya, Hunter Hendrix, Lior I. Shachaf, Jian Liu, Jie Xiao, Elijah Roberts:
  A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation. 1009788
• 
  Elena Zamfir, Peter Dayan:
  Interactions between attributions and beliefs at trial-by-trial level: Evidence from a novel computer game task. 1009920
• 
  Tianqi Yang, Ricardo Henao:
  TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile. 1009921
• 
  Michela Carlotta Massi, Lorenzo Dominoni, Francesca Ieva, Giovanni Fiorito:
  A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis. 1009959
• 
  Mitchel J. Colebank, Naomi C. Chesler:
  An in-silico analysis of experimental designs to study ventricular function: A focus on the right ventricle. 1010017
• 
  Valérie Marot-Lassauzaie, Brigitte Joanne Bouman, Fearghal Declan Donaghy, Yasmin Demerdash, Marieke Alida Gertruda Essers, Laleh Haghverdi:
  Towards reliable quantification of cell state velocities. 1010031
• 
  Lei Yu, Rafael Brüschweiler:
  Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins. 1010036
• 
  Eric Waltari, Saba Nafees, Krista M. McCutcheon, Joan Wong, John E. Pak:
  AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses. 1010052
• 
  Fredrik Orädd, Jonas Hyld Steffen, Pontus Gourdon, Magnus Andersson:
  Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B. 1010074
• 
  Johanna Senk, Birgit Kriener, Mikael Djurfeldt, Nicole Voges, Han-Jia Jiang, Lisa Schüttler, Gabriele Gramelsberger, Markus Diesmann, Hans E. Plesser, Sacha J. van Albada:
  Connectivity concepts in neuronal network modeling. 1010086
• 
  Cong Liu, Kyla Omilusik, Clara Toma, Nadia S. Kurd, John T. Chang, Ananda W. Goldrath, Wei Wang:
  Systems-level identification of key transcription factors in immune cell specification. 1010116
• 
  M. Elise Bullock, Nataly Moreno-Martinez, Kathryn Miller-Jensen:
  A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription. 1010152
• 
  Max S. Y. Lau, Alexander D. Becker, Wyatt Madden, Lance A. Waller, C. Jessica E. Metcalf, Bryan T. Grenfell:
  Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics. 1010251
• 
  Fedor Shmarov, Graham R. Smith, Sophie C. Weatherhead, Nick J. Reynolds, Paolo Zuliani:
  Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis. 1010267
• 
  Chuliang Song, Benno I. Simmons, Marie-Josée Fortin, Andrew Gonzalez:
  Generalism drives abundance: A computational causal discovery approach. 1010302
• 
  Tatjana Petrov, Matej Hajnal, Julia Klein, David Safránek, Morgane Nouvian:
  Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. 1010305
• 
  Ludmilla Figueiredo, Cédric Scherer, Juliano Sarmento Cabral:
  A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research. 1010356
• 
  Jake Lawlor, Francis Banville, Norma-Rocio Forero-Muñoz, Katherine Hébert, Juan Andrés Martínez-Lanfranco, Pierre Rogy, A. Andrew M. Macdonald:
  Ten simple rules for teaching yourself R. 1010372
• 
  Joe Hilton, Heather Riley, Lorenzo Pellis, Rabia Aziza, Samuel P. C. Brand, Ivy K. Kombe, John Ojal, Andrea Parisi, Matt J. Keeling, D. James Nokes, Robert Manson-Sawko, Thomas A. House:
  A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic. 1010390
• 
  David Laloum, Marc Robinson-Rechavi:
  Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level. 1010399
• 
  Ran Su, Haitang Yang, Leyi Wei, Siqi Chen, Quan Zou:
  A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data. 1010402
• 
  Nikos I. Bosse, Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J. Quilty, Mark Jit, Edwin van Leeuwen, Anne Cori, Sebastian Funk:
  Comparing human and model-based forecasts of COVID-19 in Germany and Poland. 1010405
• 
  Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian M. Hall, Thomas A. House, Chris P. Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe:
  EpiBeds: Data informed modelling of the COVID-19 hospital burden in England. 1010406
• 
  Tomislav D. Zbozinek, Omar D. Perez, Toby Wise, Michael Fanselow, Dean Mobbs:
  Ambiguity drives higher-order Pavlovian learning. 1010410
• 
  Fernando Soler-Toscano, Javier A. Galadí, Anira Escrichs, Yonatan Sanz Perl, Ane López-González, Jacobo D. Sitt, Jitka Annen, Olivia Gosseries, Aurore Thibaut, Rajanikant Panda, Francisco José Esteban, Steven Laureys, Morten L. Kringelbach, José A. Langa, Gustavo Deco:
  What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics. 1010412
• 
  Michael A. Kelley, Karin Leiderman:
  Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization. 1010414
• 
  Natasha Oswal, Olivier M. F. Martin, Sofia Stroustrup, Monika Anna Matusiak Bruckner, Nicholas Stroustrup:
  A hierarchical process model links behavioral aging and lifespan in C. elegans. 1010415
• 
  Christopher H. Stock, Sarah E. Harvey, Samuel A. Ocko, Surya Ganguli:
  Synaptic balancing: A biologically plausible local learning rule that provably increases neural network noise robustness without sacrificing task performance. 1010418
• 
  Gautam Upadhya, Matthias Steinrücken:
  Robust inference of population size histories from genomic sequencing data. 1010419
• 
  Matthew S. Creamer, Kevin S. Chen, Andrew M. Leifer, Jonathan W. Pillow:
  Correcting motion induced fluorescence artifacts in two-channel neural imaging. 1010421
• 
  Jianghong Shi, Bryan P. Tripp, Eric Shea-Brown, Stefan Mihalas, Michael A. Buice:
  MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex. 1010427
• 
  Mohammad Salahshour:
  Interaction between games give rise to the evolution of moral norms of cooperation. 1010429
• 
  Alex M. Casella, Carlo Colantuoni, Seth A. Ament:
  Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies. 1010430
• 
  Marilyn Gatica, Fernando E. Rosas, Pedro A. M. Mediano, Ibai Díez, Stephan P. Swinnen, Patricio Orio, Rodrigo Cofré, Jesús M. Cortés:
  High-order functional redundancy in ageing explained via alterations in the connectome in a whole-brain model. 1010431
• 
  Evgeny A. Podolskiy, Mads Peter Heide-Jørgensen:
  Strange attractor of a narwhal (Monodon monoceros). 1010432
• 
  Zhenwei Zhou, Eric D. Kolaczyk, Robin N. Thompson, Laura F. White:
  Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties. 1010434
• 
  Michelle Przedborski, David Sharon, Severine Cathelin, Steven Chan, Mohammad Kohandel:
  An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia. 1010439
• 
  Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya, Hiroshi Suzuki:
  Utility of constraints reflecting system stability on analyses for biological models. 1010441
• 
  Kapil Newar, Amith Zafal Abdulla, Hossein Salari, Eric Fanchon, Daniel Jost:
  Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells. 1010450
• 
  Erik K. Johnson, Daniel B. Larremore:
  Bayesian estimation of community size and overlap from random subsamples. 1010451
• 
  Nirvana Nursimulu, Alan M. Moses, John Parkinson:
  Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. 1010452
• 
  Florian Franke, Sebastian Aland, Hans-Joachim Böhme, Anja Voss-Böhme, Steffen Lange:
  Is cell segregation like oil and water: Asymptotic versus transitory regime. 1010460
• 
  Peter Duggins, Chris Eliasmith:
  Constructing functional models from biophysically-detailed neurons. 1010461
• 
  Qingfeng Li, Yajing Huang:
  Optimizing global COVID-19 vaccine allocation: An agent-based computational model of 148 countries. 1010463
• 
  Zdenek Straka, Jean-Paul Noel, Matej Hoffmann:
  A normative model of peripersonal space encoding as performing impact prediction. 1010464
• 
  Russell T. Johnson, Nicholas A. Bianco, James M. Finley:
  Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait. 1010466
• 
  Marco Cappellato, Giacomo Baruzzo, Barbara Di Camillo:
  Investigating differential abundance methods in microbiome data: A benchmark study. 1010467
• 
  Ye Yuan, Carlos Cosme, Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph:
  CINS: Cell Interaction Network inference from Single cell expression data. 1010468
• 
  Oscar Silfvergren, Christian Simonsson, Mattias Ekstedt, Peter Lundberg, Peter Gennemark, Gunnar Cedersund:
  Digital twin predicting diet response before and after long-term fasting. 1010469
• 
  Lin Zhang, Likai Chen, Xiaoqian (annie) Yu, Claire Duvallet, Siavash Isazadeh, Chengzhen Dai, Shinkyu Park, Katya Frois-Moniz, Fabio Duarte, Carlo Ratti, Eric J. Alm, Fangqiong Ling:
  MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes. 1010472
• 
  Christopher DiMattina, Josiah J. Burnham, Betul N. Guner, Haley B. Yerxa:
  Distinguishing shadows from surface boundaries using local achromatic cues. 1010473
• 
  Elisha M. Wood-Charlson, Zachary Crockett, Chris Erdmann, Adam P. Arkin, Carly B. Robinson:
  Ten simple rules for getting and giving credit for data. 1010476
• 
  Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi:
  Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks. 1010477
• 
  Nirag Kadakia:
  Optimal control methods for nonlinear parameter estimation in biophysical neuron models. 1010479
• 
  Wenrui Hao, Suzanne Lenhart, Jeffrey R. Petrella:
  Optimal anti-amyloid-beta therapy for Alzheimer's disease via a personalized mathematical model. 1010481
• 
  Jalil Nourisa, Berit Zeller-Plumhoff, Regine Willumeit-Römer:
  The osteogenetic activities of mesenchymal stem cells in response to Mg2+ ions and inflammatory cytokines: a numerical approach using fuzzy logic controllers. 1010482
• 
  Thomas McAndrew, Nicholas G. Reich:
  An expert judgment model to predict early stages of the COVID-19 pandemic in the United States. 1010485
• 
  Leo Zeitler, Cyril Denby Wilkes, Arach Goldar, Julie Soutourina:
  A quantitative modelling approach for DNA repair on a population scale. 1010488
• 
  Micah Allen, Andrew Levy, Thomas Parr, Karl J. Friston:
  In the Body's Eye: The computational anatomy of interoceptive inference. 1010490
• 
  Susanne Pinto, Elisa Benincà, Egbert H. van Nes, Marten Scheffer, Johannes A. Bogaards:
  Species abundance correlations carry limited information about microbial network interactions. 1010491
• 
  Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter:
  RNA velocity unraveled. 1010492
• 
  Evangelos A. Dimopoulos, Alberto Carmagnini, Irina M. Velsko, Christina Warinner, Greger Larson, Laurent A. F. Frantz, Evan K. Irving-Pease:
  HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data. 1010493
• 
  Masaki Sasai:
  Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm. 1010494
• 
  Yi-Wen Hsiao, Lin Wang, Tzu-Pin Lu:
  ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets. 1010497
• 
  Zhen Peng, Jeff T. Linderoth, David A. Baum:
  The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life. 1010498
• 
  Ali Hummos, Bin A. Wang, Sabrina Drammis, Michael M. Halassa, Burkhard Pleger:
  Thalamic regulation of frontal interactions in human cognitive flexibility. 1010500
• 
  Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W. Gray, Young Hwan Chang:
  Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays. 1010505
• 
  Tuomo Mäki-Marttunen, Verónica Mäki-Marttunen:
  Excitatory and inhibitory effects of HCN channel modulation on excitability of layer V pyramidal cells. 1010506
• 
  Yingtian Hu, Yunxiao Li, Glen A. Satten, Yi-Juan Hu:
  Testing microbiome associations with survival times at both the community and individual taxon levels. 1010509
• 
  Wenhui Yan, Wending Tang, Lihua Wang, Yannan Bin, Junfeng Xia:
  PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization. 1010511
• 
  Olivia Zahn, Jorge Bustamante, Callin Switzer, Thomas L. Daniel, J. Nathan Kutz:
  Pruning deep neural networks generates a sparse, bio-inspired nonlinear controller for insect flight. 1010512
• 
  Hamid Alinejad-Rokny, Rassa Ghavami Modegh, Hamid R. Rabiee, Ehsan Ramezani Sarbandi, Narges Rezaie, Kin Tung Tam, Alistair R. R. Forrest:
  Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments. 1010515
• 
  Daniel Krefl, Sven Bergmann:
  Cross-GWAS coherence test at the gene and pathway level. 1010517
• 
  Juan Ramon Melendez-Alvarez, Xiao-Jun Tian:
  Emergence of qualitative states in synthetic circuits driven by ultrasensitive growth feedback. 1010518
• 
  Jess Ramsay, Daniel R. Kattnig:
  Radical triads, not pairs, may explain effects of hypomagnetic fields on neurogenesis. 1010519
• 
  Theo Gibbs, Yifan Zhang, Zachary R. Miller, James P. O'Dwyer:
  Stability criteria for the consumption and exchange of essential resources. 1010521
• 
  Daniel Janini, Chris J. Hamblin, Arturo Deza, Talia Konkle:
  General object-based features account for letter perception. 1010522
• 
  Malvika Srivastava, Joshua L. Payne:
  On the incongruence of genotype-phenotype and fitness landscapes. 1010524
• 
  Yijun Liu, Ji Sun, Huiyan Sun, Yi Chang:
  Identification of key somatic oncogenic mutation based on a confounder-free causal inference model. 1010529
• 
  Gertjan Bisschop:
  Graph-based algorithms for Laplace transformed coalescence time distributions. 1010532
• 
  Christopher Brian Currin, Joseph Valentino Raimondo:
  Computational models reveal how chloride dynamics determine the optimal distribution of inhibitory synapses to minimise dendritic excitability. 1010534
• 
  Robin Pearce, Yang Li, Gilbert S. Omenn, Yang Zhang:
  Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. 1010539
• 
  Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios:
  Towards mouse genetic-specific RNA-sequencing read mapping. 1010552
• 
  Arnault H. Caillet, Andrew T. M. Phillips, Dario Farina, Luca Modenese:
  Estimation of the firing behaviour of a complete motoneuron pool by combining electromyography signal decomposition and realistic motoneuron modelling. 1010556
• 
  Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Sulc:
  Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection. 1010561
• 
  Eric Wang, Arup K. Chakraborty:
  Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants. 1010563
• 
  J. C. Dallon, Cécile Leduc, Christopher P. Grant, Emily J. Evans, Sandrine Étienne-Manneville, Stephanie Portet:
  Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics. 1010573
• 
  Qu Cheng, Philip A. Collender, Alexandra K. Heaney, Aidan Mcloughlin, Yang Yang, Yuzi Zhang, Jennifer R. Head, Rohini Dasan, Song Liang, Qiang Lv, Yaqiong Liu, Changhong Yang, Howard H. Chang, Lance A. Waller, Jon Zelner, Joseph A. Lewnard, Justin V. Remais:
  Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections. 1010575
• 
  Thomas Kaplan, Jonathan Cannon, Lorenzo Jamone, Marcus T. Pearce:
  Modeling enculturated bias in entrainment to rhythmic patterns. 1010579

Volume 18, Number 10, October 2022

• 
  Andreas Christ Sølvsten Jørgensen, Atiyo Ghosh, Marc Sturrock, Vahid Shahrezaei:
  Efficient Bayesian inference for stochastic agent-based models. 1009508
• 
  Melissa A. Iacovidou, Priscille Barreaux, Simon E. F. Spencer, Matthew B. Thomas, Erin E. Gorsich, Kat S. Rock:
  Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets. 1009540
• 
  Takahiro Hiraga, Yasufumi Yamada, Ryo Kobayashi:
  Theoretical investigation of active listening behavior based on the echolocation of CF-FM bats. 1009784
• 
  Stephen Malina, Daniel Cizin, David A. Knowles:
  Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models. 1009880
• 
  Ziwen Peng, Luning He, Rongzhen Wen, Tom Verguts, Carol A. Seger, Qi Chen:
  Obsessive-compulsive disorder is characterized by decreased Pavlovian influence on instrumental behavior. 1009945
• 
  Frédéric Crevecoeur, James Mathew, Philippe Lefèvre:
  Separability of Human Motor Memories during reaching adaptation with force cues. 1009966
• 
  John Cody Herron, Shiqiong Hu, Bei Liu, Takashi Watanabe, Klaus M. Hahn, Timothy C. Elston:
  Spatial models of pattern formation during phagocytosis. 1010092
• 
  Breschine Cummins, Francis C. Motta, Robert C. Moseley, Anastasia Deckard, Sophia Campione, Marcio Gameiro, Tomás Gedeon, Konstantin Mischaikow, Steven B. Haase:
  Experimental guidance for discovering genetic networks through hypothesis reduction on time series. 1010145
• 
  Rebecca G. Zitnay, Michael R. Herron, Keith R. Carney, Scott Potter, Lyska L. Emerson, Jeffrey A. Weiss, Michelle C. Mendoza:
  Mechanics of lung cancer: A finite element model shows strain amplification during early tumorigenesis. 1010153
• 
  Javier A. Romero, Paulina Putko, Mateusz Urbanczyk, Krzysztof Kazimierczuk, Anna Zawadzka-Kazimierczuk:
  Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins. 1010258
• 
  Rodrigo Méndez Rojano, Angela Lai, Mansur Zhussupbekov, Greg W. Burgreen, Keith Cook, James F. Antaki:
  A fibrin enhanced thrombosis model for medical devices operating at low shear regimes or large surface areas. 1010277
• 
  Mohammad A. Makrooni, Donal O'Shea, Paul Geeleher, Cathal Seoighe:
  Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis. 1010278
• 
  Sandhiya Vijayabaskaran, Sen Cheng:
  Navigation task and action space drive the emergence of egocentric and allocentric spatial representations. 1010320
• 
  Mahnaz Habibi, Golnaz Taheri:
  A new machine learning method for cancer mutation analysis. 1010332
• 
  John Hongyu Meng, Hermann Riecke:
  Structural spine plasticity: Learning and forgetting of odor-specific subnetworks in the olfactory bulb. 1010338
• 
  Dean Mobbs, Sarah M. Tashjian:
  Ten simple rules for unbiased teaching. 1010344
• 
  James T. Anibal, Alexandre G. R. Day, Erol Bahadiroglu, Liam O'Neil, Long N. Phan, Alec Peltekian, Amir Erez, Mariana Kaplan, Grégoire Altan-Bonnet, Pankaj Mehta:
  HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis. 1010349
• 
  Lucila G. Alvarez Zuzek, Casey M. Zipfel, Shweta Bansal:
  Spatial clustering in vaccination hesitancy: The role of social influence and social selection. 1010437
• 
  Laura Fontanesi, Amitai Shenhav, Sebastian Gluth:
  Disentangling choice value and choice conflict in sequential decisions under risk. 1010478
• 
  Biraj Pandey, Marius Pachitariu, Bingni W. Brunton, Kameron Decker Harris:
  Structured random receptive fields enable informative sensory encodings. 1010484
• 
  Guido España, T. Alex Perkins, Simon D. Pollett, Morgan E. Smith, Sean M. Moore, Paul O. Kwon, Tara L. Hall, Milford H. Beagle, Clinton K. Murray, Shilpa Hakre, Sheila A. Peel, Kayvon Modjarrad, Paul T. Scott:
  Prioritizing interventions for preventing COVID-19 outbreaks in military basic training. 1010489
• 
  Yingxin Lin, Lipin Loo, Andy Tran, David M. Lin, Cesar Moreno, Daniel Hesselson, G. Gregory Neely, Jean Y. H. Yang:
  Scalable workflow for characterization of cell-cell communication in COVID-19 patients. 1010495
• 
  Eric Cramer, Maisa Ziadni, Kristen Hymel Scherrer, Sean Mackey, Ming-Chih Kao:
  CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data. 1010496
• 
  Courtney Peña, Nidia Ruedas-Gracia, Jennifer R. Cohen, Ngoc Tran, Miranda B. Stratton:
  Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM. 1010499
• 
  Zi-Chun Mu, Ya-Lan Tan, Ben-gong Zhang, Jie Liu, Ya-Zhou Shi:
  Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. 1010501
• 
  Oliver Schmitt, Christian Nitzsche, Peter Eipert, Vishnu Prathapan, Marc-Thorsten Hütt, Claus C. Hilgetag:
  Reaction-diffusion models in weighted and directed connectomes. 1010507
• 
  Ryota Matsuyama, Takehisa Yamamoto, Yoko Hayama, Ryosuke Omori:
  Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan. 1010510
• 
  Edgar Perez-Lopez, Larisa Gavrilova, Janice Disla, Melissa Goodlad, Dalena Ngo, Arabi Seshappan, Farhana Sharmin, Jesús Cisneros, Christopher T. Kello, Asmeret Asefaw Berhe:
  Ten simple rules for creating and sustaining antiracist graduate programs. 1010516
• 
  Susanne Hollmann, Babette Regierer, Jaele Bechis, Lesley Tobin, Domenica D'Elia:
  Ten simple rules on how to develop a stakeholder engagement plan. 1010520
• 
  James A. R. Marshall, Andreagiovanni Reina, Célia Hay, Audrey Dussutour, Angelo Pirrone:
  Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making. 1010523
• 
  Olivia L. Lanier, Mykel D. Green, Gilda A. Barabino, Elizabeth Cosgriff-Hernandez:
  Ten simple rules in biomedical engineering to improve healthcare equity. 1010525
• 
  Jenea Imani Adams, Taylor Ferebee, Melyssa Minto, Kayla K. Pennerman, Nyasha Chambwe:
  Ten simple rules for creating a global network in computational biology. 1010528
• 
  Aaron Yip, Julien Smith-Roberge, Sara Khorasani, Marc Aucoin, Brian P. Ingalls:
  Calibrating spatiotemporal models of microbial communities to microscopy data: A review. 1010533
• 
  Dávid Deritei, Nina Kunsic, Péter Csermely:
  Probabilistic edge weights fine-tune Boolean network dynamics. 1010536
• 
  Benjamin C. Haller:
  Ten simple rules for reporting a bug. 1010540
• 
  Suran Galappaththige, Richard A. Gray, Caroline Mendonça Costa, Steven A. Niederer, Pras Pathmanathan:
  Credibility assessment of patient-specific computational modeling using patient-specific cardiac modeling as an exemplar. 1010541
• 
  Sophia Becker, Andreas Nold, Tatjana Tchumatchenko:
  Modulation of working memory duration by synaptic and astrocytic mechanisms. 1010543
• 
  Zahra M. Bagheri, Anna-Lee Jessop, Julian C. Partridge, Karen J. Osborn, Jan M. Hemmi:
  A new computational model illuminates the extraordinary eyes of Phronima. 1010545
• 
  Miranda D. Stobbe, Abel Gonzalez-Perez, Núria López-Bigas, Ivo Glynne Gut:
  Ten simple rules for a successful international consortium in big data omics. 1010546
• 
  Raymond Wang, Louis Kang:
  Multiple bumps can enhance robustness to noise in continuous attractor networks. 1010547
• 
  Behzad D. Karkaria, Angelika Manhart, Alex J. H. Fedorec, Chris P. Barnes:
  Chaos in synthetic microbial communities. 1010548
• 
  Christopher E. Overton, Luke Webb, Uma Datta, Mike Fursman, Jo Hardstaff, Iina Hiironen, Karthik Paranthaman, Heather Riley, James Sedgwick, Julia Verne, Steve Willner, Lorenzo Pellis, Ian M. Hall:
  Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England. 1010554
• 
  Patrick E. Gelbach, Dongqing Zheng, Scott E. Fraser, Kate L. White, Nicholas A. Graham, Stacey D. Finley:
  Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion. 1010555
• 
  Sara Andresen, Suraj Balakrishna, Catrina Mugglin, Axel J. Schmidt, Dominique L. Braun, Alex Marzel, Thanh Doco Lecompte, Katharine Ea Darling, Jan A. Roth, Patrick Schmid, Enos Bernasconi, Huldrych F. Günthard, Andri Rauch, Roger D. Kouyos, Luisa Salazar-Vizcaya:
  Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men. 1010559
• 
  Lorenzo Fruzzetti, Hari Teja Kalidindi, Alberto Antonietti, Cristiano Alessandro, Alice Geminiani, Claudia Casellato, Egidio Falotico, Egidio D'Angelo:
  Dual STDP processes at Purkinje cells contribute to distinct improvements in accuracy and speed of saccadic eye movements. 1010564
• 
  Sabrin Hilau, Sophia Katz, Tanya Wasserman, Ruth Hershberg, Yonatan Savir:
  Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains. 1010565
• 
  Sam C. Berens, Chris M. Bird:
  Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules. 1010566
• 
  Daniele Avitabile, Mathieu Desroches, G. Bard Ermentrout:
  Cross-scale excitability in networks of quadratic integrate-and-fire neurons. 1010569
• 
  Emma L. Henderson, Christopher D. Chambers:
  Ten simple rules for writing a Registered Report. 1010571
• 
  Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhen-Hao Guo, Kyungsook Han, De-Shuang Huang:
  DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes. 1010572
• 
  Chen Jia, Abhyudai Singh, Ramon Grima:
  Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis. 1010574
• 
  William Gasper, Francesca Rossi, Matteo Ligorio, Dario Ghersi:
  Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data. 1010576
• 
  Luqin Gan, Genevera I. Allen:
  Fast and interpretable consensus clustering via minipatch learning. 1010577
• 
  Alexandra O. M. Holmes, Adrian Goldman, Antreas C. Kalli:
  mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. 1010578
• 
  Lena Esther Ptasczynski, Isa Steinecker, Philipp Sterzer, Matthias Guggenmos:
  The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback. 1010580
• 
  Annie M. Westerlund, Akshay Sridhar, Leo Dahl, Alma Andersson, Anna-Yaroslava Bodnar, Lucie Delemotte:
  Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. 1010583
• 
  Sonja Schach, Axel Lindner, Daniel Alexander Braun:
  Bounded rational decision-making models suggest capacity-limited concurrent motor planning in human posterior parietal and frontal cortex. 1010585
• 
  Xiuyun Jiang, Lena Harker-Kirschneck, Christian Vanhille Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, Andela Saric:
  Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. 1010586
• 
  Belén Casas, Liisa Vilén, Sophie Bauer, Kajsa P. Kanebratt, Charlotte Wennberg Huldt, Lisa Magnusson, Uwe Marx, Tommy B. Andersson, Peter Gennemark, Gunnar Cedersund:
  Integrated experimental-computational analysis of a HepaRG liver-islet microphysiological system for human-centric diabetes research. 1010587
• 
  Yicong Zheng, Xiaonan L. Liu, Satoru Nishiyama, Charan Ranganath, Randall C. O'Reilly:
  Correcting the hebbian mistake: Toward a fully error-driven hippocampus. 1010589
• 
  Johannes Bracher, Evan L. Ray, Tilmann Gneiting, Nicholas G. Reich:
  Correction: Evaluating epidemic forecasts in an interval format. 1010592
• 
  Jonathan Timcheck, Jonathan Kadmon, Kwabena Boahen, Surya Ganguli:
  Optimal noise level for coding with tightly balanced networks of spiking neurons in the presence of transmission delays. 1010593
• 
  Yuxiang Wu, Shang Wu, Xin Wang, Chengtian Lang, Quanshi Zhang, Quan Wen, Tianqi Xu:
  Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans. 1010594
• 
  Michael D. Kupperman, Thomas Leitner, Ruian Ke:
  A deep learning approach to real-time HIV outbreak detection using genetic data. 1010598
• 
  Nathan Tardiff, Lalitta Suriya-Arunroj, Yale E. Cohen, Joshua I. Gold:
  Rule-based and stimulus-based cues bias auditory decisions via different computational and physiological mechanisms. 1010601
• 
  Gerardo Chowell, Sushma Dahal, Amna Tariq, Kimberlyn Roosa, James Mac Hyman, Ruiyan Luo:
  An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA. 1010602
• 
  Shichao Feng, Hong-Long Ji, Huan Wang, Bailu Zhang, Ryan Sterzenbach, Chongle Pan, Xuan Guo:
  MetaLP: An integrative linear programming method for protein inference in metaproteomics. 1010603
• 
  Marie Locard-Paulet, Oana Palasca, Lars Juhl Jensen:
  Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies. 1010604
• 
  Tsvetomira Dumbalska, Katarzyna Rudzka, Hannah E. Smithson, Christopher Summerfield:
  How do (perceptual) distracters distract? 1010609
• 
  Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio:
  DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets. 1010610
• 
  Thomas J. Attard, Julie P. I. Welburn, Joseph A. Marsh:
  Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations. 1010611
• 
  Rutger Hermsen:
  Emergent multilevel selection in a simple spatial model of the evolution of altruism. 1010612
• 
  A. S. M. Zisanur Rahman, Chengyou Liu, Hunter Sturm, Andrew M. Hogan, Rebecca L. Davis, Pingzhao Hu, Silvia T. Cardona:
  A machine learning model trained on a high-throughput antibacterial screen increases the hit rate of drug discovery. 1010613
• 
  Zubair Lalani, Gillian Chu, Silas Hsu, Shaw Kagawa, Michael Xiang, Simone Zaccaria, Mohammed El-Kebir:
  CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. 1010614
• 
  Oswaldo Gressani, Jacco Wallinga, Christian L. Althaus, Niel Hens, Christel Faes:
  EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. 1010618
• 
  Benjamin D. Maier, Luis U. Aguilera, Sven Sahle, Pascal Mutz, Priyata Kalra, Christopher Dächert, Ralf Bartenschlager, Marco Binder, Ursula Kummer:
  Stochastic dynamics of Type-I interferon responses. 1010623
• 
  Eric Lewitus, Jennifer Hoang, Yifan Li, Hongjun Bai, Morgane Rolland:
  Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens. 1010624
• 
  Sharmila Biswas, Baishakhi Tikader, Sandip Kar, Ganesh A. Viswanathan:
  Modulation of signaling cross-talk between pJNK and pAKT generates optimal apoptotic response. 1010626
• 
  Kody A. Waldstein, Jirong Yi, Myung Cho, Raghu Mudumbai, Xiaodong Wu, Steven M. Varga, Weiyu Xu:
  Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond. 1010629
• 
  Jie Deng, Washington Taylor, Serguei Saavedra:
  Understanding the impact of third-party species on pairwise coexistence. 1010630
• 
  Dhiraj Kumar Hazra, Bhalchandra S. Pujari, Snehal M. Shekatkar, Farhina Mozaffer, Sitabhra Sinha, Vishwesha Guttal, Pinaki Chaudhuri, Gautam I. Menon:
  Modelling the first wave of COVID-19 in India. 1010632
• 
  Gabriel Foley, Ariane Mora, Connie M. Ross, Scott Bottoms, Leander Sützl, Marnie L. Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine E. S. Thomson, Bostjan Kobe, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jörg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Bodén:
  Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). 1010633
• 
  Cheyu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang:
  Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. 1010636
• 
  Abhinav Dutta, David Pellow, Ron Shamir:
  Parameterized syncmer schemes improve long-read mapping. 1010638
• 
  Lea Schuh, Igor Kukhtevich, Poonam Bheda, Melanie Schulz, Maria Bordukova, Robert Schneider, Carsten Marr:
  Altered expression response upon repeated gene repression in single yeast cells. 1010640
• 
  Di Zhang, Sophia Hsin-Jung Li, Christopher G. King, Ned S. Wingreen, Zemer Gitai, Zhiyuan Li:
  Global and gene-specific translational regulation in Escherichia coli across different conditions. 1010641
• 
  Sahiti Chebolu, Peter Dayan, Kevin Lloyd:
  Vigilance, arousal, and acetylcholine: Optimal control of attention in a simple detection task. 1010642
• 
  Leonardo Trujillo, Paul Banse, Guillaume Beslon:
  Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes. 1010647
• 
  Hadar Cohen Duwek, Hamutal Slovin, Elishai Ezra Tsur:
  Computational modeling of color perception with biologically plausible spiking neural networks. 1010648
• 
  Nathaniel J. Linden, Boris Kramer, Padmini Rangamani:
  Bayesian parameter estimation for dynamical models in systems biology. 1010651
• 
  Xenia Ohmer, Michael Marino, Michael Franke, Peter König:
  Mutual influence between language and perception in multi-agent communication games. 1010658
• 
  Enrui Zhang, Bart Spronck, Jay D. Humphrey, George Em Karniadakis:
  G2Φnet: Relating genotype and biomechanical phenotype of tissues with deep learning. 1010660
• 
  Yihe Pang, Bin Liu:
  DMFpred: Predicting protein disorder molecular functions based on protein cubic language model. 1010668
• 
  Jialu Hou, Hang Wei, Bin Liu:
  iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network. 1010671
• 
  J. Andres Martinez, Matheo Delvenne, Lucas Henrion, Fabian Moreno, Samuel Telek, Christian Dusny, Frank Delvigne:
  Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages. 1010674

Volume 18, Number 11, November 2022

• 
  Noémi Élteto, Dezso Németh, Karolina Janacsek, Peter Dayan:
  Tracking human skill learning with a hierarchical Bayesian sequence model. 1009866
• 
  David M. Desmet, Joseph P. Cusumano, Jonathan B. Dingwell:
  Adaptive multi-objective control explains how humans make lateral maneuvers while walking. 1010035
• 
  Chiara Campana, Eugenio Ricci, Chiara Bartolucci, Stefano Severi, Eric A. Sobie:
  Coupling and heterogeneity modulate pacemaking capability in healthy and diseased two-dimensional sinoatrial node tissue models. 1010098
• 
  Shan Zhong, Jeong Woo Choi, Nadia G. Hashoush, Diana Babayan, Mahsa Malekmohammadi, Nader Pouratian, Vassilios N. Christopoulos:
  A neurocomputational theory of action regulation predicts motor behavior in neurotypical individuals and patients with Parkinson's disease. 1010111
• 
  Sylvain Blois, Benjamin M. Goetz, James J. Bull, Christopher S. Sullivan:
  Interpreting and de-noising genetically engineered barcodes in a DNA virus. 1010131
• 
  Kaitlyn M. Gaynor, Therese Azevedo, Clarissa Boyajian, Julien Brun, Amber E. Budden, Allie Cole, Samantha Csik, Joe Decesaro, Halina Do-Linh, Joan Dudney, Carmen Galaz García, Scout Leonard, Nicholas J. Lyon, Althea Marks, Julia Parish, Alexandra A. Phillips, Courtney Scarborough, Joshua Smith, Marcus Thompson, Camila Vargas Poulsen, Caitlin R. Fong:
  Ten simple rules to cultivate belonging in collaborative data science research teams. 1010567
• 
  Justus A. Kromer, Peter A. Tass:
  Synaptic reshaping of plastic neuronal networks by periodic multichannel stimulation with single-pulse and burst stimuli. 1010568
• 
  Jonathan M. Matthews, Brooke Schuster, Sara Saheb Kashaf, Ping Liu, Rakefet Ben-Yishay, Dana Ishay-Ronen, Evgeny Izumchenko, Le Shen, Christopher R. Weber, Margaret Bielski, Sonia S. Kupfer, Mustafa Bilgic, Andrey Rzhetsky, Savas Tay:
  OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics. 1010584
• 
  Joseph C. Ayoob, Juan S. Ramírez-Lugo:
  Ten simple rules for running a summer research program. 1010588
• 
  Niklas Smedemark-Margulies, Robin Walters, Heiko Zimmermann, Lucas Laird, Christian van der Loo, Neela Kaushik, Rajmonda Caceres, Jan-Willem van de Meent:
  Probabilistic program inference in network-based epidemiological simulations. 1010591
• 
  Daniel J. Vandenheuvel, Christopher C. Drovandi, Matthew J. Simpson:
  Computationally efficient mechanism discovery for cell invasion with uncertainty quantification. 1010599
• 
  Nestoras Karathanasis, Daniel Hwang, Vibol Heng, Rimal Abhimannyu, Phillip Slogoff-Sevilla, Gina Buchel, Victoria Frisbie, Peiyao Li, Dafni Kryoneriti, Isidore Rigoutsos:
  Reproducibility efforts as a teaching tool: A pilot study. 1010615
• 
  Hugo Menet, Vincent Daubin, Eric Tannier:
  Phylogenetic reconciliation. 1010621
• 
  Éloi Durant, Mathieu Rouard, Eric W. Ganko, Cédric Muller, Alan M. Cleary, Andrew D. Farmer, Matthieu G. Conte, François Sabot:
  Ten simple rules for developing visualization tools in genomics. 1010622
• 
  Carly Strasser, Kate L. Hertweck, Josh Greenberg, Dario Taraborelli, Elizabeth Vu:
  Ten simple rules for funding scientific open source software. 1010627
• 
  Ryan Golden, Jean Erik Delanois, Pavel Sanda, Maxim Bazhenov:
  Sleep prevents catastrophic forgetting in spiking neural networks by forming a joint synaptic weight representation. 1010628
• 
  Alfonso Nieto-Castañón:
  Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA). 1010634
• 
  Hasan Balci, Ugur Dogrusoz, Yusuf Ziya Ozgul, Perman Atayev:
  SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more. 1010635
• 
  Fabrizio Damicelli, Claus C. Hilgetag, Alexandros Goulas:
  Brain connectivity meets reservoir computing. 1010639
• 
  Correction: cytoNet: Spatiotemporal network analysis of cell communities. 1010644
• 
  Elisa Chao, Connor Chato, Reid Vender, Abayomi S. Olabode, Roux-Cil Ferreira, Art F. Y. Poon:
  Molecular source attribution. 1010649
• 
  Alexander M. Mercier, Samuel V. Scarpino, Cristopher Moore:
  Effective resistance against pandemics: Mobility network sparsification for high-fidelity epidemic simulations. 1010650
• 
  Rahul Biswas, Eli Shlizerman:
  Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm. 1010653
• 
  Mengmi Zhang, Marcelo Armendáriz, Will Xiao, Olivia Rose, Katarina Bendtz, Margaret S. Livingstone, Carlos R. Ponce, Gabriel Kreiman:
  Look twice: A generalist computational model predicts return fixations across tasks and species. 1010654
• 
  Xinyu Gu, Nicholas P. Schafer, Carlos Bueno, Wei Lu, Peter G. Wolynes:
  A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines. 1010657
• 
  Yonatan Sanz Perl, Anira Escrichs, Enzo Tagliazucchi, Morten L. Kringelbach, Gustavo Deco:
  Strength-dependent perturbation of whole-brain model working in different regimes reveals the role of fluctuations in brain dynamics. 1010662
• 
  Sigal Leviatan, Iris N. Kalka, Thomas Vogl, Shelley Klompas, Adina Weinberger, Eran Segal:
  BIPS - A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library. 1010663
• 
  Levi Solomyak, Paul B. Sharp, Eran Eldar:
  Training diversity promotes absolute-value-guided choice. 1010664
• 
  Ehsan Maleki, Saeedeh Akbari Rokn Abadi, Somayyeh Koohi:
  HELIOS: High-speed sequence alignment in optics. 1010665
• 
  Brian A. Lerch, Derek A. Smith, Thomas Koffel, Sarah C. Bagby, Karen C. Abbott:
  How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods. 1010666
• 
  Agata P. Perlinska, Adam Stasiulewicz, Mai Lan Nguyen, Karolina Swiderska, Mikolaj Zmudzinski, Alicja W. Maksymiuk, Marcin Drag, Joanna I. Sulkowska:
  Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding. 1010667
• 
  Daniel B. Cooney, Dylan H. Morris, Simon A. Levin, Daniel I. Rubenstein, Pawel Romanczuk:
  Social dilemmas of sociality due to beneficial and costly contagion. 1010670
• 
  David Arredondo, Matthew R. Lakin:
  Operant conditioning of stochastic chemical reaction networks. 1010676
• 
  Nathan D. Lee, Ivana Bozic:
  Inferring parameters of cancer evolution in chronic lymphocytic leukemia. 1010677
• 
  Joao Pinheiro Neto, F. Paul Spitzner, Viola Priesemann:
  Sampling effects and measurement overlap can bias the inference of neuronal avalanches. 1010678
• 
  Chenhui Ma, Alexandru Almasan, Evren Gurkan-Cavusoglu:
  Computational analysis of 5-fluorouracil anti-tumor activity in colon cancer using a mechanistic pharmacokinetic/pharmacodynamic model. 1010685
• 
  Georgios D. Koutsovoulos, Solène Granjeon Noriot, Marc Bailly-Bechet, Etienne G. J. Danchin, Corinne Rancurel:
  AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers. 1010686
• 
  Mubasher Rashid, Kishore Hari, John Thampi, Nived Krishnan Santhosh, Mohit Kumar Jolly:
  Network topology metrics explaining enrichment of hybrid epithelial/mesenchymal phenotypes in metastasis. 1010687
• 
  Neythen J. Treloar, Nathan Braniff, Brian P. Ingalls, Chris P. Barnes:
  Deep reinforcement learning for optimal experimental design in biology. 1010695
• 
  Mingyu Song, Persis A. Baah, Ming Bo Cai, Yael Niv:
  Humans combine value learning and hypothesis testing strategically in multi-dimensional probabilistic reward learning. 1010699
• 
  Youngmin Park, Maria N. Geffen:
  Correction: A circuit model of auditory cortex. 1010700
• 
  Nikita Sivakumar, Helen V. Warner, Shayn M. Peirce, Matthew Lazzara:
  A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. 1010701
• 
  Himangi Srivastava, Michael J. Lippincott, Jordan Currie, Robert Canfield, Maggie P. Y. Lam, Edward Lau:
  Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners. 1010702
• 
  Vivekananda Sarangi, Yeongjun Jang, Milovan Suvakov, Taejeong Bae, Liana Fasching, Shobana Sekar, Livia Tomasini, Jessica Mariani, Flora Vaccarino, Alexej Abyzov:
  Correction: All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. 1010703
• 
  Zahra Maqsood, Joanne C. Clark, Eleyna M. Martin, Yam Fung Hilaire Cheung, Luis A. Morán, Sean E. T. Watson, Jeremy A. Pike, Ying Di, Natalie S. Poulter, Alexandre Slater, Bodo M. H. Lange, Bernhard Nieswandt, Johannes A. Eble, Mike G. Tomlinson, Dylan M. Owen, David Stegner, Lloyd J. Bridge, Christoph Wierling, Steve P. Watson:
  Experimental validation of computerised models of clustering of platelet glycoprotein receptors that signal via tandem SH2 domain proteins. 1010708
• 
  Alexander Klug, Joachim Krug:
  Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations. 1010710
• 
  Javiera Cortés-Ríos, Ramón C. Hermida, Maria Rodriguez-Fernandez:
  Dosing time optimization of antihypertensive medications by including the circadian rhythm in pharmacokinetic-pharmacodynamic models. 1010711
• 
  Beatriz Seoane, Alessandra Carbone:
  Soft disorder modulates the assembly path of protein complexes. 1010713
• 
  Erick Armingol, Abbas Ghaddar, Chintan J. Joshi, Hratch Baghdassarian, Isaac Shamie, Jason Chan, Hsuan-Lin Her, Samuel Berhanu, Anushka Dar, Fabiola Rodriguez-Armstrong, Olivia Yang, Eyleen J. O'Rourke, Nathan E. Lewis:
  Inferring a spatial code of cell-cell interactions across a whole animal body. 1010715
• 
  Kyle Aitken, Marina E. Garrett, Shawn R. Olsen, Stefan Mihalas:
  The geometry of representational drift in natural and artificial neural networks. 1010716
• 
  Duncan K. Ralph, Frederick A. Matsen IV:
  Inference of B cell clonal families using heavy/light chain pairing information. 1010723
• 
  Oliver Eales, Haowei Wang, David Haw, Kylie E. C. Ainslie, Caroline E. Walters, Christina Atchison, Graham Cooke, Wendy Barclay, Helen Ward, Ara Darzi, Deborah Ashby, Christl A. Donnelly, Paul Elliott, Steven Riley:
  Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021. 1010724
• 
  Massimo Cavallaro, Juliana Coelho, Derren Ready, Valerie Decraene, Theresa Lamagni, Noel D. McCarthy, Dan Todkill, Matt J. Keeling:
  Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease. 1010726
• 
  A. Michael West Jr., Meghan E. Huber, Neville Hogan:
  Role of path information in visual perception of joint stiffness. 1010729
• 
  Alexander P. Browning, Christopher C. Drovandi, Ian W. Turner, Adrianne L. Jenner, Matthew J. Simpson:
  Efficient inference and identifiability analysis for differential equation models with random parameters. 1010734
• 
  Rong Gao, Samantha E. Brokaw, Zeyue Li, Libby J. Helfant, Ti Wu, Muhammad Malik, Ann M. Stock:
  Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites. 1010738
• 
  Connor Chato, Yi Feng, Yuhua Ruan, Hui Xing, Joshua T. Herbeck, Marcia Kalish, Art F. Y. Poon:
  Optimized phylogenetic clustering of HIV-1 sequence data for public health applications. 1010745
• 
  Quentin J. Leclerc, Jodi A. Lindsay, Gwenan M. Knight:
  Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: Killers and drivers of resistance evolution. 1010746

Volume 18, Number 12, December 2022

• 
  Xuexia Jiang, Tadamoto Isogai, Joseph Chi, Gaudenz Danuser:
  Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. 1009667
• 
  Frederik Van de Steen, Dimitris A. Pinotsis, Wouter Devos, Nigel Colenbier, Iege Bassez, Karl J. Friston, Daniele Marinazzo:
  Dynamic causal modelling shows a prominent role of local inhibition in alpha power modulation in higher visual cortex. 1009988
• 
  Darshak Kartikey Bhatt, Thijs Janzen, Toos Daemen, Franz J. Weissing:
  Modelling the spatial dynamics of oncolytic virotherapy in the presence of virus-resistant tumour cells. 1010076
• 
  Yunjun Zhang, Tom Britton, Xiaohua Zhou:
  Monitoring real-time transmission heterogeneity from incidence data. 1010078
• 
  Guillem Via, Román Baravalle, Fernando R. Fernandez, John A. White, Carmen C. Canavier:
  Interneuronal network model of theta-nested fast oscillations predicts differential effects of heterogeneity, gap junctions and short term depression for hyperpolarizing versus shunting inhibition. 1010094
• 
  Hannah Kurtenbach, Eduard Ort, Monja Isabel Froböse, Gerhard Jocham:
  Removal of reinforcement improves instrumental performance in humans by decreasing a general action bias rather than unmasking learnt associations. 1010201
• 
  Marion F. S. Fischer, James E. Crowe Jr., Jens Meiler:
  Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. 1010230
• 
  Yulia Fridman, Zihan Wang, Sergei Maslov, Akshit Goyal:
  Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments. 1010244
• 
  Or Zruya, Ilana Nisky:
  Orientation control strategies and adaptation to a visuomotor perturbation in rotational hand movements. 1010248
• 
  Thibault Tubiana, Ian Sillitoe, Christine A. Orengo, Nathalie Reuter:
  Dissecting peripheral protein-membrane interfaces. 1010346
• 
  Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga:
  Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. 1010384
• 
  Sahar Aghakhani, Sylvain Soliman, Anna Niarakis:
  Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach. 1010408
• 
  Stefan Gaillard, Tara van Viegen, Michele Veldsman, Melanie I. Stefan, Veronika Cheplygina:
  Ten simple rules for failing successfully in academia. 1010538
• 
  Rainer Engelken, Alessandro Ingrosso, Ramin Khajeh, Sven Goedeke, L. F. Abbott:
  Input correlations impede suppression of chaos and learning in balanced firing-rate networks. 1010590
• 
  Melissa M. Stadt, Jessica Leete, Sophia Devinyak, Anita T. Layton:
  A mathematical model of potassium homeostasis: Effect of feedforward and feedback controls. 1010607
• 
  Ashalatha Sreshty Mamidi, Avadhesha Surolia:
  Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins. 1010661
• 
  Qingzhen Hou, Katharina Waury, Dea Gogishvili, K. Anton Feenstra:
  Ten quick tips for sequence-based prediction of protein properties using machine learning. 1010669
• 
  Matthias C. Rillig:
  Ten simple rules for how you can help make your lab a better place as a graduate student or postdoc. 1010673
• 
  Paton Vuong, Michael J. Wise, Andrew S. Whiteley, Parwinder Kaur:
  Ten simple rules for investigating (meta)genomic data from environmental ecosystems. 1010675
• 
  Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV:
  Comparing T cell receptor repertoires using optimal transport. 1010681
• 
  Christoph Miehl, Julijana Gjorgjieva:
  Stability and learning in excitatory synapses by nonlinear inhibitory plasticity. 1010682
• 
  Adrien Coulier, Prashant Singh, Marc Sturrock, Andreas Hellander:
  Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation. 1010683
• 
  Nidia Ruedas-Gracia, Crystal M. Botham, Amber R. Moore, Courtney Peña:
  Ten simple rules for creating a sense of belonging in your research group. 1010688
• 
  Jason A. Papin, Jessica Keim-Malpass, Sana Syed:
  Ten simple rules for launching an academic research career. 1010689
• 
  Isaac H. Goldstein, Damon Bayer, Ivan Barilar, Balladiah Kizito, Ogopotse Matsiri, Chawangwa Modongo, Nicola M. Zetola, Stefan Niemann, Volodymyr M. Minin, Sanghyuk S. Shin:
  Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission. 1010696
• 
  Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Nalagampalli Papudeshi, Scott A. Handley, C. Titus Brown, Nathan S. Watson-Haigh, Robert A. Edwards:
  Ten simple rules and a template for creating workflows-as-applications. 1010705
• 
  Rikuto Kamiura, Ryo Mizuuchi, Norikazu Ichihashi:
  Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution. 1010709
• 
  Albane Ruaud, Niklas Pfister, Ruth E. Ley, Nicholas D. Youngblut:
  Interpreting tree ensemble machine learning models with endoR. 1010714
• 
  Davide Chicco, Luca Oneto, Erica Tavazzi:
  Eleven quick tips for data cleaning and feature engineering. 1010718
• 
  Lu Bin Liu, Attila Losonczy, Zhenrui Liao:
  tension: A Python package for FORCE learning. 1010722
• 
  Alessandro Filazzola, Garland Xie, Kimberly Barrett, Andrea Dunn, Marc T. J. Johnson, James Scott Macivor:
  Using smartphone-GPS data to quantify human activity in green spaces. 1010725
• 
  Kieran Elmes, Astra Heywood, Zhiyi Huang, Alex Gavryushkin:
  A fast lasso-based method for inferring higher-order interactions. 1010730
• 
  Patricia Guevara-Ramírez, Viviana A. Ruiz-Pozo, Santiago Cadena-Ullauri, Gabriela Salazar-Navas, Ana Acosta Bedón, J. Faustino V.-Vázquez, Ana Karina Zambrano:
  Ten simple rules for empowering women in STEM. 1010731
• 
  Mohammadreza Mohaghegh Neyshabouri, Jens Lagergren:
  ToMExO: A probabilistic tree-structured model for cancer progression. 1010732
• 
  Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan:
  Regional mutational signature activities in cancer genomes. 1010733
• 
  Dimitri Rodarie, Csaba Verasztó, Yann Roussel, Michael W. Reimann, Daniel X. Keller, Srikanth Ramaswamy, Henry Markram, Marc-Oliver Gewaltig:
  A method to estimate the cellular composition of the mouse brain from heterogeneous datasets. 1010739
• 
  Casey F. Breen, Ayesha S. Mahmud, Dennis M. Feehan:
  Novel estimates reveal subnational heterogeneities in disease-relevant contact patterns in the United States. 1010742
• 
  Yao Jiang, Jia-Xuan Zhang, Rong Liu:
  Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing. 1010744
• 
  Stefan Appelhoff, Ralph Hertwig, Bernhard Spitzer:
  EEG-representational geometries and psychometric distortions in approximate numerical judgment. 1010747
• 
  Andrew F. Brouwer, Marisa C. Eisenberg, Kevin M. Bakker, Savannah N. Boerger, Mondal H. Zahid, Matthew C. Freeman, Joseph N. S. Eisenberg:
  Leveraging infectious disease models to interpret randomized controlled trials: Controlling enteric pathogen transmission through water, sanitation, and hygiene interventions. 1010748
• 
  Nana Wei, Yating Nie, Lin Liu, Xiaoqi Zheng, Hua-Jun Wu:
  Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data. 1010753
• 
  Yogita Sharma, Jared B. Bennett, Gordana Rasic, John M. Marshall:
  Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes. 1010755
• 
  Denis Turcu, L. F. Abbott:
  Sparse RNNs can support high-capacity classification. 1010759
• 
  Xueer Chen, Lujia Chen, Cornelius H. L. Kürten, Fattaneh Jabbari, Lazar Vujanovic, Ying Ding, Binfeng Lu, Kevin Lu, Aditi Kulkarni, Tracy Tabib, Robert Lafyatis, Gregory F. Cooper, Robert Ferris, Xinghua Lu:
  An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors. 1010761
• 
  Alejandro Torres-Sánchez, Max Kerr Winter, Guillaume Salbreux:
  Interacting active surfaces: A model for three-dimensional cell aggregates. 1010762
• 
  Giulia Corniani, Miguel A. Casal, Stefano Panzeri, Hannes P. Saal:
  Population coding strategies in human tactile afferents. 1010763
• 
  Jinke Liu, Martin A. Vinck:
  Improved visualization of high-dimensional data using the distance-of-distance transformation. 1010764
• 
  Peter A. Embacher, Tsvetelina E. Germanova, Emanuele Roscioli, Andrew D. McAinsh, Nigel J. Burroughs:
  Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution. 1010765
• 
  Xinxin Wang, Gaudenz Danuser:
  Remeshing flexible membranes under the control of free energy. 1010766
• 
  Fanny Bergström, Felix Günther, Michael Höhle, Tom Britton:
  Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden. 1010767
• 
  Aaron Rumack, Ryan J. Tibshirani, Roni Rosenfeld:
  Recalibrating probabilistic forecasts of epidemics. 1010771
• 
  Haiyun Wang, Jianping Zhao, Chunhou Zheng, Yansen Su:
  scDSSC: Deep Sparse Subspace Clustering for scRNA-seq Data. 1010772
• 
  Correction: Humans combine value learning and hypothesis testing strategically in multi-dimensional probabilistic reward learning. 1010775
• 
  Leo Kozachkov, John Tauber, Mikael Lundqvist, Scott L. Brincat, Jean-Jacques E. Slotine, Earl K. Miller:
  Robust and brain-like working memory through short-term synaptic plasticity. 1010776
• 
  Olivier Mailhot, Vincent Frappier, François Major, Rafael J. Najmanovich:
  Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation. 1010777
• 
  Yansong Wang, Zilong Hou, Yuning Yang, Ka-Chun Wong, Xiangtao Li:
  Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework. 1010779
• 
  David Mathar, Mani Erfanian Abdoust, Tobias Marrenbach, Deniz Tuzsus, Jan Peters:
  The catecholamine precursor Tyrosine reduces autonomic arousal and decreases decision thresholds in reinforcement learning and temporal discounting. 1010785
• 
  Jakub Wojciechowski, Emirhan Tekoglu, Marlena Gasior-Glogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczynska, Sven J. Saupe, Witold Dyrka:
  Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. 1010787
• 
  Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel:
  CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. 1010788
• 
  Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang:
  Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. 1010793
• 
  Tingting Zhao, Nischal Karki, Brian D. Zoltowski, Devin A. Matthews:
  Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant. 1010794
• 
  Brandon K. Ashinoff, Justin Buck, Michael Woodford, Guillermo Horga:
  The effects of base rate neglect on sequential belief updating and real-world beliefs. 1010796
• 
  Nicolas Sundqvist, Sebastian Sten, Peter Thompson, Benjamin Jan Andersson, Maria Engström, Gunnar Cedersund:
  Mechanistic model for human brain metabolism and its connection to the neurovascular coupling. 1010798
• 
  Sarah M. Tashjian, Toby Wise, Dean Mobbs:
  Model-based prioritization for acquiring protection. 1010805
• 
  Eloi Martinez-Rabert, Chiel van Amstel, Cindy Smith, William T. Sloan, Rebeca Gonzalez-Cabaleiro:
  Environmental and ecological controls of the spatial distribution of microbial populations in aggregates. 1010807
• 
  Bastian Pietras, Valentin Schmutz, Tilo Schwalger:
  Mesoscopic description of hippocampal replay and metastability in spiking neural networks with short-term plasticity. 1010809