PLoS Computational Biology, Volume 16

Volume 16, Number 1, January 2020

Education

• 
  Alex Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel:
  An educational guide for nanopore sequencing in the classroom.

Research Articles

• 
  Anand Pathak, Nivedita Chatterjee, Sitabhra Sinha:
  Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization.
• 
  Simon Valentin, Maximilian Harkotte, Tzvetan Popov:
  Interpreting neural decoding models using grouped model reliance.
• 
  Filip Melinscak, Dominik R. Bach:
  Computational optimization of associative learning experiments.
• 
  Jeremy M. Chacón, Allison K. Shaw, William R. Harcombe:
  Increasing growth rate slows adaptation when genotypes compete for diffusing resources.
• 
  Yong Chen, Wentao Ma:
  The origin of biological homochirality along with the origin of life.
• 
  Jaideep Joshi, Åke Brännström, Ulf Dieckmann:
  Emergence of social inequality in the spatial harvesting of renewable public goods.
• 
  Henghui Zhu, Hao Liu, Armin Ataei, Yonatan Munk, Thomas Daniel, Ioannis Ch. Paschalidis:
  Learning from animals: How to Navigate Complex Terrains.
• 
  Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson:
  Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power.
• 
  Anton M. Unakafov, Thomas Schultze, Alexander Gail, Sebastian Möller, Igor Kagan, Stephan Eule, Fred Wolf:
  Emergence and suppression of cooperation by action visibility in transparent games.
• 
  Jake P. Taylor-King, Asbjørn Nilsen Riseth, Will Macnair, Manfred Claassen:
  Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming.
• 
  Alba Solsona-Berga, Kaitlin E. Frasier, Simone Baumann-Pickering, Sean M. Wiggins, John A. Hildebrand:
  DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data.
• 
  Jiwoong Kim, David E. Greenberg, Reed Pifer, Shuang Jiang, Guanghua Xiao, Samuel A. Shelburne, Andrew Y. Koh, Yang Xie, Xiaowei Zhan:
  VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.
• 
  Tommy Heck, Diego A. Vargas, Bart Smeets, Herman Ramon, Paul Van Liedekerke, Hans Van Oosterwyck:
  The role of actin protrusion dynamics in cell migration through a degradable viscoelastic extracellular matrix: Insights from a computational model.
• 
  Manoj Kumar, Cameron T. Ellis, Qihong Lu, Hejia Zhang, Mihai Capota, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk-Browne, Kenneth A. Norman:
  BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis.
• 
  Sungrim Seirin-Lee, Yuhki Yanase, Shunsuke Takahagi, Michihiro Hide:
  A single reaction-diffusion equation for the multifarious eruptions of urticaria.
• 
  Christie A. Bahlai, Elise F. Zipkin:
  The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations.
• 
  Maria Bargués-Ribera, Chaitanya S. Gokhale:
  Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations.
• 
  Benjamin Allen, Christine Sample, Robert Jencks, James Withers, Patricia Steinhagen, Lori Brizuela, Joshua Kolodny, Darren Parke, Gabor Lippner, Yulia Dementieva:
  Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs.
• 
  Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, Martin A. Nowak:
  Limits on amplifiers of natural selection under death-Birth updating.
• 
  Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar:
  A new method for inferring timetrees from temporally sampled molecular sequences.
• 
  Melanie Gerken, Sergej Kakorin, Kamel Chibani, Karl-Josef Dietz:
  Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism.
• 
  Simon D. Angus, Jonathan Newton:
  Collaboration leads to cooperation on sparse networks.
• 
  Jennifer Hannig, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
  Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma.
• 
  Amadeus Maes, Mauricio Barahona, Claudia Clopath:
  Learning spatiotemporal signals using a recurrent spiking network that discretizes time.
• 
  Veena Padmanaban, Yohannes Tsehay, Kevin J. Cheung, Andrew J. Ewald, Joel S. Bader:
  Between-tumor and within-tumor heterogeneity in invasive potential.
• 
  Edward W. Huang, Ameya Bhope, Jing Lim, Saurabh Sinha, Amin Emad:
  Tissue-guided LASSO for prediction of clinical drug response using preclinical samples.
• 
  Christopher A. Lavender, Andrew J. Shapiro, Frank S. Day, David C. Fargo:
  ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
• 
  Rasmus S. Petersen, Andrea Colins Rodriguez, Mathew H. Evans, Dario Campagner, Michaela S. E. Loft:
  A system for tracking whisker kinematics and whisker shape in three dimensions.
• 
  Erinija Pranckeviciene, Sergey Hosid, Nathan Liang, Ilya Ioshikhes:
  Nucleosome positioning sequence patterns as packing or regulatory.
• 
  Daan H. de Groot, Josephus Hulshof, Bas Teusink, Frank J. Bruggeman, Robert Planqué:
  Elementary Growth Modes provide a molecular description of cellular self-fabrication.
• 
  Sean M. Cascarina, Mikaela R. Elder, Eric D. Ross:
  Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.
• 
  Rocío Vega, Manuel Carretero, Rui D. M. Travasso, Luis L. Bonilla:
  Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model.
• 
  Tomasz Konopka, Damian Smedley:
  Incremental data integration for tracking genotype-disease associations.
• 
  Roger J. W. Hill, Pasquale F. Innominato, Francis Lévi, Annabelle Ballesta:
  Optimizing circadian drug infusion schedules towards personalized cancer chronotherapy.
• 
  Subhodh Kotekal, Jason N. MacLean:
  Recurrent interactions can explain the variance in single trial responses.
• 
  Yichao Han, Fuzhong Zhang:
  Heterogeneity coordinates bacterial multi-gene expression in single cells.
• 
  Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter:
  XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.

Volume 16, Number 2, February 2020

Editorials

• 
  Veronika Cheplygina, Felienne Hermans, Casper J. Albers, Natalia Z. Bielczyk, Ionica Smeets:
  Ten simple rules for getting started on Twitter as a scientist.
• 
  John S. Tregoning, Jason E. McDermott:
  Ten Simple Rules to becoming a principal investigator.

Research Articles

• 
  Janine Arloth, Gökcen Eraslan, Till F. M. Andlauer, Jade Martins, Stella Iurato, Brigitte Kühnel, Melanie Waldenberger, Josef Frank, Ralf Gold, Bernhard Hemmer, Felix Luessi, Sandra Nischwitz, Friedemann Paul, Heinz Wiendl, Christian Gieger, Stefanie Heilmann-Heimbach, Tim Kacprowski, Matthias Laudes, Thomas Meitinger, Annette Peters, Rajesh Rawal, Konstantin Strauch, Susanne Lucae, Bertram Müller-Myhsok, Marcella Rietschel, Fabian J. Theis, Elisabeth B. Binder, Nikola S. Müller:
  DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
• 
  Nadim A. A. Atiya, Arkady Zgonnikov, Denis O'Hora, Martin Schoemann, Stefan Scherbaum, KongFatt Wong-Lin:
  Changes-of-mind in the absence of new post-decision evidence.
• 
  Collins Assisi, Mark Stopfer, Maxim Bazhenov:
  Optimality of sparse olfactory representations is not affected by network plasticity.
• 
  Hadar Levi-Aharoni, Oren Shriki, Naftali Tishby:
  Surprise response as a probe for compressed memory states.
• 
  Flavia Corsi, Richard Lavery, Elodie Laine, Alessandra Carbone:
  Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.
• 
  Aleksandr Ianevski, Sanna Timonen, Alexander Kononov, Tero Aittokallio, Anil K. Giri:
  SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy.
• 
  Antoine Allard, M. Ángeles Serrano:
  Navigable maps of structural brain networks across species.
• 
  Ana Moyano, Gila Lustig, Hylton E. Rodel, Tibor Antal, Alex Sigal:
  Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition.
• 
  Brian Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel:
  Predicting colorectal cancer risk from adenoma detection via a two-type branching process model.
• 
  Florent Le Möel, Antoine Wystrach:
  Opponent processes in visual memories: A model of attraction and repulsion in navigating insects' mushroom bodies.
• 
  Manuel Stritt, Anna Stalder, Enrico Vezzali:
  Orbit Image Analysis: An open-source whole slide image analysis tool.
• 
  Alice E. Milne, Timothy R. Gottwald, Stephen Parnell, Vasthi Alonso Chávez, Frank van den Bosch:
  What makes or breaks a campaign to stop an invading plant pathogen?
• 
  Kaeser Md. Sabrin, Yongbin Wei, Martijn P. van den Heuvel, Constantine Dovrolis:
  The hourglass organization of the Caenorhabditis elegans connectome.
• 
  Susanne Reimering, Sebastian Muñoz, Alice C. McHardy:
  Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
• 
  Marion F. Sauer, Alexander M. Sevy, James E. Crowe Jr., Jens Meiler:
  Multi-state design of flexible proteins predicts sequences optimal for conformational change.
• 
  Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein, Tim Jeske:
  SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases.
• 
  Shubham Tripathi, Priyanka Chakraborty, Herbert Levine, Mohit Kumar Jolly:
  A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells.
• 
  Ernesto Segredo-Otero, Rafael Sanjuán:
  The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model.
• 
  Xiangying Sun, Zhezhen Wang, Johnathon M. Hall, Carlos Perez-Cervantes, Alexander J. Ruthenburg, Ivan P. Moskowitz, Michael Gribskov, Xinan Holly Yang:
  Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq.
• 
  Daniel Majoral, Ajmal Zemmar, Raul Vicente:
  A model for time interval learning in the Purkinje cell.
• 
  Simon Dirmeier, Christopher Dächert, Martijn van Hemert, Ali Tas, Natacha S. Ogando, Frank J. M. van Kuppeveld, Ralf Bartenschlager, Lars Kaderali, Marco Binder, Niko Beerenwinkel:
  Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation.
• 
  Shuang Song, Wei Jiang, Lin Hou, Hongyu Zhao:
  Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies.
• 
  Eric C. Dykeman:
  A stochastic model for simulating ribosome kinetics in vivo.
• 
  Paco Derouault, Jasmine Chauzeix, David Rizzo, Federica Miressi, Corinne Magdelaine, Sylvie Bourthoumieu, Karine Durand, Hélène Dzugan, Jean Feuillard, Franck Sturtz, Stéphane Mérillou, Anne-Sophie Lia:
  CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer.
• 
  Lu Li, Massimo Lai, Stephen Cole, Nicolas Le Novère, Stuart J. Edelstein:
  Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies.
• 
  Pegah Kassraian-Fard, Michael Pfeiffer, Roman Bauer:
  A generative growth model for thalamocortical axonal branching in primary visual cortex.
• 
  Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski:
  SuperFreq: Integrated mutation detection and clonal tracking in cancer.
• 
  Qian-Yuan Tang, Kunihiko Kaneko:
  Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis.
• 
  Giulio Bondanelli, Srdjan Ostojic:
  Coding with transient trajectories in recurrent neural networks.
• 
  Jordan Douglas, Richard Kingston, Alexei J. Drummond:
  Bayesian inference and comparison of stochastic transcription elongation models.
• 
  Kosuke Hamazaki, Hiroyoshi Iwata:
  RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method.
• 
  Pol Kennel, Jules Dichamp, Corinne Barreau, Christophe Guissard, Lise Teyssedre, Jacques Rouquette, Julien Colombelli, Anne Lorsignol, Louis Casteilla, Franck Plouraboué:
  From whole-organ imaging to in-silico blood flow modeling: A new multi-scale network analysis for revisiting tissue functional anatomy.
• 
  Joël R. Pradines, Victor Farutin, Nicholas A. Cilfone, Abouzar Ghavami, Elma Kurtagic, Jamey Guess, Anthony M. Manning, Ishan Capila:
  Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein.
• 
  Jong Hoon Lee, Xiaoqin Wang, Daniel Bendor:
  The role of adaptation in generating monotonic rate codes in auditory cortex.
• 
  Chieh Lin, Jun Ding, Ziv Bar-Joseph:
  Inferring TF activation order in time series scRNA-Seq studies.
• 
  Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane:
  Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice.
• 
  Bruno Junior Neves, Rodolpho C. Braga, Vinicius M. Alves, Marília N. N. Lima, Gustavo C. Cassiano, Eugene N. Muratov, Fabio T. M. Costa, Carolina Horta Andrade:
  Deep Learning-driven research for drug discovery: Tackling Malaria.
• 
  W. Jeffrey Johnston, Stephanie E. Palmer, David J. Freedman:
  Nonlinear mixed selectivity supports reliable neural computation.
• 
  Andrei Yu. Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky:
  Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.
• 
  Florian Ott, Dimitrije Markovic, Alexander Strobel, Stefan J. Kiebel:
  Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit.
• 
  Lauren Castro, Trevor Bedford, Lauren Ancel Meyers:
  Early prediction of antigenic transitions for influenza A/H3N2.
• 
  Stefan Sellman, Michael J. Tildesley, Christopher L. Burdett, Ryan S. Miller, Clayton Hallman, Colleen Webb, Uno Wennergren, Katie Portacci, Tom Lindström:
  Realistic assumptions about spatial locations and clustering of premises matter for models of foot-and-mouth disease spread in the United States.
• 
  Toshinori Namba, Shuji Ishihara:
  Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells.
• 
  Hao Hong, Shuai Jiang, Hao Li, Guifang Du, Yu Sun, Huan Tao, Cheng Quan, Chenghui Zhao, Ruijiang Li, Wanying Li, Xiaoyao Yin, Yangchen Huang, Cheng Li, Hebing Chen, Xiaochen Bo:
  DeepHiC: A generative adversarial network for enhancing Hi-C data resolution.
• 
  Nadine S. Schaadt, Ralf Schönmeyer, Germain Forestier, Nicolas Brieu, Peter Braubach, Katharina Nekolla, Michael Meyer-Hermann, Friedrich Feuerhake:
  Graph-based description of tertiary lymphoid organs at single-cell level.
• 
  Natacha Comandante-Lou, Mehwish Khaliq, Divya Venkat, Mohan Manikkam, Mohammad Fallahi-Sichani:
  Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy.
• 
  Daniel B. Reeves, Yunda Huang, Elizabeth R. Duke, Bryan T. Mayer, E. Fabian Cardozo-Ojeda, Florencia A. Boshier, David A. Swan, Morgane Rolland, Merlin L. Robb, John R. Mascola, Myron S. Cohen, Lawrence Corey, Peter B. Gilbert, Joshua T. Schiffer:
  Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials.
• 
  Muhammad Ali Al-Radhawi, David Angeli, Eduardo D. Sontag:
  A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks.
• 
  Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James Gonzalo King, Werner Van Geit, Arseny V. Povolotsky, Eilif Müller, Jean-Denis Courcol, Anton Arkhipov:
  The SONATA data format for efficient description of large-scale network models.
• 
  Franziska Hörhold, David Eisel, Marcus Oswald, Amol Kolte, Daniela Röll, Wolfram Osen, Stefan B. Eichmüller, Rainer König:
  Reprogramming of macrophages employing gene regulatory and metabolic network models.
• 
  Jieyun Bai, Andy Lo, Patrick A. Gladding, Martin K. Stiles, Vadim V. Fedorov, Jichao Zhao:
  In silico investigation of the mechanisms underlying atrial fibrillation due to impaired Pitx2.
• 
  Daniel E. Hurtado, Javiera Jilberto, Grigory Panasenko:
  Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions.
• 
  Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullino, Joseph Ciccolini, Jonathan Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sébastien Benzekry:
  Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors.
• 
  Julia A. K. Chartove, Michelle M. McCarthy, Benjamin R. Pittman-Polletta, Nancy J. Kopell:
  A biophysical model of striatal microcircuits suggests gamma and beta oscillations interleaved at delta/theta frequencies mediate periodicity in motor control.
• 
  Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori A. Shepherd, Martin Morgan, Rob Patro:
  Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
• 
  Rok Grah, Tamar Friedlander:
  The relation between crosstalk and gene regulation form revisited.
• 
  Chuang Liu, Junfei Zhao, Weiqiang Lu, Yao Dai, Jennifer Hockings, Yadi Zhou, Ruth Nussinov, Charis Eng, Feixiong Cheng:
  Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes.
• 
  Jill Gallaher, Susan Christine Massey, Andrea Hawkins-Daarud, Sonal S. Noticewala, Russell C. Rockne, Sandra K. Johnston, Luis Gonzalez-Cuyar, Joseph Juliano, Orlando Gil, Kristin R. Swanson, Peter D. Canoll, Alexander R. A. Anderson:
  From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response.
• 
  Isaac Fradkin, Casimir J. H. Ludwig, Eran Eldar, Jonathan D. Huppert:
  Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms.
• 
  Joshua B. Moskowitz, Daniel J. Gale, Jason P. Gallivan, Daniel M. Wolpert, J. Randall Flanagan:
  Human decision making anticipates future performance in motor learning.
• 
  Bastien Berret, Frédéric Jean:
  Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction.
• 
  Lenka Stejskal, William D. Lees, David S. Moss, Machaela Palor, Richard J. Bingham, Adrian J. Shepherd, Joe Grove:
  Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein.

Volume 16, Number 3, March 2020

Editorials

• 
  Ana Arnal, Irene Epifanio, Pablo Gregori, Vicente Martínez:
  Ten Simple Rules for organizing a non-real-time web conference.
• 
  Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne M. Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass:
  Ten simple rules for providing effective bioinformatics research support.

Education

• 
  Marijn van Vliet:
  Seven quick tips for analysis scripts in neuroimaging.

Research Articles

• 
  Jason C. Hyun, Erol S. Kavvas, Jonathan M. Monk, Bernhard O. Palsson:
  Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.
• 
  Barbara Bravi, Riccardo Ravasio, Carolina Brito, Matthieu Wyart:
  Direct coupling analysis of epistasis in allosteric materials.
• 
  Daniel Priego-Espinosa, Alberto Darszon, Adán Guerrero, Ana Laura González-Cota, Takuya Nishigaki, Gustavo Martinez-Mekler, Jorge Carneiro:
  Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm.
• 
  Elba Raimúndez-Álvarez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J. Theis, Dieter Maier, Birgit Luber, Jan Hasenauer:
  Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.
• 
  Sebastian M. Bernasek, Nicolás Peláez, Richard W. Carthew, Neda Bagheri, Luis A. Nunes Amaral:
  Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila.
• 
  Tessa Altair Morris, Jasmine Naik, Kirby Sinclair Fibben, Xiangduo Kong, Tohru Kiyono, Kyoko Yokomori, Anna Grosberg:
  Striated myocyte structural integrity: Automated analysis of sarcomeric z-discs.
• 
  Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann:
  ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.
• 
  Tobias S. Brett, Marco Ajelli, Quan-Hui Liu, Mary G. Krauland, John J. Grefenstette, Willem G. van Panhuis, Alessandro Vespignani, John M. Drake, Pejman Rohani:
  Detecting critical slowing down in high-dimensional epidemiological systems.
• 
  Kiara C. Eldred, Cameron M. Avelis, Robert J. Johnston Jr, Elijah Roberts:
  Modeling binary and graded cone cell fate patterning in the mouse retina.
• 
  Arshag D. Mooradian, Sjoerd van der Post, Kristen M. Naegle, Jason M. Held:
  ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis.
• 
  Michael A. Boemo, Luca Cardelli, Conrad A. Nieduszynski:
  The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.
• 
  Sanjana Gupta, Robin E. C. Lee, James R. Faeder:
  Parallel Tempering with Lasso for model reduction in systems biology.
• 
  Hanah Goetz, Juan Ramon Melendez-Alvarez, Luonan Chen, Xiao-Jun Tian:
  A plausible accelerating function of intermediate states in cancer metastasis.
• 
  Rafael R. Bravo, Etienne Baratchart, Jeffrey West, Ryan O. Schenck, Anna K. Miller, Jill Gallaher, Chandler Gatenbee, David Basanta, Mark Robertson-Tessi, Alexander R. A. Anderson:
  Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization.
• 
  Jan-Eirik W. Skaar, Alexander J. Stasik, Espen Hagen, Torbjørn V. Ness, Gaute T. Einevoll:
  Estimation of neural network model parameters from local field potentials (LFPs).
• 
  Michele Tizzoni, André Panisson, Daniela Paolotti, Ciro Cattuto:
  The impact of news exposure on collective attention in the United States during the 2016 Zika epidemic.
• 
  Dmitrii S. Shcherbinin, Vlad A. Belousov, Mikhail Shugay:
  Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex.
• 
  Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons G. Hoekstra, Omolola Eniola-Adefeso:
  The influence of red blood cell deformability on hematocrit profiles and platelet margination.
• 
  Ryohei Shibue, Fumiyasu Komaki:
  Deconvolution of calcium imaging data using marked point processes.
• 
  Mariama Jaiteh, Ismael Rodriguez-Espigares, Jana Selent, Jens Carlsson:
  Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity.
• 
  Rodrigo M. Corder, Marcelo U. Ferreira, M. Gabriela M. Gomes:
  Modelling the epidemiology of residual Plasmodium vivax malaria in a heterogeneous host population: A case study in the Amazon Basin.
• 
  Xiaochu Li, Floricel Gonzalez, Nathaniel Esteves, Birgit E. Scharf, Jing Chen:
  Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria.
• 
  Ruairi Donnelly, Geofrey W. Sikazwe, Christopher A. Gilligan:
  Estimating epidemiological parameters from experiments in vector access to host plants, the method of matching gradients.
• 
  Lisa M. Bramer, Amanda M. White, Kelly G. Stratton, Allison M. Thompson, Daniel Claborne, Kirsten Hofmockel, Lee Ann McCue:
  ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data.
• 
  Baudouin Forgeot d'Arc, Marie Devaine, Jean Daunizeau:
  Social behavioural adaptation in Autism.
• 
  Thilde Terkelsen, Anders Krogh, Elena Papaleo:
  CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data.
• 
  Wieland Brendel, Ralph Bourdoukan, Pietro Vertechi, Christian K. Machens, Sophie Denève:
  Learning to represent signals spike by spike.
• 
  Lei Liu, Ramón Escobedo, Clément Sire, Guy Theraulaz:
  Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish.
• 
  Christopher N. Davis, T. Déirdre Hollingsworth, Quentin Caudron, Michael A. Irvine:
  The use of mixture density networks in the emulation of complex epidemiological individual-based models.
• 
  Mathias Foo, Declan G. Bates, Ozgur E. Akman:
  A simplified modelling framework facilitates more complex representations of plant circadian clocks.
• 
  Kunal Kathuria, Aakrosh Ratan:
  SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.
• 
  David Laloum, Marc Robinson-Rechavi:
  Methods detecting rhythmic gene expression are biologically relevant only for strong signal.
• 
  Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, David Vallenet:
  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
• 
  Benny Da'adoosh, Kon Kaito, Keishi Miyashita, Minoru Sakaguchi, Amiram Goldblum:
  Computational design of substrate selective inhibition.
• 
  Isobel Routledge, Shengjie Lai, Katherine E. Battle, Azra C. Ghani, Manuel Gomez-Rodriguez, Kyle Gustafson, Swapnil Mishra, Juliette Unwin, Joshua L. Proctor, Andrew J. Tatem, Zhongjie Li, Samir Bhatt:
  Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach.
• 
  Hanna Märkle, Aurélien Tellier:
  Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments.
• 
  Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge:
  An Evolutionary Trace method defines functionally important bases and sites common to RNA families.
• 
  Zhaleh Ghaemi, Joseph R. Peterson, Martin Gruebele, Zaida Luthey-Schulten:
  An in-silico human cell model reveals the influence of spatial organization on RNA splicing.
• 
  Carly Adams, David Young, Paul A. Gastañaduy, Prabasaj Paul, Zach Marsh, Aron J. Hall, Benjamin A. Lopman:
  Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks.
• 
  Ellen Brooks-Pollock, Leon Danon, Hester Korthals Altes, Jennifer A. Davidson, Andrew M. T. Pollock, Dick van Soolingen, Colin Campbell, Maeve K. Lalor:
  A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015.
• 
  Shani Inbar, Pnina Cohen, Tal Yahav, Eyal Privman:
  Comparative study of population genomic approaches for mapping colony-level traits.
• 
  Liangyu Tao, Siddhi Ozarkar, Vikas Bhandawat:
  Mechanisms underlying attraction to odors in walking Drosophila.
• 
  Jyotika Bahuguna, Ajith Sahasranamam, Arvind Kumar:
  Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations.
• 
  Keri A. McKiernan, Anna K. Koster, Merritt Maduke, Vijay S. Pande:
  Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating.
• 
  Elina Numminen, Anna-Liisa Laine:
  The spread of a wild plant pathogen is driven by the road network.
• 
  Kevin C. Cassidy, Jan Sefcik, Yogindra Raghav, Alexander Chang, Jacob D. Durrant:
  ProteinVR: Web-based molecular visualization in virtual reality.

Volume 16, Number 4, April 2020

Editorials

• 
  Kuan-Lin Huang:
  Ten Simple Rules for landing on the right job after your PhD or postdoc.
• 
  Paul Medvedev:
  Ten Simple Rules for writing algorithmic bioinformatics conference papers.
• 
  Anthony C. Fletcher, Georges A. Wagner, Philip E. Bourne:
  Ten simple rules for more objective decision-making.
• 
  Tony Ross-Hellauer, Jonathan P. Tennant, Vilte Banelyte, Edit Görögh, Daniela Luzi, Peter Kraker, Lucio Pisacane, Roberta Ruggieri, Electra Sifacaki, Michela Vignoli:
  Ten simple rules for innovative dissemination of research.

Education Articles

• 
  Yazan Haddad, Vojtech Adam, Zbynek Heger:
  Ten quick tips for homology modeling of high-resolution protein 3D structures.
• 
  Simone Carlo Surace, Jean-Pascal Pfister, Wulfram Gerstner, Johanni Brea:
  On the choice of metric in gradient-based theories of brain function.

Reviews

• 
  Nam D. Nguyen, Daifeng Wang:
  Multiview learning for understanding functional multiomics.
• 
  Shiva Kamkar, Fatemeh Ghezloo, Hamid Abrishami Moghaddam, Ali Borji, Reza Lashgari:
  Multiple-target tracking in human and machine vision.

Research Articles

• 
  Cedoljub Bundalovic-Torma, Gregory B. Whitfield, Lindsey S. Marmont, P. Lynne Howell, John Parkinson:
  A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.
• 
  Winston Garira:
  The research and development process for multiscale models of infectious disease systems.
• 
  David Pellow, Itzik Mizrahi, Ron Shamir:
  PlasClass improves plasmid sequence classification.
• 
  Momchil S. Tomov, Samyukta Yagati, Agni Kumar, Wanqian Yang, Samuel J. Gershman:
  Discovery of hierarchical representations for efficient planning.
• 
  Parisa Rahmani, Fernando Peruani, Pawel Romanczuk:
  Flocking in complex environments - Attention trade-offs in collective information processing.
• 
  David M. Richards, Jamie J. Walker, Joël Tabak:
  Ion channel noise shapes the electrical activity of endocrine cells.
• 
  Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael J. Holst, Padmini Rangamani:
  3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.
• 
  Scott S. Terhune, Yongwoon Jung, Katie M. Cataldo, Ranjan K. Dash:
  Network mechanisms and dysfunction within an integrated computational model of progression through mitosis in the human cell cycle.
• 
  Avtar Roopra:
  MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data.
• 
  Luca Ponzoni, Nga H. Nguyen, Ivet Bahar, Jeffrey L. Brodsky:
  Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel.
• 
  Sarah F. McGough, Michael A. Johansson, Marc Lipsitch, Nicolas A. Menzies:
  Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking.
• 
  Hadel Al Asafen, Prasad U. Bandodkar, Sophia Carrell-Noel, Allison E. Schloop, Jeramey Friedman, Gregory T. Reeves:
  Robustness of the Dorsal morphogen gradient with respect to morphogen dosage.
• 
  Hans-Ulrich Klein, Martin Schäfer, David A. Bennett, Holger Schwender, Philip L. De Jager:
  Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.
• 
  Jamie L. Nosbisch, Anisur Rahman, Krithika Mohan, Timothy C. Elston, James E. Bear, Jason M. Haugh:
  Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing.
• 
  Lara S. Burchardt, Mirjam Knörnschild:
  Comparison of methods for rhythm analysis of complex animals' acoustic signals.
• 
  Fude Sun, Carsten F. E. Schroer, Carlos Ramírez-Palacios, Lida Xu, Shi-Zhong Luo, Siewert J. Marrink:
  Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2.
• 
  Megan L. Matthews, Jack P. Wang, Ronald R. Sederoff, Vincent L. Chiang, Cranos M. Williams:
  Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa.
• 
  Guido Maiello, Manuela Chessa, Peter J. Bex, Fabio Solari:
  Near-optimal combination of disparity across a log-polar scaled visual field.
• 
  Luis Busto-Moner, Julien Morival, Honglei Ren, Arjang Fahim, Zachary Reitz, Timothy L. Downing, Elizabeth L. Read:
  Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
• 
  Jacob Pfeil, Lauren M. Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong T. Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena Morozova Vaske:
  Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.
• 
  Neythen J. Treloar, Alex J. H. Fedorec, Brian P. Ingalls, Chris P. Barnes:
  Deep reinforcement learning for the control of microbial co-cultures in bioreactors.
• 
  Augusto Anguita-Ruiz, Alberto Segura-Delgado, Rafael Alcalá, Concepción Maria Aguilera, Jesús Alcalá-Fdez:
  eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research.
• 
  Pablo Rodríguez-Sánchez, Egbert H. van Nes, Marten Scheffer:
  Climbing Escher's stairs: A way to approximate stability landscapes in multidimensional systems.
• 
  Loïc Marrec, Anne-Florence Bitbol:
  Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial.
• 
  David Frank Little, Joel S. Snyder, Mounya Elhilali:
  Ensemble modeling of auditory streaming reveals potential sources of bistability across the perceptual hierarchy.
• 
  Parker W. de Waal, Jingjing Shi, Erli You, Xiaoxi Wang, Karsten Melcher, Yi Jiang, H. Eric Xu, Bradley M. Dickson:
  Molecular mechanisms of fentanyl mediated β-arrestin biased signaling.
• 
  Yangqing Deng, Wei Pan:
  A powerful and versatile colocalization test.
• 
  Jean-Baptiste Lugagne, Haonan Lin, Mary J. Dunlop:
  DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.
• 
  Nicholas T. Franklin, Michael J. Frank:
  Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning.
• 
  Chloé Pasturel, Anna Montagnini, Laurent U. Perrinet:
  Humans adapt their anticipatory eye movements to the volatility of visual motion properties.
• 
  Marco Mauri, Jean-Luc Gouzé, Hidde de Jong, Eugenio Cinquemani:
  Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs.
• 
  Miguel Brun-Usan, Christoph Thies, Richard A. Watson:
  How to fit in: The learning principles of cell differentiation.
• 
  Yi Jiang, Gina Giase, Kay Grennan, Annie W. Shieh, Yan Xia, Lide Han, Quan Wang, Qiang Wei, Rui Chen, Sihan Liu, Kevin P. White, Chao Chen, Bingshan Li, Chunyu Liu:
  DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.
• 
  Christian Quirouette, Nada P. Younis, Micaela B. Reddy, Catherine A. A. Beauchemin:
  A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract.
• 
  Anna Hutchinson, Hope Watson, Chris Wallace:
  Improving the coverage of credible sets in Bayesian genetic fine-mapping.
• 
  Shreya Saxena, Ian Kinsella, Simon Musall, Sharon H. Kim, Jozsef Meszaros, David N. Thibodeaux, Carla Kim, John J. Cunningham, Elizabeth M. C. Hillman, Anne Churchland, Liam Paninski:
  Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.
• 
  Olga A. Vsevolozhskaya, Min Shi, Fengjiao Hu, Dmitri V. Zaykin:
  DOT: Gene-set analysis by combining decorrelated association statistics.
• 
  Pierre Millard, Uwe Schmitt, Patrick Kiefer, Julia A. Vorholt, Stéphanie Heux, Jean-Charles Portais:
  ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks.
• 
  Aurel A. Lazar, Chung-Heng Yeh:
  A molecular odorant transduction model and the complexity of spatio-temporal encoding in the Drosophila antenna.
• 
  Paul Curtin, Christine Austin, Austen Curtin, Chris Gennings, Claudia Figueroa-Romero, Kristen A. Mikhail, Tatiana M. Botero, Stephen A. Goutman, Eva L. Feldman, Manish Arora:
  Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis.
• 
  João Vasconcelos e Sá, Daniel Simão, Ana P. Terrasso, Marta M. Silva, Catarina Brito, Inês A. Isidro, Paula M. Alves, Manuel J. T. Carrondo:
  Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells.
• 
  Agustín Bruzzese, James A. R. Dalton, Jesús Giraldo:
  Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions.
• 
  Matthew L. Jenior, Thomas J. Moutinho Jr., Bonnie V. Dougherty, Jason A. Papin:
  Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments.
• 
  Adam Ponzi, Scott J. Barton, Kendra D. Bunner, Claudia Rangel-Barajas, Emily S. Zhang, Benjamin R. Miller, George V. Rebec, James R. Kozloski:
  Striatal network modeling in Huntington's Disease.
• 
  Chengwen Luo, Botao Fa, Yuting Yan, Yang Wang, Yiwang Zhou, Yue Zhang, Zhangsheng Yu:
  High-dimensional mediation analysis in survival models.
• 
  Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert:
  Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE.
• 
  Semidán Robaina-Estévez, Zoran Nikoloski:
  Flux-based hierarchical organization of Escherichia coli's metabolic network.
• 
  Weimin Wu, Norman R. Watts, Naiqian Cheng, Rick Huang, Alasdair C. Steven, Paul T. Wingfield:
  Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae.
• 
  Robert P. Gowers, Yulia Timofeeva, Magnus J. E. Richardson:
  Low-rate firing limit for neurons with axon, soma and dendrites driven by spatially distributed stochastic synapses.
• 
  Sean M. Cavany, Guido España, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Helvio Astete, William H. Elson, Gonzalo M. Vazquez-Prokopec, Thomas W. Scott, Amy C. Morrison, Robert C. Reiner Jr., T. Alex Perkins:
  Optimizing the deployment of ultra-low volume and targeted indoor residual spraying for dengue outbreak response.
• 
  Jan Peters, Mark D'Esposito:
  The drift diffusion model as the choice rule in inter-temporal and risky choice: A case study in medial orbitofrontal cortex lesion patients and controls.
• 
  Juhwan Lee, Mooseok Kang, Sangyeol Kim, Iksoo Chang:
  Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity.
• 
  Francisco Y. Cai, Tiffany M. DeSimone, Elsa Hansen, Cameron V. Jennings, Amy K. Bei, Ambroise D. Ahouidi, Souleymane Mboup, Manoj Duraisingh, Caroline O. Buckee:
  Accounting for red blood cell accessibility reveals distinct invasion strategies in Plasmodium falciparum strains.
• 
  Jordanna D. H. Sprayberry:
  Compounds without borders: A mechanism for quantifying complex odors and responses to scent-pollution in bumblebees.
• 
  Sean L. Wu, Héctor M. Sánchez C., John M. Henry, Daniel T. Citron, Qian Zhang, Kelly Compton, Biyonka Liang, Amit Verma, Derek A. T. Cummings, Arnaud Le Menach, Thomas W. Scott, Anne L. Wilson, Steven W. Lindsay, Catherine L. Moyes, Penny A. Hancock, Tanya L. Russell, Thomas R. Burkot, John M. Marshall, Samson S. Kiware, Robert C. Reiner Jr., David L. Smith:
  Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.
• 
  Alexander Tschantz, Anil K. Seth, Christopher L. Buckley:
  Learning action-oriented models through active inference.
• 
  Chuliang Song, Serguei Saavedra:
  Telling ecological networks apart by their structure: An environment-dependent approach.
• 
  Caglar Cakan, Klaus Obermayer:
  Biophysically grounded mean-field models of neural populations under electrical stimulation.
• 
  Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
  BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
• 
  Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le:
  LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer.
• 
  Ramón Bartolo, Richard C. Saunders, Andrew R. Mitz, Bruno B. Averbeck:
  Dimensionality, information and learning in prefrontal cortex.
• 
  Xiangyu Yao, Shihoko Kojima, Jing Chen:
  Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.
• 
  Xinmeng Li, James Van Deventer, Soha Hassoun:
  ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.
• 
  Andreas Haahr Larsen, Yong Wang, Sandro Bottaro, Sergei Grudinin, Lise Arleth, Kresten Lindorff-Larsen:
  Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.
• 
  Vinnu Bhardwaj, Massimo Franceschetti, Ramesh Rao, Pavel A. Pevzner, Yana Safonova:
  Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.
• 
  Yuanchao Zhang, Mansuck Kim, Erin R. Reichenberger, Ben Stear, Deanne M. Taylor:
  Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis.
• 
  Malte Schilling, Holk Cruse:
  Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results.
• 
  Mirko Klukas, Marcus Lewis, Ila Fiete:
  Efficient and flexible representation of higher-dimensional cognitive variables with grid cells.
• 
  Karren D. Yang, Karthik Damodaran, Saradha Venkatachalapathy, Ali Soylemezoglu, G. V. Shivashankar, Caroline Uhler:
  Predicting cell lineages using autoencoders and optimal transport.
• 
  Xiaoning Zheng, Alireza Yazdani, He Li, Jay D. Humphrey, George E. Karniadakis:
  A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels.
• 
  Maximilian Puelma Touzel, Aleksandra M. Walczak, Thierry Mora:
  Inferring the immune response from repertoire sequencing.
• 
  Gregory L. Medlock, Thomas J. Moutinho Jr., Jason A. Papin:
  Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions.
• 
  Marte J. Sætra, Gaute T. Einevoll, Geir Halnes:
  An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms.
• 
  Agus Hartoyo, Peter J. Cadusch, David T. J. Liley, Damien G. Hicks:
  Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.
• 
  Ian J. Aitkenhead, Grant A. Duffy, Citsabehsan Devendran, Michael R. Kearney, Adrian Neild, Steven L. Chown:
  Tracheal branching in ants is area-decreasing, violating a central assumption of network transport models.
• 
  Daniele Raimondi, Gabriele Orlando, Piero Fariselli, Yves Moreau:
  Insight into the protein solubility driving forces with neural attention.
• 
  Shakti N. Menon, P. Varuni, Gautam I. Menon:
  Information integration and collective motility in phototactic cyanobacteria.

Volume 16, Number 5, May 2020

Editorials

• 
  Kevin R. Burgio, Caitlin McDonough MacKenzie, Stephanie B. Borrelle, S. K. Morgan Ernest, Jacquelyn L. Gill, Kurt E. Ingeman, Amy Teffer, Ethan P. White:
  Ten Simple Rules for a successful remote postdoc.
• 
  Deborah D. Rupert, Alexandra C. Nowlan, Oliver H. Tam, Molly Hammell:
  Ten simple rules for running a successful women-in-STEM organization on an academic campus.
• 
  Leyla J. García, Erick Antezana, Alexander García Castro, Evan Bolton, Rafael C. Jiménez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama:
  Ten simple rules to run a successful BioHackathon.
• 
  Alastair M. Kilpatrick, Audra Anjum, Lonnie R. Welch:
  Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles.
• 
  Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath:
  Improving reproducibility in computational biology research.
• 
  Leyla J. García, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis E. Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi:
  Ten simple rules for making training materials FAIR.

Education

• 
  Orianna Demasi, Alexandra Paxton, Kevin Koy:
  Ad hoc efforts for advancing data science education.

Review

• 
  Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau:
  Better together: Elements of successful scientific software development in a distributed collaborative community.

Research Articles

• 
  Jue Tao Lim, Borame Sue Dickens, Haoyang Sun, Ng Lee Ching, Alex R. Cook:
  Inference on dengue epidemics with Bayesian regime switching models.
• 
  Tal Einav, Jesse D. Bloom:
  When two are better than one: Modeling the mechanisms of antibody mixtures.
• 
  Amanda Brucker, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz, Tzu-Pin Lu, Jung-Ying Tzeng:
  Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis.
• 
  Andrew J. Bernoff, Michael Culshaw-Maurer, Rebecca A. Everett, Maryann E. Hohn, W. Christopher Strickland, Jasper Weinburd:
  Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.
• 
  James A. Hay, Amanda Minter, Kylie E. C. Ainslie, Justin Lessler, Bingyi Yang, Derek A. T. Cummings, Adam J. Kucharski, Steven Riley:
  An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver.
• 
  Christine A. Tataru, Maude M. David:
  Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease.
• 
  Erik D. Fagerholm, W. Matthew C. Foulkes, Yasir Gallero-Salas, Fritjof Helmchen, Karl J. Friston, Rosalyn J. Moran, Robert Leech:
  Conservation laws by virtue of scale symmetries in neural systems.
• 
  Juami Hermine Mariama van Gils, Erik van Dijk, Alessia Peduzzo, Alexander Hofmann, Nicola Vettore, Marie P. Schützmann, Georg Groth, Halima Mouhib, Daniel E. Otzen, Alexander K. Buell, Sanne Abeln:
  The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth.
• 
  Kee-Myoung Nam, Benjamin M. Gyori, Silviana V. Amethyst, Daniel J. Bates, Jeremy Gunawardena:
  Robustness and parameter geography in post-translational modification systems.
• 
  Elan Shatoff, Ralf Bundschuh:
  Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures.
• 
  Sevan K. Harootonian, Robert C. Wilson, Lukás Hejtmánek, Eli M. Ziskin, Arne D. Ekstrom:
  Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models.
• 
  Audrey J. Sederberg, Ilya Nemenman:
  Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons.
• 
  Leonardo Pacciani-Mori, Andrea Giometto, Samir Suweis, Amos Maritan:
  Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities.
• 
  Sara Jamous, Andrea Comba, Pedro R. Lowenstein, Sébastien Motsch:
  Self-organization in brain tumors: How cell morphology and cell density influence glioma pattern formation.
• 
  Mohsen Ranjbaran, Mina Solhtalab, Ashim K. Datta:
  Mechanistic modeling of light-induced chemotactic infiltration of bacteria into leaf stomata.
• 
  Lisandro Montangie, Christoph Miehl, Julijana Gjorgjieva:
  Autonomous emergence of connectivity assemblies via spike triplet interactions.
• 
  Magali Richard, Clémentine Decamps, Florent Chuffart, Elisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost:
  PenDA, a rank-based method for personalized differential analysis: Application to lung cancer.
• 
  Julian Q. Kosciessa, Niels A. Kloosterman, Douglas D. Garrett:
  Standard multiscale entropy reflects neural dynamics at mismatched temporal scales: What's signal irregularity got to do with it?
• 
  Alan Le Goallec, Braden T. Tierney, Jacob M. Luber, Evan M. Cofer, Aleksandar D. Kostic, Chirag J. Patel:
  A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type.
• 
  C. Marijn Hazelbag, Jonathan Dushoff, Emanuel M. Dominic, Zinhle E. Mthombothi, Wim Delva:
  Calibration of individual-based models to epidemiological data: A systematic review.
• 
  Alexander Rivkind, Hallel Schreier, Naama Brenner, Omri Barak:
  Scale free topology as an effective feedback system.
• 
  Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke, Nathan E. Lewis:
  StanDep: Capturing transcriptomic variability improves context-specific metabolic models.
• 
  Ting-En Wang, Tai-Ling Chao, Hsin-Tsuen Tsai, Pi-Han Lin, Yen-Lung Tsai, Sui-Yuan Chang:
  Differentiation of Cytopathic Effects (CPE) induced by influenza virus infection using deep Convolutional Neural Networks (CNN).
• 
  Eric Wright, Mauricio H. Ferrato, Alexander J. Bryer, Robert Searles, Juan R. Perilla, Sunita Chandrasekaran:
  Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.
• 
  Nicolò Gozzi, Daniela Perrotta, Daniela Paolotti, Nicola Perra:
  Towards a data-driven characterization of behavioral changes induced by the seasonal flu.
• 
  Guang Song:
  Shape-preserving elastic solid models of macromolecules.
• 
  Felix Roy, Matthieu Barbier, Giulio Biroli, Guy Bunin:
  Complex interactions can create persistent fluctuations in high-diversity ecosystems.
• 
  Jimin Pei, Lisa N. Kinch, Zbyszek Otwinowski, Nick V. Grishin:
  Mutation severity spectrum of rare alleles in the human genome is predictive of disease type.
• 
  Tim Loossens, Merijn Mestdagh, Egon Dejonckheere, Peter Kuppens, Francis Tuerlinckx, Stijn Verdonck:
  The Affective Ising Model: A computational account of human affect dynamics.
• 
  Joseph Farris, Barbara Calhoun, Md. Suhail Alam, Shaun Lee, Kasturi Haldar:
  Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity.
• 
  Vincent Cabeli, Louis Verny, Nadir Sella, Guido Uguzzoni, Marc Verny, Hervé Isambert:
  Learning clinical networks from medical records based on information estimates in mixed-type data.
• 
  Kai Zheng, Zhu-Hong You, Jian-Qiang Li, Lei Wang, Zhen-Hao Guo, Yu-An Huang:
  iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation.
• 
  Abhishek Varghese, Christopher C. Drovandi, Antonietta Mira, Kerrie L. Mengersen:
  Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation.
• 
  Yuan Zhao, Jacob L. Yates, Aaron J. Levi, Alexander C. Huk, Il Memming Park:
  Stimulus-choice (mis)alignment in primate area MT.
• 
  Jannes Jegminat, Maya A. Jastrzebowska, Matthew V. Pachai, Michael H. Herzog, Jean-Pascal Pfister:
  Bayesian regression explains how human participants handle parameter uncertainty.
• 
  Chao Kong, Yu-Xiang Yao, Zhi-Tong Bing, Bing-Hui Guo, Liang Huang, Zi-Gang Huang, Ying-Cheng Lai:
  Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer.
• 
  Timothy Wessler, Louis R. Joslyn, H. Jacob Borish, Hannah P. Gideon, JoAnne L. Flynn, Denise E. Kirschner, Jennifer J. Linderman:
  A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination.
• 
  Martí Català, Jordi Bechini, Montserrat Tenesa, Ricardo Pérez, Mariano Moya, Cristina Vilaplana, Joaquim Valls, Sergio Alonso, Daniel López, Pere-Joan Cardona, Clara Prats:
  Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection.
• 
  Lei Wang, Zhu-Hong You, Yang-Ming Li, Kai Zheng, Yu-An Huang:
  GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm.
• 
  Attila Horvath, Márton Miskei, Viktor Ambrus, Michele Vendruscolo, Mónika Fuxreiter:
  Sequence-based prediction of protein binding mode landscapes.
• 
  Francesca Young, Simon Rogers, David L. Robertson:
  Predicting host taxonomic information from viral genomes: A comparison of feature representations.
• 
  Arumay Pal, Yaakov Levy:
  Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA.
• 
  Jose Cadena, Ana Paula Sales, Doris Lam, Heather A. Enright, Elizabeth K. Wheeler, Nicholas O. Fischer:
  Modeling the temporal network dynamics of neuronal cultures.
• 
  Agata P. Perlinska, Adam Stasiulewicz, Ewa K. Nawrocka, Krzysztof Kazimierczuk, Piotr Setny, Joanna I. Sulkowska:
  Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.
• 
  Maaike M. H. van Swieten, Rafal Bogacz:
  Modeling the effects of motivation on choice and learning in the basal ganglia.
• 
  Paul Lemarre, Laurent Pujo-Menjouet, Suzanne S. Sindi:
  A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion.
• 
  Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters:
  Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system.
• 
  Haleh Alimohamadi, Alyson S. Smith, Roberta B. Nowak, Velia M. Fowler, Padmini Rangamani:
  Non-uniform distribution of myosin-mediated forces governs red blood cell membrane curvature through tension modulation.
• 
  Christopher Brian Currin, Andrew J. Trevelyan, Colin J. Akerman, Joseph Valentino Raimondo:
  Chloride dynamics alter the input-output properties of neurons.
• 
  Clare I. Abreu, Vilhelm L. Andersen Woltz, Jonathan Friedman, Jeff Gore:
  Microbial communities display alternative stable states in a fluctuating environment.
• 
  Cameron Meaney, Sander Rhebergen, Mohammad Kohandel:
  In silico analysis of hypoxia activated prodrugs in combination with anti angiogenic therapy through nanocell delivery.
• 
  Yuval Hart, Maryam Vaziri-Pashkam, L. Mahadevan:
  Early warning signals in motion inference.
• 
  Tyler A. Joseph, Liat Shenhav, João B. Xavier, Eran Halperin, Itsik Pe'er:
  Compositional Lotka-Volterra describes microbial dynamics in the simplex.
• 
  M-Hossein Moeinzadeh, Jun Yang, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan A. Haas, Martin Vingron:
  Ranbow: A fast and accurate method for polyploid haplotype reconstruction.
• 
  Martín Carballo-Pacheco, Michael D. Nicholson, Elin E. Lilja, Rosalind J. Allen, Bartlomiej Waclaw:
  Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications.

Volume 16, Number 6, June 2020

Editorials

• 
  Joseph C. Ayoob, Joshua D. Kangas:
  10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats.
• 
  Hoe-Han Goh, Philip E. Bourne:
  Ten simple rules for researchers while in isolation from a pandemic.

Education

• 
  Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin:
  G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.

Research Articles

• 
  Miguel Capllonch-Juan, Francisco Sepulveda:
  Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves.
• 
  Jonathan Carruthers, Grant Lythe, Martín López-García, Joseph Gillard, Thomas R. Laws, Roman Lukaszewski, Carmen Molina-París:
  Stochastic dynamics of Francisella tularensis infection and replication.
• 
  Giulio Ruffini, Ricardo Salvador, Ehsan Tadayon, Roser Sanchez-Todo, Alvaro Pascual-Leone, Emiliano Santarnecchi:
  Realistic modeling of mesoscopic ephaptic coupling in the human brain.
• 
  Bartlomiej Tomiczek, Wojciech Delewski, Lukasz Nierzwicki, Milena Stolarska, Igor Grochowina, Brenda Schilke, Rafal Dutkiewicz, Marta A. Uzarska, Szymon J. Ciesielski, Jacek Czub, Elizabeth A. Craig, Jaroslaw Marszalek:
  Two-step mechanism of J-domain action in driving Hsp70 function.
• 
  Andrew K. Smith, Glen E. P. Ropella, Mitchell R. McGill, Preethi Krishnan, Lopamudra Dutta, Ryan C. Kennedy, Hartmut Jaeschke, C. Anthony Hunt:
  Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms.
• 
  Florent Meyniel:
  Brain dynamics for confidence-weighted learning.
• 
  Hélène Ruffieux, Jérôme Carayol, Radu Popescu, Mary-Ellen Harper, Robert Dent, Wim H. M. Saris, Arne Astrup, Jörg Hager, Anthony C. Davison, Armand Valsesia:
  A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma.
• 
  Dirke Imig, Nadine Pollak, Frank Allgöwer, Markus Rehm:
  Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis.
• 
  Zhenxing Wu, Kai Zhao:
  Taste of time: A porous-medium model for human tongue surface with implications for early taste perception.
• 
  Abolfazl Ramezanpour, Alireza Mashaghi:
  Disease evolution in reaction networks: Implications for a diagnostic problem.
• 
  Jan J. Domanski, Mark S. P. Sansom, Phillip J. Stansfeld, Robert B. Best:
  Atomistic mechanism of transmembrane helix association.
• 
  Federico Sevlever, Juan Pablo Di-Bella, Alejandra C. Ventura:
  Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves.
• 
  Philip Kleinert, Beth K. Martin, Martin Kircher:
  HemoMIPs - Automated analysis and result reporting pipeline for targeted sequencing data.
• 
  Yu Hu, Kai Wang, Mingyao Li:
  Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers.
• 
  Rebecca H. Chisholm, Nikki Sonenberg, Jake A. Lacey, Malcolm I. McDonald, Manisha Pandey, Mark R. Davies, Steven Y. C. Tong, Jodie McVernon, Nicholas Geard:
  Epidemiological consequences of enduring strain-specific immunity requiring repeated episodes of infection.
• 
  David V. Conesa, Blas Echebarria, Angelina Peñaranda, Inmaculada R. Cantalapiedra, Yohannes Shiferaw, Enrique Alvarez-Lacalle:
  Two-variable nullcline analysis of ionic general equilibrium predicts calcium homeostasis in ventricular myocytes.
• 
  Hanxin Zhang, Torsten Dahlén, Atif Ali Khan, Gustaf Edgren, Andrey Rzhetsky:
  Measurable health effects associated with the daylight saving time shift.
• 
  Hui Yu, Shilin Zhao, Scott Ness, Huining Kang, Quanhu Sheng, David C. Samuels, Olufunmilola Oyebamiji, Ying-Yong Zhao, Yan Guo:
  Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats.
• 
  Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke A. Ojewole, Bruce Randall Donald:
  Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface.
• 
  Matthijs Pals, Terrence C. Stewart, Elkan G. Akyürek, Jelmer P. Borst:
  A functional spiking-neuron model of activity-silent working memory in humans based on calcium-mediated short-term synaptic plasticity.
• 
  David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T. Grant Belgard, Alice Zhang, Victor Hanson-Smith:
  A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.
• 
  Yuxiu Shao, Jiwei Zhang, Louis Tao:
  Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure.
• 
  Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P. Trzeciakowski, Andreea Trache, Yi Jiang:
  Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry.
• 
  Lauren A. White, Sue VandeWoude, Meggan E. Craft:
  A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence.
• 
  Víctor A. López-Agudelo, Tom A. Mendum, Emma Laing, HuiHai Wu, Andres Baena, Luis F. Barrera, Dany J. V. Beste, Rigoberto Ríos-Estepa:
  A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks.
• 
  Guosheng Yi, Warren M. Grill:
  Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block.
• 
  Lindsay Rutter, Dianne Cook:
  bigPint: A Bioconductor visualization package that makes big data pint-sized.
• 
  Will Xiao, Gabriel Kreiman:
  XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization.
• 
  Wan Yang, Eric H. Y. Lau, Benjamin J. Cowling:
  Dynamic interactions of influenza viruses in Hong Kong during 1998-2018.
• 
  Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse:
  Circuits with broken fibration symmetries perform core logic computations in biological networks.
• 
  Mario J. C. Ayala, Daniel A. M. Villela:
  Early transmission of sensitive strain slows down emergence of drug resistance in Plasmodium vivax.
• 
  Alexey Savelyev, Gary Gorbet, Amy Henrickson, Borries Demeler:
  Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment.
• 
  Fatemeh Khatami, Monty A. Escabí:
  Spiking network optimized for word recognition in noise predicts auditory system hierarchy.
• 
  Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric T. Dawson, Garan Jones, Daniel J. Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E. Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook:
  A crowdsourced set of curated structural variants for the human genome.
• 
  Bruno Miranda, W. M. Nishantha Malalasekera, Timothy Edward John Behrens, Peter Dayan, Steven W. Kennerley:
  Combined model-free and model-sensitive reinforcement learning in non-human primates.
• 
  Damiano Piovesan, András Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon, Silvio C. E. Tosatto:
  Assessing predictors for new post translational modification sites: A case study on hydroxylation.
• 
  Satoshi Ii, Hiroki Kitade, Shunichi Ishida, Yohsuke Imai, Yoshiyuki Watanabe, Shigeo Wada:
  Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm.
• 
  Alexander Ivanenko, Paul V. Watkins, Marcel A. J. van Gerven, K. Hammerschmidt, Bernhard Englitz:
  Classifying sex and strain from mouse ultrasonic vocalizations using deep learning.
• 
  Nima Nouri, Steven H. Kleinstein:
  Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.
• 
  Emili Balaguer-Ballester, Ramon Nogueira, Juan M. Abofalia, Rubén Moreno-Bote, Maria V. Sanchez-Vives:
  Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions.
• 
  Jakob Rosenbauer, Chengting Zhang, Benjamin Mattes, Ines Reinartz, Kyle Wedgwood, Simone Schindler, Claude Sinner, Steffen Scholpp, Alexander Schug:
  Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis.
• 
  Seha Kim, Johannes Burge:
  Natural scene statistics predict how humans pool information across space in surface tilt estimation.
• 
  Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell:
  Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans.
• 
  Hadi Rahmaninejad, Tom Pace, Shashank Bhatt, Bin Sun, Peter M. Kekenes-Huskey:
  Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.
• 
  Atte S. A. Eskelinen, Petri Tanska, Cristina Florea, Gustavo A. Orozco, Petro Julkunen, Alan J. Grodzinsky, Rami K. Korhonen:
  Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus.
• 
  Garikoitz Lerma-Usabiaga, Noah C. Benson, Jonathan Winawer, Brian A. Wandell:
  A validation framework for neuroimaging software: The case of population receptive fields.
• 
  Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein:
  Epigenome-based splicing prediction using a recurrent neural network.
• 
  Fabian Konrath, Anna Mittermeier, Elena Cristiano, Jana Wolf, Alexander Loewer:
  A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics.
• 
  Aleksey V. Zimin, Steven L. Salzberg:
  The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.
• 
  Stefanie Duvigneau, Robert Dürr, Tanja Laske, Mandy Bachmann, Melanie Dostert, Achim Kienle:
  Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing - Application to influenza vaccine production.
• 
  A. Armean Wright, Ghassan N. Fayad, James F. Selgrade, Mette S. Olufsen:
  Mechanistic model of hormonal contraception.
• 
  Nimrod Sherf, Maoz Shamir:
  Multiplexing rhythmic information by spike timing dependent plasticity.
• 
  Shintaro Nagata, Macoto Kikuchi:
  Emergence of cooperative bistability and robustness of gene regulatory networks.
• 
  Ethan D. Evans, Chengzhen Dai, Siavash Isazadeh, Shinkyu Park, Carlo Ratti, Eric J. Alm:
  Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites.
• 
  Samuel R. Bray, Bo Wang:
  Forecasting unprecedented ecological fluctuations.
• 
  Mikkel Herholdt Jensen, Eliza J. Morris, Hai Tran, Michael A. Nash, Cheemeng Tan:
  Stochastic ordering of complexoform protein assembly by genetic circuits.
• 
  Niklas Korsbo, Henrik Jönsson:
  It's about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology.
• 
  Jens Karschau, André Scholich, Jonathan Wise, Hernán Morales-Navarrete, Yannis Kalaidzidis, Marino Zerial, Benjamin M. Friedrich:
  Resilience of three-dimensional sinusoidal networks in liver tissue.
• 
  Sandra Mayr, Fabian Hauser, Sujitha Puthukodan, Markus Axmann, Janett Göhring, Jaroslaw Jacak:
  Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model.

Volume 16, Number 7, July 2020

Editorial

• 
  Maureen A. Carey, Kevin L. Steiner, William A. Petri Jr.:
  Ten simple rules for reading a scientific paper.

Education Articles

• 
  Kim T. Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee D. Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez Del Angel, Pedro L. Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskosek, Jessica M. Lindvall, Diana Marek, Paula Andrea Martínez, Tuur Muyldermans, Ståle Nygård, Patricia M. Palagi, Hedi Peterson, Fotis E. Psomopoulos, Vojtech Spiwok, Celia W. G. van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L. Morgan, Gabriella Rustici:
  A framework to assess the quality and impact of bioinformatics training across ELIXIR.
• 
  Susan McClatchy, Kristin M. Bass, Daniel M. Gatti, Adam Moylan, Gary Churchill:
  Nine quick tips for efficient bioinformatics curriculum development and training.

Research Articles

• 
  Payam Piray, Nathaniel D. Daw:
  A simple model for learning in volatile environments.
• 
  Tomasz Pienko, Joanna Trylska:
  Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli.
• 
  Kris V. Parag, Christl A. Donnelly:
  Using information theory to optimise epidemic models for real-time prediction and estimation.
• 
  August George, Paola Bisignano, John M. Rosenberg, Michael Grabe, Daniel M. Zuckerman:
  A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms.
• 
  Paola Bisignano, Michael A. Lee, August George, Daniel M. Zuckerman, Michael Grabe, John M. Rosenberg:
  A kinetic mechanism for enhanced selectivity of membrane transport.
• 
  Alex C. Ferris, Richard O. J. H. Stutt, David Godding, Christopher A. Gilligan:
  Computational models to improve surveillance for cassava brown streak disease and minimize yield loss.
• 
  Julia Berezutskaya, Zachary Freudenburg, Umut Güçlü, Marcel A. J. van Gerven, Nick F. Ramsey:
  Brain-optimized extraction of complex sound features that drive continuous auditory perception.
• 
  Joe Hilton, Matt J. Keeling:
  Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices.
• 
  Elisa Benincà, Thomas J. Hagenaars, Gert Jan Boender, Jan van de Kassteele, Michiel van Boven:
  Trade-off between local transmission and long-range dispersal drives infectious disease outbreak size in spatially structured populations.
• 
  Tom L. Kaufmann, Ulrich S. Schwarz:
  Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments.
• 
  Madison S. Krieger, Carson E. Denison, Thayer L. Anderson, Martin A. Nowak, Alison L. Hill:
  Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections.
• 
  Thuy T. T. Le, Frederick R. Adler:
  Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality.
• 
  Konstantin Butenko, Christian Bahls, Max Schröder, Rüdiger Köhling, Ursula van Rienen:
  OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling.
• 
  Philippe Carmona, Sylvain Gandon:
  Winter is coming: Pathogen emergence in seasonal environments.
• 
  Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte:
  Real time structural search of the Protein Data Bank.
• 
  Samuel V. Scarpino, James G. Scott, Rosalind M. Eggo, Bruce Clements, Nedialko B. Dimitrov, Lauren Ancel Meyers:
  Socioeconomic bias in influenza surveillance.
• 
  Samuel F. Rosenblatt, Jeffrey A. Smith, G. Robin Gauthier, Laurent Hébert-Dufresne:
  Immunization strategies in networks with missing data.
• 
  Mathilde Foglierini, Leontios Pappas, Antonio Lanzavecchia, Davide Corti, Laurent Perez:
  AncesTree: An interactive immunoglobulin lineage tree visualizer.
• 
  Doron Levin, Tamir Tuller:
  Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics.
• 
  Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling:
  Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling.
• 
  Victor Pedrosa, Claudia Clopath:
  The interplay between somatic and dendritic inhibition promotes the emergence and stabilization of place fields.
• 
  Richard J. Beck, Dario I. Bijker, Joost B. Beltman:
  Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data.
• 
  Xian F. Mallory, Mohammad Amin Edrisi, Nicholas Navin, Luay Nakhleh:
  Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data.
• 
  Na Zhao, Qince Li, Kevin Zhang, Kuanquan Wang, Runnan He, Yongfeng Yuan, Henggui Zhang:
  Heart failure-induced atrial remodelling promotes electrical and conduction alternans.
• 
  Ulisse Ferrari, Stéphane Deny, Abhishek Sengupta, Romain Caplette, Francesco Trapani, José-Alain Sahel, Deniz Dalkara, Serge Picaud, Jens Duebel, Olivier Marre:
  Towards optogenetic vision restoration with high resolution.
• 
  Huiyuan Chen, Feixiong Cheng, Jing Li:
  iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding.
• 
  Elin Nyman, Richard R. Stein, Xiaohong Jing, Weiqing Wang, Benjamin Marks, Ioannis K. Zervantonakis, Anil Korkut, Nicholas Paul Gauthier, Chris Sander:
  Perturbation biology links temporal protein changes to drug responses in a melanoma cell line.
• 
  Shixin Xu, Joshua C. Chang, Carson C. Chow, K. C. Brennan, Huaxiong Huang:
  A mathematical model for persistent post-CSD vasoconstriction.
• 
  Alberto Aleta, Guilherme Ferraz de Arruda, Yamir Moreno:
  Data-driven contact structures: From homogeneous mixing to multilayer networks.
• 
  Joseph D. Taylor, Samuel Winnall, Alain Nogaret:
  Estimation of neuron parameters from imperfect observations.
• 
  Mariam Ordyan, Tom Bartol, Mary B. Kennedy, Padmini Rangamani, Terrence J. Sejnowski:
  Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator.
• 
  Andrew J. Page, Sarah Bastkowski, Muhammad Yasir, A. Keith Turner, Thanh Le Viet, George M. Savva, Mark A. Webber, Ian G. Charles:
  AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments.
• 
  Timo Oess, Marc O. Ernst, Heiko Neumann:
  Computational principles of neural adaptation for binaural signal integration.
• 
  David R. Kelley:
  Cross-species regulatory sequence activity prediction.
• 
  Filip Z. Klawe, Thomas Stiehl, Peter Bastian, Christophe Gaillochet, Jan U. Lohmann, Anna K. Marciniak-Czochra:
  Mathematical modeling of plant cell fate transitions controlled by hormonal signals.
• 
  Solomon Shiferaw Beyene, Tianyi Ling, Blagoj Ristevski, Ming Chen:
  A novel riboswitch classification based on imbalanced sequences achieved by machine learning.
• 
  Céline N. Martineau, André E. X. Brown, Patrick Laurent:
  Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans.
• 
  Adrien Doerig, Lynn Schmittwilken, Bilge Sayim, Mauro Manassi, Michael H. Herzog:
  Capsule networks as recurrent models of grouping and segmentation.
• 
  Andrew R. Ghazi, Xianguo Kong, Edward S. Chen, Leonard C. Edelstein, Chad A. Shaw:
  Bayesian modelling of high-throughput sequencing assays with malacoda.
• 
  Morgan E. Smith, Emily Griswold, Brajendra K. Singh, Emmanuel Miri, Abel Eigege, Solomon Adelamo, John Umaru, Kenrick Nwodu, Yohanna Sambo, Jonathan Kadimbo, Jacob Danyobi, Frank O. Richards, Edwin Michael:
  Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery.
• 
  Doina Bucur, Petter Holme:
  Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities.
• 
  David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz:
  Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.
• 
  Christophe Verbist, Michael G. Müller, Huibert D. Mansvelder, Robert Legenstein, Michele Giugliano:
  The location of the axon initial segment affects the bandwidth of spike initiation dynamics.
• 
  Jennifer L. Wilson, Dan Lu, Nick Corr, Aaron Fullerton, James Lu:
  An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias.
• 
  Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Shin Ishii:
  Signaling models for dopamine-dependent temporal contiguity in striatal synaptic plasticity.
• 
  Noor Seijdel, Nikos Tsakmakidis, Edward H. F. de Haan, Sander M. Bohté, H. Steven Scholte:
  Depth in convolutional neural networks solves scene segmentation.
• 
  Jinhee Park, Hyerin Kim, Jaekwang Kim, Mookyung Cheon:
  A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease.
• 
  Xiao Zheng, Yuan Huang, Xiufen Zou:
  scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data.
• 
  Margaret L. DeMaegd, Wolfgang Stein:
  Temperature-robust activity patterns arise from coordinated axonal Sodium channel properties.
• 
  Philipp Schneider, Axel von Kamp, Steffen Klamt:
  An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets.
• 
  William Davis Haselden, Ravi Teja Kedarasetti, Patrick J. Drew:
  Spatial and temporal patterns of nitric oxide diffusion and degradation drive emergent cerebrovascular dynamics.
• 
  Youngmin Park, Maria N. Geffen:
  A circuit model of auditory cortex.
• 
  Edward C. Schrom II, Simon A. Levin, Andrea L. Graham:
  Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells.
• 
  Ian F. Coccimiglio, David C. Clarke:
  ADP is the dominant controller of AMP-activated protein kinase activity dynamics in skeletal muscle during exercise.
• 
  Huu Hoang, Eric J. Lang, Yoshito Hirata, Isao T. Tokuda, Kazuyuki Aihara, Keisuke Toyama, Mitsuo Kawato, Nicolas Schweighofer:
  Electrical coupling controls dimensionality and chaotic firing of inferior olive neurons.
• 
  Rafael D'Andrea, Theo Gibbs, James P. O'Dwyer:
  Emergent neutrality in consumer-resource dynamics.
• 
  Kathryn Asalone, Kara M. Ryan, Maryam Yamadi, Annastelle L. Cohen, William G. Farmer, Deborah J. George, Claudia Joppert, Kaitlyn Kim, Madeeha Froze Mughal, Rana Said, Metin Toksoz-Exley, Evgeny Bisk, John R. Bracht:
  Regional sequence expansion or collapse in heterozygous genome assemblies.
• 
  Samy Castro, Wael El-Deredy, Demian Battaglia, Patricio Orio:
  Cortical ignition dynamics is tightly linked to the core organisation of the human connectome.

Volume 16, Number 8, August 2020

Education

• 
  Ada K. Hagan, Nicholas A. Lesniak, Marcy J. Balunas, Lucas Bishop, William L. Close, Matthew D. Doherty, Amanda G. Elmore, Kaitlin J. Flynn, Geoffrey D. Hannigan, Charlie C. Koumpouras, Matthew L. Jenior, Ariangela J. Kozik, Kathryn McBride, Samara B. Rifkin, Joshua M. A. Stough, Kelly L. Sovacool, Marc A. Sze, Sarah Tomkovich, Begüm D. Topçuoglu, Patrick D. Schloss:
  Ten simple rules to increase computational skills among biologists with Code Clubs.

Perspective

• 
  Enrico Ferrero, Sophie Brachat, Jeremy L. Jenkins, Philippe Marc, Peter Skewes-Cox, Robert C. Altshuler, Caroline Gubser Keller, Audrey Kauffmann, Erik K. Sassaman, Jason M. Laramie, Birgit Schoeberl, Mark L. Borowsky, Nikolaus Stiefl:
  Ten simple rules to power drug discovery with data science.

Research Articles

• 
  Giorgos Minas, Dan J. Woodcock, Louise Ashall, Claire V. Harper, Michael R. H. White, David A. Rand:
  Multiplexing information flow through dynamic signalling systems.
• 
  Takuya Ito, Scott L. Brincat, Markus Siegel, Ravi D. Mill, Biyu J. He, Earl K. Miller, Horacio G. Rotstein, Michael W. Cole:
  Task-evoked activity quenches neural correlations and variability across cortical areas.
• 
  Sara Hamis, Mohammad Kohandel, Ludwig J. Dubois, Ala Yaromina, Philippe Lambin, Gibin G. Powathil:
  Combining hypoxia-activated prodrugs and radiotherapy in silico: Impact of treatment scheduling and the intra-tumoural oxygen landscape.
• 
  Andy Hoyle, David E. Cairns, Iona Paterson, Stuart McMillan, Gabriela Ochoa, Andrew P. Desbois:
  Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times.
• 
  Gabriel Koch Ocker, Michael A. Buice:
  Flexible neural connectivity under constraints on total connection strength.
• 
  Lina K. Klein, Guido Maiello, Vivian C. Paulun, Roland W. Fleming:
  Predicting precision grip grasp locations on three-dimensional objects.
• 
  Leonila Lagunes, Lee Bardwell, Germán A. Enciso:
  Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes.
• 
  Coryandar Gilvary, Jamal Elkhader, Neel Madhukar, Claire Henchcliffe, Marcus D. Goncalves, Olivier Elemento:
  A machine learning and network framework to discover new indications for small molecules.
• 
  Laura Bella Naumann, Henning Sprekeler:
  Presynaptic inhibition rapidly stabilises recurrent excitation in the face of plasticity.
• 
  Leo Kozachkov, Mikael Lundqvist, Jean-Jacques E. Slotine, Earl K. Miller:
  Achieving stable dynamics in neural circuits.
• 
  Maria Salfer, Javier F. Collado, Wolfgang Baumeister, Rubén Fernández-Busnadiego, Antonio Martínez-Sánchez:
  Reliable estimation of membrane curvature for cryo-electron tomography.
• 
  Hedyeh Rezaei, Ad Aertsen, Arvind Kumar, Alireza Valizadeh:
  Facilitating the propagation of spiking activity in feedforward networks by including feedback.
• 
  Laura de Arroyo Garcia, Patrik R. Jones:
  In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli.
• 
  Chen Hu, Philippe Domenech, Mathias Pessiglione:
  Order matters: How covert value updating during sequential option sampling shapes economic preference.
• 
  Eli Pollock, Mehrdad Jazayeri:
  Engineering recurrent neural networks from task-relevant manifolds and dynamics.
• 
  Gabriel Schweizer, Andreas Wagner:
  Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis.
• 
  Jingwen Pei, Yiming Zhang, Rasmus Nielsen, Yufeng Wu:
  Inferring the ancestry of parents and grandparents from genetic data.
• 
  Alok K. Maity, Roy Wollman:
  Information transmission from NFkB signaling dynamics to gene expression.
• 
  Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C. Censin, Samantha Laber, Hanieh Yaghootkar, Nilufer Rahmioglu, Emilie Pastel, Katerina Kos, Andrew Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren:
  Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits.
• 
  Divya C. Kernik, Pei-Chi Yang, Junko Kurokawa, Joseph C. Wu, Colleen E. Clancy:
  A computational model of induced pluripotent stem-cell derived cardiomyocytes for high throughput risk stratification of KCNQ1 genetic variants.
• 
  Fabrizio Clarelli, Adam Palmer, Bhupender Singh, Merete Storflor, Silje Lauksund, Ted Cohen, Sören Abel, Pia Abel zur Wiesch:
  Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones.
• 
  Prashanth Selvaraj, Edward A. Wenger, Daniel Bridenbecker, Nikolai Windbichler, Jonathan R. Russell, Jaline Gerardin, Caitlin A. Bever, Milen Nikolov:
  Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination.
• 
  Isaias Lans, Ernesto Anoz-Carbonell, Karen Palacio-Rodríguez, José Antonio Aínsa, Milagros Medina, Pilar Cossio:
  In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target.
• 
  Wai Kit Ong, Dylan K. Courtney, Shu Pan, Ramon Bonela Andrade, Patricia J. Kiley, Brian F. Pfleger, Jennifer L. Reed:
  Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4.
• 
  Ellis Patrick, Mariko Taga, Ayla Ergün, Bernard Ng, William Casazza, Maria Cimpean, Christina Yung, Julie A. Schneider, David A. Bennett, Chris Gaiteri, Philip L. De Jager, Elizabeth M. Bradshaw, Sara Mostafavi:
  Deconvolving the contributions of cell-type heterogeneity on cortical gene expression.
• 
  Hongtao Yu, Sanchita Basu, K. Melissa Hallow:
  Cardiac and renal function interactions in heart failure with reduced ejection fraction: A mathematical modeling analysis.
• 
  Emily L. Aiken, Sarah F. McGough, Maimuna S. Majumder, Gal Wachtel, André T. Nguyen, Cécile Viboud, Mauricio Santillana:
  Real-time estimation of disease activity in emerging outbreaks using internet search information.
• 
  Amrit Dhar, Duncan K. Ralph, Vladimir N. Minin, Frederick A. Matsen IV:
  A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.
• 
  David Pascucci, Maria Rubega, Gijs Plomp:
  Modeling time-varying brain networks with a self-tuning optimized Kalman filter.
• 
  Joshua Adam Bull, Franziska Mech, Tom Quaiser, Sarah L. Waters, Helen M. Byrne:
  Mathematical modelling reveals cellular dynamics within tumour spheroids.
• 
  Eric Yao, Robert M. Buels, Lincoln Stein, Taner Z. Sen, Ian H. Holmes:
  JBrowse Connect: A server API to connect JBrowse instances and users.
• 
  Chen Liao, Tong Wang, Sergei Maslov, João B. Xavier:
  Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence.
• 
  John Fors, Natasha Strydom, William S. Fox, Ron J. Keizer, Radojka M. Savic:
  Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis.
• 
  Ru-Yuan Zhang, Xue-Xin Wei, Kendrick N. Kay:
  Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging.
• 
  Jan Jaap R. van Assen, Shin'ya Nishida, Roland W. Fleming:
  Visual perception of liquids: Insights from deep neural networks.
• 
  Sina Miran, Alessandro Presacco, Jonathan Z. Simon, Michael C. Fu, Steven I. Marcus, Behtash Babadi:
  Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise.
• 
  Donald A. Belcher, Alfredo Lucas, Pedro J. Cabrales, Andre F. Palmer:
  Tumor vascular status controls oxygen delivery facilitated by infused polymerized hemoglobins with varying oxygen affinity.
• 
  Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J. Zartman, Mark S. Alber:
  Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix.
• 
  Rajat Desikan, Rubesh Raja, Narendra M. Dixit:
  Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection.
• 
  Tomer Stern, Stanislav Y. Shvartsman, Eric F. Wieschaus:
  Template-based mapping of dynamic motifs in tissue morphogenesis.
• 
  Jeffery Demers, Sharon Bewick, Folashade Agusto, Kevin A. Caillouët, William F. Fagan, Suzanne L. Robertson:
  Managing disease outbreaks: The importance of vector mobility and spatially heterogeneous control.
• 
  Ashkan Tabibian, Siavash Ghaffari, Diego A. Vargas, Hans Van Oosterwyck, Elizabeth A. V. Jones:
  Simulating flow induced migration in vascular remodelling.
• 
  Xiaomei Li, Lin Liu, Gregory J. Goodall, Andreas W. Schreiber, Taosheng Xu, Jiuyong Li, Thuc Duy Le:
  A novel single-cell based method for breast cancer prognosis.
• 
  Linda Irons, Jay D. Humphrey:
  Cell signaling model for arterial mechanobiology.
• 
  Claudia Bachmann, Tom Tetzlaff, Renato C. Duarte, Abigail Morrison:
  Firing rate homeostasis counteracts changes in stability of recurrent neural networks caused by synapse loss in Alzheimer's disease.
• 
  Thiago S. Guzella, Vasco M. Barreto, Jorge Carneiro:
  Partitioning stable and unstable expression level variation in cell populations: A theoretical framework and its application to the T cell receptor.
• 
  John R. Casey, Michael J. Follows:
  A steady-state model of microbial acclimation to substrate limitation.
• 
  Saurav Mallik, Dan S. Tawfik:
  Determining the interaction status and evolutionary fate of duplicated homomeric proteins.
• 
  Quynh-Anh Nguyen, John Rinzel, Rodica Curtu:
  Buildup and bistability in auditory streaming as an evidence accumulation process with saturation.
• 
  Ondrej Maxian, Alex Mogilner, Wanda Strychalski:
  Computational estimates of mechanical constraints on cell migration through the extracellular matrix.
• 
  Zhiyuan Li, Bo Liu, Sophia Hsin-Jung Li, Christopher G. King, Zemer Gitai, Ned S. Wingreen:
  Modeling microbial metabolic trade-offs in a chemostat.
• 
  Yoonjoo Choi, Sukyo Jeong, Jung-Min Choi, Christian NDong, Karl E. Griswold, Chris Bailey-Kellogg, Hak-Sung Kim:
  Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination.

Volume 16, Number 9, September 2020

Editorials

• 
  Pleuni S. Pennings, Mayra M. Banuelos, Francisca L. Catalan, Victoria R. Caudill, Bozhidar Chakalov, Selena Hernandez, Jeanice Jones, Chinomnso Okorie, Sepideh Modrek, Rori Rohlfs, Nicole Adelstein:
  Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates.
• 
  Aïda Bafeta, Jason Bobe, Jon Clucas, Pattie Pramila Gonsalves, Célya Gruson-Daniel, Kathy L. Hudson, Arno Klein, Anirudh Krishnakumar, Anna McCollister-Slipp, Ariel B. Lindner, Dusan Misevic, John A. Naslund, Camille Nebeker, Aki Nikolaidis, Irene V. Pasquetto, Gabriela Sánchez, Matthieu Schapira, Tohar Scheininger, Felix Schoeller, Anibal Sólon Heinsfeld, François Taddei:
  Ten simple rules for open human health research.
• 
  Susanne Hollmann, Marcus Frohme, Christoph Endrullat, Andreas Kremer, Domenica D'Elia, Babette Regierer, Alina S. Nechyporenko:
  Ten simple rules on how to write a standard operating procedure.

Education Articles

• 
  Alexander Johan Nederbragt, Rayna Michelle Harris, Alison Presmanes Hill, Greg Wilson:
  Ten quick tips for teaching with participatory live coding.
• 
  Anne-Laure Ligozat, Aurélie Névéol, Bénédicte Daly, Emmanuelle Frenoux:
  Ten simple rules to make your research more sustainable.

Perspective

• 
  Hoe-Han Goh, Philip E. Bourne:
  Ten simple rules for writing scientific op-ed articles.

Research Articles

• 
  Maxim Igaev, Helmut Grubmüller:
  Microtubule instability driven by longitudinal and lateral strain propagation.
• 
  Stewart Heitmann, G. Bard Ermentrout:
  Direction-selective motion discrimination by traveling waves in visual cortex.
• 
  Ignasius Joanito, Ching-Cher Sanders Yan, Jhih-Wei Chu, Shu-Hsing Wu, Chao-Ping Hsu:
  Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops.
• 
  William Pilcher, Xingyu Yang, Anastasia Zhurikhina, Olga Chernaya, Yinghan Xu, Peng Qiu, Denis Tsygankov:
  Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images.
• 
  Yunjun Zhang, Thomas Leitner, Jan Albert, Tom Britton:
  Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention.
• 
  Lia Papadopoulos, Christopher W. Lynn, Demian Battaglia, Danielle S. Bassett:
  Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state.
• 
  Wei Xiong Wen, Adam J. Mead, Supat Thongjuea:
  VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution.
• 
  Bo Chen, Wei Xu:
  Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures.
• 
  Philip Pärnamets, Andreas Olsson:
  Integration of social cues and individual experiences during instrumental avoidance learning.
• 
  Nikolaus Korfhage, Markus Mühling, Stephan Ringshandl, Anke Becker, Bernd Schmeck, Bernd Freisleben:
  Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion.
• 
  Charley M. Wu, Eric Schulz, Mona M. Garvert, Björn Meder, Nicolas W. Schuck:
  Similarities and differences in spatial and non-spatial cognitive maps.
• 
  Thinh N. Tran, Gary D. Bader:
  Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data.
• 
  Gabriella J. Gerlach, Rachel Carrock, Robyn Stix, Elliott J. Stollar, K. Aurelia Ball:
  A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.
• 
  Juan F. Poyatos:
  Genetic buffering and potentiation in metabolism.
• 
  Kassi T. Stein, Sun Jin Moon, Athena N. Nguyen, Hadley D. Sikes:
  Kinetic modeling of H2O2 dynamics in the mitochondria of HeLa cells.
• 
  Linfeng Yang, Rajarshi P. Ghosh, J. Matthew Franklin, Simon B. Chen, Chenyu You, Raja R. Narayan, Marc L. Melcher, Jan T. Liphardt:
  NuSeT: A deep learning tool for reliably separating and analyzing crowded cells.
• 
  Carlos Barajas, Domitilla Del Vecchio:
  Effects of spatial heterogeneity on bacterial genetic circuits.
• 
  Cristina Herencias, Sergio Salgado-Briegas, M. Auxiliadora Prieto, Juan Nogales:
  Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling.
• 
  Nimrod Rappoport, Roy Safra, Ron Shamir:
  MONET: Multi-omic module discovery by omic selection.
• 
  Ziqiang Wei, Bei-Jung Lin, Tsai-Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann:
  A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.
• 
  Xue Zhang, Wangxin Xiao, Weijia Xiao:
  DeepHE: Accurately predicting human essential genes based on deep learning.
• 
  Patrick C. Fiaux, Hsiuyi V. Chen, Poshen B. Chen, Aaron R. Chen, Graham McVicker:
  Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
• 
  Zhengqiao Zhao, Bahrad A. Sokhansanj, Charvi Malhotra, Kitty Zheng, Gail L. Rosen:
  Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
• 
  Alessandro Sanzeni, Mark H. Histed, Nicolas Brunel:
  Response nonlinearities in networks of spiking neurons.
• 
  Mengjia Xu, Zhijiang Wang, Haifeng Zhang, Dimitrios Pantazis, Huali Wang, Quanzheng Li:
  A new Graph Gaussian embedding method for analyzing the effects of cognitive training.
• 
  Daniel J. Laydon, Vikram Sunkara, Lies Boelen, Charles R. M. Bangham, Becca Asquith:
  The relative contributions of infectious and mitotic spread to HTLV-1 persistence.
• 
  Hyeon-Jin Kim, Galip Gürkan Yardimci, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhi-jun Duan, William Stafford Noble:
  Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
• 
  Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R. Requena, Emiliano Biasini, Pietro Faccioli:
  All-atom simulation of the HET-s prion replication.
• 
  Cody Baker, Vicky Zhu, Robert Rosenbaum:
  Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance.
• 
  Mikael Jagan, Michelle S. deJonge, Olga Krylova, David J. D. Earn:
  Fast estimation of time-varying infectious disease transmission rates.
• 
  Ryan E. Pavlovicz, Hahnbeom Park, Frank DiMaio:
  Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination.
• 
  Emma Southall, Michael J. Tildesley, Louise Dyson:
  Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data.
• 
  Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen:
  Alcoholic liver disease: A registry view on comorbidities and disease prediction.
• 
  J. Kyle Medley, Jonathan J. Y. Teo, Sung Sik Woo, Joseph L. Hellerstein, Rahul Sarpeshkar, Herbert M. Sauro:
  A compiler for biological networks on silicon chips.
• 
  Camila P. E. de Souza, Mirela Andronescu, Tehmina Masud, Farhia Kabeer, Justina Biele, Emma Laks, Daniel Lai, Patricia Ye, Jazmine Brimhall, Beixi Wang, Edmund Su, Tony Hui, Qi Cao, Marcus Wong, Michelle Moksa, Richard A. Moore, Martin Hirst, Samuel Aparicio, Sohrab P. Shah:
  Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data.
• 
  Aditi Roy, Marta Varela, Henry Chubb, Robert S. MacLeod, Jules C. Hancox, Tobias Schaeffter, Oleg V. Aslanidi:
  Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium.
• 
  Thomas E. Yerxa, Eric Kee, Michael Robert DeWeese, Emily A. Cooper:
  Efficient sensory coding of multidimensional stimuli.
• 
  Miquel Marchena, Blas Echebarria, Yohannes Shiferaw, Enrique Alvarez-Lacalle:
  Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells.
• 
  Rajib Mukherjee, Burcu Beykal, Adam T. Szafran, Melis Onel, Fabio Stossi, Maureen G. Mancini, Dillon Lloyd, Fred A. Wright, Lan Zhou, Michael A. Mancini, Efstratios N. Pistikopoulos:
  Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms.
• 
  Fabien Raphel, Tessa De Korte, Damiano Lombardi, Stefan Braam, Jean-Frédéric Gerbeau:
  A greedy classifier optimization strategy to assess ion channel blocking activity and pro-arrhythmia in hiPSC-cardiomyocytes.
• 
  Quirine A. ten Bosch, Joseph M. Wagman, Fanny Castro-Llanos, Nicole L. Achee, John P. Grieco, T. Alex Perkins:
  Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes.
• 
  Nicolas Deperrois, Michael Graupner:
  Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity.
• 
  Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine A. Wells:
  A simple, scalable approach to building a cross-platform transcriptome atlas.
• 
  Kwang Su Kim, Tatsunari Kondoh, Yusuke Asai, Ayato Takada, Shingo Iwami:
  Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule.
• 
  Alejandro V. Cano, Joshua L. Payne:
  Mutation bias interacts with composition bias to influence adaptive evolution.
• 
  Wen Jun Xie, Yifeng Qi, Bin Zhang:
  Characterizing chromatin folding coordinate and landscape with deep learning.
• 
  François Bertaux, Julius von Kügelgen, Samuel Marguerat, Vahid Shahrezaei:
  A bacterial size law revealed by a coarse-grained model of cell physiology.
• 
  Jingwen Li, Woodrow L. Shew:
  Tuning network dynamics from criticality to an asynchronous state.
• 
  Jennifer L. Creaser, Congping Lin, Thomas Ridler, Jonathan T. Brown, Wendyl D'Souza, Udaya Seneviratne, Mark J. Cook, John R. Terry, Krasimira Tsaneva-Atanasova:
  Domino-like transient dynamics at seizure onset in epilepsy.
• 
  James D. Brunner, Nicholas Chia:
  Minimizing the number of optimizations for efficient community dynamic flux balance analysis.
• 
  Zachary R. Sailer, Sarah H. Shafik, Robert L. Summers, Alex Joule, Alice Patterson-Robert, Rowena E. Martin, Michael J. Harms:
  Inferring a complete genotype-phenotype map from a small number of measured phenotypes.
• 
  Kyle Bojanek, Yuqing Zhu, Jason N. MacLean:
  Cyclic transitions between higher order motifs underlie sustained asynchronous spiking in sparse recurrent networks.
• 
  Frans M. van der Kloet, Jeroen Buurmans, Martijs J. Jonker, Age K. Smilde, Johan A. Westerhuis:
  Increased comparability between RNA-Seq and microarray data by utilization of gene sets.
• 
  Lara Henco, Andreea O. Diaconescu, Juha M. Lahnakoski, Marie-Luise Brandi, Sophia Hörmann, Johannes Hennings, Alkomiet Hasan, Irina Papazova, Wolfgang Strube, Dimitris Bolis, Leonhard Schilbach, Christoph Mathys:
  Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder.
• 
  Gianfranco Politano, Alfredo Benso:
  IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
• 
  Marieke Jepma, Jessica V. Schaaf, Ingmar Visser, Hilde M. Huizenga:
  Uncertainty-driven regulation of learning and exploration in adolescents: A computational account.

Volume 16, Number 10, October 2020

Editorials

• 
  Emily Nordmann, Chiara Horlin, Jacqui Hutchison, Jo-Anne Murray, Louise Robson, Michael K. Seery, Jill R. D. MacKay:
  Ten simple rules for supporting a temporary online pivot in higher education.
• 
  V. Bala Chaudhary, Asmeret Asefaw Berhe:
  Ten simple rules for building an antiracist lab.
• 
  Alexa R. Warwick, Angela Kolonich, Kristin M. Bass, Louise S. Mead, Frieda Reichsman:
  Ten simple rules for partnering with K-12 teachers to support broader impact goals.
• 
  Irene Stevens, Abdul Kadir Mukarram, Matthias Hörtenhuber, Terrence F. Meehan, Johan Rung, Carsten O. Daub:
  Ten simple rules for annotating sequencing experiments.
• 
  Georges Hattab, Theresa-Marie Rhyne, Dominik Heider:
  Ten simple rules to colorize biological data visualization.
• 
  Alise J. Ponsero, Ryan Bartelme, Gustavo de Oliveira Almeida, Alex Bigelow, Reetu Tuteja, Holly Ellingson, Tyson Lee Swetnam, Nirav C. Merchant, Maliaca Oxnam, Eric Lyons:
  Ten simple rules for organizing a data science workshop.
• 
  Monika Cechova:
  Ten simple rules for biologists initiating a collaboration with computer scientists.

Perspective

• 
  Pamela K. Kreeger, Amy Brock, Holly C. Gibbs, K. Jane Grande-Allen, Alice H. Huang, Kristyn S. Masters, Padmini Rangamani, Michaela R. Reagan, Shannon L. Servoss:
  Ten simple rules for women principal investigators during a pandemic.

Review

• 
  Jae Kyoung Kim, John J. Tyson:
  Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy.

Research Articles

• 
  Abdur Rahman Mohd Abul Basher, Ryan J. McLaughlin, Steven J. Hallam:
  Metabolic pathway inference using multi-label classification with rich pathway features.
• 
  Kaname Kojima, Shu Tadaka, Fumiki Katsuoka, Gen Tamiya, Masayuki Yamamoto, Kengo Kinoshita:
  A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.
• 
  Christiaan H. van Dorp, Jessica M. Conway, Dan H. Barouch, James B. Whitney, Alan S. Perelson:
  Models of SIV rebound after treatment interruption that involve multiple reactivation events.
• 
  Leah L. Weber, Nuraini Aguse, Nicholas Chia, Mohammed El-Kebir:
  PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.
• 
  Jack Pattee, Wei Pan:
  Penalized regression and model selection methods for polygenic scores on summary statistics.
• 
  Antonello Caruso, Jannik Vollmer, Matthias Machacek, Elod Kortvely:
  Modeling the activation of the alternative complement pathway and its effects on hemolysis in health and disease.
• 
  Han Yan, Jin Wang:
  Non-equilibrium landscape and flux reveal the stability-flexibility-energy tradeoff in working memory.
• 
  Ewa Szczurek, Tyll Krüger, Barbara Klink, Niko Beerenwinkel:
  A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment.
• 
  Courtney J. Spoerer, Tim C. Kietzmann, Johannes Mehrer, Ian Charest, Nikolaus Kriegeskorte:
  Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision.
• 
  Emilia Kozlowska, Rafal Suwinski, Monika Giglok, Andrzej Swierniak, Marek Kimmel:
  Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet.
• 
  Michael J. Lydeamore, Patricia T. Campbell, David J. Price, Yue Wu, Adrian J. Marcato, Will Cuningham, Jonathan R. Carapetis, Ross M. Andrews, Malcolm I. McDonald, Jodie McVernon, Steven Y. C. Tong, James M. McCaw:
  Estimation of the force of infection and infectious period of skin sores in remote Australian communities using interval-censored data.
• 
  José Manuel Rodriguez, Fernando Pozo, Tomás Di Domenico, Jesús Vázquez, Michael L. Tress:
  An analysis of tissue-specific alternative splicing at the protein level.
• 
  Zhen Song, Zhilin Qu:
  Delayed global feedback in the genesis and stability of spatiotemporal excitation patterns in paced biological excitable media.
• 
  James E. Lucas, Tanja Kortemme:
  New computational protein design methods for de novo small molecule binding sites.
• 
  Vikas Dubey, Behruz Bozorg, Daniel Wüstner, Himanshu Khandelia:
  Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.
• 
  Edward M. Hill, Stavros Petrou, Henry Forster, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling:
  Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation.
• 
  Ugne Klibaite, Joshua W. Shaevitz:
  Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster.
• 
  Francesco Regazzoni, Luca Dedè, Alfio Quarteroni:
  Biophysically detailed mathematical models of multiscale cardiac active mechanics.
• 
  Yu Yang Fredrik Liu, Yin Lu, Steve Oh, Gareth John Conduit:
  Machine learning to predict mesenchymal stem cell efficacy for cartilage repair.
• 
  Bridget S. Penman, Sylvain Gandon:
  Adaptive immunity selects against malaria infection blocking mutations.
• 
  Tsukushi Kamiya, Megan A. Greischar, David S. Schneider, Nicole Mideo:
  Uncovering drivers of dose-dependence and individual variation in malaria infection outcomes.
• 
  Mehrshad Sadria, Anita T. Layton:
  Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers During the COVID-19 Pandemic: A Modeling Analysis.
• 
  Mohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun, Jens Lagergren:
  Inferring tumor progression in large datasets.
• 
  Maureen Muscat, Giancarlo Croce, Edoardo Sarti, Martin Weigt:
  FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution.
• 
  Abhishek Mukherjee, Amlan Barai, Ramesh Kumar Singh, Wenyi Yan, Shamik Sen:
  Nuclear plasticity increases susceptibility to damage during confined migration.
• 
  Alexander I Manolov, Dmitry Konanov, Dmitry V. Fedorov, Ivan Osmolovsky, Rinat Vereshchagin, Elena Ilina:
  Genome Complexity Browser: Visualization and quantification of genome variability.
• 
  Jan Mikelson, Mustafa Khammash:
  Likelihood-free nested sampling for parameter inference of biochemical reaction networks.
• 
  Jue Tao Lim, Yiting Han, Borame Sue Dickens, Ng Lee Ching, Alex R. Cook:
  Time varying methods to infer extremes in dengue transmission dynamics.
• 
  Itay Dalmedigos, Guy Bunin:
  Dynamical persistence in high-diversity resource-consumer communities.
• 
  Matthieu Gilson, David Dahmen, Rubén Moreno-Bote, Andrea Insabato, Moritz Helias:
  The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks.
• 
  Michael D. Karcher, Luiz Max Carvalho, Marc A. Suchard, Gytis Dudas, Vladimir N. Minin:
  Estimating effective population size changes from preferentially sampled genetic sequences.
• 
  Barbara Schnitzer, Johannes Borgqvist, Marija Cvijovic:
  The synergy of damage repair and retention promotes rejuvenation and prolongs healthy lifespans in cell lineages.
• 
  Sarah F. Beul, Claus C. Hilgetag:
  Systematic modelling of the development of laminar projection origins in the cerebral cortex: Interactions of spatio-temporal patterns of neurogenesis and cellular heterogeneity.
• 
  Pengfei Tian, Robert B. Best:
  Exploring the sequence fitness landscape of a bridge between protein folds.
• 
  Charlotte Doussot, Olivier J. N. Bertrand, Martin Egelhaaf:
  Visually guided homing of bumblebees in ambiguous situations: A behavioural and modelling study.
• 
  Travis B. Thompson, Pavanjit Chaggar, Ellen Kuhl, Alain Goriely, Alzheimer's Disease Neuroimaging Initiative:
  Protein-protein interactions in neurodegenerative diseases: A conspiracy theory.
• 
  Anton Chizhov, Natalia Merkulyeva:
  Refractory density model of cortical direction selectivity: Lagged-nonlagged, transient-sustained, and On-Off thalamic neuron-based mechanisms and intracortical amplification.
• 
  Sarah C. Kramer, Sen Pei, Jeffrey Shaman:
  Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel.
• 
  David G. Nagy, Balázs Török, Gergo Orbán:
  Optimal forgetting: Semantic compression of episodic memories.
• 
  Tim Sainburg, Marvin Thielk, Timothy Q. Gentner:
  Finding, visualizing, and quantifying latent structure across diverse animal vocal repertoires.
• 
  Audrey McCombs, Claus Kadelka:
  A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies.
• 
  Joseph M. Barnby, Vaughan Bell, Mitul A. Mehta, Michael Moutoussis:
  Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game.
• 
  Lucas Lehnert, Michael L. Littman, Michael J. Frank:
  Reward-predictive representations generalize across tasks in reinforcement learning.
• 
  Brandon Hollingsworth, Kenichi W. Okamoto, Alun L. Lloyd:
  After the honeymoon, the divorce: Unexpected outcomes of disease control measures against endemic infections.
• 
  Manuel Muñoz-Aguirre, Vasilis F. Ntasis, Santiago Rojas, Roderic Guigó:
  PyHIST: A Histological Image Segmentation Tool.
• 
  Marcus Nguyen, Robert Olson, Maulik Shukla, Margo VanOeffelen, James J. Davis:
  Predicting antimicrobial resistance using conserved genes.
• 
  Iveta Jancigová, Kristína Kovalcíková, Rudolf Weeber, Ivan Cimrák:
  PyOIF: Computational tool for modelling of multi-cell flows in complex geometries.
• 
  Nils Neupärtl, Fabian Tatai, Constantin A. Rothkopf:
  Intuitive physical reasoning about objects' masses transfers to a visuomotor decision task consistent with Newtonian physics.
• 
  David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose:
  BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management.
• 
  Alejandro Pereira-Santana, Samuel David Gamboa-Tuz, Tao Zhao, M. Eric Schranz, Pablo Vinuesa, Andrea Bayona, Luis C. Rodríguez-Zapata, Enrique Castaño:
  Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin.
• 
  Marion Forano, David W. Franklin:
  Timescales of motor memory formation in dual-adaptation.
• 
  Ruijin Wu, Rahul Prabhu, Aysegul Ozkan, Meera Sitharam:
  Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis.
• 
  Marcos Latorre, Jay D. Humphrey:
  Numerical knockouts-In silico assessment of factors predisposing to thoracic aortic aneurysms.
• 
  Mohamed Chaabane, Kalina Andreeva, Jae Yeon Hwang, Tae Lim Kook, Juw Won Park, Nigel G. F. Cooper:
  seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data.
• 
  Dharmeshkumar Patel, Jonathan E. Barnes, Wayne I. L. Davies, Deborah L. Stenkamp, Jagdish Suresh Patel:
  Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance.
• 
  Kiersten Utsey, James P. Keener:
  A mathematical model of flagellar gene regulation and construction in Salmonella enterica.
• 
  Naim Panjwani, Fan Wang, Scott Mastromatteo, Allen Bao, Cheng Wang, Gengming He, Jiafen Gong, Johanna M. Rommens, Lei Sun, Lisa J. Strug:
  LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS.
• 
  Sen Pei, Jeffrey Shaman:
  Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness.
• 
  Adrián Cordido, Eva Cernadas, Manuel Fernández Delgado, Miguel A. García-González:
  CystAnalyser: A new software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders.
• 
  Calvin McCarter, Judie A. Howrylak, Seyoung Kim:
  Learning gene networks underlying clinical phenotypes using SNP perturbation.
• 
  Emilio Dorigatti, Benjamin Schubert:
  Graph-theoretical formulation of the generalized epitope-based vaccine design problem.
• 
  Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker:
  Multiscale community detection in Cytoscape.
• 
  Klaudia Kozlowska, Miroslaw Latka, Bruce J. West:
  Significance of trends in gait dynamics.
• 
  Peter D. Tonner, Cynthia L. Darnell, Francesca M. L. Bushell, Peter A. Lund, Amy K. Schmid, Scott C. Schmidler:
  A Bayesian non-parametric mixed-effects model of microbial growth curves.
• 
  Michael Schmutzer, Andreas Wagner:
  Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments.
• 
  Amir Alavi, Ziv Bar-Joseph:
  Iterative point set registration for aligning scRNA-seq data.
• 
  Arash Mohammadzadeh Gonabadi, Prokopios Antonellis, Philippe Malcolm:
  Differences between joint-space and musculoskeletal estimations of metabolic rate time profiles.
• 
  Jinchan Liu, James C. Gumbart:
  Membrane thinning and lateral gating are consistent features of BamA across multiple species.
• 
  Andrew F. Magee, Sebastian Höhna, Tetyana I. Vasylyeva, Adam D. Leaché, Vladimir N. Minin:
  Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts.
• 
  Brian Joseph Bender, Brennica Marlow, Jens Meiler:
  Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs.
• 
  David M. Watson, Ben B. Brown, Alan Johnston:
  A data-driven characterisation of natural facial expressions when giving good and bad news.
• 
  Komal S. Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S. Naqvi, Deanne M. Taylor, Phillip B. Storm, Adam C. Resnick, Jo Lynne Rokita, Pichai Raman:
  A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
• 
  Etienne Combrisson, Timothy Nest, Andrea Brovelli, Robin A. A. Ince, Juan L. P. Soto, Aymeric Guillot, Karim Jerbi:
  Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals.
• 
  Elena Rivas:
  RNA structure prediction using positive and negative evolutionary information.
• 
  Tony J. Lam, Moses Stamboulian, Wontack Han, Yuzhen Ye:
  Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species.
• 
  Oliver M. Cliff, Natalia Mclean, Vitali Sintchenko, Kristopher M. Fair, Tania C. Sorrell, Stuart A. Kauffman, Mikhail Prokopenko:
  Inferring evolutionary pathways and directed genotype networks of foodborne pathogens.

Corrections

• 
  Shira Warszawski, Aliza Borenstein Katz, Rosalie Lipsh, Lev Khmelnitsky, Gili Ben Nissan, Gabriel Javitt, Orly Dym, Tamar Unger, Orli Knop, Shira Albeck, Ron Diskin, Deborah Fass, Michal Sharon, Sarel Jacob Fleishman:
  Correction: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces.
• 
  Charley M. Wu, Eric Schulz, Mona M. Garvert, Björn Meder, Nicolas W. Schuck:
  Correction: Similarities and differences in spatial and non-spatial cognitive maps.
• 
  PLOS Computational Biology Staff:
  Correction: Humans adapt their anticipatory eye movements to the volatility of visual motion properties.

Volume 16, Number 11, November 2020

Editorials

• 
  Daniel Nüst, Vanessa V. Sochat, Ben Marwick, Stephen J. Eglen, Tim Head, Tony Hirst, Benjamin D. Evans:
  Ten simple rules for writing Dockerfiles for reproducible data science.
• 
  Joseph D. Romano, Jason H. Moore:
  Ten simple rules for writing a paper about scientific software.
• 
  Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne:
  Ten simple rules for starting research in your late teens.

Education

• 
  Hyungtaek Jung, Tomer Ventura, J. Sook Chung, Woo-Jin Kim, Bo-Hye Nam, Hee Jeong Kong, Young-Ok Kim, Min-Seung Jeon, Seong-il Eyun:
  Twelve quick steps for genome assembly and annotation in the classroom.

Perspective

• 
  Matthias C. Rillig, Milos Bielcik, V. Bala Chaudhary, Leonie Grünfeld, Stefanie Maaß, India Mansour, Masahiro Ryo, Stavros D. Veresoglou:
  Ten simple rules for increased lab resilience.

Review

• 
  Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel:
  Transforming the study of organisms: Phenomic data models and knowledge bases.

Research Articles

• 
  Tiina Manninen, Ausra Saudargiene, Marja-Leena Linne:
  Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex.
• 
  Teresa Maria Rosaria Noviello, Francesco Ceccarelli, Michele Ceccarelli, Luigi Cerulo:
  Deep learning predicts short non-coding RNA functions from only raw sequence data.
• 
  Doruk Cakmakci, Emin Onur Karakaslar, Elisa Ruhland, Marie-Pierre Chenard, Francois Proust, Martial Piotto, Izzie-Jacques Namer, A. Ercüment Çiçek:
  Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy.
• 
  Duncan K. Ralph, Frederick A. Matsen IV:
  Using B cell receptor lineage structures to predict affinity.
• 
  Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu:
  Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.
• 
  Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Skrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz:
  Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines.
• 
  Roman Frolov, Irina Ignatova:
  Speed of phototransduction in the microvillus regulates the accuracy and bandwidth of the rhabdomeric photoreceptor.
• 
  Amir Bitran, William M. Jacobs, Eugene Shakhnovich:
  Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.
• 
  Jingwei Ma, Myan Do, Mark A. Le Gros, Charles S. Peskin, Carolyn A. Larabell, Yoichiro Mori, Samuel A. Isaacson:
  Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus.
• 
  Romain Amyot, Holger Flechsig:
  BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
• 
  Maxat Kulmanov, Robert Hoehndorf:
  DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier.
• 
  Alireza Yazdani, Lu Lu, Maziar Raissi, George Em Karniadakis:
  Systems biology informed deep learning for inferring parameters and hidden dynamics.
• 
  Yuriy Pichugin, Arne Traulsen:
  Evolution of multicellular life cycles under costly fragmentation.
• 
  Colin T. Barker, Naveen K. Vaidya:
  Modeling HIV-1 infection in the brain.
• 
  Auss Abbood, Alexander Ullrich, Rüdiger Busche, Stéphane Ghozzi:
  EventEpi - A natural language processing framework for event-based surveillance.
• 
  Camille E. Rullán Buxó, Jonathan W. Pillow:
  Poisson balanced spiking networks.
• 
  Lindsey S. Brown, Francis J. Doyle III:
  A dual-feedback loop model of the mammalian circadian clock for multi-input control of circadian phase.
• 
  Chiara Vanalli, Lorenzo Mari, Lorenzo Righetto, Renato Casagrandi, Marino Gatto, Isabella M. Cattadori:
  Within-host mechanisms of immune regulation explain the contrasting dynamics of two helminth species in both single and dual infections.
• 
  Riccha Sethi, Julia Becker, Jos de Graaf, Martin Löwer, Martin Suchan, Ugur Sahin, David Weber:
  Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.
• 
  Howard Bowman, Joseph L. Brooks, Omid Hajilou, Alexia Zoumpoulaki, Vladimir Litvak:
  Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach.
• 
  Shane D. Anderson, Asna Tabassum, Jae Kyung Yeon, Garima Sharma, Priscilla Santos, Tik Hang Soong, Yin Win Thu, Isaac Nies, Tomomi Kurita, Andrew Chandler, Abdelaziz Alsamarah, Rhye-Samuel Kanassatega, Yun Lyna Luo, Wesley M. Botello-Smith, Bradley T. Andresen:
  In silico prediction of ARB resistance: A first step in creating personalized ARB therapy.
• 
  András Szilágyi, Peter Szabó, Mauro Santos, Eörs Szathmáry:
  Phenotypes to remember: Evolutionary developmental memory capacity and robustness.
• 
  Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu, Binghuang Cai, Nicholas Cain, Atle E. Rimehaug, Alexander J. Stasik, Gaute T. Einevoll, Stefan Mihalas, Christof Koch, Anton Arkhipov:
  Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits.
• 
  Magdalena San Román, Andreas Wagner:
  Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli.
• 
  Yufang Qin, Weiwei Zhang, Xiaoqiang Sun, Siwei Nan, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng:
  Deconvolution of heterogeneous tumor samples using partial reference signals.
• 
  Ananya Saha, Narendra M. Dixit:
  Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection.
• 
  Kathleen Wiencke, Annette Horstmann, David Mathar, Arno Villringer, Jane Neumann:
  Dopamine release, diffusion and uptake: A computational model for synaptic and volume transmission.
• 
  Corey Weistuch, Luca Agozzino, Lilianne R. Mujica-Parodi, Ken A. Dill:
  Inferring a network from dynamical signals at its nodes.
• 
  Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums:
  Inference of mutability landscapes of tumors from single cell sequencing data.
• 
  F. William Townes, Kareem Carr, Jeffrey W. Miller:
  Identifying longevity associated genes by integrating gene expression and curated annotations.
• 
  Yanli Zhou, Luigi Acerbi, Wei Ji Ma:
  The role of sensory uncertainty in simple contour integration.
• 
  Grey W. Wilburn, Sean R. Eddy:
  Remote homology search with hidden Potts models.
• 
  Torsten Johann Paul, Philip Kollmannsberger:
  Biological network growth in complex environments: A computational framework.
• 
  Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka:
  Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.
• 
  Kris V. Parag, Christl A. Donnelly, Rahul Jha, Robin N. Thompson:
  An exact method for quantifying the reliability of end-of-epidemic declarations in real time.
• 
  Christoph Stelzer, Yaakov Benenson:
  Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection.
• 
  Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein:
  Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
• 
  Marcus Anthony Triplett, Zac Pujic, Biao Sun, Lilach Avitan, Geoffrey J. Goodhill:
  Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data.
• 
  Monika J. Piotrowska, Konrad Sakowski, André Karch, Hannan Tahir, Johannes Horn, Mirjam E. Kretzschmar, Rafael T. Mikolajczyk:
  Modelling pathogen spread in a healthcare network: Indirect patient movements.
• 
  Pei-Yau Lung, Dongrui Zhong, Xiaodong Pang, Yan Li, Jinfeng Zhang:
  Maximizing the reusability of gene expression data by predicting missing metadata. 1007450
• 
  Toshiyuki Ishii, Toshihiko Hosoya:
  Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features. 1007726
• 
  Vito Adrian Cantu, Peter Salamon, Victor Seguritan, Jackson Redfield, David Salamon, Robert A. Edwards, Anca M. Segall:
  PhANNs, a fast and accurate tool and web server to classify phage structural proteins. 1007845
• 
  Sequoia I. Leuba, Reza Yaesoubi, Marina Antillon, Ted Cohen, Christoph Zimmer:
  Tracking and predicting U.S. influenza activity with a real-time surveillance network. 1008180
• 
  Jolene Ramsey, Helena Rasche, Cory Maughmer, Anthony Criscione, Eleni Mijalis, Mei Liu, James C. Hu, Ry Young, Jason J. Gill:
  Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. 1008214
• 
  Mario Castro, Rob J. De Boer:
  Testing structural identifiability by a simple scaling method. 1008248
• 
  Oliver M. Crook, Aikaterini Geladaki, Daniel J. H. Nightingale, Owen L. Vennard, Kathryn S. Lilley, Laurent Gatto, Paul D. W. Kirk:
  A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. 1008288
• 
  Dylan Girodat, Avik K. Pati, Daniel S. Terry, Scott C. Blanchard, Karissa Y. Sanbonmatsu:
  Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein. 1008293
• 
  Yumin Zheng, Haohan Wang, Yang Zhang, Xin Gao, Eric P. Xing, Min Xu:
  Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species. 1008297
• 
  Peter M. C. Harrison, Roberta Bianco, Maria Chait, Marcus T. Pearce:
  PPM-Decay: A computational model of auditory prediction with memory decay. 1008304
• 
  Wei Liu, Mo Li, Wenfeng Zhang, Geyu Zhou, Xing Wu, Jiawei Wang, Qiongshi Lu, Hongyu Zhao:
  Leveraging functional annotation to identify genes associated with complex diseases. 1008315
• 
  Mahdi Golkaram, Chen Zhao, Kristina Kruglyak, Shile Zhang, Sven Bilke:
  The interplay between cancer type, panel size and tumor mutational burden threshold in patient selection for cancer immunotherapy. 1008332
• 
  Ling Chen, John A. Capra:
  Learning and interpreting the gene regulatory grammar in a deep learning framework. 1008334
• 
  Joshua Kimrey, Theodore Vo, Richard Bertram:
  Canard analysis reveals why a large Ca2+ window current promotes early afterdepolarizations in cardiac myocytes. 1008341
• 
  Zhewei Zhang, Huzi Cheng, Tianming Yang:
  A recurrent neural network framework for flexible and adaptive decision making based on sequence learning. 1008342
• 
  Laura E. Liao, Jonathan Carruthers, Sophie J. Smither, Simon A. Weller, Diane Williamson, Thomas R. Laws, Isabel García-Dorival, Julian A. Hiscox, Benjamin P. Holder, Catherine A. A. Beauchemin, Alan S. Perelson, Martín López-García, Grant Lythe, John N. Barr, Carmen Molina-París:
  Quantification of Ebola virus replication kinetics in vitro. 1008375
• 
  Richard Wilton, Alexander S. Szalay:
  Arioc: High-concurrency short-read alignment on multiple GPUs. 1008383
• 
  Román Zapién-Campos, Michael Sieber, Arne Traulsen:
  Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium. 1008392
• 
  Gregory McInnes, Rachel Dalton, Katrin Sangkuhl, Michelle Whirl Carrillo, Seung-been Lee, Philip S. Tsao, Andrea Gaedigk, Russ B. Altman, Erica L. Woodahl:
  Transfer learning enables prediction of CYP2D6 haplotype function. 1008399
• 
  Kamran Kaveh, Alex McAvoy, Krishnendu Chatterjee, Martin A. Nowak:
  The Moran process on 2-chromatic graphs. 1008402
• 
  Hai Yang, Qiang Wei, Dongdong Li, Zhe Wang:
  Cancer classification based on chromatin accessibility profiles with deep adversarial learning model. 1008405
• 
  Anahita Bayani, Joanne L. Dunster, Jonathan J. Crofts, Martin R. Nelson:
  Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model. 1008413
• 
  Carolin Zitzmann, Lars Kaderali, Alan S. Perelson:
  Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release. 1008421
• 
  Christine A. Tataru, Maude M. David:
  Correction: Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease. 1008423
• 
  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. 1008424
• 
  Elif Köksal Ersöz, Julien Modolo, Fabrice Bartolomei, Fabrice Wendling:
  Neural mass modeling of slow-fast dynamics of seizure initiation and abortion. 1008430

Volume 16, Number 12, December 2020

Editorial

• 
  Scott Rich, Andreea O. Diaconescu, John D. Griffiths, Milad Lankarany:
  Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic).

Education Articles

• 
  Lars Ole Schwen:
  Ten simple rules for typographically appealing scientific texts.
• 
  Sarah Lin, Ibraheem Ali, Greg Wilson:
  Ten quick tips for making things findable.

Perspective

• 
  Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey:
  Practical considerations for measuring the effective reproductive number, Rt.

Reviews

• 
  Andreas Buttenschön, Leah Edelstein-Keshet:
  Bridging from single to collective cell migration: A review of models and links to experiments.
• 
  Sebastian Gottwald, Daniel A. Braun:
  The two kinds of free energy and the Bayesian revolution.

Research Articles

• 
  Vít Novácek, Gavin McGauran, David Matallanas, Adrián Vallejo Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Muhammad Zeeshan Nawaz, Brian Walsh, Sameh K. Mohamed, Pierre-Yves Vandenbussche, Colm J. Ryan, Walter Kolch, Dirk Fey:
  Accurate prediction of kinase-substrate networks using knowledge graphs.
• 
  Ruggero Basanisi, Andrea Brovelli, Emilio Cartoni, Gianluca Baldassarre:
  A generative spiking neural-network model of goal-directed behaviour and one-step planning.
• 
  Jack E. Bowyer, Chloe Ding, Benjamin H. Weinberg, Wilson W. Wong, Declan G. Bates:
  A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits.
• 
  Noa Malem-Shinitski, Manfred Opper, Sebastian Reich, Lisa Schwetlick, Stefan A. Seelig, Ralf Engbert:
  A mathematical model of local and global attention in natural scene viewing.
• 
  Stefano Masoli, Alessandra Ottaviani, Stefano Casali, Egidio D'Angelo:
  Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity.
• 
  Jiayin Hong, Bo Hua, Michael Springer, Chao Tang:
  Computational study on ratio-sensing in yeast galactose utilization pathway.
• 
  Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Soti, Peter Csermely:
  Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network.
• 
  Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter:
  Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases.
• 
  Sean C. Anderson, Andrew M. Edwards, Madi Yerlanov, Nicola Mulberry, Jessica E. Stockdale, Sarafa A. Iyaniwura, Rebeca C. Falcao, Michael C. Otterstatter, Michael A. Irvine, Naveed Z. Janjua, Daniel Coombs, Caroline Colijn:
  Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing.
• 
  Fernando E. Rosas, Pedro A. M. Mediano, Henrik J. Jensen, Anil K. Seth, Adam B. Barrett, Robin L. Carhart-Harris, Daniel Bor:
  Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data.
• 
  Etay Hay, J. Andrew Pruszynski:
  Orientation processing by synaptic integration across first-order tactile neurons.
• 
  Anton Sobinov, Matthew T. Boots, Valeriya Gritsenko, Lee E. Fisher, Robert A. Gaunt, Sergiy Yakovenko:
  Approximating complex musculoskeletal biomechanics using multidimensional autogenerating polynomials.
• 
  Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M. Walczak, Yuval Elhanati:
  Population variability in the generation and selection of T-cell repertoires.
• 
  Natalia Sanchez de Groot, Marc Torrent Burgas:
  Bacteria use structural imperfect mimicry to hijack the host interactome.
• 
  Luis L. Bonilla, Ana Carpio, Carolina Trenado:
  Tracking collective cell motion by topological data analysis.
• 
  André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabian Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher, Benjamin M. Friedrich:
  Quantification of nematic cell polarity in three-dimensional tissues.
• 
  Thomas F. Varley, Olaf Sporns, Aina Puce, John M. Beggs:
  Differential effects of propofol and ketamine on critical brain dynamics.
• 
  Ananya Rastogi, Philippe A. Robert, Stephan Halle, Michael Meyer-Hermann:
  Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments.
• 
  Martí Català, Sergio Alonso, Enrique Alvarez-Lacalle, Daniel López, Pere-Joan Cardona, Clara Prats:
  Empirical model for short-time prediction of COVID-19 spreading.
• 
  Wataru Morita, Naoki Morimoto, Jukka Jernvall:
  Mapping molar shapes on signaling pathways.
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  Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan A. Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky:
  Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation.
• 
  Jennifer Lu, Steven L. Salzberg:
  SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.
• 
  Arnab Datta, David Harbage, Jané Kondev:
  Control of filament length by a depolymerizing gradient.
• 
  Julienne LaChance, Daniel J. Cohen:
  Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging.
• 
  Samuel Christensen, Yitong Huang, Olivia J. Walch, Daniel B. Forger:
  Optimal adjustment of the human circadian clock in the real world.
• 
  Christopher Mark Pooley, Glenn Marion, Stephen C. Bishop, Richard I. Bailey, Andrea B. Doeschl-Wilson:
  Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data.
• 
  Erik D. Fagerholm, Chayanin Tangwiriyasakul, Karl J. Friston, Inês R. Violante, Steven C. R. Williams, David W. Carmichael, Suejen Perani, Federico E. Turkheimer, Rosalyn J. Moran, Robert Leech, Mark P. Richardson:
  Neural diffusivity and pre-emptive epileptic seizure intervention.
• 
  João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt:
  Insights on cross-species transmission of SARS-CoV-2 from structural modeling.
• 
  Javier Delgado Blanco, Xavier Hernandez-Alias, Damiano Cianferoni, Luis Serrano:
  In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species.
• 
  T. J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica R. Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier:
  A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.
• 
  Sreejan Kumar, Cameron T. Ellis, Thomas P. O'Connell, Marvin M. Chun, Nicholas B. Turk-Browne:
  Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain.
• 
  Adam M. R. de Graff, David E. Mosedale, Tilly Sharp, Ken A. Dill, David J. Grainger:
  Proteostasis is adaptive: Balancing chaperone holdases against foldases.
• 
  Pranesh Padmanabhan, Rajat Desikan, Narendra M. Dixit:
  Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection.
• 
  John H. Lagergren, John T. Nardini, Ruth E. Baker, Matthew J. Simpson, Kevin B. Flores:
  Biologically-informed neural networks guide mechanistic modeling from sparse experimental data.
• 
  Saeed Farjami, Ryan P. D. Alexander, Derek Bowie, Anmar Khadra:
  Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding.
• 
  Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
  Drug2ways: Reasoning over causal paths in biological networks for drug discovery.
• 
  Niklas Hartung, Jens Markus Borghardt:
  A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs.
• 
  Quanhui Liu, Ana I. Bento, Kexin Yang, Hang Zhang, Xiaohan Yang, Stefano Merler, Alessandro Vespignani, Jiancheng Lv, Hongjie Yu, Wei Zhang, Tao Zhou, Marco Ajelli:
  The COVID-19 outbreak in Sichuan, China: Epidemiology and impact of interventions.
• 
  Andrey Kechin, Viktoria Borobova, Ulyana Boyarskikh, Evgeniy Khrapov, Sergey Subbotin, Maxim Filipenko:
  NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions.
• 
  Dongheon Lee, Arul Jayaraman, Joseph Sang-Il Kwon:
  Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling.
• 
  Pamela N. Luna, Jonathan M. Mansbach, Chad A. Shaw:
  A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease.
• 
  Marko Vendelin, Martin Laasmaa, Mari Kalda, Jelena Branovets, Niina Karro, Karina Barsunova, Rikke Birkedal:
  IOCBIO Kinetics: An open-source software solution for analysis of data traces.
• 
  Samuel Ingram, Nicholas T. Henthorn, John W. Warmenhoven, Norman F. Kirkby, Ranald I. MacKay, Karen J. Kirkby, Michael J. Merchant:
  Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage.
• 
  Qu Cheng, Philip A. Collender, Alexandra K. Heaney, Xintong Li, Rohini Dasan, Charles Li, Joseph A. Lewnard, Jonathan L. Zelner, Song Liang, Howard H. Chang, Lance A. Waller, Benjamin A. Lopman, Changhong Yang, Justin V. Remais:
  The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures.
• 
  Daniel F. Nino, Daniel Djayakarsana, Joshua N. Milstein:
  FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy.
• 
  Pantelis Leptourgos, Vincent Bouttier, Renaud Jardri, Sophie Denève:
  A functional theory of bistable perception based on dynamical circular inference.
• 
  Amjad Khan, Alita R. Burmeister, Lindi M. Wahl:
  Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages.
• 
  Bas van Opheusden, Luigi Acerbi, Wei Ji Ma:
  Unbiased and efficient log-likelihood estimation with inverse binomial sampling.
• 
  Ryan Smith, Rayus Kuplicki, Justin S. Feinstein, Katherine L. Forthman, Jennifer L. Stewart, Martin P. Paulus, Tulsa 1000 Investigators, Sahib S. Khalsa:
  A Bayesian computational model reveals a failure to adapt interoceptive precision estimates across depression, anxiety, eating, and substance use disorders.
• 
  Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini:
  On the NF-Y regulome as in ENCODE (2019).
• 
  Haiping Zhang, Yang Yang, Junxin Li, Min Wang, Konda Mani Saravanan, Jinli Wei, Justin Tze-Yang Ng, Md. Tofazzal Hossain, Maoxuan Liu, Huiling Zhang, Xiaohu Ren, Yi Pan, Yin Peng, Yi Shi, Xiaochun Wan, Yingxia Liu, Yanjie Wei:
  A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro.
• 
  Ali Khalilimeybodi, Alexander M. Paap, Steven L. M. Christiansen, Jeffrey J. Saucerman:
  Context-specific network modeling identifies new crosstalk in β-adrenergic cardiac hypertrophy.
• 
  Ivan Carcamo-Orive, Marc Y. R. Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D'Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang:
  Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness.
• 
  Abhishek Mallela, Maulik K. Nariya, Eric J. Deeds:
  Crosstalk and ultrasensitivity in protein degradation pathways.
• 
  Christopher L. Dembia, Nicholas A. Bianco, Antoine Falisse, Jennifer L. Hicks, Scott L. Delp:
  OpenSim Moco: Musculoskeletal optimal control.
• 
  Ivan I. Borisov, Eugeny A. Metelkin:
  Confidence intervals by constrained optimization - An algorithm and software package for practical identifiability analysis in systems biology.
• 
  Nadav Amir, Reut Suliman-Lavie, Maayan Tal, Sagiv Shifman, Naftali Tishby, Israel Nelken:
  Value-complexity tradeoff explains mouse navigational learning.
• 
  Dongdong Lin, Hima B. Yalamanchili, Xinmin Zhang, Nathan E. Lewis, Christina S. Alves, Joost Groot, Johnny Arnsdorf, Sara P. Bjørn, Tune Wulff, Bjørn G. Voldborg, Yizhou Zhou, Baohong Zhang:
  CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
• 
  Sebastian Bittrich, Stephen K. Burley, Alexander S. Rose:
  Real-time structural motif searching in proteins using an inverted index strategy.
• 
  Tanguy Fardet, Anna Levina:
  Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions.
• 
  Julian Libiseller-Egger, Jody Phelan, Susana G. Campino, Fady R. Mohareb, Taane G. Clark:
  Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers.
• 
  Colin G. Cess, Stacey D. Finley:
  Multi-scale modeling of macrophage - T cell interactions within the tumor microenvironment.
• 
  Stephanie Evans, J. Russell Butler, Joshua T. Mattila, Denise E. Kirschner:
  Systems biology predicts that fibrosis in tuberculous granulomas may arise through macrophage-to-myofibroblast transformation.
• 
  Edoardo Pinzuti, Patricia Wollstadt, Aaron J. Gutknecht, Oliver Tüscher, Michael Wibral:
  Measuring spectrally-resolved information transfer.
• 
  Halgurd Taher, Alessandro Torcini, Simona Olmi:
  Exact neural mass model for synaptic-based working memory.
• 
  Alessandro Ingrosso:
  Optimal learning with excitatory and inhibitory synapses.
• 
  Otto Pulkkinen, Prson Gautam, Ville Mustonen, Tero Aittokallio:
  Multiobjective optimization identifies cancer-selective combination therapies.
• 
  Timothy C. Matisziw, Ashkan Gholamialam, Kathleen M. Trauth:
  Modeling habitat connectivity in support of multiobjective species movement: An application to amphibian habitat systems.
• 
  Yuting Chen, Haoyu Lu, Ning Zhang, Zefeng Zhu, Shuqin Wang, Minghui Li:
  PremPS: Predicting the impact of missense mutations on protein stability.