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ORCIDF1000Research, Volume 9
Volume 9, 2020
- Saif Aldeen AlRyalat
, Osama El khatib, Ola Al-qawasmi, Hadeel Alkasrawi, Raneem al Zu'bi, Maram Abu-Halaweh, Yara alkanash, Ibrahim Habash:
The impact of the National Heart, Lung, and Blood Institute data: analyzing published articles that used BioLINCC open access data. 30 - Stefan T. Arold:
Intrinsic negative feedback as a limiting factor for the evolution of higher forms of intelligence. 34 - Colby T. Ford, Daniel Janies:
Ensemble machine learning modeling for the prediction of artemisinin resistance in malaria. 62 - Maxime Garcia, Szilveszter Juhos, Malin Larsson, Páll Ísólfur Ólason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Diaz de Ståhl, Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt:
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. 63 - Sander de Ridder, Jeroen A. M. Beliën:
The iCRF Generator: Generating interoperable electronic case report forms using online codebooks. 81 - Martin Vogt, Jürgen Bajorath:
ccbmlib - a Python package for modeling Tanimoto similarity value distributions. 100 - Marcel Baltruschat, Paul Czodrowski:
Machine learning meets pKa. 113 - Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi:
BioHackathon 2015: Semantics of data for life sciences and reproducible research. 136 - Ann Cochrane, Charlie Welch, Caroline Fairhurst, Sarah Cockayne, David J. Torgerson, OTIS Study Group:
An evaluation of a personalised text message reminder compared to a standard text message on postal questionnaire response rates: an embedded randomised controlled trial. 154 - Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen:
Visualize omics data on networks with Omics Visualizer, a Cytoscape App. 157 - Marco Bilucaglia, Gian Marco Duma, Giovanni Mento, Luca Semenzato, Patrizio Tressoldi:
Applying machine learning EEG signal classification to emotion‑related brain anticipatory activity. 173 - Lena Schmidt, Babatunde K. Olorisade, Luke A. McGuinness, Julian P. T. Higgins:
Data extraction methods for systematic review (semi)automation: A living review protocol. 210 - Roc Reguant, Yevgeniy Antipin, Robert P. Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier:
AlignmentViewer: Sequence Analysis of Large Protein Families. 213 - Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, Firmin Martin, Michael McManus, Philippe Hupé:
QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing. 240 - Alif Choyon, Ashiqur Rahman, Md. Hasanuzzaman, Dewan Md. Farid, Swakkhar Shatabda:
PRESa2i: incremental decision trees for prediction of Adenosine to Inosine RNA editing sites. 262 - Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojciech Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H. C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Jörg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekermann, Stefan Unger, Rudolf Weeber:
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. 295 - Sari Sabban, Mikhail Markovsky:
RamaNet: Computational de novo helical protein backbone design using a long short-term memory generative adversarial neural network. 298 - Andrew J. McKay, Ashley P. Jones, Carrol Gamble, Andrew J. Farmer, Paula R. Williamson:
Use of routinely collected data in a UK cohort of publicly funded randomised clinical trials. 323 - Sandeep Kasaragod, Varshasnata Mohanty, Ankur Tyagi, Santosh Kumar Behera, Arun H. Patil, Sneha M. Pinto, T. S. Keshava Prasad, Prashant Kumar Modi, Harsha Gowda:
CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets. 344 - Matthew N. Bernstein, Ariella L. Gladstein, Khun Zaw Latt, Emily Clough, Ben Busby, Allissa Dillman:
Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive. 376 - Aysha Rooha, Malavika Anakkathil Anil, Jayashree S. Bhat:
Pictures over words: a cross-sectional study reporting short term memory abilities in children. 380 - Justin A. Ehrlich, Shankar Ghimire:
COVID-19 countermeasures, Major League Baseball, and the home field advantage: Simulating the 2020 season using logit regression and a neural network. 414 - Matias Carrasco Kind, Mantas Zurauskas, Aneesh Alex, Marina Marjanovic, Prabuddha Mukherjee, Minh Doan, Darold R. Spillman Jr., Steve Hood, Stephen A. Boppart:
flimview : A software framework to handle, visualize and analyze FLIM data. 574 - Paola A. Sánchez-Sánchez, José Rafael García-González, Juan Manuel Rúa Ascar:
Automatic migraine classification using artificial neural networks. 618 - Choumouss Kamoun, Julien Roméjon, Henri de Soyres, Apolline Gallois, Elodie Girard, Philippe Hupé:
biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab. 632 - Michael Hewera, Ann-Christin Nickel, Nina Knipprath, Sajjad Muhammad, Xiaolong Fan, Hans-Jakob Steiger, Daniel Hänggi, Ulf Dietrich Kahlert:
Measures to increase value of preclinical research - an inexpensive and easy-to-implement approach to a QMS for an academic research lab. 660 - Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson:
gprofiler2 - an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. 709 - Antti Väänänen, Keijo Haataja, Pekka J. Toivanen:
Survey to healthcare professionals on the practicality of AI services for healthcare. 760 - Martha Fors, Paloma González:
Who is making clinical trials for treatment or prevention of COVID-19? A review of Clinicaltrials.gov, May 2020. 823 - Finn Kuusisto, Daniel Ng, John W. Steill, Ian Ross, Miron Livny, James A. Thomson, David Page, Ron M. Stewart:
KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. 832 - Liesbeth François, Jonathan van Eyll, Patrice Godard:
Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies. 942 - Emmanuel S. Adabor, George K. Acquaah-Mensah, Gaston K. Mazandu:
MSclassifier: median-supplement model-based classification tool for automated knowledge discovery. 1114 - Anthony Nash, M. Zameel Cader:
Extraction of CPRD additional clinical data using R. 1124 - Christopher P. Cheng, Yaroslav O. Halchenko:
A new virtue of phantom MRI data: explaining variance in human participant data. 1131 - Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis A. Dean:
BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations. 1144 - Caitlin E. Coombes, Zachary B. Abrams, Samantha Nakayiza, Guy N. Brock, Kevin R. Coombes:
Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning. 1186 - Caroline Jay, Robert Haines, Daniel S. Katz, Jeffrey C. Carver, Sandra Gesing, Steven R. Brandt, James Howison, Anshu Dubey, James C. Phillips, Hui Wan, Matthew J. Turk:
The challenges of theory-software translation. 1192 - Danielle L. Kurtin, Daniel A. J. Parsons, Scott Stagg:
VTES: a stochastic Python-based tool to simulate viral transmission. 1198 - Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen, Heidi Marjonen, Mats R. K. Lindstedt, Kati Kristiansson, Sarah E. Hunt, Fiona Cunningham, Ilkka Lappalainen, Michael J. E. Sternberg:
Annotation and curation of human genomic variations: an ELIXIR Implementation Study. 1207 - Dustin B. Miller, Stephen R. Piccolo:
CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline. 1211 - Henry Inegbedion, Emmanuel Inegbedion, Abiola Asaleye, Eseosa Obadiaru, Festus Asamu:
Use of social media in the marketing of agricultural products and farmers' turnover in South-South Nigeria. 1220 - David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutiérrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquín Dopazo, Laura I. Furlong, Bo Gao, Leyla Jael García Castro, Dietlind Gerloff, Ivo Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskosek, David Lloyd, Tomàs Marquès-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud:
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. 1229 - Alok Atreya, Samata Nepal, Prakash Thapa:
Cross-sectional study of Facebook addiction in a sample of Nepalese population. 1237 - Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader:
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. 1239 - Ruizhu Huang, Charlotte Soneson, Felix G. M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson:
TreeSummarizedExperiment: a S4 class for data with hierarchical structure. 1246 - Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig:
Fiji plugins for qualitative image annotations: routine analysis and application to image classification. 1248 - Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe:
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME. 1255 - Helena L. Crowell, Stéphane Chevrier, Andrea Jacobs, Sujana Sivapatham, Tumor Profiler consortium, Bernd Bodenmiller, Mark D. Robinson:
An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. 1263 - Jonathan K. Black, Jonathan M. Koller, Kevin J. Black:
TicTimer Web: software for measuring tic suppression remotely. 1264 - Rick Seifert, Sebastian M. Markert, Sebastian Britz, Veronika Perschin, Christoph Erbacher, Christian Stigloher, Philip Kollmannsberger:
DeepCLEM: automated registration for correlative light and electron microscopy using deep learning. 1275 - Elnaz Fazeli, Nathan H. Roy, Gautier Follain, Romain F. Laine, Lucas von Chamier, Pekka E. Hänninen, John E. Eriksson, Jean-Yves Tinevez, Guillaume Jacquemet:
Automated cell tracking using StarDist and TrackMate. 1279 - Louise Bezuidenhout, Johanna Havemann:
The varying openness of digital open science tools. 1292 - Judi R. Walters, Kate Light, Nathan Robinson:
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database. 1305 - Jessica L. Thomson, Alicia S. Landry:
Three datasets for nutrition environment measures of food outlets located in the Lower Mississippi Delta region of the United States. 1307 - Sébastien Tosi, Lídia Bardia, Maria Jose Barallobre, Arrate Muñoz-Barrutia, María Luisa Soto-Montenegro, Julien Colombelli:
MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy. 1308 - Christopher Schmied, Helena Klara Jambor:
Effective image visualization for publications - a workflow using open access tools and concepts. 1373 - Minh Son Phan, Anatole Chessel:
GeNePy3D: a quantitative geometry python toolbox for large scale bioimaging. 1374 - Romain Guiet, Olivier Burri, Nicolas Chiaruttini, Olivier Hagens, Arne Seitz:
DEVILS: a tool for the visualization of large datasets with a high dynamic range. 1380 - Anna H. Klemm:
Semi-automated analysis of dot blots using ImageJ/Fiji. 1385 - Julian Hirt, Thomas Nordhausen, Christian Appenzeller-Herzog, Hannah Ewald:
Using citation tracking for systematic literature searching - study protocol for a scoping review of methodological studies and an expert survey. 1386 - Dennis Psaroudakis, Feng Liu, Patrick König, Uwe Scholz, Astrid Junker, Matthias Lange, Daniel Arend:
isa4j: a scalable Java library for creating ISA-Tab metadata. 1388 - Susanne Hollmann, Andreas Kremer, Spela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. A. Evelo, Alina S. Nechyporenko, Marcus Frohme, David Safránek, Babette Regierer, Domenica D'Elia:
The need for standardisation in life science research - an approach to excellence and trust. 1398 - Maryam Jamshidi, Cavus Falamaki:
Image analysis method for heterogeneity and porosity characterization of biomimetic hydrogels. 1461 - Jenna Oberstaller, Swamy Rakesh Adapa, Guy W. Dayhoff II, Justin Gibbons, Thomas E. Keller, Chang Li, Shen Jean Lim, Minh Pham, Anujit Sarkar, Ravi Sharma, Agaz H. Wani, Andrea Vianello, Linh M. Duong, Chenggi Wang, Celine Grace F. Atkinson, Madeleine Barrow, Nathan W. Van Bibber, Jan Dahrendorff, David A. E. Dean, Omkar Dokur, Gloria C. Ferreira, Mitchell Hastings, Gregory S. Herbert, Khandaker Tasnim Huq, Youngchul Kim, Xiangyun Liao, XiaoMing Liu, Fahad Mansuri, Lynn B. Martin, Elizabeth M. Miller, Ojas Natarajan, Jinyong Pang, Francesca Prieto, Peter W. Radulovic, Vyoma Sheth, Matthew Sumpter, Desirae Sutherland, Nisha Vijayakumar, Rays H. Y. Jiang:
Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences. 1478 - Abdulkerim Çapar, Sibel Cimen, Zeynep Aladag, Dursun Ali Ekinci, Umut Engin Ayten, Bilal Ersen Kerman, Behçet Ugur Töreyin:
A multi-spectral myelin annotation tool for machine learning based myelin quantification. 1492
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