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Improving reproducibility in computational biology research

Anand Rampadarath,David Nickerson,Feilim Mac Gabhann,Herbert M. Sauro,Jason A. Papin

Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles

Alastair M. Kilpatrick,Audra Anjum,Lonnie Welch

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth

Alessia Peduzzo,Alexander Hofmann,Alexander K. Buell,Daniel E. Otzen,Erik van Dijk,Georg Groth,Halima Mouhib,Juami Hermine Mariama van Gils,Marie P. Schützmann,Nicola Vettore,Sanne Abeln

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

Alan Le Goallec,Aleksandar D. Kostic,Braden T. Tierney,Chirag J. Patel,Evan M. Cofer,Jacob M. Luber

Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures

Elan Shatoff,Ralf Bundschuh

Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons

Audrey Sederberg,Ilya Nemenman

Shape-preserving elastic solid models of macromolecules

Guang Song

Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation

Abhishek Varghese,Antonietta Mira,Christopher Drovandi,Kerrie Mengersen

Early warning signals in motion inference

L. Mahadevan,Maryam Vaziri-Pashkam,Yuval Hart

An educational guide for nanopore sequencing in the classroom

Ahmed Mahfouz,Alex N. Salazar,Ana Rita Costa,Anna C. Haagsma,Anwar Hiralal,Christine Anyansi,Cristian Aparicio-Maldonado,Franklin L. Nobrega,Rebecca E. McKenzie,Stan J. J. Brouns,Teunke van Rossum,Thomas Abeel

Increasing growth rate slows adaptation when genotypes compete for diffusing resources

Allison K. Shaw,Jeremy M. Chacón,William R. Harcombe

Emergence and suppression of cooperation by action visibility in transparent games

Alexander Gail,Anton M. Unakafov,Fred Wolf,Igor Kagan,Sebastian Moeller,Stephan Eule,Thomas Schultze

Learning from animals: How to Navigate Complex Terrains

Armin Ataei,Hao Liu,Henghui Zhu,Ioannis Ch. Paschalidis,Thomas Daniel,Yonatan Munk

A single reaction-diffusion equation for the multifarious eruptions of urticaria

Michihiro Hide,Shunsuke Takahagi,Sungrim Seirin-Lee,Yuhki Yanase

Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs

Benjamin Allen,Christine Sample,Darren Parke,Gabor Lippner,James Withers,Joshua Kolodny,Lori Brizuela,Patricia Steinhagen,Robert Jencks,Yulia A. Dementieva

Collaboration leads to cooperation on sparse networks

Jonathan Newton,Simon D. Angus

Recurrent interactions can explain the variance in single trial responses

Jason N. MacLean,Subhodh Kotekal

Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model

Luis L. Bonilla,Manuel Carretero,Rocío Vega,Rui D. M. Travasso

Ten Simple Rules to becoming a principal investigator

Jason E. McDermott,John S. Tregoning

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

Aleksandr Ianevski,Alexander Kononov,Anil K. Giri,Sanna Timonen,Tero Aittokallio

What makes or breaks a campaign to stop an invading plant pathogen?

Alice E. Milne,Frank van den Bosch,Stephen R. Parnell,Tim Gottwald,Vasthi Alonso Chavez

Nonlinear mixed selectivity supports reliable neural computation

David J. Freedman,Stephanie E. Palmer,W. Jeffrey Johnston

Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis

Kunihiko Kaneko,Qian-Yuan Tang

Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit

Alexander Strobel,Dimitrije Markovi？,Florian Ott,Stefan J. Kiebel

CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer

Anne-Sophie Lia,Corinne Magdelaine,David Rizzo,Federica Miressi,Franck Sturtz,Hélène Dzugan,Jasmine Chauzeix,Jean Feuillard,Karine Durand,Paco Derouault,Stéphane Mérillou,Sylvie Bourthoumieu

Reprogramming of macrophages employing gene regulatory and metabolic network models

Amol Kolte,Daniela R？ll,David Eisel,Franziska H？rhold,Marcus Oswald,Rainer K？nig,Stefan B. Eichmüller,Wolfram Osen

Human decision making anticipates future performance in motor learning

Daniel J. Gale,Daniel M. Wolpert,J. Randall Flanagan,Jason P. Gallivan,Joshua B. Moskowitz

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution

Cheng Li,Cheng Quan,Chenghui Zhao,Guifang Du,Hao Hong,Hao Li,Hebing Chen,Huan Tao,Ruijiang Li,Shuai Jiang,Wanying Li,Xiaochen Bo,Xiaoyao Yin,Yangchen Huang,Yu Sun

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Arshag D. Mooradian,Jason M. Held,Kristen M. Naegle,Sjoerd van der Post

Parallel Tempering with Lasso for model reduction in systems biology

James R. Faeder,Robin E. C. Lee,Sanjana Gupta

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Luís A. N. Amaral,Neda Bagheri,Nicolás Peláez,Richard W. Carthew,Sebastian M. Bernasek

A plausible accelerating function of intermediate states in cancer metastasis

Hanah Goetz,Juan R. Melendez-Alvarez,Luonan Chen,Xiao-Jun Tian

Direct coupling analysis of epistasis in allosteric materials

Barbara Bravi,Carolina Brito,Matthieu Wyart,Riccardo Ravasio

Ten simple rules for more objective decision-making

Anthony C. Fletcher,Georges A. Wagner,Philip E. Bourne

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Christopher T. Lee,J. Andrew McCammon,Justin G. Laughlin,Michael Holst,Nils Angliviel de La Beaumelle,Padmini Rangamani,Ravi Ramamoorthi,Rommie E. Amaro

Near-optimal combination of disparity across a log-polar scaled visual field

Fabio Solari,Guido Maiello,Manuela Chessa,Peter J. Bex

Deep reinforcement learning for the control of microbial co-cultures in bioreactors

Alex J. H. Fedorec,Brian Ingalls,Chris P. Barnes,Neythen J. Treloar

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex

Dmitrii S. Shcherbinin,Mikhail Shugay,Vlad A. Belousov

Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization

Alexander R. A. Anderson,Anna K. Miller,Chandler D. Gatenbee,David Basanta,Etienne Baratchart,Jeffrey West,Jill Gallaher,Mark Robertson-Tessi,Rafael R. Bravo,Ryan O. Schenck

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

Allison M. Thompson,Amanda M. White,Daniel Claborne,Kelly G. Stratton,Kirsten Hofmockel,Lee Ann McCue,Lisa M. Bramer

Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria

Birgit E. Scharf,Floricel Gonzalez,Jing Chen,Nathaniel Esteves,Xiaochu Li

Efficient and flexible representation of higher-dimensional cognitive variables with grid cells

Ila Fiete,Marcus Lewis,Mirko Klukas

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis

Ben Stear,Deanne M. Taylor,Erin R. Reichenberger,Man S. Kim,Yuanchao Zhang

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE

Ali Hadizadeh Esfahani,Andreas Schuppert,Lisa-Katrin Sch？tzle

Climbing Escher’s stairs: A way to approximate stability landscapes in multidimensional systems

Egbert H. van Nes,Marten Scheffer,Pablo Rodríguez-Sánchez

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

Andreas Haahr Larsen,Kresten Lindorff-Larsen,Lise Arleth,Sandro Bottaro,Sergei Grudinin,Yong Wang

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

Gregory L. Medlock,Jason A. Papin,Thomas J. Moutinho

Better together: Elements of successful scientific software development in a distributed collaborative community

Andrew Leaver-Fay,Andrew M. Watkins,Brian D. Weitzner,Brian Kuhlman,Charlie E. M. Strauss,Christopher Bystroff,David Baker,Dominik Gront,Jared Adolf-Bryfogle,Jason W. Labonte,Jeffrey J. Gray,Jens Meiler,Julia Koehler Leman,Justyna Krys,Ora Schueler-Furman,P. Douglas Renfrew,Philip Bradley,Richard Bonneau,Rocco Moretti,Roland Dunbrack,RosettaCommons Consortium,Sergey Lyskov,Steven M. Lewis,Tanja Kortemme,Vikram Khipple Mulligan,William Schief

Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis

Amanda Brucker,Ching-Heng Lin,Chuhsing Kate Hsiao,Jin P. Szatkiewicz,Jung-Ying Tzeng,Patrick F. Sullivan,Patrik K. E. Magnusson,Qi-You Yu,Rachel Marceau West,Tzu-Hung Hsiao,Tzu-Pin Lu,Wenbin Lu

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry

Andrew J. Bernoff,Jasper Weinburd,Maryann E. Hohn,Michael Culshaw-Maurer,Rebecca A. Everett,W. Christopher Strickland

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