PLOS Computational Biology

2005 - 2022

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Volume 16, issue 12, 2020

Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage pp. 1-26

Samuel P Ingram, Nicholas T Henthorn, John W Warmenhoven, Norman F Kirkby, Ranald I Mackay, Karen J Kirkby and Michael J Merchant

A mathematical model of local and global attention in natural scene viewing pp. 1-21

Noa Malem-Shinitski, Manfred Opper, Sebastian Reich, Lisa Schwetlick, Stefan A Seelig and Ralf Engbert

Population variability in the generation and selection of T-cell repertoires pp. 1-21

Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M Walczak and Yuval Elhanati

Practical considerations for measuring the effective reproductive number, Rt pp. 1-21

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 Sherrat, Robin N Thompson, Laura F White, Jana S Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch and Sarah Cobey

Neural diffusivity and pre-emptive epileptic seizure intervention pp. 1-21

Erik D Fagerholm, Chayanin Tangwiriyasakul, Karl J Friston, Inês R Violante, Steven Williams, David W Carmichael, Suejen Perani, Federico E Turkheimer, Rosalyn J Moran, Robert Leech and Mark P Richardson

Drug2ways: Reasoning over causal paths in biological networks for drug discovery pp. 1-21

Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius and Daniel Domingo-Fernández

Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments pp. 1-27

Ananya Rastogi, Philippe A Robert, Stephan Halle and Michael Meyer-Hermann

A functional theory of bistable perception based on dynamical circular inference pp. 1-23

Pantelis Leptourgos, Vincent Bouttier, Renaud Jardri and Sophie Denève

Modeling habitat connectivity in support of multiobjective species movement: An application to amphibian habitat systems pp. 1-23

Timothy C Matisziw, Ashkan Gholamialam and Kathleen M Trauth

A generative spiking neural-network model of goal-directed behaviour and one-step planning pp. 1-32

Ruggero Basanisi, Andrea Brovelli, Emilio Cartoni and Gianluca Baldassarre

The two kinds of free energy and the Bayesian revolution pp. 1-32

Sebastian Gottwald and Daniel A Braun

Estimating individuals’ genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data pp. 1-32

Christopher M Pooley, Glenn Marion, Stephen C Bishop, Richard I Bailey and Andrea B Doeschl-Wilson

Unbiased and efficient log-likelihood estimation with inverse binomial sampling pp. 1-32

Bas van Opheusden, Luigi Acerbi and Wei Ji Ma

Ten quick tips for making things findable pp. 1-10

Sarah Lin, Ibraheem Ali and Greg Wilson

Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging pp. 1-24

Julienne LaChance and Daniel J Cohen

Optimal learning with excitatory and inhibitory synapses pp. 1-24

Alessandro Ingrosso

Differential effects of propofol and ketamine on critical brain dynamics pp. 1-29

Thomas F Varley, Olaf Sporns, Aina Puce and John Beggs

Biologically-informed neural networks guide mechanistic modeling from sparse experimental data pp. 1-29

John H Lagergren, John T Nardini, Ruth E Baker, Matthew J Simpson and Kevin B Flores

Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding pp. 1-29

Saeed Farjami, Ryan P D Alexander, Derek Bowie and Anmar Khadra

IOCBIO Kinetics: An open-source software solution for analysis of data traces pp. 1-9

Marko Vendelin, Martin Laasmaa, Mari Kalda, Jelena Branovets, Niina Karro, Karina Barsunova and Rikke Birkedal

Optimal adjustment of the human circadian clock in the real world pp. 1-18

Samuel Christensen, Yitong Huang, Olivia J Walch and Daniel B Forger

Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain pp. 1-18

Sreejan Kumar, Cameron T Ellis, Thomas P O’Connell, Marvin M Chun and Nicholas B Turk-Browne

Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing pp. 1-15

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 and Caroline Colijn

Control of filament length by a depolymerizing gradient pp. 1-15

Arnab Datta, David Harbage and Jane Kondev

Proteostasis is adaptive: Balancing chaperone holdases against foldases pp. 1-15

Adam MR de Graff, David E Mosedale, Tilly Sharp, Ken A Dill and David J Grainger

Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling pp. 1-31

Dongheon Lee, Arul Jayaraman and Joseph S Kwon

Value-complexity tradeoff explains mouse navigational learning pp. 1-31

Nadav Amir, Reut Suliman, Maayan Tal, Sagiv Shifman, Naftali Tishby and Israel Nelken

Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data pp. 1-22

Fernando E Rosas, Pedro A M Mediano, Henrik J Jensen, Anil K Seth, Adam B Barrett, Robin L Carhart-Harris and Daniel Bor

Quantification of nematic cell polarity in three-dimensional tissues pp. 1-22

André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabián Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher and Benjamin M Friedrich

Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions pp. 1-22

Tanguy Fardet and Anna Levina

The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures pp. 1-25

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 and Justin V Remais

Accurate prediction of kinase-substrate networks using knowledge graphs pp. 1-30

Vít Nováček, Gavin McGauran, David Matallanas, Adrián Vallejo Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Zeeshan Nawaz, Brian Walsh, Sameh K Mohamed, Pierre-Yves Vandenbussche, Colm J Ryan, Walter Kolch and Dirk Fey

Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology pp. 1-13

Ivan Borisov and Evgeny Metelkin

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines pp. 1-13

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 and Baohong Zhang

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease pp. 1-17

Pamela N Luna, Jonathan M Mansbach and Chad A Shaw

Multiobjective optimization identifies cancer-selective combination therapies pp. 1-17

Otto I Pulkkinen, Prson Gautam, Ville Mustonen and Tero Aittokallio

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy pp. 1-19

Daniel F Nino, Daniel Djayakarsana and Joshua N Milstein

Measuring spectrally-resolved information transfer pp. 1-40

Edoardo Pinzuti, Patricia Wollstadt, Aaron Gutknecht, Oliver Tüscher and Michael Wibral

Volume 16, issue 11, 2020

Tracking and predicting U.S. influenza activity with a real-time surveillance network pp. 1-14

Sequoia I Leuba, Reza Yaesoubi, Marina Antillon, Ted Cohen and Christoph Zimmer

Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy pp. 1-14

Doruk Cakmakci, Emin Onur Karakaslar, Elisa Ruhland, Marie-Pierre Chenard, Francois Proust, Martial Piotto, Izzie Jacques Namer and A Ercument Cicek

Systems biology informed deep learning for inferring parameters and hidden dynamics pp. 1-19

Alireza Yazdani, Lu Lu, Maziar Raissi and George Em Karniadakis

Ten simple rules for starting research in your late teens pp. 1-11

Cameron Mura, Mike Chalupa, Abigail M Newbury, Jack Chalupa and Philip E Bourne

EventEpi—A natural language processing framework for event-based surveillance pp. 1-16

Auss Abbood, Alexander Ullrich, Rüdiger Busche and Stéphane Ghozzi

Biological network growth in complex environments: A computational framework pp. 1-20

Torsten Johann Paul and Philip Kollmannsberger

Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium pp. 1-20

Román Zapién-Campos, Michael Sieber and Arne Traulsen

Identifying longevity associated genes by integrating gene expression and curated annotations pp. 1-20

F William Townes, Kareem Carr and Jeffrey W Miller

Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features pp. 1-30

Toshiyuki Ishii and Toshihiko Hosoya

Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection pp. 1-30

Christoph Stelzer and Yaakov Benenson

A dual-feedback loop model of the mammalian circadian clock for multi-input control of circadian phase pp. 1-25

Lindsey S Brown and Francis J Doyle

Ten simple rules for writing a paper about scientific software pp. 1-8

Joseph D Romano and Jason H Moore

Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model pp. 1-31

Anahita Bayani, Joanne L Dunster, Jonathan J Crofts and Martin R Nelson

Neural mass modeling of slow-fast dynamics of seizure initiation and abortion pp. 1-31

Elif Köksal Ersöz, Julien Modolo, Fabrice Bartolomei and Fabrice Wendling

Modelling pathogen spread in a healthcare network: Indirect patient movements pp. 1-22

Monika J Piotrowska, Konrad Sakowski, André Karch, Hannan Tahir, Johannes Horn, Mirjam E Kretzschmar and Rafael T Mikolajczyk

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier pp. 1-22

Maxat Kulmanov and Robert Hoehndorf

Testing structural identifiability by a simple scaling method pp. 1-15

Mario Castro and Rob J de Boer

Quantification of Ebola virus replication kinetics in vitro pp. 1-15

Laura E Liao, Jonathan Carruthers, Sophie J Smither, Virology Team Cl4, Simon A Weller, Diane Williamson, Thomas R Laws, Isabel García-Dorival, Julian Hiscox, Benjamin P Holder, Catherine A A Beauchemin, Alan S Perelson, Martín López-García, Grant Lythe, John N Barr and Carmen Molina-París

Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach pp. 1-34

Howard Bowman, Joseph L Brooks, Omid Hajilou, Alexia Zoumpoulaki and Vladimir Litvak

PPM-Decay: A computational model of auditory prediction with memory decay pp. 1-41

Peter M C Harrison, Roberta Bianco, Maria Chait and Marcus T Pearce

Maximizing the reusability of gene expression data by predicting missing metadata pp. 1-18

Pei-Yau Lung, Dongrui Zhong, Xiaodong Pang, Yan Li and Jinfeng Zhang

The Moran process on 2-chromatic graphs pp. 1-18

Kamran Kaveh, Alex McAvoy, Krishnendu Chatterjee and Martin A Nowak

Inferring a network from dynamical signals at its nodes pp. 1-18

Corey Weistuch, Luca Agozzino, Lilianne R Mujica-Parodi and Ken A Dill

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein pp. 1-24

Dylan Girodat, Avik K Pati, Daniel S Terry, Scott C Blanchard and Karissa Y Sanbonmatsu

Ten simple rules for writing Dockerfiles for reproducible data science pp. 1-24

Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J Eglen, Tim Head, Tony Hirst and Benjamin D Evans

Poisson balanced spiking networks pp. 1-27

Camille E Rullán Buxó and Jonathan W Pillow

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells pp. 1-27

Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga and Masao Matsuoka

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits pp. 1-23

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 and Anton Arkhipov

Dopamine release, diffusion and uptake: A computational model for synaptic and volume transmission pp. 1-26

Kathleen Wiencke, Annette Horstmann, David Mathar, Arno Villringer and Jane Neumann

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection pp. 1-21

Oliver M Crook, Aikaterini Geladaki, Daniel J H Nightingale, Owen L Vennard, Kathryn S Lilley, Laurent Gatto and Paul D W Kirk

Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species pp. 1-21

Yumin Zheng, Haohan Wang, Yang Zhang, Xin Gao, Eric P Xing and Min Xu

An exact method for quantifying the reliability of end-of-epidemic declarations in real time pp. 1-21

Kris V Parag, Christl A Donnelly, Rahul Jha and Robin N Thompson

Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins pp. 1-32

Amir Bitran, William M Jacobs and Eugene Shakhnovich

Volume 16, issue 10, 2020

Membrane thinning and lateral gating are consistent features of BamA across multiple species pp. 1-15

Jinchan Liu and James C Gumbart

Biophysically detailed mathematical models of multiscale cardiac active mechanics pp. 1-42

Francesco Regazzoni, Luca Dedè and Alfio Quarteroni

Refractory density model of cortical direction selectivity: Lagged-nonlagged, transient-sustained, and On-Off thalamic neuron-based mechanisms and intracortical amplification pp. 1-42

Anton Chizhov and Natalia Merkulyeva

Timescales of motor memory formation in dual-adaptation pp. 1-33

Marion Forano and David W Franklin

Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision pp. 1-27

Courtney J Spoerer, Tim C Kietzmann, Johannes Mehrer, Ian Charest and Nikolaus Kriegeskorte

Penalized regression and model selection methods for polygenic scores on summary statistics pp. 1-27

Jack Pattee and Wei Pan

Reward-predictive representations generalize across tasks in reinforcement learning pp. 1-27

Lucas Lehnert, Michael L Littman and Michael J Frank

Delayed global feedback in the genesis and stability of spatiotemporal excitation patterns in paced biological excitable media pp. 1-23

Zhen Song and Zhilin Qu

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts pp. 1-23

Andrew F Magee, Sebastian Höhna, Tetyana I Vasylyeva, Adam D Leaché and Vladimir N Minin

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 pp. 1-23

Joseph M Barnby, Vaughan Bell, Mitul A Mehta and Michael Moutoussis

Protein-protein interactions in neurodegenerative diseases: A conspiracy theory pp. 1-41

Travis B Thompson, Pavanjit Chaggar, Ellen Kuhl, Alain Goriely and for the Alzheimer’s Disease Neuroimaging Initiative

Ten simple rules for building an antiracist lab pp. 1-9

V Bala Chaudhary and Asmeret Asefaw Berhe

Ten simple rules for women principal investigators during a pandemic pp. 1-9

Pamela K Kreeger, Amy Brock, Holly C Gibbs, K Jane Grande-Allen, Alice H Huang, Kristyn S Masters, Padmini Rangamani, Michaela R Reagan and Shannon L Servoss

Estimation of the force of infection and infectious period of skin sores in remote Australian communities using interval-censored data pp. 1-18

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 and James M McCaw

Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals pp. 1-18

Etienne Combrisson, Timothy Nest, Andrea Brovelli, Robin A A Ince, Juan L P Soto, Aymeric Guillot and Karim Jerbi

A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies pp. 1-18

Audrey McCombs and Claus Kadelka

LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS pp. 1-8

Naim Panjwani, Fan Wang, Scott Mastromatteo, Allen Bao, Cheng Wang, Gengming He, Jiafen Gong, Johanna M Rommens, Lei Sun and Lisa J Strug

Significance of trends in gait dynamics pp. 1-25

Klaudia Kozlowska, Miroslaw Latka and Bruce J West

Models of SIV rebound after treatment interruption that involve multiple reactivation events pp. 1-25

Christiaan H van Dorp, Jessica M Conway, Dan H Barouch, James B Whitney and Alan S Perelson

The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks pp. 1-38

Matthieu Gilson, David Dahmen, Rubén Moreno-Bote, Andrea Insabato and Moritz Helias

Estimating effective population size changes from preferentially sampled genetic sequences pp. 1-22

Michael D Karcher, Luiz Max Carvalho, Marc A Suchard, Gytis Dudas and Vladimir N Minin

Metabolic pathway inference using multi-label classification with rich pathway features pp. 1-22

Abdur Rahman M. A. Basher, Ryan J McLaughlin and Steven J Hallam

A data-driven characterisation of natural facial expressions when giving good and bad news pp. 1-22

David M Watson, Ben B Brown and Alan Johnston

A mathematical model of flagellar gene regulation and construction in Salmonella enterica pp. 1-21

Kiersten Utsey and James P Keener

Iterative point set registration for aligning scRNA-seq data pp. 1-21

Amir Alavi and Ziv Bar-Joseph

A genotype imputation method for de-identified haplotype reference information by using recurrent neural network pp. 1-21

Kaname Kojima, Shu Tadaka, Fumiki Katsuoka, Gen Tamiya, Masayuki Yamamoto and Kengo Kinoshita

Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster pp. 1-21

Ugne Klibaite and Joshua W Shaevitz

Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel pp. 1-21

Sarah C Kramer, Sen Pei and Jeffrey Shaman

A Bayesian non-parametric mixed-effects model of microbial growth curves pp. 1-21

Peter D Tonner, Cynthia L Darnell, Francesca M L Bushell, Peter A Lund, Amy K Schmid and Scott C Schmidler

Intuitive physical reasoning about objects’ masses transfers to a visuomotor decision task consistent with Newtonian physics pp. 1-26

Nils Neupärtl, Fabian Tatai and Constantin A Rothkopf

Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation pp. 1-32

Edward M Hill, Stavros Petrou, Henry Forster, Simon de Lusignan, Ivelina Yonova and Matt J Keeling

Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis pp. 1-32

Ruijin Wu, Rahul Prabhu, Aysegul Ozkan and Meera Sitharam

Multiscale community detection in Cytoscape pp. 1-10

Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng and Trey Ideker

Learning gene networks underlying clinical phenotypes using SNP perturbation pp. 1-24

Calvin McCarter, Judie Howrylak and Seyoung Kim

Likelihood-free nested sampling for parameter inference of biochemical reaction networks pp. 1-24

Jan Mikelson and Mustafa Khammash

Inferring tumor progression in large datasets pp. 1-16

Mohammadreza Mohaghegh Neyshabouri, Seong-Hwan Jun and Jens Lagergren

Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet pp. 1-16

Emilia Kozłowska, Rafał Suwiński, Monika Giglok, Andrzej Świerniak and Marek Kimmel

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance pp. 1-20

Dharmeshkumar Patel, Jonathan E Barnes, Wayne I L Davies, Deborah L Stenkamp and Jagdish Suresh Patel

Genome Complexity Browser: Visualization and quantification of genome variability pp. 1-20

Alexander Manolov, Dmitry Konanov, Dmitry Fedorov, Ivan Osmolovsky, Rinat Vereshchagin and Elena Ilina

Finding, visualizing, and quantifying latent structure across diverse animal vocal repertoires pp. 1-48

Tim Sainburg, Marvin Thielk and Timothy Q Gentner

Dynamical persistence in high-diversity resource-consumer communities pp. 1-14

Itay Dalmedigos and Guy Bunin

Time varying methods to infer extremes in dengue transmission dynamics pp. 1-19

Jue Tao Lim, Yiting Han, Borame Sue Lee Dickens, Lee Ching Ng and Alex R Cook

Exploring the sequence fitness landscape of a bridge between protein folds pp. 1-19

Pengfei Tian and Robert B Best

Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness pp. 1-19

Sen Pei and Jeffrey Shaman

Ten simple rules for organizing a data science workshop pp. 1-7

Alise Ponsero, Ryan Bartelme, Gustavo de Oliveira Almeida, Alex Bigelow, Reetu Tuteja, Holly Ellingson, Tyson Swetnam, Nirav Merchant, Maliaca Oxnam and Eric Lyons

Volume 16, issue 9, 2020

Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates pp. 1-7

Pleuni Pennings, Mayra M Banuelos, Francisca L Catalan, Victoria R Caudill, Bozhidar Chakalov, Selena Hernandez, Jeanice Jones, Chinomnso Okorie, Sepideh Modrek, Rori Rohlfs and Nicole Adelstein

Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells pp. 1-28

Miquel Marchena, Blas Echebarria, Yohannes Shiferaw and Enrique Alvarez-Lacalle

Similarities and differences in spatial and non-spatial cognitive maps pp. 1-28

Charley M Wu, Eric Schulz, Mona M Garvert, Björn Meder and Nicolas W Schuck

Domino-like transient dynamics at seizure onset in epilepsy pp. 1-28

Jennifer Creaser, Congping Lin, Thomas Ridler, Jonathan T Brown, Wendyl D’Souza, Udaya Seneviratne, Mark Cook, John R Terry and Krasimira Tsaneva-Atanasova

Alcoholic liver disease: A registry view on comorbidities and disease prediction pp. 1-19

Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak and Lars Juhl Jensen

Characterizing chromatin folding coordinate and landscape with deep learning pp. 1-19

Wen Jun Xie, Yifeng Qi and Bin Zhang

Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule pp. 1-14

Kwang Su Kim, Tatsunari Kondoh, Yusuke Asai, Ayato Takada and Shingo Iwami

Minimizing the number of optimizations for efficient community dynamic flux balance analysis pp. 1-20

James D Brunner and Nicholas Chia

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination pp. 1-20

Ryan E Pavlovicz, Hahnbeom Park and Frank DiMaio

NuSeT: A deep learning tool for reliably separating and analyzing crowded cells pp. 1-20

Linfeng Yang, Rajarshi P Ghosh, J Matthew Franklin, Simon Chen, Chenyu You, Raja R Narayan, Marc L Melcher and Jan T Liphardt

DeepHE: Accurately predicting human essential genes based on deep learning pp. 1-17

Xue Zhang, Wangxin Xiao and Weijia Xiao

Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion pp. 1-16

Nikolaus Korfhage, Markus Mühling, Stephan Ringshandl, Anke Becker, Bernd Schmeck and Bernd Freisleben

Ten simple rules to make your research more sustainable pp. 1-11

Anne-Laure Ligozat, Aurélie Névéol, Bénédicte Daly and Emmanuelle Frenoux

The relative contributions of infectious and mitotic spread to HTLV-1 persistence pp. 1-25

Daniel J Laydon, Vikram Sunkara, Lies Boelen, Charles R M Bangham and Becca Asquith

Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images pp. 1-25

William Pilcher, Xingyu Yang, Anastasia Zhurikhina, Olga Chernaya, Yinghan Xu, Peng Qiu and Denis Tsygankov

Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium pp. 1-25

Aditi Roy, Marta Varela, Henry Chubb, Robert MacLeod, Jules C Hancox, Tobias Schaeffter and Oleg Aslanidi

Efficient sensory coding of multidimensional stimuli pp. 1-25

Thomas E Yerxa, Eric Kee, Michael R DeWeese and Emily A Cooper

Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity pp. 1-25

Nicolas Deperrois and Michael Graupner

Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data pp. 1-22

Emma Southall, Michael J Tildesley and Louise Dyson

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures pp. 1-22

Bo Chen and Wei Xu

Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder pp. 1-22

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 and Christoph Mathys

Fast estimation of time-varying infectious disease transmission rates pp. 1-39

Mikael Jagan, Michelle S deJonge, Olga Krylova and David J D Earn

Ten simple rules for open human health research pp. 1-18

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 Pasquetto, Gabriela Sanchez, Matthieu Schapira, Tohar Scheininger, Félix Schoeller, Anibal Sólon Heinsfeld and François Taddei

All-atom simulation of the HET-s prion replication pp. 1-18

Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R Requena, Emiliano Biasini and Pietro Faccioli

Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms pp. 1-24

Rajib Mukherjee, Burcu Beykal, Adam T Szafran, Melis Onel, Fabio Stossi, Maureen G Mancini, Dillon Lloyd, Fred A Wright, Lan Zhou, Michael A Mancini and Efstratios N Pistikopoulos

Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data pp. 1-24

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 and Sohrab P Shah

Uncertainty-driven regulation of learning and exploration in adolescents: A computational account pp. 1-29

Marieke Jepma, Jessica V Schaaf, Ingmar Visser and Hilde M Huizenga

Ten simple rules on how to write a standard operating procedure pp. 1-10

Susanne Hollmann, Marcus Frohme, Christoph Endrullat, Andreas Kremer, Domenica D’Elia, Babette Regierer, Alina Nechyporenko and on behalf of Cost Action Ca15110

Discovering functional sequences with RELICS, an analysis method for CRISPR screens pp. 1-23

Patrick C Fiaux, Hsiuyi V Chen, Poshen B Chen, Aaron R Chen and Graham McVicker

A compiler for biological networks on silicon chips pp. 1-27

J Kyle Medley, Jonathan Teo, Sung Sik Woo, Joseph Hellerstein, Rahul Sarpeshkar and Herbert M Sauro

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention pp. 1-27

Yunjun Zhang, Thomas Leitner, Jan Albert and Tom Britton

Response nonlinearities in networks of spiking neurons pp. 1-27

Alessandro Sanzeni, Mark H Histed and Nicolas Brunel

Inferring a complete genotype-phenotype map from a small number of measured phenotypes pp. 1-27

Zachary R Sailer, Sarah H Shafik, Robert L Summers, Alex Joule, Alice Patterson-Robert, Rowena E Martin and Michael J Harms

Ten simple rules for writing scientific op-ed articles pp. 1-4

Hoe-Han Goh and Philip Bourne

Microtubule instability driven by longitudinal and lateral strain propagation pp. 1-21

Maxim Igaev and Helmut Grubmüller

A simple, scalable approach to building a cross-platform transcriptome atlas pp. 1-21

Paul W Angel, Nadia Rajab, Yidi Deng, Chris M Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi and Christine A Wells

Increased comparability between RNA-Seq and microarray data by utilization of gene sets pp. 1-21

Frans M van der Kloet, Jeroen Buurmans, Martijs J Jonker, Age K Smilde and Johan A Westerhuis

Volume 16, issue 8, 2020

Modeling time-varying brain networks with a self-tuning optimized Kalman filter pp. 1-29

D Pascucci, M Rubega and G Plomp

Reliable estimation of membrane curvature for cryo-electron tomography pp. 1-29

Maria Salfer, Javier F Collado, Wolfgang Baumeister, Rubén Fernández-Busnadiego and Antonio Martínez-Sánchez

Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging pp. 1-29

Ru-Yuan Zhang, Xue-Xin Wei and Kendrick Kay

Multiplexing information flow through dynamic signalling systems pp. 1-18

Giorgos Minas, Dan J Woodcock, Louise Ashall, Claire V Harper, Michael R H White and David A Rand

JBrowse Connect: A server API to connect JBrowse instances and users pp. 1-21

Eric Yao, Robert Buels, Lincoln Stein, Taner Z Sen and Ian Holmes

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits pp. 1-21

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 and Cecilia M Lindgren

Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination pp. 1-21

Prashanth Selvaraj, Edward A Wenger, Daniel Bridenbecker, Nikolai Windbichler, Jonathan R Russell, Jaline Gerardin, Caitlin A Bever and Milen Nikolov

Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes pp. 1-26

Leonila Lagunes, Lee Bardwell and German A Enciso

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis pp. 1-27

Amrit Dhar, Duncan K Ralph, Vladimir N Minin and Frederick A Matsen Iv

Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones pp. 1-27

Fabrizio Clarelli, Adam Palmer, Bhupender Singh, Merete Storflor, Silje Lauksund, Ted Cohen, Sören Abel and Pia Abel zur Wiesch

Simulating flow induced migration in vascular remodelling pp. 1-23

Ashkan Tabibian, Siavash Ghaffari, Diego A Vargas, Hans Van Oosterwyck and Elizabeth A V Jones

Order matters: How covert value updating during sequential option sampling shapes economic preference pp. 1-23

Chen Hu, Philippe Domenech and Mathias Pessiglione

Engineering recurrent neural networks from task-relevant manifolds and dynamics pp. 1-23

Eli Pollock and Mehrdad Jazayeri

Inferring the ancestry of parents and grandparents from genetic data pp. 1-22

Jingwen Pei, Yiming Zhang, Rasmus Nielsen and Yufeng Wu

Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis pp. 1-36

John Fors, Natasha Strydom, William S Fox, Ron J Keizer and Radojka M Savic

Task-evoked activity quenches neural correlations and variability across cortical areas pp. 1-39

Takuya Ito, Scott L Brincat, Markus Siegel, Ravi D Mill, Biyu J He, Earl K Miller, Horacio G Rotstein and Michael W Cole

Buildup and bistability in auditory streaming as an evidence accumulation process with saturation pp. 1-34

Quynh-Anh Nguyen, John Rinzel and Rodica Curtu

Achieving stable dynamics in neural circuits pp. 1-15

Leo Kozachkov, Mikael Lundqvist, Jean-Jacques Slotine and Earl K Miller

Ten simple rules to increase computational skills among biologists with Code Clubs pp. 1-7

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, Begum D Topcuoglu and Patrick D Schloss

Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise pp. 1-28

Sina Miran, Alessandro Presacco, Jonathan Z Simon, Michael C Fu, Steven I Marcus and Behtash Babadi

Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times pp. 1-20

Andy Hoyle, David Cairns, Iona Paterson, Stuart McMillan, Gabriela Ochoa and Andrew P Desbois

Template-based mapping of dynamic motifs in tissue morphogenesis pp. 1-20

Tomer Stern, Stanislav Y Shvartsman and Eric F Wieschaus

A novel single-cell based method for breast cancer prognosis pp. 1-20

Xiaomei Li, Lin Liu, Gregory J Goodall, Andreas Schreiber, Taosheng Xu, Jiuyong Li and Thuc D Le

Information transmission from NFkB signaling dynamics to gene expression pp. 1-16

Alok Maity and Roy Wollman

Deconvolving the contributions of cell-type heterogeneity on cortical gene expression pp. 1-17

Ellis Patrick, Mariko Taga, Ayla Ergun, Bernard Ng, William Casazza, Maria Cimpean, Christina Yung, Julie A Schneider, David A Bennett, Chris Gaiteri, Philip L De Jager, Elizabeth M Bradshaw and Sara Mostafavi

Volume 16, issue 7, 2020

A framework to assess the quality and impact of bioinformatics training across ELIXIR pp. 1-12

Kim T Gurwitz, Prakash Singh Gaur, Louisa J Bellis, Lee 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 Leskošek, Jessica M Lindvall, Diana Marek, Paula A Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia W G van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L Morgan and Gabriella Rustici

Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data pp. 1-25

Richard J Beck, Dario I Bijker and Joost B Beltman

Socioeconomic bias in influenza surveillance pp. 1-19

Samuel V Scarpino, James G Scott, Rosalind M Eggo, Bruce Clements, Nedialko B Dimitrov and Lauren Ancel Meyers

Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans pp. 1-14

Céline N Martineau, André E X Brown and Patrick Laurent

Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality pp. 1-16

Thuy T T Le and Frederick R Adler

Using information theory to optimise epidemic models for real-time prediction and estimation pp. 1-20

Kris V Parag and Christl A Donnelly

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding pp. 1-20

Huiyuan Chen, Feixiong Cheng and Jing Li

Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities pp. 1-20

Doina Bucur and Petter Holme

A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease pp. 1-20

Jinhee Park, Hyerin Kim, Jaekwang Kim and Mookyung Cheon

An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias pp. 1-24

Jennifer L Wilson, Dan Lu, Nick Corr, Aaron Fullerton and James Lu

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data pp. 1-24

Xian F Mallory, Mohammadamin Edrisi, Nicholas Navin and Luay Nakhleh

Heart failure-induced atrial remodelling promotes electrical and conduction alternans pp. 1-24

Na Zhao, Qince Li, Kevin Zhang, Kuanquan Wang, Runnan He, Yongfeng Yuan and Henggui Zhang

Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator pp. 1-29

Mariam Ordyan, Tom Bartol, Mary Kennedy, Padmini Rangamani and Terrence Sejnowski

Bayesian modelling of high-throughput sequencing assays with malacoda pp. 1-18

Andrew R Ghazi, Xianguo Kong, Ed S Chen, Leonard C Edelstein and Chad A Shaw

OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling pp. 1-18

Konstantin Butenko, Christian Bahls, Max Schröder, Rüdiger Köhling and Ursula van Rienen

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line pp. 1-26

Elin Nyman, Richard R Stein, Xiaohong Jing, Weiqing Wang, Benjamin Marks, Ioannis K Zervantonakis, Anil Korkut, Nicholas P Gauthier and Chris Sander

A simple model for learning in volatile environments pp. 1-26

Payam Piray and Nathaniel D Daw

Mathematical modeling of plant cell fate transitions controlled by hormonal signals pp. 1-21

Filip Z Klawe, Thomas Stiehl, Peter Bastian, Christophe Gaillochet, Jan U Lohmann and Anna Marciniak-Czochra

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms pp. 1-21

August George, Paola Bisignano, John M Rosenberg, Michael Grabe and Daniel M Zuckerman

Immunization strategies in networks with missing data pp. 1-21

Samuel F Rosenblatt, Jeffrey Smith, G Robin Gauthier and Laurent Hébert-Dufresne

Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells pp. 1-21

Edward C Schrom, Simon A Levin and Andrea L Graham

Cortical ignition dynamics is tightly linked to the core organisation of the human connectome pp. 1-23

Samy Castro, Wael El-Deredy, Demian Battaglia and Patricio Orio

A novel riboswitch classification based on imbalanced sequences achieved by machine learning pp. 1-23

Solomon Shiferaw Beyene, Tianyi Ling, Blagoj Ristevski and Ming Chen

Cross-species regulatory sequence activity prediction pp. 1-27

David R Kelley

Nine quick tips for efficient bioinformatics curriculum development and training pp. 1-10

Susan McClatchy, Kristin M Bass, Daniel M Gatti, Adam Moylan and Gary Churchill

Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices pp. 1-10

Joe Hilton and Matt J Keeling

Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery pp. 1-22

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 and Edwin Michael

Estimation of neuron parameters from imperfect observations pp. 1-22

Joseph D Taylor, Samuel Winnall and Alain Nogaret

Ten simple rules for reading a scientific paper pp. 1-6

Maureen A Carey, Kevin L Steiner and William A Petri

Brain-optimized extraction of complex sound features that drive continuous auditory perception pp. 1-34

Julia Berezutskaya, Zachary V Freudenburg, Umut Güçlü, Marcel A J van Gerven and Nick F Ramsey

Volume 16, issue 6, 2020

Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block pp. 1-21

Guosheng Yi and Warren M Grill

bigPint: A Bioconductor visualization package that makes big data pint-sized pp. 1-21

Lindsay Rutter and Dianne Cook

Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves pp. 1-21

Federico Sevlever, Juan Pablo Di Bella and Alejandra C Ventura

Stochastic dynamics of Francisella tularensis infection and replication pp. 1-26

Jonathan Carruthers, Grant Lythe, Martín López-García, Joseph Gillard, Thomas R Laws, Roman Lukaszewski and Carmen Molina-París

Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves pp. 1-26

Miguel Capllonch-Juan and Francisco Sepulveda

Natural scene statistics predict how humans pool information across space in surface tilt estimation pp. 1-26

Seha Kim and Johannes Burge

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 pp. 1-27

Anna U Lowegard, Marcel S Frenkel, Graham T Holt, Jonathan D Jou, Adegoke A Ojewole and Bruce R Donald

A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data pp. 1-27

David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T Grant Belgard, Alice Zhang and Victor Hanson-Smith

Classifying sex and strain from mouse ultrasonic vocalizations using deep learning pp. 1-27

A Ivanenko, P Watkins, M A J van Gerven, K Hammerschmidt and B Englitz

Brain dynamics for confidence-weighted learning pp. 1-27

Florent Meyniel

It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology pp. 1-29

Niklas Korsbo and Henrik Jönsson

Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites pp. 1-29

Ethan D Evans, Chengzhen Dai, Siavash Isazadeh, Shinkyu Park, Carlo Ratti and Eric J Alm

Emergence of cooperative bistability and robustness of gene regulatory networks pp. 1-24

Shintaro Nagata and Macoto Kikuchi

A validation framework for neuroimaging software: The case of population receptive fields pp. 1-18

Garikoitz Lerma-Usabiaga, Noah Benson, Jonathan Winawer and Brian A Wandell

Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model pp. 1-34

Sandra Mayr, Fabian Hauser, Sujitha Puthukodan, Markus Axmann, Janett Göhring and Jaroslaw Jacak

10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats pp. 1-6

Joseph C Ayoob and Joshua D Kangas

Assessing predictors for new post translational modification sites: A case study on hydroxylation pp. 1-15

Damiano Piovesan, Andras Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon and Silvio C E Tosatto

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization pp. 1-15

Will Xiao and Gabriel Kreiman

Resilience of three-dimensional sinusoidal networks in liver tissue pp. 1-22

Jens Karschau, André Scholich, Jonathan Wise, Hernán Morales-Navarrete, Yannis Kalaidzidis, Marino Zerial and Benjamin M Friedrich

Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data pp. 1-22

Nima Nouri and Steven H Kleinstein

A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks pp. 1-31

Víctor A López-Agudelo, Tom A Mendum, Emma Laing, HuiHai Wu, Andres Baena, Luis F Barrera, Dany J V Beste and Rigoberto Rios-Estepa

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies pp. 1-8

Aleksey V Zimin and Steven L Salzberg

Realistic modeling of mesoscopic ephaptic coupling in the human brain pp. 1-25

Giulio Ruffini, Ricardo Salvador, Ehsan Tadayon, Roser Sanchez-Todo, Alvaro Pascual-Leone and Emiliano Santarnecchi

Combined model-free and model-sensitive reinforcement learning in non-human primates pp. 1-25

Bruno Miranda, W M Nishantha Malalasekera, Timothy E Behrens, Peter Dayan and Steven W Kennerley

Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus pp. 1-25

Atte S A Eskelinen, Petri Tanska, Cristina Florea, Gustavo A Orozco, Petro Julkunen, Alan J Grodzinsky and Rami K Korhonen

Multiplexing rhythmic information by spike timing dependent plasticity pp. 1-25

Nimrod Sherf and Shamir Maoz

Measurable health effects associated with the daylight saving time shift pp. 1-13

Hanxin Zhang, Torsten Dahlén, Atif Khan, Gustaf Edgren and Andrey Rzhetsky

Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis pp. 1-17

Dirke Imig, Nadine Pollak, Frank Allgöwer and Markus Rehm

Disease evolution in reaction networks: Implications for a diagnostic problem pp. 1-17

Abolfazl Ramezanpour and Alireza Mashaghi

Forecasting unprecedented ecological fluctuations pp. 1-17

Samuel R Bray and Bo Wang

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers pp. 1-19

Yu Hu, Kai Wang and Mingyao Li

Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment pp. 1-19

Alexey Savelyev, Gary E Gorbet, Amy Henrickson and Borries Demeler

Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm pp. 1-28

Satoshi Ii, Hiroki Kitade, Shunichi Ishida, Yohsuke Imai, Yoshiyuki Watanabe and Shigeo Wada

HemoMIPs—Automated analysis and result reporting pipeline for targeted sequencing data pp. 1-7

Philip Kleinert, Beth Martin and Martin Kircher

Volume 16, issue 5, 2020

Calibration of individual-based models to epidemiological data: A systematic review pp. 1-17

C Marijn Hazelbag, Jonathan Dushoff, Emanuel M Dominic, Zinhle E Mthombothi and Wim Delva

Microbial communities display alternative stable states in a fluctuating environment pp. 1-17

Clare I Abreu, Vilhelm L Andersen Woltz, Jonathan Friedman and Jeff Gore

Early warning signals in motion inference pp. 1-16

Yuval Hart, Maryam Vaziri-Pashkam and L Mahadevan

Conservation laws by virtue of scale symmetries in neural systems pp. 1-16

Erik D Fagerholm, W M C Foulkes, Yasir Gallero-Salas, Fritjof Helmchen, Karl J Friston, Rosalyn J Moran and Robert Leech

Modeling the temporal network dynamics of neuronal cultures pp. 1-20

Jose Cadena, Ana Paula Sales, Doris Lam, Heather A Enright, Elizabeth K Wheeler and Nicholas O Fischer

GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm pp. 1-19

Lei Wang, Zhu-Hong You, Yang-Ming Li, Kai Zheng and Yu-An Huang

Towards a data-driven characterization of behavioral changes induced by the seasonal flu pp. 1-19

Nicolò Gozzi, Daniela Perrotta, Daniela Paolotti and Nicola Perra

Complex interactions can create persistent fluctuations in high-diversity ecosystems pp. 1-14

Felix Roy, Matthieu Barbier, Giulio Biroli and Guy Bunin

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth pp. 1-25

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 and Sanne Abeln

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease pp. 1-25

Christine A Tataru and Maude M David

Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles pp. 1-12

Alastair M Kilpatrick, Audra Anjum and Lonnie Welch

Improving reproducibility in computational biology research pp. 1-3

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

A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion pp. 1-15

Paul Lemarre, Laurent Pujo-Menjouet and Suzanne S Sindi

Inference on dengue epidemics with Bayesian regime switching models pp. 1-15

Jue Tao Lim, Borame Sue Dickens, Sun Haoyang, Ng Lee Ching and Alex R Cook

Robustness and parameter geography in post-translational modification systems pp. 1-50

Kee-Myoung Nam, Benjamin M Gyori, Silviana V Amethyst, Daniel J Bates and Jeremy Gunawardena

Modeling the effects of motivation on choice and learning in the basal ganglia pp. 1-33

Maaike M H van Swieten and Rafal Bogacz

Self-organization in brain tumors: How cell morphology and cell density influence glioma pattern formation pp. 1-22

Sara Jamous, Andrea Comba, Pedro R Lowenstein and Sebastien Motsch

iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation pp. 1-22

Kai Zheng, Zhu-Hong You, Jian-Qiang Li, Lei Wang, Zhen-Hao Guo and Yu-An Huang

Compositional Lotka-Volterra describes microbial dynamics in the simplex pp. 1-22

Tyler A Joseph, Liat Shenhav, Joao B Xavier, Eran Halperin and Itsik Pe’er

Chloride dynamics alter the input-output properties of neurons pp. 1-22

Christopher B Currin, Andrew J Trevelyan, Colin J Akerman and Joseph V Raimondo

Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis pp. 1-23

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 and Jung-Ying Tzeng

Ranbow: A fast and accurate method for polyploid haplotype reconstruction pp. 1-23

M-Hossein Moeinzadeh, Jun Yang, Evgeny Muzychenko, Giuseppe Gallone, David Heller, Knut Reinert, Stefan Haas and Martin Vingron

Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation pp. 1-23

Abhishek Varghese, Christopher Drovandi, Antonietta Mira and Kerrie Mengersen

Bayesian regression explains how human participants handle parameter uncertainty pp. 1-23

Jannes Jegminat, Maya A Jastrzębowska, Matthew V Pachai, Michael H Herzog and Jean-Pascal Pfister

Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models pp. 1-27

Sevan K Harootonian, Robert C Wilson, Lukáš Hejtmánek, Eli M Ziskin and Arne D Ekstrom

The Affective Ising Model: A computational account of human affect dynamics pp. 1-27

Tim Loossens, Merijn Mestdagh, Egon Dejonckheere, Peter Kuppens, Francis Tuerlinckx and Stijn Verdonck

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type pp. 1-21

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

In silico analysis of hypoxia activated prodrugs in combination with anti angiogenic therapy through nanocell delivery pp. 1-21

Cameron Meaney, Sander Rhebergen and Mohammad Kohandel

Autonomous emergence of connectivity assemblies via spike triplet interactions pp. 1-44

Lisandro Montangie, Christoph Miehl and Julijana Gjorgjieva

Ad hoc efforts for advancing data science education pp. 1-18

Orianna DeMasi, Alexandra Paxton and Kevin Koy

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system pp. 1-18

Sinu Paul, Nathan P Croft, Anthony W Purcell, David C Tscharke, Alessandro Sette, Morten Nielsen and Bjoern Peters

Scale free topology as an effective feedback system pp. 1-24

Alexander Rivkind, Hallel Schreier, Naama Brenner and Omri Barak

Shape-preserving elastic solid models of macromolecules pp. 1-24

Guang Song

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry pp. 1-29

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

Ten simple rules for running a successful women-in-STEM organization on an academic campus pp. 1-9

Deborah D Rupert, Alexandra C Nowlan, Oliver H Tam and Molly Gale Hammell

Ten Simple Rules for a successful remote postdoc pp. 1-9

Kevin R Burgio, Caitlin McDonough MacKenzie, Stephanie B Borrelle, S K Morgan Ernest, Jacquelyn L Gill, Kurt E Ingeman, Amy Teffer and Ethan P White

Ten simple rules for making training materials FAIR pp. 1-9

Leyla Garcia, Bérénice Batut, Melissa L Burke, Mateusz Kuzak, Fotis 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 and Patricia M Palagi

Volume 16, issue 4, 2020

Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning pp. 1-33

Nicholas T Franklin and Michael J Frank

High-dimensional mediation analysis in survival models pp. 1-15

Chengwen Luo, Botao Fa, Yuting Yan, Yang Wang, Yiwang Zhou, Yue Zhang and Zhangsheng Yu

Telling ecological networks apart by their structure: An environment-dependent approach pp. 1-15

Chuliang Song and Serguei Saavedra

Discovery of hierarchical representations for efficient planning pp. 1-42

Momchil S Tomov, Samyukta Yagati, Agni Kumar, Wanqian Yang and Samuel J Gershman

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning pp. 1-18

Jean-Baptiste Lugagne, Haonan Lin and Mary J Dunlop

A powerful and versatile colocalization test pp. 1-18

Yangqing Deng and Wei Pan

Deep reinforcement learning for the control of microbial co-cultures in bioreactors pp. 1-18

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

ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks pp. 1-18

Pierre Millard, Uwe Schmitt, Patrick Kiefer, Julia A Vorholt, Stéphanie Heux and Jean-Charles Portais

Information integration and collective motility in phototactic cyanobacteria pp. 1-18

Shakti N Menon, P Varuni and Gautam I Menon

Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation pp. 1-23

Luis Busto-Moner, Julien Morival, Honglei Ren, Arjang Fahim, Zachary Reitz, Timothy L Downing and Elizabeth L Read

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE pp. 1-23

Lisa-Katrin Schätzle, Ali Hadizadeh Esfahani and Andreas Schuppert

Striatal network modeling in Huntington’s Disease pp. 1-44

Adam Ponzi, Scott J Barton, Kendra D Bunner, Claudia Rangel-Barajas, Emily S Zhang, Benjamin R Miller, George V Rebec and James Kozloski

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries pp. 1-35

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

Humans adapt their anticipatory eye movements to the volatility of visual motion properties pp. 1-28

Chloé Pasture, Anna Montagnini and Laurent Udo Perrinet

Multiple-target tracking in human and machine vision pp. 1-28

Shiva Kamkar, Fatemeh Ghezloo, Hamid Abrishami Moghaddam, Ali Borji and Reza Lashgari

Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response pp. 1-28

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 and T Alex Perkins

On the choice of metric in gradient-based theories of brain function pp. 1-13

Simone Carlo Surace, Jean-Pascal Pfister, Wulfram Gerstner and Johanni Brea

Ten Simple Rules for landing on the right job after your PhD or postdoc pp. 1-5

Kuan-lin Huang

Ten Simple Rules for writing algorithmic bioinformatics conference papers pp. 1-5

Paul Medvedev

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 pp. 1-25

Jan Peters and Mark D’Esposito

DOT: Gene-set analysis by combining decorrelated association statistics pp. 1-25

Olga A Vsevolozhskaya, Min Shi, Fengjiao Hu and Dmitri V Zaykin

Ensemble modeling of auditory streaming reveals potential sources of bistability across the perceptual hierarchy pp. 1-31

David F Little, Joel S Snyder and Mounya Elhilali

An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms pp. 1-36

Marte J Sætra, Gaute T Einevoll and Geir Halnes

Comparison of methods for rhythm analysis of complex animals’ acoustic signals pp. 1-22

Lara S Burchardt and Mirjam Knörnschild

Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis pp. 1-22

Paul Curtin, Christine Austin, Austen Curtin, Chris Gennings, Claudia Figueroa-Romero, Kristen A Mikhail, Tatiana M Botero, Stephen A Goutman, Eva L Feldman and Manish Arora

LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer pp. 1-22

Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao and Thuc Duy Le

The research and development process for multiscale models of infectious disease systems pp. 1-39

Winston Garira

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research pp. 1-34

Augusto Anguita-Ruiz, Alberto Segura-Delgado, Rafael Alcalá, Concepción M Aguilera and Jesús Alcalá-Fdez

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution pp. 1-29

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

A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels pp. 1-24

Xiaoning Zheng, Alireza Yazdani, He Li, Jay D Humphrey and George E Karniadakis

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis pp. 1-24

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

Multiview learning for understanding functional multiomics pp. 1-26

Nam D Nguyen and Daifeng Wang

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage pp. 1-21

Hadel Al Asafen, Prasad U Bandodkar, Sophia Carrell-Noel, Allison E Schloop, Jeramey Friedman and Gregory T Reeves

Improving the coverage of credible sets in Bayesian genetic fine-mapping pp. 1-21

Anna Hutchinson, Hope Watson and Chris Wallace

Inferring the immune response from repertoire sequencing pp. 1-21

Maximilian Puelma Touzel, Aleksandra M Walczak and Thierry Mora

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology pp. 1-32

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 Kiware, Robert C Reiner and David L Smith

Ten simple rules for more objective decision-making pp. 1-7

Anthony C Fletcher, Georges A Wagner and Philip E Bourne

DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data pp. 1-19

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 and Chunyu Liu

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions pp. 1-11

Gregory L Medlock, Thomas J Moutinho and Jason A Papin

Climbing Escher’s stairs: A way to approximate stability landscapes in multidimensional systems pp. 1-16

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

Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking pp. 1-20

Sarah F McGough, Michael A Johansson, Marc Lipsitch and Nicolas A Menzies

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data pp. 1-20

Avtar Roopra

Predicting cell lineages using autoencoders and optimal transport pp. 1-20

Karren Dai Yang, Karthik Damodaran, Saradha Venkatachalapathy, Ali C Soylemezoglu, G V Shivashankar and Caroline Uhler

Learning action-oriented models through active inference pp. 1-30

Alexander Tschantz, Anil K Seth and Christopher L Buckley

Ten simple rules for innovative dissemination of research pp. 1-12

Tony Ross-Hellauer, Jonathan P Tennant, Viltė Banelytė, Edit Gorogh, Daniela Luzi, Peter Kraker, Lucio Pisacane, Roberta Ruggieri, Electra Sifacaki and Michela Vignoli

Volume 16, issue 3, 2020

A simplified modelling framework facilitates more complex representations of plant circadian clocks pp. 1-34

Mathias Foo, Declan G Bates and Ozgur E Akman

Parallel Tempering with Lasso for model reduction in systems biology pp. 1-22

Sanjana Gupta, Robin E C Lee and James R Faeder

A plausible accelerating function of intermediate states in cancer metastasis pp. 1-22

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

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines pp. 1-21

Elba Raimúndez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J Theis, Dieter Maier, Birgit Luber and Jan Hasenauer

The spread of a wild plant pathogen is driven by the road network pp. 1-21

Elina Numminen and Anna-Liisa Laine

Mechanisms underlying attraction to odors in walking Drosophila pp. 1-26

Liangyu Tao, Siddhi Ozarkar and Vikas Bhandawat

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph pp. 1-27

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 and David Vallenet

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures pp. 1-23

Kunal Kathuria and Aakrosh Ratan

Ten simple rules for providing effective bioinformatics research support pp. 1-10

Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi and Lyndon Zass

Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating pp. 1-24

Keri A McKiernan, Anna K Koster, Merritt Maduke and Vijay S Pande

The influence of red blood cell deformability on hematocrit profiles and platelet margination pp. 1-18

Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra and Omolola Eniola-Adefeso

The use of mixture density networks in the emulation of complex epidemiological individual-based models pp. 1-16

Christopher N Davis, T Deirdre Hollingsworth, Quentin Caudron and Michael A Irvine

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex pp. 1-17

Dmitrii S Shcherbinin, Vlad A Belousov and Mikhail Shugay

ProteinVR: Web-based molecular visualization in virtual reality pp. 1-17

Kevin C Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang and Jacob D Durrant

CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data pp. 1-20

Thilde Terkelsen, Anders Krogh and Elena Papaleo

Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach pp. 1-20

Isobel Routledge, Shengjie Lai, Katherine E Battle, Azra C Ghani, Manuel Gomez-Rodriguez, Kyle B Gustafson, Swapnil Mishra, Juliette Unwin, Joshua L Proctor, Andrew J Tatem, Zhongjie Li and Samir Bhatt

Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks pp. 1-14

Carly Adams, David Young, Paul A Gastañaduy, Prabasaj Paul, Zach Marsh, Aron J Hall and Benjamin A Lopman

A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015 pp. 1-14

Ellen Brooks-Pollock, Leon Danon, Hester Korthals Altes, Jennifer A Davidson, Andrew M T Pollock, Dick van Soolingen, Colin Campbell and Maeve K Lalor

Detecting critical slowing down in high-dimensional epidemiological systems pp. 1-19

Tobias Brett, Marco Ajelli, Quan-Hui Liu, Mary G Krauland, John J Grefenstette, Willem G van Panhuis, Alessandro Vespignani, John M Drake and Pejman Rohani

Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization pp. 1-28

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

Deconvolution of calcium imaging data using marked point processes pp. 1-25

Ryohei Shibue and Fumiyasu Komaki

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity pp. 1-25

Mariama Jaiteh, Ismael Rodríguez-Espigares, Jana Selent and Jens Carlsson

Modeling binary and graded cone cell fate patterning in the mouse retina pp. 1-25

Kiara C Eldred, Cameron Avelis, Robert J Johnston and Elijah Roberts

Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish pp. 1-45

Liu Lei, Ramón Escobedo, Clément Sire and Guy Theraulaz

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data pp. 1-12

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

Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments pp. 1-30

Hanna Märkle and Aurélien Tellier

Volume 16, issue 2, 2020

Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms pp. 1-26

Isaac Fradkin, Casimir Ludwig, Eran Eldar and Jonathan D Huppert

Bayesian inference and comparison of stochastic transcription elongation models pp. 1-21

Jordan Douglas, Richard Kingston and Alexei J Drummond

Surprise response as a probe for compressed memory states pp. 1-21

Hadar Levi-Aharoni, Oren Shriki and Naftali Tishby

Changes-of-mind in the absence of new post-decision evidence pp. 1-21

Nadim A A Atiya, Arkady Zgonnikov, Denis O’Hora, Martin Schoemann, Stefan Scherbaum and KongFatt Wong-Lin

Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials pp. 1-27

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 and Joshua T Schiffer

From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response pp. 1-27

Jill A Gallaher, Susan C Massey, Andrea Hawkins-Daarud, Sonal S Noticewala, Russell C Rockne, Sandra K Johnston, Luis Gonzalez-Cuyar, Joseph Juliano, Orlando Gil, Kristin R Swanson, Peter Canoll and Alexander R A Anderson

Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit pp. 1-27

Florian Ott, Dimitrije Marković, Alexander Strobel and Stefan J Kiebel

A generative growth model for thalamocortical axonal branching in primary visual cortex pp. 1-23

Pegah Kassraian-Fard, Michael Pfeiffer and Roman Bauer

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model pp. 1-23

Brian M Lang, Jack Kuipers, Benjamin Misselwitz and Niko Beerenwinkel

Early prediction of antigenic transitions for influenza A/H3N2 pp. 1-23

Lauren A Castro, Trevor Bedford and Lauren Ancel Meyers

Multi-state design of flexible proteins predicts sequences optimal for conformational change pp. 1-29

Marion F Sauer, Alexander M Sevy, James E Crowe and Jens Meiler

Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein pp. 1-29

Lenka Stejskal, William D Lees, David S Moss, Machaela Palor, Richard J Bingham, Adrian J Shepherd and Joe Grove

Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors pp. 1-24

Cristina Vaghi, Anne Rodallec, Raphaëlle Fanciullino, Joseph Ciccolini, Jonathan P Mochel, Michalis Mastri, Clair Poignard, John M L Ebos and Sébastien Benzekry

The relation between crosstalk and gene regulation form revisited pp. 1-24

Rok Grah and Tamar Friedlander

Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein pp. 1-24

Joël R Pradines, Victor Farutin, Nicholas A Cilfone, Abouzar Ghavami, Elma Kurtagic, Jamey Guess, Anthony M Manning and Ishan Capila

The SONATA data format for efficient description of large-scale network models pp. 1-24

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 G King, Werner A H Van Geit, Arseny V Povolotsky, Eilif Muller, Jean-Denis Courcol and Anton Arkhipov

Ten simple rules for getting started on Twitter as a scientist pp. 1-9

Veronika Cheplygina, Felienne Hermans, Casper Albers, Natalia Bielczyk and Ionica Smeets

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies pp. 1-18

Shuang Song, Wei Jiang, Lin Hou and Hongyu Zhao

Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells pp. 1-18

Toshinori Namba and Shuji Ishihara

Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic pp. 1-16

Susanne Reimering, Sebastian Muñoz and Alice C McHardy

Ten Simple Rules to becoming a principal investigator pp. 1-13

John S Tregoning and Jason E McDermott

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method pp. 1-17

Kosuke Hamazaki and Hiroyoshi Iwata

Navigable maps of structural brain networks across species pp. 1-20

Antoine Allard and M Ángeles Serrano

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice pp. 1-20

Aleksandr Kovaltsuk, Matthew I J Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück and Charlotte M Deane

Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions pp. 1-19

Daniel E Hurtado, Javiera Jilberto and Grigory Panasenko

Orbit Image Analysis: An open-source whole slide image analysis tool pp. 1-19

Manuel Stritt, Anna K Stalder and Enrico Vezzali

Inferring TF activation order in time series scRNA-Seq studies pp. 1-19

Chieh Lin, Jun Ding and Ziv Bar-Joseph

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network pp. 1-19

Andrei Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M Frahm and Dima L Shepelyansky

Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction pp. 1-28

Bastien Berret and Frédéric Jean

SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases pp. 1-12

Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein and Tim Jeske

Volume 16, issue 1, 2020

Emergence of social inequality in the spatial harvesting of renewable public goods pp. 1-25

Jaideep Joshi, Åke Brännström and Ulf Dieckmann

BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis pp. 1-12

Manoj Kumar, Cameron T Ellis, Qihong Lu, Hejia Zhang, Mihai Capotă, Theodore L Willke, Peter J Ramadge, Nicholas B Turk-Browne and Kenneth A Norman

The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations pp. 1-16

Christie A Bahlai and Elise F Zipkin

Collaboration leads to cooperation on sparse networks pp. 1-11

Simon Angus and Jonathan Newton

Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism pp. 1-17

Melanie Gerken, Sergej Kakorin, Kamel Chibani and Karl-Josef Dietz

Interpreting neural decoding models using grouped model reliance pp. 1-17

Simon Valentin, Maximilian Harkotte and Tzvetan Popov

Learning from animals: How to Navigate Complex Terrains pp. 1-17

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

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning pp. 1-17

Jiwoong Kim, David E Greenberg, Reed Pifer, Shuang Jiang, Guanghua Xiao, Samuel A Shelburne, Andrew Koh, Yang Xie and Xiaowei Zhan

Limits on amplifiers of natural selection under death-Birth updating pp. 1-13

Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee and Martin A Nowak

Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs pp. 1-20

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

Increasing growth rate slows adaptation when genotypes compete for diffusing resources pp. 1-14

Jeremy M Chacón, Allison K Shaw and William R Harcombe

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power pp. 1-19

Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam and Thomas Simonson

Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming pp. 1-21

Jake P Taylor-King, Asbjørn N Riseth, Will Macnair and Manfred Claassen

Computational optimization of associative learning experiments pp. 1-23

Filip Melinscak and Dominik R Bach

Emergence and suppression of cooperation by action visibility in transparent games pp. 1-32

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

A new method for inferring timetrees from temporally sampled molecular sequences pp. 1-24

Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L Kosakovsky Pond, Jessica Priest, Jiamin Deng and Sudhir Kumar

A system for tracking whisker kinematics and whisker shape in three dimensions pp. 1-24

Rasmus S Petersen, Andrea Colins Rodriguez, Mathew H Evans, Dario Campagner and Michaela S E Loft

A single reaction-diffusion equation for the multifarious eruptions of urticaria pp. 1-18

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

Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model pp. 1-31

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

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples pp. 1-22

Edward W Huang, Ameya Bhope, Jing Lim, Saurabh Sinha and Amin Emad