PLOS Computational Biology

2005 - 2025

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Volume 17, issue 12, 2021

Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant pp. 1-28

Joseph R Larsen, Margaret R Martin, John D Martin, James B Hicks and Peter Kuhn

Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat pp. 1-28

Jessica R Parker, Alexander N Klishko, Boris I Prilutsky and Gennady S Cymbalyuk

Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble pp. 1-20

Icíar Civantos-Gómez, Javier García-Algarra, David García-Callejas, Javier Galeano, Oscar Godoy and Ignasi Bartomeus

Motif-pattern dependence of biomolecular phase separation driven by specific interactions pp. 1-17

Benjamin G Weiner, Andrew G T Pyo, Yigal Meir and Ned S Wingreen

A data-informed mean-field approach to mapping of cortical parameter landscapes pp. 1-30

Zhuo-Cheng Xiao, Kevin K Lin and Lai-Sang Young

Preparing to move: Setting initial conditions to simplify interactions with complex objects pp. 1-38

Rashida Nayeem, Salah Bazzi, Mohsen Sadeghi, Neville Hogan and Dagmar Sternad

Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example pp. 1-14

Guoyang Zou, Yang Zou, Chenglong Ma, Jiaojiao Zhao and Lei Li

One-carbon metabolism during the menstrual cycle and pregnancy pp. 1-21

Ruby Kim, H Frederik Nijhout and Michael C Reed

Dissociable influences of reward and punishment on adaptive cognitive control pp. 1-21

Xiamin Leng, Debbie Yee, Harrison Ritz and Amitai Shenhav

Benchmarking of tools for axon length measurement in individually-labeled projection neurons pp. 1-22

Mario Rubio-Teves, Sergio Díez-Hermano, César Porrero, Abel Sánchez-Jiménez, Lucía Prensa, Francisco Clascá, María García-Amado and José Antonio Villacorta-Atienza

Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis) pp. 1-22

Shanel C Pickard, David J Bertsch, Zoe Le Garrec, Roy E Ritzmann, Roger D Quinn and Nicholas S Szczecinski

Dynamic maximum entropy provides accurate approximation of structured population dynamics pp. 1-22

Katarína Bod’ová, Enikő Szép and Nicholas H Barton

Combination treatment optimization using a pan-cancer pathway model pp. 1-22

Robin Schmucker, Gabriele Farina, James Faeder, Fabian Fröhlich, Ali Sinan Saglam and Tuomas Sandholm

A systems genomics approach uncovers molecular associates of RSV severity pp. 1-19

Matthew N McCall, Chin-Yi Chu, Lu Wang, Lauren Benoodt, Juilee Thakar, Anthony Corbett, Jeanne Holden-Wiltse, Christopher Slaunwhite, Alex Grier, Steven R Gill, Ann R Falsey, David J Topham, Mary T Caserta, Edward E Walsh, Xing Qiu and Thomas J Mariani

GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder pp. 1-19

Lei Li, Yu-Tian Wang, Cun-Mei Ji, Chun-Hou Zheng, Jian-Cheng Ni and Yan-Sen Su

Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study pp. 1-19

Deus Thindwa, Nicole Wolter, Amy Pinsent, Maimuna Carrim, John Ojal, Stefano Tempia, Jocelyn Moyes, Meredith McMorrow, Jackie Kleynhans, Anne von Gottberg, Neil French, Group Phirst, Cheryl Cohen and Stefan Flasche

Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? pp. 1-23

Juan Diaz-Colunga and Ramon Diaz-Uriarte

DeepCME: A deep learning framework for computing solution statistics of the chemical master equation pp. 1-23

Ankit Gupta, Christoph Schwab and Mustafa Khammash

Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity pp. 1-31

Elishai Ezra-Tsur, Oren Amsalem, Lea Ankri, Pritish Patil, Idan Segev and Michal Rivlin-Etzion

Decision prioritization and causal reasoning in decision hierarchies pp. 1-39

Ariel Zylberberg

Ten simple rules for developing bioinformatics capacity at an academic institution pp. 1-13

Shaun Aron, C Victor Jongeneel, Paballo Abel Chauke, Melek Chaouch, Judit Kumuthini, Lyndon Zass, Fouzia Radouani, Samar Kamal Kassim, Faisal M Fadlelmola and Nicola Mulder

Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization pp. 1-13

Fuminari Miura, Ka Yin Leung, Don Klinkenberg, Kylie E C Ainslie and Jacco Wallinga

SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction pp. 1-15

Akshaya V Annapragada, Joseph L Greenstein, Sanjukta N Bose, Bradford D Winters, Sridevi V Sarma and Raimond L Winslow

Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes pp. 1-24

Lanxin Zhang, Junyu Wang and Max von Kleist

When shared concept cells support associations: Theory of overlapping memory engrams pp. 1-44

Chiara Gastaldi, Tilo Schwalger, Emanuela De Falco, Rodrigo Quian Quiroga and Wulfram Gerstner

Volume 17, issue 11, 2021

Identifying prognostic pairwise relationships among bacterial species in microbiome studies pp. 1-12

Sean M Devlin, Axel Martin and Irina Ostrovnaya

A gap-filling algorithm for prediction of metabolic interactions in microbial communities pp. 1-26

Dafni Giannari, Cleo Hanchen Ho and Radhakrishnan Mahadevan

Optimizing network propagation for multi-omics data integration pp. 1-26

Konstantina Charmpi, Manopriya Chokkalingam, Ronja Johnen and Andreas Beyer

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance pp. 1-26

Mathurin Dorel, Bertram Klinger, Tommaso Mari, Joern Toedling, Eric Blanc, Clemens Messerschmidt, Michal Nadler-Holly, Matthias Ziehm, Anja Sieber, Falk Hertwig, Dieter Beule, Angelika Eggert, Johannes H Schulte, Matthias Selbach and Nils Blüthgen

Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones pp. 1-24

Erik B Nordquist, Charles A English, Eugenia M Clerico, Woody Sherman, Lila M Gierasch and Jianhan Chen

Cross-population coupling of neural activity based on Gaussian process current source densities pp. 1-24

Natalie Klein, Joshua H Siegle, Tobias Teichert and Robert E Kass

Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception pp. 1-37

Fangfang Hong, Stephanie Badde and Michael S Landy

Multivariable association discovery in population-scale meta-omics studies pp. 1-27

Himel Mallick, Ali Rahnavard, Lauren J McIver, Siyuan Ma, Yancong Zhang, Long H Nguyen, Timothy L Tickle, George Weingart, Boyu Ren, Emma H Schwager, Suvo Chatterjee, Kelsey N Thompson, Jeremy E Wilkinson, Ayshwarya Subramanian, Yiren Lu, Levi Waldron, Joseph N Paulson, Eric A Franzosa, Hector Corrada Bravo and Curtis Huttenhower

Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases pp. 1-34

Tunca Doğan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R Baxendale, Maria Martin and Rengul Cetin-Atalay

Approximate distance correlation for selecting highly interrelated genes across datasets pp. 1-18

Qunlun Shen and Shihua Zhang

The meaning of significant mean group differences for biomarker discovery pp. 1-16

Eva Loth, Jumana Ahmad, Chris Chatham, Beatriz López, Ben Carter, Daisy Crawley, Bethany Oakley, Hannah Hayward, Jennifer Cooke, Antonia San José Cáceres, Danilo Bzdok, Emily Jones, Tony Charman, Christian Beckmann, Thomas Bourgeron, Roberto Toro, Jan Buitelaar, Declan Murphy and Guillaume Dumas

The role of competition versus cooperation in microbial community coalescence pp. 1-16

Pablo Lechón-Alonso, Tom Clegg, Jacob Cook, Thomas P Smith and Samraat Pawar

Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling pp. 1-16

Danial Pourjafar-Dehkordi and Martin Zacharias

Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data pp. 1-14

Tania Mendonca, Ana A Jones, Jose M Pozo, Sarah Baxendale, Tanya T Whitfield and Alejandro F Frangi

Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans pp. 1-38

Javier J How, Saket Navlakha and Sreekanth H Chalasani

Comparison of metabolic states using genome-scale metabolic models pp. 1-25

Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E Adriaens, Chris T Evelo and Ilja C W Arts

Crowd control: Reducing individual estimation bias by sharing biased social information pp. 1-28

Bertrand Jayles, Clément Sire and Ralf H J M Kurvers

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data pp. 1-19

Pavel I Kos, Aleksandra A Galitsyna, Sergey V Ulianov, Mikhail S Gelfand, Sergey V Razin and Alexander V Chertovich

Estimating the dimensionality of the manifold underlying multi-electrode neural recordings pp. 1-23

Ege Altan, Sara A Solla, Lee E Miller and Eric J Perreault

Cluster size distribution of cells disseminating from a primary tumor pp. 1-23

Mrinmoy Mukherjee and Herbert Levine

Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data pp. 1-21

Torfinn S Madssen, Guro F Giskeødegård, Age K Smilde and Johan A Westerhuis

Intriguing effects of selection intensity on the evolution of prosocial behaviors pp. 1-21

Alex McAvoy, Andrew Rao and Christoph Hauert

Volume 17, issue 10, 2021

Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention pp. 1-23

Stacy Tessler Lindau, Jennifer A Makelarski, Chaitanya Kaligotla, Emily M Abramsohn, David G Beiser, Chiahung Chou, Nicholson Collier, Elbert S Huang, Charles M Macal, Jonathan Ozik and Elizabeth L Tung

RgCop-A regularized copula based method for gene selection in single-cell RNA-seq data pp. 1-19

Snehalika Lall, Sumanta Ray and Sanghamitra Bandyopadhyay

Narrative event segmentation in the cortical reservoir pp. 1-31

Peter Ford Dominey

Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans pp. 1-32

Vince Enachescu, Paul Schrater, Stefan Schaal and Vassilios Christopoulos

Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity pp. 1-32

Daniel E Mattox and Chris Bailey-Kellogg

PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes pp. 1-22

Charlie M Carpenter, Weiming Zhang, Lucas Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russell Bowler, Katerina Kechris and Debashis Ghosh

Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities pp. 1-21

Yun Min Song, Hyukpyo Hong and Jae Kyoung Kim

Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns pp. 1-21

Maxwell W Libbrecht, Rachel C W Chan and Michael M Hoffman

Steady-state measures of visual suppression pp. 1-21

Daniel H Baker, Greta Vilidaite and Alex R Wade

Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons pp. 1-21

Ziniu Wu, Harold Rockwell, Yimeng Zhang, Shiming Tang and Tai Sing Lee

Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans pp. 1-38

Yashika Arora, Pushpinder Walia, Mitsuhiro Hayashibe, Makii Muthalib, Shubhajit Roy Chowdhury, Stephane Perrey and Anirban Dutta

pyActigraphy: Open-source python package for actigraphy data visualization and analysis pp. 1-16

Grégory Hammad, Mathilde Reyt, Nikita Beliy, Marion Baillet, Michele Deantoni, Alexia Lesoinne, Vincenzo Muto and Christina Schmidt

Cortical feedback and gating in odor discrimination and generalization pp. 1-35

Gaia Tavoni, David E Chen Kersen and Vijay Balasubramanian

Extended graphical lasso for multiple interaction networks for high dimensional omics data pp. 1-20

Yang Xu, Hongmei Jiang and Wenxin Jiang

Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration pp. 1-20

Daniel Cresta, Donald C Warren, Christian Quirouette, Amanda P Smith, Lindey C Lane, Amber M Smith and Catherine A A Beauchemin

Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model pp. 1-28

Hua-Chun Sun, David St-Amand, Curtis L Baker and Frederick A A Kingdom

Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies pp. 1-28

Junho Lee, Jin Su Kim and Yangjin Kim

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites pp. 1-28

Bikash K Bhandari, Chun Shen Lim, Daniela M Remus, Augustine Chen, Craig van Dolleweerd and Paul P Gardner

Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty pp. 1-17

Qingchu Jin, Joseph L Greenstein and Raimond L Winslow

Tracking calcium dynamics from individual neurons in behaving animals pp. 1-25

Thibault Lagache, Alison Hanson, Jesús E Pérez-Ortega, Adrienne Fairhall and Rafael Yuste

Better tired than lost: Turtle ant trail networks favor coherence over short edges pp. 1-24

Arjun Chandrasekhar, James A R Marshall, Cortnea Austin, Saket Navlakha and Deborah M Gordon

A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC pp. 1-18

Jason Bennett, Mikhail Pomaznoy, Akul Singhania and Bjoern Peters

A data-driven approach for constructing mutation categories for mutational signature analysis pp. 1-15

Gal Gilad, Mark D M Leiserson and Roded Sharan

How conformity can lead to polarised social behaviour pp. 1-27

Folco Panizza, Alexander Vostroknutov and Giorgio Coricelli

Point-estimating observer models for latent cause detection pp. 1-29

Jennifer Laura Lee and Wei Ji Ma

Ten simple rules for training yourself in an emerging field pp. 1-12

Whitney M Woelmer, L M Bradley, Lisa T Haber, David H Klinges, Abigail S L Lewis, Elizabeth J Mohr, Christa L Torrens, Kathryn I Wheeler and Alyssa M Willson

Volume 17, issue 9, 2021

An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City pp. 1-29

Sheng Zhang, Joan Ponce, Zhen Zhang, Guang Lin and George Karniadakis

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters pp. 1-29

Mar González-Ramírez, Cecilia Ballaré, Francesca Mugianesi, Malte Beringer, Alexandra Santanach, Enrique Blanco and Luciano Di Croce

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo pp. 1-39

Charles-Elie Rabier, Vincent Berry, Marnus Stoltz, João D Santos, Wensheng Wang, Jean-Christophe Glaszmann, Fabio Pardi and Celine Scornavacca

Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment pp. 1-12

Sepideh Mazrouee, Susan J Little and Joel O Wertheim

Ten simple rules for choosing a PhD supervisor pp. 1-8

Loay Jabre, Catherine Bannon, J Scott P McCain and Yana Eglit

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome pp. 1-26

Ilario De Toma, Cesar Sierra and Mara Dierssen

Neighbor-enhanced diffusivity in dense, cohesive cell populations pp. 1-26

Hyun Gyu Lee and Kyoung J Lee

Personalized brain stimulation for effective neurointervention across participants pp. 1-24

Nienke E R van Bueren, Thomas L Reed, Vu Nguyen, James G Sheffield, Sanne H G van der Ven, Michael A Osborne, Evelyn H Kroesbergen and Roi Cohen Kadosh

Optima TB: A tool to help optimally allocate tuberculosis spending pp. 1-24

Lara Goscé, Gerard Abou Jaoude, David J Kedziora, Clemens Benedikt, Azfar Hussain, Sarah Jarvis, Alena Skrahina, Dzmitry Klimuk, Henadz Hurevich, Feng Zhao, Nicole Fraser-Hurt, Nejma Cheikh, Marelize Gorgens, David J Wilson, Romesh Abeysuriya, Rowan Martin-Hughes, Sherrie L Kelly, Anna Roberts, Robyn M Stuart, Tom Palmer, Jasmina Panovska-Griffiths, Cliff C Kerr, David P Wilson, Hassan Haghparast-Bidgoli, Jolene Skordis and Ibrahim Abubakar

Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model pp. 1-24

Federica Gugole, Luc E Coffeng, Wouter Edeling, Benjamin Sanderse, Sake J de Vlas and Daan Crommelin

Ten simple rules for being a faculty advocate of first-year graduate students pp. 1-6

Kevin A Janes

Hemodynamics-driven mathematical model of first and second heart sound generation pp. 1-14

Mehrdad Shahmohammadi, Hongxing Luo, Philip Westphal, Richard N Cornelussen, Frits W Prinzen and Tammo Delhaas

Ten simple rules for supporting historically underrepresented students in science pp. 1-16

Suchinta Arif, Melanie Duc Bo Massey, Natalie Klinard, Julie Charbonneau, Loay Jabre, Ana Barbosa Martins, Danielle Gaitor, Rhiannon Kirton, Catalina Albury and Karma Nanglu

Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections pp. 1-16

Thomas Beneteau, Christian Selinger, Mircea T Sofonea and Samuel Alizon

Ten simple rules for avoiding predatory publishing scams pp. 1-5

Michelle Leonard, Suzanne Stapleton, Perry Collins, Terry Kit Selfe and Tara Cataldo

Inter-trial effects in priming of pop-out: Comparison of computational updating models pp. 1-35

Fredrik Allenmark, Ahu Gokce, Thomas Geyer, Artyom Zinchenko, Hermann J Müller and Zhuanghua Shi

Basis profile curve identification to understand electrical stimulation effects in human brain networks pp. 1-20

Kai J Miller, Klaus-Robert Müller and Dora Hermes

Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics pp. 1-20

Eric W Bridgeford, Shangsi Wang, Zeyi Wang, Ting Xu, Cameron Craddock, Jayanta Dey, Gregory Kiar, William Gray-Roncal, Carlo Colantuoni, Christopher Douville, Stephanie Noble, Carey E Priebe, Brian Caffo, Michael Milham, Xi-Nian Zuo, Consortium for Reliability and Reproducibility and Joshua T Vogelstein

Latching dynamics as a basis for short-term recall pp. 1-28

Kwang Il Ryom, Vezha Boboeva, Oleksandra Soldatkina and Alessandro Treves

Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models pp. 1-28

Michelle F Craft, Andrea K Barreiro, Shree Hari Gautam, Woodrow L Shew and Cheng Ly

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C pp. 1-25

Susana Posada-Céspedes, Gert Van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger Kouyos, Huldrych F Günthard and Niko Beerenwinkel

Learning brain dynamics for decoding and predicting individual differences pp. 1-25

Joyneel Misra, Srinivas Govinda Surampudi, Manasij Venkatesh, Chirag Limbachia, Joseph Jaja and Luiz Pessoa

Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing pp. 1-25

Michael Smith, Rachel Chan, Maaz Khurram and Paul M K Gordon

ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves pp. 1-19

Eric D Musselman, Jake E Cariello, Warren M Grill and Nicole A Pelot

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants pp. 1-23

Rui Yin, Johnathan D Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush and Brian G Pierce

Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies pp. 1-32

Nathaniel J Zuk, Jeremy W Murphy, Richard B Reilly and Edmund C Lalor

Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation pp. 1-21

Magali Tournus, Miguel Escobedo, Wei-Feng Xue and Marie Doumic

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers pp. 1-21

Jack B Maguire, Daniele Grattarola, Vikram Khipple Mulligan, Eugene Klyshko and Hans Melo

Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds pp. 1-21

Alison Pereira Ribeiro, Nádia Felix Felipe da Silva, Fernanda Neiva Mesquita, Priscila de Cássia Souza Araújo, Thierson Couto Rosa and José Neiva Mesquita-Neto

Drug-induced resistance evolution necessitates less aggressive treatment pp. 1-22

Teemu Kuosmanen, Johannes Cairns, Robert Noble, Niko Beerenwinkel, Tommi Mononen and Ville Mustonen

Volume 17, issue 8, 2021

Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster pp. 1-9

Jamie J Alnasir

Critical behaviour of the stochastic Wilson-Cowan model pp. 1-23

Antonio de Candia, Alessandro Sarracino, Ilenia Apicella and Lucilla de Arcangelis

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations pp. 1-22

Jenny M Vo-Phamhi, Kevin A Yamauchi and Rafael Gómez-Sjöberg

Review of machine learning methods for RNA secondary structure prediction pp. 1-22

Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao and Yudong Yao

A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease pp. 1-21

Luke Tait, Marinho A Lopes, George Stothart, John Baker, Nina Kazanina, Jiaxiang Zhang and Marc Goodfellow

Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows pp. 1-33

Daniel Schindler, Ted Moldenhawer, Maike Stange, Valentino Lepro, Carsten Beta, Matthias Holschneider and Wilhelm Huisinga

Interspike interval correlations in neuron models with adaptation and correlated noise pp. 1-35

Lukas Ramlow and Benjamin Lindner

Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space pp. 1-30

Daisuke Imoto, Nen Saito, Akihiko Nakajima, Gen Honda, Motohiko Ishida, Toyoko Sugita, Sayaka Ishihara, Koko Katagiri, Chika Okimura, Yoshiaki Iwadate and Satoshi Sawai

A probabilistic model for the ultradian timing of REM sleep in mice pp. 1-30

Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung and Franz Weber

An uncertainty-based model of the effects of fixation on choice pp. 1-17

Zhi-Wei Li and Wei Ji Ma

The role of memory in non-genetic inheritance and its impact on cancer treatment resistance pp. 1-25

Tyler Cassidy, Daniel Nichol, Mark Robertson-Tessi, Morgan Craig and Alexander R A Anderson

A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms pp. 1-28

Indie C Garwood, Sourish Chakravarty, Jacob Donoghue, Meredith Mahnke, Pegah Kahali, Shubham Chamadia, Oluwaseun Akeju, Earl K Miller and Emery N Brown

Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence pp. 1-28

Simon M Lichtinger, Adiran Garaizar, Rosana Collepardo-Guevara and Aleks Reinhardt

Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread pp. 1-24

John R Giles, Derek A T Cummings, Bryan T Grenfell, Andrew J Tatem, Elisabeth zu Erbach-Schoenberg, Metcalf Cje and Amy Wesolowski

A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes pp. 1-24

Karoline Horgmo Jæger, Andrew G Edwards, Wayne R Giles and Aslak Tveito

A multi-objective genetic algorithm to find active modules in multiplex biological networks pp. 1-24

Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit and Anaïs Baudot

PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions pp. 1-18

Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W Ritchie and Marie-Dominique Devignes

A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers pp. 1-18

Frances L Heredia, Abiel Roche-Lima and Elsie I Parés-Matos

Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base pp. 1-18

Tomasz Konopka, Sandra Ng and Damian Smedley

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data pp. 1-18

Ariel A Hippen, Matias M Falco, Lukas M Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S Greene and Stephanie C Hicks

Ten simple rules for aspiring graduate students pp. 1-10

Andrea I Luppi, Charlotte Coco Newton, Lynde Folsom, Elisa Galliano and Rafael Romero-Garcia

Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters pp. 1-29

Natalie Schaworonkow and Bradley Voytek

SiGMoiD: A super-statistical generative model for binary data pp. 1-13

Xiaochuan Zhao, Germán Plata and Purushottam D Dixit

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries pp. 1-12

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas and Nicola Mulder

Volume 17, issue 7, 2021

Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson’s disease pp. 1-42

Benoit Duchet, Filippo Ghezzi, Gihan Weerasinghe, Gerd Tinkhauser, Andrea A Kühn, Peter Brown, Christian Bick and Rafal Bogacz

Modelling locust foraging: How and why food affects group formation pp. 1-22

Fillipe Georgiou, Camille Buhl, J E F Green, Bishnu Lamichhane and Ngamta Thamwattana

Risk sensitivity and theory of mind in human coordination pp. 1-22

Pedro L Ferreira, Francisco C Santos and Sérgio Pequito

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements pp. 1-22

Xi Chen, Andrew F Neuwald, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan

Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic pp. 1-22

Tenglong Li and Laura F White

Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching pp. 1-22

Matthias Niemann, Nils Lachmann, Kirsten Geneugelijk and Eric Spierings

Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection pp. 1-21

Gustav Markkula, Zeynep Uludağ, Richard McGilchrist Wilkie and Jac Billington

Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology pp. 1-16

Adrian J Green, Martin J Mohlenkamp, Jhuma Das, Meenal Chaudhari, Lisa Truong, Robyn L Tanguay and David M Reif

Multitask learning over shared subspaces pp. 1-25

Nicholas Menghi, Kemal Kacar and Will Penny

Noise suppression in stochastic genetic circuits using PID controllers pp. 1-25

Saurabh Modi, Supravat Dey and Abhyudai Singh

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization pp. 1-20

Lei Li, Zhen Gao, Yu-Tian Wang, Ming-Wen Zhang, Jian-Cheng Ni, Chun-Hou Zheng and Yansen Su

Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors pp. 1-20

Shirit Dvorkin, Reut Levi and Yoram Louzoun

Accurate influenza forecasts using type-specific incidence data for small geographic units pp. 1-20

James Turtle, Pete Riley, Michal Ben-Nun and Steven Riley

Selection of stimulus parameters for enhancing slow wave sleep events with a neural-field theory thalamocortical model pp. 1-28

Felipe A Torres, Patricio Orio and María-José Escobar

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2 pp. 1-37

Asaminew H Aytenfisu, Daniel Deredge, Erik H Klontz, Jonathan Du, Eric J Sundberg and Alexander D MacKerell

Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes pp. 1-24

Davin Lunz, Gregory Batt, Jakob Ruess and J Frédéric Bonnans

Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans pp. 1-26

Omer Yuval, Yael Iosilevskii, Anna Meledin, Benjamin Podbilewicz and Tom Shemesh

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis pp. 1-15

Pol Castellano-Escuder, Raúl González-Domínguez, Francesc Carmona-Pontaque, Cristina Andrés-Lacueva and Alex Sánchez-Pla

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread pp. 1-34

Meysam Hashemi, Anirudh N Vattikonda, Viktor Sip, Sandra Diaz-Pier, Alexander Peyser, Huifang Wang, Maxime Guye, Fabrice Bartolomei, Marmaduke M Woodman and Viktor K Jirsa

Predicting seasonal influenza using supermarket retail records pp. 1-18

Ioanna Miliou, Xinyue Xiong, Salvatore Rinzivillo, Qian Zhang, Giulio Rossetti, Fosca Giannotti, Dino Pedreschi and Alessandro Vespignani

Ten simple rules for attending your first conference pp. 1-13

Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo and Anna Ritz

Volume 17, issue 6, 2021

Stochastic optimal feedforward-feedback control determines timing and variability of arm movements with or without vision pp. 1-24

Bastien Berret, Adrien Conessa, Nicolas Schweighofer and Etienne Burdet

A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2 pp. 1-24

Edward M Hill, Benjamin D Atkins, Matt J Keeling, Louise Dyson and Michael J Tildesley

De novo mutational signature discovery in tumor genomes using SparseSignatures pp. 1-24

Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow and Daniele Ramazzotti

Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints pp. 1-18

Diego del Alamo, Kevin L Jagessar, Jens Meiler and Hassane S Mchaourab

Embedding optimization reveals long-lasting history dependence in neural spiking activity pp. 1-51

Lucas Rudelt, Daniel González Marx, Michael Wibral and Viola Priesemann

Identifying the combinatorial control of signal-dependent transcription factors pp. 1-29

Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li and Alexander Hoffmann

Ten simple rules for doing a postdoc in pharma pp. 1-8

Jitao David Zhang

Three-dimensional topology optimization model to simulate the external shapes of bone pp. 1-23

Misaki Sakashita, Shintaro Yamasaki, Kentaro Yaji, Atsushi Kawamoto and Shigeru Kondo

Learning divisive normalization in primary visual cortex pp. 1-31

Max F Burg, Santiago A Cadena, George H Denfield, Edgar Y Walker, Andreas S Tolias, Matthias Bethge and Alexander S Ecker

Novelty is not surprise: Human exploratory and adaptive behavior in sequential decision-making pp. 1-32

He A Xu, Alireza Modirshanechi, Marco P Lehmann, Wulfram Gerstner and Michael H Herzog

High-affinity P2Y2 and low-affinity P2X7 receptor interaction modulates ATP-mediated calcium signaling in murine osteoblasts pp. 1-22

Nicholas Mikolajewicz, Delaney Smith, Svetlana V Komarova and Anmar Khadra

GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction pp. 1-22

Zhong Li, Kaiyancheng Jiang, Shengwei Qin, Yijun Zhong and Arne Elofsson

BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration pp. 1-22

Andreas Deutsch, Josué Manik Nava-Sedeño, Simon Syga and Haralampos Hatzikirou

PHENSIM: Phenotype Simulator pp. 1-21

Salvatore Alaimo, Rosaria Valentina Rapicavoli, Gioacchino P Marceca, Alessandro La Ferlita, Oksana B Serebrennikova, Philip N Tsichlis, Bud Mishra, Alfredo Pulvirenti and Alfredo Ferro

CytoPy: An autonomous cytometry analysis framework pp. 1-21

Ross J Burton, Raya Ahmed, Simone M Cuff, Sarah Baker, Andreas Artemiou and Matthias Eberl

Iliski, a software for robust calculation of transfer functions pp. 1-14

Ali-Kemal Aydin, William D Haselden, Julie Dang, Patrick J Drew, Serge Charpak and Davide Boido

Behavioral correlates of cortical semantic representations modeled by word vectors pp. 1-35

Satoshi Nishida, Antoine Blanc, Naoya Maeda, Masataka Kado and Shinji Nishimoto

Categorical judgments do not modify sensory representations in working memory pp. 1-28

Long Luu and Alan A Stocker

A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma pp. 1-28

Sonja Langthaler, Theresa Rienmüller, Susanne Scheruebel, Brigitte Pelzmann, Niroj Shrestha, Klaus Zorn-Pauly, Wolfgang Schreibmayer, Andrew Koff and Christian Baumgartner

pyTFM: A tool for traction force and monolayer stress microscopy pp. 1-17

Andreas Bauer, Magdalena Prechová, Lena Fischer, Ingo Thievessen, Martin Gregor and Ben Fabry

A zero inflated log-normal model for inference of sparse microbial association networks pp. 1-17

Vincent Prost, Stéphane Gazut and Thomas Brüls

Volume 17, issue 5, 2021

Ten steps to investigate a cellular system with mathematical modeling pp. 1-8

Jasia King, Kerbaï Saïd Eroumé, Roman Truckenmüller, Stefan Giselbrecht, Ann E Cowan, Leslie Loew and Aurélie Carlier

Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections pp. 1-18

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

Sequence learning recodes cortical representations instead of strengthening initial ones pp. 1-34

Kristjan Kalm and Dennis Norris

MetaGSCA: A tool for meta-analysis of gene set differential coexpression pp. 1-15

Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott Ness, Yu Shyr and Fei Ye

A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila pp. 1-27

Claudio D T Barros, Maira A Cardoso, Paulo M Bisch, Helena M Araujo and Francisco J P Lopes

Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10 pp. 1-24

Leonard Campanello, Maria K Traver, Hari Shroff, Brian C Schaefer and Wolfgang Losert

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data pp. 1-24

Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan and Zuoheng Wang

Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport pp. 1-26

Daniel Ch Haspinger, Sandra Klinge and Gerhard A Holzapfel

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage pp. 1-26

Jonathan Liu, Donald Hansen, Elizabeth Eck, Yang Joon Kim, Meghan Turner, Simon Alamos and Hernan G Garcia

What we can and what we cannot see with extracellular multielectrodes pp. 1-20

Chaitanya Chintaluri, Marta Bejtka, Władysław Średniawa, Michał Czerwiński, Jakub M Dzik, Joanna Jędrzejewska-Szmek, Kacper Kondrakiewicz, Ewa Kublik and Daniel K Wójcik

PRER: A patient representation with pairwise relative expression of proteins on biological networks pp. 1-20

Halil İbrahim Kuru, Mustafa Buyukozkan and Oznur Tastan

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs pp. 1-28

Antoine Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, Alain Denise and Jérôme Waldispühl

Red blood cell phenotyping from 3D confocal images using artificial neural networks pp. 1-17

Greta Simionato, Konrad Hinkelmann, Revaz Chachanidze, Paola Bianchi, Elisa Fermo, Richard van Wijk, Marc Leonetti, Christian Wagner, Lars Kaestner and Stephan Quint

On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins pp. 1-17

Edwin Rodriguez Horta and Martin Weigt

A deep learning algorithm for 3D cell detection in whole mouse brain image datasets pp. 1-17

Adam L Tyson, Charly V Rousseau, Christian J Niedworok, Sepiedeh Keshavarzi, Chryssanthi Tsitoura, Lee Cossell, Molly Strom and Troy W Margrie

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data pp. 1-14

Xinjun Li, Fan Feng, Hongxi Pu, Wai Yan Leung and Jie Liu

Evaluation of residue-residue contact prediction methods: From retrospective to prospective pp. 1-33

Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo and Yanjie Wei

A first-takes-all model of centriole copy number control based on cartwheel elongation pp. 1-22

Marco António Dias Louro, Mónica Bettencourt-Dias and Jorge Carneiro

Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition pp. 1-22

Christian Schulz, Tjasa Kumelj, Emil Karlsen and Eivind Almaas

Patterns of selection against centrosome amplification in human cell lines pp. 1-22

Marco António Dias Louro, Mónica Bettencourt-Dias and Claudia Bank

CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation pp. 1-21

Christopher J Arthurs, Rostislav Khlebnikov, Alex Melville, Marija Marčan, Alberto Gomez, Desmond Dillon-Murphy, Federica Cuomo, Miguel Silva Vieira, Jonas Schollenberger, Sabrina R Lynch, Christopher Tossas-Betancourt, Kritika Iyer, Sara Hopper, Elizabeth Livingston, Pouya Youssefi, Alia Noorani, Sabrina Ben Ahmed, Foeke J H Nauta, Theodorus M J van Bakel, Yunus Ahmed, Petrus A J van Bakel, Jonathan Mynard, Paolo Di Achille, Hamid Gharahi, Kevin D Lau, Vasilina Filonova, Miquel Aguirre, Nitesh Nama, Nan Xiao, Seungik Baek, Krishna Garikipati, Onkar Sahni, David Nordsletten and C Alberto Figueroa

Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder pp. 1-21

Mads L Pedersen, Maria Ironside, Ken-ichi Amemori, Callie L McGrath, Min S Kang, Ann M Graybiel, Diego A Pizzagalli and Michael J Frank

Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways pp. 1-23

Juho A J Kontio, Tanja Pyhäjärvi and Mikko J Sillanpää

Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication pp. 1-31

JaeAnn M Dwulet, Jennifer K Briggs and Richard K P Benninger

Volume 17, issue 4, 2021

Behavioral discrimination and time-series phenotyping of birdsong performance pp. 1-21

Avishek Paul, Helen McLendon, Veronica Rally, Jon T Sakata and Sarah C Woolley

Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment pp. 1-21

Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz and Alexis Joly

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads pp. 1-41

Rohan N Shah and Alexander J Ruthenburg

VolPy: Automated and scalable analysis pipelines for voltage imaging datasets pp. 1-27

Changjia Cai, Johannes Friedrich, Amrita Singh, M Hossein Eybposh, Eftychios A Pnevmatikakis, Kaspar Podgorski and Andrea Giovannucci

Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions pp. 1-22

Yao Jiang, Hui-Fang Liu and Rong Liu

Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories pp. 1-33

Christopher Wills, Bin Wang, Shuai Fang, Yunquan Wang, Yi Jin, James Lutz, Jill Thompson, Kyle E Harms, Sandeep Pulla, Bonifacio Pasion, Sara Germain, Heming Liu, Joseph Smokey, Sheng-Hsin Su, Nathalie Butt, Chengjin Chu, George Chuyong, Chia-Hao Chang-Yang, H S Dattaraja, Stuart Davies, Sisira Ediriweera, Shameema Esufali, Christine Dawn Fletcher, Nimal Gunatilleke, Savi Gunatilleke, Chang-Fu Hsieh, Fangliang He, Stephen Hubbell, Zhanqing Hao, Akira Itoh, David Kenfack, Buhang Li, Xiankun Li, Keping Ma, Michael Morecroft, Xiangcheng Mi, Yadvinder Malhi, Perry Ong, Lillian Jennifer Rodriguez, H S Suresh, I Fang Sun, Raman Sukumar, Sylvester Tan, Duncan Thomas, Maria Uriarte, Xihua Wang, Xugao Wang, T L Yao and Jess Zimmermann

Using Hawkes Processes to model imported and local malaria cases in near-elimination settings pp. 1-18

H Juliette T Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin Cohen, Daniel J Weiss, Swapnil Mishra and Samir Bhatt

Mistakes can stabilise the dynamics of rock-paper-scissors games pp. 1-16

Maria Kleshnina, Sabrina S Streipert, Jerzy A Filar and Krishnendu Chatterjee

MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging pp. 1-16

Alex Baranski, Idan Milo, Shirley Greenbaum, John-Paul Oliveria, Dunja Mrdjen, Michael Angelo and Leeat Keren

Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data pp. 1-45

David P Shorten, Richard E Spinney and Joseph T Lizier

Individual differences in the perception of probability pp. 1-25

Mel W Khaw, Luminita Stevens and Michael Woodford

A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation pp. 1-20

Diego Vidaurre

Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy pp. 1-20

Claude Gérard, Laurane De Mot, Sabine Cordi, Jonathan van Eyll and Frédéric P Lemaigre

WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans pp. 1-20

Laetitia Hebert, Tosif Ahamed, Antonio C Costa, Liam O’Shaughnessy and Greg J Stephens

Volume 17, issue 3, 2021

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry pp. 1-30

Ya-Wei Eileen Lin, Tal Shnitzer, Ronen Talmon, Franz Villarroel-Espindola, Shruti Desai, Kurt Schalper and Yuval Kluger

Neural modelling of the encoding of fast frequency modulation pp. 1-30

Alejandro Tabas and Katharina von Kriegstein

Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance pp. 1-16

Anton J M Larsson, Christoph Ziegenhain, Michael Hagemann-Jensen, Björn Reinius, Tina Jacob, Tim Dalessandri, Gert-Jan Hendriks, Maria Kasper and Rickard Sandberg

JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters pp. 1-16

Hong Seo Lim and Peng Qiu

How does Sec63 affect the conformation of Sec61 in yeast? pp. 1-28

Pratiti Bhadra, Lalitha Yadhanapudi, Karin Römisch and Volkhard Helms

Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease pp. 1-20

Mark J Panaggio, Daniel M Abrams, Fan Yang, Tanvi Banerjee and Nirmish R Shah

Predicting microbial growth dynamics in response to nutrient availability pp. 1-20

Olga A Nev, Richard J Lindsay, Alys Jepson, Lisa Butt, Robert E Beardmore and Ivana Gudelj

Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model pp. 1-20

Gregory L Watson, Di Xiong, Lu Zhang, Joseph A Zoller, John Shamshoian, Phillip Sundin, Teresa Bufford, Anne W Rimoin, Marc A Suchard and Christina M Ramirez

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD pp. 1-17

Yannick Marcon, Tom Bishop, Demetris Avraam, Xavier Escriba-Montagut, Patricia Ryser-Welch, Stuart Wheater, Paul Burton and Juan R González

Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability pp. 1-25

Javier Rasero, Amy Isabella Sentis, Fang-Cheng Yeh and Timothy Verstynen

Modelling the impact of clot fragmentation on the microcirculation after thrombectomy pp. 1-25

Wahbi K El-Bouri, Andrew MacGowan, Tamás I Józsa, Matthew J Gounis and Stephen J Payne

Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators pp. 1-25

Alberto Pérez-Cervera and Jaroslav Hlinka

Mechanical coupling in the nitrogenase complex pp. 1-25

Qi Huang, Monika Tokmina-Lukaszewska, Lewis E Johnson, Hayden Kallas, Bojana Ginovska, John W Peters, Lance C Seefeldt, Brian Bothner and Simone Raugei

Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance pp. 1-25

Vincent Brault, Bastien Mallein and Jean-François Rupprecht

Inferring phenomenological models of first passage processes pp. 1-25

Catalina Rivera, David Hofmann and Ilya Nemenman

Optimal timing of one-shot interventions for epidemic control pp. 1-25

Francesco Di Lauro, István Z Kiss and Joel C Miller

Prediction of amphipathic helix—membrane interactions with Rosetta pp. 1-25

Alican Gulsevin and Jens Meiler

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach pp. 1-25

Josh L Espinoza, Chris L Dupont, Aubrie O’Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J Meyer, Agnes P Chan, Yongwook Choi, William C Nierman, Kim Lewis and Karen E Nelson

Health inequities in influenza transmission and surveillance pp. 1-23

Casey M Zipfel, Vittoria Colizza and Shweta Bansal

Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements pp. 1-23

Kseniia Cheloshkina and Maria Poptsova

Public Baseline and shared response structures support the theory of antibody repertoire functional commonality pp. 1-23

Matthew I J Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P Lewis, Jiye Shi and Charlotte M Deane

Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models pp. 1-23

Denis A Shah, Erick D De Wolf, Pierce A Paul and Laurence V Madden

Signal-to-signal neural networks for improved spike estimation from calcium imaging data pp. 1-19

Jilt Sebastian, Mriganka Sur, Hema A Murthy and Mathew Magimai-Doss

Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder pp. 1-19

Haider Al-Tahan and Yalda Mohsenzadeh

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks pp. 1-19

Yang Li, Chengxin Zhang, Eric W Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu and Yang Zhang

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds pp. 1-9

Brian Coventry and David Baker

Connectivity, reproduction number, and mobility interact to determine communities’ epidemiological superspreader potential in a metapopulation network pp. 1-22

Brandon Lieberthal and Allison M Gardner

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli pp. 1-22

Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia Rodrigues and Oscar Dias

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases pp. 1-21

Janani Durairaj, Elena Melillo, Harro J Bouwmeester, Jules Beekwilder, Dick de Ridder and Aalt D J van Dijk

Collective predator evasion: Putting the criticality hypothesis to the test pp. 1-21

Pascal P Klamser and Pawel Romanczuk

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling pp. 1-21

Yekaterina S Pavlova, David Paez-Espino, Andrew Yu Morozov and Ilya S Belalov

Fixation patterns in simple choice reflect optimal information sampling pp. 1-29

Frederick Callaway, Antonio Rangel and Thomas L Griffiths

PDKit: A data science toolkit for the digital assessment of Parkinson’s Disease pp. 1-11

Cosmin Stamate, Joan Saez Pons, David Weston and George Roussos

Principles for data analysis workflows pp. 1-26

Sara Stoudt, Váleri N Vásquez and Ciera C Martinez

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data pp. 1-10

Song He, Xinyu Song, Xiaoxi Yang, Jijun Yu, Yuqi Wen, Lianlian Wu, Bowei Yan, Jiannan Feng and Xiaochen Bo

Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex pp. 1-18

Annika Hagemann, Jens Wilting, Bita Samimizad, Florian Mormann and Viola Priesemann

DCMD: Distance-based classification using mixture distributions on microbiome data pp. 1-18

Konstantin Shestopaloff, Mei Dong, Fan Gao and Wei Xu

Ten simple rules for quick and dirty scientific programming pp. 1-15

Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer and Geir Kjetil Sandve

Linear-nonlinear cascades capture synaptic dynamics pp. 1-27

Julian Rossbroich, Daniel Trotter, John Beninger, Katalin Tóth and Richard Naud

Optimal prediction with resource constraints using the information bottleneck pp. 1-27

Vedant Sachdeva, Thierry Mora, Aleksandra M Walczak and Stephanie E Palmer

Volume 17, issue 2, 2021

Integrated information structure collapses with anesthetic loss of conscious arousal in Drosophila melanogaster pp. 1-27

Angus Leung, Dror Cohen, Bruno van Swinderen and Naotsugu Tsuchiya

Evaluating epidemic forecasts in an interval format pp. 1-15

Johannes Bracher, Evan L Ray, Tilmann Gneiting and Nicholas G Reich

Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species pp. 1-15

Zutan Li, Hangjin Jiang, Lingpeng Kong, Yuanyuan Chen, Kun Lang, Xiaodan Fan, Liangyun Zhang and Cong Pian

Deriving fine-scale models of human mobility from aggregated origin-destination flow data pp. 1-18

Constanze Ciavarella and Neil M Ferguson

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships pp. 1-18

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H Spaaks, Faruk Diblen, Simon Rogers and Justin J J van der Hooft

Ten simple rules for running and managing virtual internships pp. 1-10

Johannes Werner and Debora Jeske

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes pp. 1-26

Johannes Asplund-Samuelsson and Elton P Hudson

A model of developmental canalization, applied to human cranial form pp. 1-24

Philipp Mitteroecker and Ekaterina Stansfield

Dynamics of chromosomal target search by a membrane-integrated one-component receptor pp. 1-24

Linda Martini, Sophie Brameyer, Elisabeth Hoyer, Kirsten Jung and Ulrich Gerland

Ten simple rules for starting (and sustaining) an academic data science initiative pp. 1-12

Micaela S Parker, Arlyn E Burgess and Philip E Bourne

Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective pp. 1-12

Hwai-Ray Tung and Rick Durrett

Ten simple rules for engaging with artificial intelligence in biomedicine pp. 1-11

Avni Malik, Paranjay Patel, Lubaina Ehsan, Shan Guleria, Thomas Hartka, Sodiq Adewole and Sana Syed

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways pp. 1-13

Martín Garrido-Rodriguez, Daniel Lopez-Lopez, Francisco M Ortuno, María Peña-Chilet, Eduardo Muñoz, Marco A Calzado and Joaquin Dopazo

Quantitative profiling of protease specificity pp. 1-29

Boris I Ratnikov, Piotr Cieplak, Albert G Remacle, Elise Nguyen and Jeffrey W Smith

Ancestral haplotype reconstruction in endogamous populations using identity-by-descent pp. 1-29

Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, Yuval B Simons, Shweta Ramdas, Alejandro A Schäffer, Rachel L Kember, Maja Bućan and Sara Mathieson

On the importance of evolving phenotype distributions on evolutionary diversification pp. 1-21

Gil Jorge Barros Henriques, Koichi Ito, Christoph Hauert and Michael Doebeli

From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach pp. 1-21

Ann-Kristin Becker, Marcus Dörr, Stephan B Felix, Fabian Frost, Hans J Grabe, Markus M Lerch, Matthias Nauck, Uwe Völker, Henry Völzke and Lars Kaderali

End-to-end neural system identification with neural information flow pp. 1-22

K Seeliger, L Ambrogioni, Y Güçlütürk, L M van den Bulk, U Güçlü and M A J van Gerven

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations pp. 1-22

Qiao Liu and Lei Xie

Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography pp. 1-31

Viktor Sip, Meysam Hashemi, Anirudh N Vattikonda, Marmaduke M Woodman, Huifang Wang, Julia Scholly, Samuel Medina Villalon, Maxime Guye, Fabrice Bartolomei and Viktor K Jirsa

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins pp. 1-31

Rahmatullah Roche, Sutanu Bhattacharya and Debswapna Bhattacharya

A numerical framework for mechano-regulated tendon healing—Simulation of early regeneration of the Achilles tendon pp. 1-19

Thomas Notermans, Petri Tanska, Rami K Korhonen, Hanifeh Khayyeri and Hanna Isaksson

FastTrack: An open-source software for tracking varying numbers of deformable objects pp. 1-19

Benjamin Gallois and Raphaël Candelier

Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches pp. 1-19

Judith A Bouman, Julien Riou, Sebastian Bonhoeffer and Roland R Regoes

Generating functional protein variants with variational autoencoders pp. 1-23

Alex Hawkins-Hooker, Florence Depardieu, Sebastien Baur, Guillaume Couairon, Arthur Chen and David Bikard

Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas pp. 1-25

Mari Ganesh Kumar, Ming Hu, Aadhirai Ramanujan, Mriganka Sur and Hema A Murthy

Fixation probabilities in graph-structured populations under weak selection pp. 1-25

Benjamin Allen, Christine Sample, Patricia Steinhagen, Julia Shapiro, Matthew King, Timothy Hedspeth and Megan Goncalves

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity pp. 1-25

John P Lloyd, Matthew B Soellner, Sofia D Merajver and Jun Z Li

Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings pp. 1-25

Viktor Sip, Julia Scholly, Maxime Guye, Fabrice Bartolomei and Viktor Jirsa

Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex pp. 1-25

Christof Fehrman, Tyler D Robbins and C Daniel Meliza

Unsupervised manifold learning of collective behavior pp. 1-20

Mathew Titus, George Hagstrom and James R Watson

Evolution of heterogeneous perceptual limits and indifference in competitive foraging pp. 1-20

Richard P Mann

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees pp. 1-35

George G Vega Yon, Duncan C Thomas, John Morrison, Huaiyu Mi, Paul D Thomas and Paul Marjoram

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model pp. 1-30

Jordan Douglas, Rong Zhang and Remco Bouckaert

Volume 17, issue 1, 2021

Modeling multi-sensory feedback control of zebrafish in a flow pp. 1-24

Daniel A Burbano-L. and Maurizio Porfiri

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference pp. 1-26

Katharine Best, Dan H Barouch, Jeremie Guedj, Ruy M Ribeiro and Alan S Perelson

Real-time resolution of short-read assembly graph using ONT long reads pp. 1-18

Son Hoang Nguyen, Minh Duc Cao and Lachlan J M Coin

mbkmeans: Fast clustering for single cell data using mini-batch k-means pp. 1-18

Stephanie C Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom and Davide Risso

Estimating the time-varying reproduction number of COVID-19 with a state-space method pp. 1-18

Shinsuke Koyama, Taiki Horie and Shigeru Shinomoto

Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach pp. 1-27

Vikki Neville, Peter Dayan, Iain D Gilchrist, Elizabeth S Paul and Michael Mendl

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk pp. 1-27

Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stephane Guindon and Nicola De Maio

Post-lockdown abatement of COVID-19 by fast periodic switching pp. 1-34

Michelangelo Bin, Peter Y K Cheung, Emanuele Crisostomi, Pietro Ferraro, Hugo Lhachemi, Roderick Murray-Smith, Connor Myant, Thomas Parisini, Robert Shorten, Sebastian Stein and Lewi Stone

Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome pp. 1-29

Marco Aqil, Selen Atasoy, Morten L Kringelbach and Rikkert Hindriks

Chemical graph generators pp. 1-11

Mehmet Aziz Yirik and Christoph Steinbeck

Structured environments foster competitor coexistence by manipulating interspecies interfaces pp. 1-23

Tristan Ursell

A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans pp. 1-43

Samuel Planton, Timo van Kerkoerle, Leïla Abbih, Maxime Maheu, Florent Meyniel, Mariano Sigman, Liping Wang, Santiago Figueira, Sergio Romano and Stanislas Dehaene

Online analysis of microendoscopic 1-photon calcium imaging data streams pp. 1-32

Johannes Friedrich, Andrea Giovannucci and Eftychios A Pnevmatikakis

Predicting synchronous firing of large neural populations from sequential recordings pp. 1-21

Oleksandr Sorochynskyi, Stéphane Deny, Olivier Marre and Ulisse Ferrari

Sensor-based localization of epidemic sources on human mobility networks pp. 1-21

Jun Li, Juliane Manitz, Enrico Bertuzzo and Eric D Kolaczyk

Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains pp. 1-22

Antonino Casile, Rose T Faghih and Emery N Brown

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data pp. 1-22

Andreas Tjärnberg, Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel A Christiaen and Richard A Bonneau

Reconciling kinetic and thermodynamic models of bacterial transcription pp. 1-30

Muir Morrison, Manuel Razo-Mejia and Rob Phillips

The risks of using the chi-square periodogram to estimate the period of biological rhythms pp. 1-16

Michael C Tackenberg and Jacob J Hughey

Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing pp. 1-16

Bansho Masutani, Shin-ichi Arimura and Shinichi Morishita

Improving probabilistic infectious disease forecasting through coherence pp. 1-20

Graham Casey Gibson, Kelly R Moran, Nicholas G Reich and Dave Osthus

Modeling invasion patterns in the glioblastoma battlefield pp. 1-20

Martina Conte, Sergio Casas-Tintò and Juan Soler

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine pp. 1-28

Linda K Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye and Quaid Morris

Friendly-rivalry solution to the iterated n-person public-goods game pp. 1-17

Yohsuke Murase and Seung Ki Baek