PLOS Computational Biology

2005 - 2022

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Volume 15, issue 12, 2019

Motion prediction enables simulated MR-imaging of freely moving model organisms pp. 1-16

Markus Reischl, Mazin Jouda, Neil MacKinnon, Erwin Fuhrer, Natalia Bakhtina, Andreas Bartschat, Ralf Mikut and Jan G Korvink

Statistical inference in ensemble modeling of cellular metabolism pp. 1-16

Tuure Hameri, Marc-Olivier Boldi and Vassily Hatzimanikatis

Representation learning of genomic sequence motifs with convolutional neural networks pp. 1-17

Peter K Koo and Sean R Eddy

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters pp. 1-20

Christine Jandrasits, Stefan Kröger, Walter Haas and Bernhard Y Renard

Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs pp. 1-20

Yongcui Wang, Shilong Chen, Luonan Chen and Yong Wang

Benchmarking network algorithms for contextualizing genes of interest pp. 1-14

Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy Jenkins and Melody K Morris

Statistics of correlated percolation in a bacterial community pp. 1-19

Xiaoling Zhai, Joseph W Larkin, Kaito Kikuchi, Samuel E Redford, Ushasi Roy, Gürol M Süel and Andrew Mugler

Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication pp. 1-19

Razie Yousefi and Maga Rowicka

Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model pp. 1-28

John E Mittler, James T Murphy, Sarah E Stansfield, Kathryn Peebles, Geoffrey S Gottlieb, Neil F Abernethy, Molly C Reid, Steven M Goodreau and Joshua T Herbeck

The dynamics of motor learning through the formation of internal models pp. 1-25

Camilla Pierella, Maura Casadio, Ferdinando A Mussa-Ivaldi and Sara A Solla

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory pp. 1-25

Shu Wang, Jia-Ren Lin, Eduardo D Sontag and Peter K Sorger

Stability of spontaneous, correlated activity in mouse auditory cortex pp. 1-25

Richard F Betzel, Katherine C Wood, Christopher Angeloni, Maria Neimark Geffen and Danielle S Bassett

Neuronal population model of globular bushy cells covering unit-to-unit variability pp. 1-38

Go Ashida, Helen T Heinermann and Jutta Kretzberg

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest pp. 1-30

Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B Freimer and Jae Hoon Sul

Molecular sampling at logarithmic rates for next-generation sequencing pp. 1-12

Caroline Horn and Julia Salzman

Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models pp. 1-21

Colette Mair, Sema Nickbakhsh, Richard Reeve, Jim McMenamin, Arlene Reynolds, Rory N Gunson, Pablo R Murcia and Louise Matthews

Protons in small spaces: Discrete simulations of vesicle acidification pp. 1-21

Apeksha Singh, Frank V Marcoline, Salome Veshaguri, Aimee W Kao, Marcel Bruchez, Joseph A Mindell, Dimitrios Stamou and Michael Grabe

Overlap matrix completion for predicting drug-associated indications pp. 1-21

Mengyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu and Jianxin Wang

The effect of inhibition on rate code efficiency indicators pp. 1-21

Tomas Barta and Lubomir Kostal

A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation pp. 1-26

Matthew C Pharris, Neal M Patel, Tyler G VanDyk, Thomas M Bartol, Terrence J Sejnowski, Mary B Kennedy, Melanie I Stefan and Tamara L Kinzer-Ursem

Chemotaxis in external fields: Simulations for active magnetic biological matter pp. 1-26

Agnese Codutti, Klaas Bente, Damien Faivre and Stefan Klumpp

Incomplete information about the partner affects the development of collaborative strategies in joint action pp. 1-23

Vinil T Chackochan and Vittorio Sanguineti

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities pp. 1-23

Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P Curtis and Paolo Zuliani

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling pp. 1-23

Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini and Alessandro Paiardini

From energy to cellular forces in the Cellular Potts Model: An algorithmic approach pp. 1-23

Elisabeth G Rens and Leah Edelstein-Keshet

Probing neural networks for dynamic switches of communication pathways pp. 1-23

Holger Finger, Richard Gast, Christian Gerloff, Andreas K Engel and Peter König

Nine quick tips for analyzing network data pp. 1-10

Vincent Miele, Catherine Matias, Stéphane Robin and Stéphane Dray

Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation pp. 1-24

Marina A Ferreira, Evangeline Despin-Guitard, Fernando Duarte, Pierre Degond and Eric Theveneau

Regulatory context drives conservation of glycine riboswitch aptamers pp. 1-24

Matt Crum, Nikhil Ram-Mohan and Michelle M Meyer

Autistic traits influence the strategic diversity of information sampling: Insights from two-stage decision models pp. 1-29

Haoyang Lu, Li Yi and Hang Zhang

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data pp. 1-18

Kai Kang, Qian Meng, Igor Shats, David M Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li and Leping Li

Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15 pp. 1-18

Akira Endo, Mitsuo Uchida, Adam J Kucharski and Sebastian Funk

Volume 15, issue 11, 2019

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process pp. 1-17

Jifan Shi, Tiejun Li, Luonan Chen and Kazuyuki Aihara

Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture pp. 1-35

Jilin W J L Wang, Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet and Plamen Ch Ivanov

Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance pp. 1-28

Charlotte Le Mouel and Romain Brette

A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology pp. 1-28

Chen Zhao, Adam C Mirando, Richard J Sové, Thalyta X Medeiros, Brian H Annex and Aleksander S Popel

Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex pp. 1-19

Marilia Menezes de Oliveira, James C Pang, Peter A Robinson, Xiaochen Liu and Mark M Schira

Uncovering the subtype-specific temporal order of cancer pathway dysregulation pp. 1-19

Sahand Khakabimamaghani, Dujian Ding, Oliver Snow and Martin Ester

Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S pp. 1-19

Nicholas G Reich, Craig J McGowan, Teresa K Yamana, Abhinav Tushar, Evan L Ray, Dave Osthus, Sasikiran Kandula, Logan C Brooks, Willow Crawford-Crudell, Graham Casey Gibson, Evan Moore, Rebecca Silva, Matthew Biggerstaff, Michael A Johansson, Roni Rosenfeld and Jeffrey Shaman

Neural field models for latent state inference: Application to large-scale neuronal recordings pp. 1-23

Michael E Rule, David Schnoerr, Matthias H Hennig and Guido Sanguinetti

No substantial change in the balance between model-free and model-based control via training on the two-step task pp. 1-23

Elmar D Grosskurth, Dominik R Bach, Marcos Economides, Quentin J M Huys and Lisa Holper

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences pp. 1-27

Ilya Plyusnin, Liisa Holm and Petri Törönen

Predicting neuronal dynamics with a delayed gain control model pp. 1-27

Jingyang Zhou, Noah C Benson, Kendrick Kay and Jonathan Winawer

Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer pp. 1-27

Miranda D Stobbe, Gian A Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P Whalley, Emanuele Raineri and Ivo G Gut

A novel network control model for identifying personalized driver genes in cancer pp. 1-27

Wei-Feng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao and Luonan Chen

Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps pp. 1-32

Yichen Zheng and Thomas Wiehe

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets pp. 1-29

M S Vijayabaskar, Debbie K Goode, Nadine Obier, Monika Lichtinger, Amber M L Emmett, Fatin N Zainul Abidin, Nisar Shar, Rebecca Hannah, Salam A Assi, Michael Lie-A-Ling, Berthold Gottgens, Georges Lacaud, Valerie Kouskoff, Constanze Bonifer and David R Westhead

A model of how depth facilitates scene-relative object motion perception pp. 1-29

Oliver W Layton and D C Niehorster

Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data pp. 1-24

Prashant Rangarajan, Sandeep K Mody and Madhav Marathe

Large-scale cortical travelling waves predict localized future cortical signals pp. 1-34

David M Alexander, Tonio Ball, Andreas Schulze-Bonhage and Cees van Leeuwen

Tonic exploration governs both flexibility and lapses pp. 1-37

R Becket Ebitz, Brianna J Sleezer, Hank P Jedema, Charles W Bradberry and Benjamin Y Hayden

Volume 15, issue 10, 2019

Ten simple rules to aid in achieving a vision pp. 1-5

Philip E Bourne

Evaluation of linear and non-linear activation dynamics models for insect muscle pp. 1-30

Nalin Harischandra, Anthony J Clare, Jure Zakotnik, Laura M L Blackburn, Tom Matheson and Volker Dürr

A Kuramoto model of self-other integration across interpersonal synchronization strategies pp. 1-17

Ole Adrian Heggli, Joana Cabral, Ivana Konvalinka, Peter Vuust and Morten L Kringelbach

A simulation of the random and directed motion of dendritic cells in chemokine fields pp. 1-16

Avery Parr, Nicholas R Anderson and Daniel A Hammer

Uncovering and characterizing splice variants associated with survival in lung cancer patients pp. 1-16

Sean West, Sushil Kumar, Surinder K Batra, Hesham Ali and Dario Ghersi

Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi pp. 1-20

Guillermo Vidal-Diez de Ulzurrun, Tsung-Yu Huang, Ching-Wen Chang, Hung-Che Lin and Yen-Ping Hsueh

Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism pp. 1-1

The PLOS Computational Biology Staff

Correction: Generation of Binary Tree-Child phylogenetic networks pp. 1-1

Gabriel Cardona, Joan Carles Pons and Celine Scornavacca

Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer pp. 1-1

Margaret P Chapman, Tyler Risom, Anil J Aswani, Ellen M Langer, Rosalie C Sears and Claire J Tomlin

Correction: Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer pp. 1-1

Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello and Erik de Schutter

Correction: Bayesian hypothesis testing and experimental design for two-photon imaging data pp. 1-1

Luke E Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler and Philipp Berens

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways pp. 1-28

Elisa Salviato, Vera Djordjilović, Monica Chiogna and Chiara Romualdi

Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling pp. 1-28

Parul Maheshwari, Hao Du, Jen Sheen, Sarah M Assmann and Reka Albert

Estimating influenza incidence using search query deceptiveness and generalized ridge regression pp. 1-23

Reid Priedhorsky, Ashlynn R Daughton, Martha Barnard, Fiona O’Connell and Dave Osthus

Categorical encoding of decision variables in orbitofrontal cortex pp. 1-27

Arno Onken, Jue Xie, Stefano Panzeri and Camillo Padoa-Schioppa

Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations pp. 1-27

Carmichael F Ong, Thomas Geijtenbeek, Jennifer L Hicks and Scott L Delp

Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation pp. 1-27

Alireza Kazemi, Bruno Louis, Daniel Isabey, Gary F Nieman, Louis A Gatto, Joshua Satalin, Sarah Baker, James B Grotberg and Marcel Filoche

Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity pp. 1-27

Siva Venkadesh, Alexander O Komendantov, Diek W Wheeler, David J Hamilton and Giorgio A Ascoli

A computational account of threat-related attentional bias pp. 1-21

Toby Wise, Jochen Michely, Peter Dayan and Raymond J Dolan

Hypergraph-based connectivity measures for signaling pathway topologies pp. 1-26

Nicholas Franzese, Adam Groce, T M Murali and Anna Ritz

Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach pp. 1-32

Iran R Roman, Auriel Washburn, Edward W Large, Chris Chafe and Takako Fujioka

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals pp. 1-32

Neil J Bruce, Daniele Narzi, Daniel Trpevski, Siri C van Keulen, Anu G Nair, Ursula Röthlisberger, Rebecca C Wade, Paolo Carloni and Jeanette Hellgren Kotaleski

Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort pp. 1-18

Gabriel Balaban, Brian P Halliday, Wenjia Bai, Bradley Porter, Carlotta Malvuccio, Pablo Lamata, Christopher A Rinaldi, Gernot Plank, Daniel Rueckert, Sanjay K Prasad and Martin J Bishop

The folded X-pattern is not necessarily a statistical signature of decision confidence pp. 1-18

Manuel Rausch and Michael Zehetleitner

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations pp. 1-29

Bogdan Barz, Jennifer Loschwitz and Birgit Strodel

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers pp. 1-29

David J Wooten, Sarah M Groves, Darren R Tyson, Qi Liu, Jing S Lim, Réka Albert, Carlos F Lopez, Julien Sage and Vito Quaranta

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein pp. 1-29

Ruchi Lohia, Reza Salari and Grace Brannigan

Ten simple rules for providing optimal administrative support to research teams pp. 1-9

Romina Garrido, Casandra A Trowbridge and Nana Tamura

TAPES: A tool for assessment and prioritisation in exome studies pp. 1-9

Alexandre Xavier, Rodney J Scott and Bente A Talseth-Palmer

Phylogenetic correlations can suffice to infer protein partners from sequences pp. 1-24

Guillaume Marmier, Martin Weigt and Anne-Florence Bitbol

Color improves edge classification in human vision pp. 1-15

Camille Breuil, Ben J Jennings, Simon Barthelmé, Nathalie Guyader and Frederick A A Kingdom

Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice pp. 1-31

Mehran Spitmaan, Oihane Horno, Emily Chu and Alireza Soltani

Bayesian inference of neuronal assemblies pp. 1-31

Giovanni Diana, Thomas T J Sainsbury and Martin P Meyer

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature pp. 1-22

Qiao Liu, Di He and Lei Xie

Volume 15, issue 9, 2019

Network trade-offs and homeostasis in Arabidopsis shoot architectures pp. 1-19

Adam Conn, Arjun Chandrasekhar, Martin van Rongen, Ottoline Leyser, Joanne Chory and Saket Navlakha

Perspective: Dimensions of the scientific method pp. 1-14

Eberhard O Voit

Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination pp. 1-14

Alexander D Becker, Amy Wesolowski, Ottar N Bjørnstad and Bryan T Grenfell

Close spatial arrangement of mutants favors and disfavors fixation pp. 1-20

Yunming Xiao and Bin Wu

Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space pp. 1-22

Michaëlle N Mayalu, Min-Cheol Kim and H Harry Asada

Fast and near-optimal monitoring for healthcare acquired infection outbreaks pp. 1-22

Bijaya Adhikari, Bryan Lewis, Anil Vullikanti, José Mauricio Jiménez and B Aditya Prakash

Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making pp. 1-22

Amir Dezfouli and Bernard W Balleine

Time scales and wave formation in non-linear spatial public goods games pp. 1-22

Gregory J Kimmel, Philip Gerlee and Philipp M Altrock

Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform pp. 1-22

Anna Matveeva, Michael Fichtner, Katherine McAllister, Christopher McCann, Marc Sturrock, Daniel B Longley and Jochen H M Prehn

A flexible and generalizable model of online latent-state learning pp. 1-31

Amy L Cochran and Josh M Cisler

Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons pp. 1-34

Timothy Rumbell and James Kozloski

Benchmarking network propagation methods for disease gene identification pp. 1-24

Sergio Picart-Armada, Steven J Barrett, David R Willé, Alexandre Perera-Lluna, Alex Gutteridge and Benoit H Dessailly

Loop analysis of blood pressure/volume homeostasis pp. 1-24

Bruno Burlando, Franco Blanchini and Giulia Giordano

Generation of Binary Tree-Child phylogenetic networks pp. 1-29

Gabriel Cardona, Joan Carles Pons and Celine Scornavacca

Invariant neural responses for sensory categories revealed by the time-varying information for communication calls pp. 1-43

Julie E Elie and Frédéric E Theunissen

Ten simple rules for helping newcomers become contributors to open projects pp. 1-10

Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye and Greg Wilson

The FACTS model of speech motor control: Fusing state estimation and task-based control pp. 1-26

Benjamin Parrell, Vikram Ramanarayanan, Srikantan Nagarajan and John Houde

Executable pathway analysis using ensemble discrete-state modeling for large-scale data pp. 1-21

Rohith Palli, Mukta G Palshikar and Juilee Thakar

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data pp. 1-21

Allison L Hicks, Nicole Wheeler, Leonor Sánchez-Busó, Jennifer L Rakeman, Simon R Harris and Yonatan H Grad

Cost-benefit trade-offs in decision-making and learning pp. 1-28

Nura Sidarus, Stefano Palminteri and Valérian Chambon

Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints pp. 1-17

Srinivasan Venkatramanan, Jiangzhuo Chen, Arindam Fadikar, Sandeep Gupta, Dave Higdon, Bryan Lewis, Madhav Marathe, Henning Mortveit and Anil Vullikanti

Designing combination therapies with modeling chaperoned machine learning pp. 1-17

Yin Zhang, Julie M Huynh, Guan-Sheng Liu, Richard Ballweg, Kayenat S Aryeh, Andrew L Paek and Tongli Zhang

MHC binding affects the dynamics of different T-cell receptors in different ways pp. 1-17

Bernhard Knapp, P Anton van der Merwe, Omer Dushek and Charlotte M Deane

EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology pp. 1-13

Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée and Pauline Ezanno

Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity pp. 1-38

Kaiser Niknam, Amir Akbarian, Kelsey Clark, Yasin Zamani, Behrad Noudoost and Neda Nategh

Estimating information in time-varying signals pp. 1-33

Sarah Anhala Cepeda-Humerez, Jakob Ruess and Gašper Tkačik

Prepaid parameter estimation without likelihoods pp. 1-42

Merijn Mestdagh, Stijn Verdonck, Kristof Meers, Tim Loossens and Francis Tuerlinckx

On measuring selection in cancer from subclonal mutation frequencies pp. 1-15

Ivana Bozic, Chay Paterson and Bartlomiej Waclaw

Deconvolving multiplexed protease signatures with substrate reduction and activity clustering pp. 1-18

Qinwei Zhuang, Brandon Alexander Holt, Gabriel A Kwong and Peng Qiu

Quantifying model evidence for yellow fever transmission routes in Africa pp. 1-18

Katy A M Gaythorpe, Kévin Jean, Laurence Cibrelus and Tini Garske

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes pp. 1-27

Olivier Collier, Véronique Stoven and Jean-Philippe Vert

Volume 15, issue 8, 2019

A generative learning model for saccade adaptation pp. 1-35

Carlos R Cassanello, Florian Ostendorf and Martin Rolfs

Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI pp. 1-35

Georgia Koppe, Hazem Toutounji, Peter Kirsch, Stefanie Lis and Daniel Durstewitz

Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions pp. 1-35

Joel A Paulson, Marc Martin-Casas and Ali Mesbah

Predicting the effects of deep brain stimulation using a reduced coupled oscillator model pp. 1-28

Gihan Weerasinghe, Benoit Duchet, Hayriye Cagnan, Peter Brown, Christian Bick and Rafal Bogacz

A computational model for gonadotropin releasing cells in the teleost fish medaka pp. 1-28

Geir Halnes, Simen Tennøe, Trude M Haug, Gaute T Einevoll, Finn-Arne Weltzien and Kjetil Hodne

Transient crosslinking kinetics optimize gene cluster interactions pp. 1-28

Benjamin Walker, Dane Taylor, Josh Lawrimore, Caitlin Hult, David Adalsteinsson, Kerry Bloom and M Gregory Forest

Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer pp. 1-19

Morgan Craig, Kamran Kaveh, Alec Woosley, Andrew S Brown, David Goldman, Elliot Eton, Ravindra M Mehta, Andrew Dhawan, Kazuya Arai, M Mamunur Rahman, Sidi Chen, Martin A Nowak and Aaron Goldman

Directed migration shapes cooperation in spatial ecological public goods games pp. 1-14

Felix Funk and Christoph Hauert

PanoView: An iterative clustering method for single-cell RNA sequencing data pp. 1-17

Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J Zack, Seth Blackshaw and Jiang Qian

Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study pp. 1-17

Laura W Pomeroy, Hyeyoung Kim, Ningchuan Xiao, Mark Moritz and Rebecca Garabed

Reappraising the utility of Google Flu Trends pp. 1-16

Sasikiran Kandula and Jeffrey Shaman

A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes pp. 1-30

Jung Min Han and Vipul Periwal

Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma pp. 1-25

Pieter Verbeke and Tom Verguts

The formation of preference in risky choice pp. 1-25

Moshe Glickman, Orian Sharoni, Dino J Levy, Ernst Niebur, Veit Stuphorn and Marius Usher

Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease pp. 1-25

Song Cui, Qiang Wu, James West and Jiangping Bai

Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability pp. 1-25

Vladimir A Fedorov, Philipp S Orekhov, Ekaterina G Kholina, Artem A Zhmurov, Fazoil I Ataullakhanov, Ilya B Kovalenko and Nikita B Gudimchuk

Twelve quick tips for designing sound dynamical models for bioprocesses pp. 1-8

Francis Mairet and Olivier Bernard

Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity pp. 1-33

Audrey Denizot, Misa Arizono, U Valentin Nägerl, Hédi Soula and Hugues Berry

On the optimal design of metabolic RNA labeling experiments pp. 1-22

Alexey Uvarovskii, Isabel S Naarmann- de Vries and Christoph Dieterich

Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation pp. 1-34

Michael A Colman

Predicting kinase inhibitors using bioactivity matrix derived informer sets pp. 1-29

Huikun Zhang, Spencer S Ericksen, Ching-pei Lee, Gene E Ananiev, Nathan Wlodarchak, Peng Yu, Julie C Mitchell, Anthony Gitter, Stephen J Wright, F Michael Hoffmann, Scott A Wildman and Michael A Newton

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties pp. 1-29

Ljubisa Miskovic, Jonas Béal, Michael Moret and Vassily Hatzimanikatis

Every which way? On predicting tumor evolution using cancer progression models pp. 1-29

Ramon Diaz-Uriarte and Claudia Vasallo

FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics pp. 1-23

Michael Gabel, Tobias Hohl, Andrea Imle, Oliver T Fackler and Frederik Graw

Variation in plastic responses to light results from selection in different competitive environments—A game theoretical approach using virtual plants pp. 1-23

Franca J Bongers, Jacob C Douma, Yoh Iwasa, Ronald Pierik, Jochem B Evers and Niels P R Anten

Bayesian hypothesis testing and experimental design for two-photon imaging data pp. 1-27

Luke E Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler and Philipp Berens

Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models pp. 1-26

Thi Mui Pham, Mirjam Kretzschmar, Xavier Bertrand, Martin Bootsma and on behalf of COMBACTE-MAGNET Consortium

Volume 15, issue 7, 2019

With an eye on uncertainty: Modelling pupillary responses to environmental volatility pp. 1-22

Peter Vincent, Thomas Parr, David Benrimoh and Karl J Friston

Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned pp. 1-22

David Zwicker

Depressive symptoms are associated with blunted reward learning in social contexts pp. 1-22

Lou Safra, Coralie Chevallier and Stefano Palminteri

Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks pp. 1-4

Christian L Vestergaard and Mathieu Génois

Human online adaptation to changes in prior probability pp. 1-26

Elyse H Norton, Luigi Acerbi, Wei Ji Ma and Michael S Landy

Identifying determinants of persistent MRSA bacteremia using mathematical modeling pp. 1-26

Tsuyoshi Mikkaichi, Michael R Yeaman, Alexander Hoffmann and Systems Immunobiology Group Mrsa

Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers pp. 1-26

Jessica M Conway, Alan S Perelson and Jonathan Z Li

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data pp. 1-26

Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J Williams, Weini Huang, Giulio Caravagna, Trevor A Graham and Andrea Sottoriva

Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction pp. 1-21

Maarten H G Heusinkveld, Wouter Huberts, Joost Lumens, Theo Arts, Tammo Delhaas and Koen D Reesink

Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential pp. 1-21

Aleksandra Karolak, Sharan Poonja and Katarzyna A Rejniak

Robustness of respiratory rhythm generation across dynamic regimes pp. 1-27

Jonathan E Rubin and Jeffrey C Smith

Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications pp. 1-23

Joseph A Lewnard, Benjamin A Lopman, Umesh D Parashar, Aisleen Bennett, Naor Bar-Zeev, Nigel A Cunliffe, Prasanna Samuel, M Lourdes Guerrero, Guillermo Ruiz-Palacios, Gagandeep Kang and Virginia E Pitzer

Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks pp. 1-23

Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf and Thomas Dandekar

Information-theoretic analysis of multivariate single-cell signaling responses pp. 1-23

Tomasz Jetka, Karol Nienałtowski, Tomasz Winarski, Sławomir Błoński and Michał Komorowski

Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation pp. 1-32

Nicolas Cazin, Martin Llofriu Alonso, Pablo Scleidorovich Chiodi, Tatiana Pelc, Bruce Harland, Alfredo Weitzenfeld, Jean-Marc Fellous and Peter Ford Dominey

Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity pp. 1-29

Stefano Recanatesi, Gabriel Koch Ocker, Michael A Buice and Eric Shea-Brown

Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference pp. 1-29

Chunhui Cai, Gregory F Cooper, Kevin N Lu, Xiaojun Ma, Shuping Xu, Zhenlong Zhao, Xueer Chen, Yifan Xue, Adrian V Lee, Nathan Clark, Vicky Chen, Songjian Lu, Lujia Chen, Liyue Yu, Harry S Hochheiser, Xia Jiang, Q Jane Wang and Xinghua Lu

Modeling human intuitions about liquid flow with particle-based simulation pp. 1-29

Christopher J Bates, Ilker Yildirim, Joshua B Tenenbaum and Peter Battaglia

Machine and deep learning meet genome-scale metabolic modeling pp. 1-24

Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske and Claudio Angione

Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas pp. 1-17

Víctor M Pérez-García, Luis E Ayala-Hernández, Juan Belmonte-Beitia, Philippe Schucht, Michael Murek, Andreas Raabe and Juan Sepúlveda

Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources pp. 1-1

Yoram Zarai and Tamir Tuller

Disease gene prediction for molecularly uncharacterized diseases pp. 1-14

Juan J Cáceres and Alberto Paccanaro

A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth pp. 1-28

Shiva Rudraraju, Derek E Moulton, Régis Chirat, Alain Goriely and Krishna Garikipati

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks pp. 1-8

Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H Nguyen, Sara Brin Rosenthal, Fernando Pérez and Peter W Rose

Ten simple rules for giving an effective academic job talk pp. 1-8

Shayna A Sura, Lauren L Smith, Monique R Ambrose, C Eduardo Guerra Amorim, Annabel C Beichman, Ana C R Gomez, Mark Juhn, Gaurav S Kandlikar, Julie S Miller, Jazlyn Mooney, Riley O Mummah, Kirk E Lohmueller and James O Lloyd-Smith

Foraging as an evidence accumulation process pp. 1-25

Jacob D Davidson and Ahmed El Hady

Think: Theory for Africa pp. 1-5

Christopher B Currin, Phumlani N Khoza, Alexander D Antrobus, Peter E Latham, Tim P Vogels and Joseph V Raimondo

DART-ID increases single-cell proteome coverage pp. 1-30

Albert Tian Chen, Alexander Franks and Nikolai Slavov

Volume 15, issue 6, 2019

Evolution of interface binding strengths in simplified model of protein quaternary structure pp. 1-15

Alexander S Leonard and Sebastian E Ahnert

Evidence accumulation is biased by motivation: A computational account pp. 1-15

Filip Gesiarz, Donal Cahill and Tali Sharot

Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes pp. 1-15

Atsushi Kamimura, Yoshiya J Matsubara, Kunihiko Kaneko and Nobuto Takeuchi

Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies pp. 1-34

Payam Piray, Amir Dezfouli, Tom Heskes, Michael J Frank and Nathaniel D Daw

Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model pp. 1-36

Mahua Roy and Stacey D Finley

A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model pp. 1-31

Erlend Hodneland, Erik Hanson, Ove Sævareid, Geir Nævdal, Arvid Lundervold, Veronika Šoltészová, Antonella Z Munthe-Kaas, Andreas Deistung, Jürgen R Reichenbach and Jan M Nordbotten

Models that learn how humans learn: The case of decision-making and its disorders pp. 1-33

Amir Dezfouli, Kristi Griffiths, Fabio Ramos, Peter Dayan and Bernard W Balleine

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame pp. 1-22

Rohan V Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Participants and Rhiju Das

Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations pp. 1-27

Hanne Hoitzing, Payam A Gammage, Lindsey Van Haute, Michal Minczuk, Iain G Johnston and Nick S Jones

Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis pp. 1-27

Takaaki Yonekura, Akitoshi Iwamoto, Hironori Fujita and Munetaka Sugiyama

Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons pp. 1-27

Sharmila Venugopal, Soju Seki, David H Terman, Antonios Pantazis, Riccardo Olcese, Martina Wiedau-Pazos and Scott H Chandler

Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells pp. 1-26

Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay and Marek Kimmel

Modeling the temporal dynamics of the gut microbial community in adults and infants pp. 1-21

Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D Silverman, Itzhak Mizrahi and Eran Halperin

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome pp. 1-21

Kymberleigh A Pagel, Danny Antaki, AoJie Lian, Matthew Mort, David N Cooper, Jonathan Sebat, Lilia M Iakoucheva, Sean D Mooney and Predrag Radivojac

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH) pp. 1-21

Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis and Dani Or

Open collaborative writing with Manubot pp. 1-21

Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene and Anthony Gitter

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences pp. 1-21

Ingoo Lee, Jongsoo Keum and Hojung Nam

Ten simple rules for successfully hosting an intern at a scientific software company pp. 1-4

Kristine Briedis, Yi-Shiou Chen and Scott Markel

Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants pp. 1-18

Romain Ligneul

A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test pp. 1-24

David Hasler, Pinelopi Anagnostopoulou, Sylvia Nyilas, Philipp Latzin, Johannes Schittny and Dominik Obrist

Telling ecological networks apart by their structure: A computational challenge pp. 1-13

Matthew J Michalska-Smith and Stefano Allesina

Charting pathways to climate change mitigation in a coupled socio-climate model pp. 1-16

Thomas M Bury, Chris T Bauch and Madhur Anand

Learning to use past evidence in a sophisticated world model pp. 1-20

Sanjeevan Ahilan, Rebecca B Solomon, Yannick-André Breton, Kent Conover, Ritwik K Niyogi, Peter Shizgal and Peter Dayan

Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria pp. 1-1

The PLOS Computational Biology Staff

Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses pp. 1-1

Sven Zenker, Jonathan Rubin and Gilles Clermont

How single neuron properties shape chaotic dynamics and signal transmission in random neural networks pp. 1-35

Samuel P Muscinelli, Wulfram Gerstner and Tilo Schwalger

Ten quick tips for effective dimensionality reduction pp. 1-19

Lan Huong Nguyen and Susan Holmes

Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales pp. 1-25

Joshua M Mueller, Primoz Ravbar, Julie H Simpson and Jean M Carlson

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training pp. 1-12

Annette McGrath, Katherine Champ, Catherine A Shang, Ellen van Dam, Cath Brooksbank and Sarah L Morgan

Volume 15, issue 5, 2019

Noise-precision tradeoff in predicting combinations of mutations and drugs pp. 1-17

Avichai Tendler, Anat Zimmer, Avi Mayo and Uri Alon

Notice of Republication: Ten simple rules for organizing a webinar series pp. 1-1

The PLOS Computational Biology Staff

Beyond Bouma's window: How to explain global aspects of crowding? pp. 1-28

Adrien Doerig, Alban Bornet, Ruth Rosenholtz, Gregory Francis, Aaron M Clarke and Michael H Herzog

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis pp. 1-25

Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias and Christoforos Nikolaou

Perturbing low dimensional activity manifolds in spiking neuronal networks pp. 1-23

Emil Wärnberg and Arvind Kumar

Parameter estimation and identifiability in a neural population model for electro-cortical activity pp. 1-27

Agus Hartoyo, Peter J Cadusch, David T J Liley and Damien G Hicks

Correction: How pupil responses track value-based decision-making during and after reinforcement learning pp. 1-2

Joanne C Van Slooten, Sara Jahfari, Tomas Knapen and Jan Theeuwes

Wisdom of crowds in computational biology pp. 1-2

Jason A Papin and Feilim Mac Gabhann

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features pp. 1-18

David A Knowles, Gina Bouchard and Sylvia Plevritis

Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes pp. 1-18

Anupama Sharma, Shakti N Menon, V Sasidevan and Sitabhra Sinha

A quick guide for using Microsoft OneNote as an electronic laboratory notebook pp. 1-9

Santiago Guerrero, Andrés López-Cortés, Jennyfer M García-Cárdenas, Pablo Saa, Alberto Indacochea, Isaac Armendáriz-Castillo, Ana Karina Zambrano, Verónica Yumiceba, Andy Pérez-Villa, Patricia Guevara-Ramírez, Oswaldo Moscoso-Zea, Joel Paredes, Paola E Leone and César Paz-y-Miño

Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis pp. 1-16

Yaser Saffar Talori, Jing-Shan Zhao, Yun-Fei Liu, Wen-Xiu Lu, Zhi-Heng Li and Jingmai Kathleen O'Connor

Interacting cells driving the evolution of multicellular life cycles pp. 1-16

Yuanxiao Gao, Arne Traulsen and Yuriy Pichugin

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions pp. 1-16

Matti Javanainen, Giray Enkavi, Ramon Guixà-Gonzaléz, Waldemar Kulig, Hector Martinez-Seara, Ilya Levental and Ilpo Vattulainen

Ten quick tips for using a Raspberry Pi pp. 1-11

Anthony C Fletcher and Cameron Mura

Uncovering functional signature in neural systems via random matrix theory pp. 1-20

Assaf Almog, M Renate Buijink, Ori Roethler, Stephan Michel, Johanna H Meijer, Jos H T Rohling and Diego Garlaschelli

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images pp. 1-20

Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne Carpenter, Mark Bathe and Victor Lempitsky

Forecasting national and regional influenza-like illness for the USA pp. 1-20

Michal Ben-Nun, Pete Riley, James Turtle, David P Bacon and Steven Riley

Ten quick tips for biocuration pp. 1-7

Y Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C Munoz-Torres, Drashtti V Vasant, Eleanor Williams and Melissa Haendel

Ten simple rules for carrying out and writing meta-analyses pp. 1-7

Diego A Forero, Sandra Lopez-Leon, Yeimy González-Giraldo and Pantelis G Bagos

The statistics of epidemic transitions pp. 1-14

John M Drake, Tobias S Brett, Shiyang Chen, Bogdan I Epureanu, Matthew J Ferrari, Éric Marty, Paige B Miller, Eamon B O’Dea, Suzanne M O’Regan, Andrew W Park and Pejman Rohani

Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal pp. 1-19

Jakob Lund Dideriksen and Dario Farina

Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias pp. 1-30

Ming Bo Cai, Nicolas W Schuck, Jonathan W Pillow and Yael Niv

A neuromechanistic model for rhythmic beat generation pp. 1-30

Amitabha Bose, Áine Byrne and John Rinzel

Modeling enamel matrix secretion in mammalian teeth pp. 1-12

Teemu J Häkkinen, S Susanna Sova, Ian J Corfe, Leo Tjäderhane, Antti Hannukainen and Jukka Jernvall

Comprehensively benchmarking applications for detecting copy number variation pp. 1-12

Le Zhang, Wanyu Bai, Na Yuan and Zhenglin Du

Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG pp. 1-22

Natalie Schaworonkow and Vadim V Nikulin

Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares pp. 1-21

Yuning Hao, Ming Yan, Blake R Heath, Yu L Lei and Yuying Xie

Differential sustained and transient temporal processing across visual streams pp. 1-26

Anthony Stigliani, Brianna Jeska and Kalanit Grill-Spector

State-aware detection of sensory stimuli in the cortex of the awake mouse pp. 1-24

Audrey J Sederberg, Aurélie Pala, He J V Zheng, Biyu J He and Garrett B Stanley

Efficient algorithms to discover alterations with complementary functional association in cancer pp. 1-24

Rebecca Sarto Basso, Dorit S Hochbaum and Fabio Vandin

Human representation of multimodal distributions as clusters of samples pp. 1-29

Jingwei Sun, Jian Li and Hang Zhang

Volume 15, issue 4, 2019

SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species pp. 1-30

Đorđe Miladinović, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian Baumann, Antoine Adamantidis, Steven A Brown and Joachim M Buhmann

The intrinsic dimension of protein sequence evolution pp. 1-16

Elena Facco, Andrea Pagnani, Elena Tea Russo and Alessandro Laio

Revealing evolutionary constraints on proteins through sequence analysis pp. 1-16

Shou-Wen Wang, Anne-Florence Bitbol and Ned S Wingreen

A quick guide for student-driven community genome annotation pp. 1-11

Prashant S Hosmani, Teresa Shippy, Sherry Miller, Joshua B Benoit, Monica Munoz-Torres, Mirella Flores-Gonzalez, Lukas A Mueller, Helen Wiersma-Koch, Tom D’Elia, Susan J Brown and Surya Saha

Physical constraints on accuracy and persistence during breast cancer cell chemotaxis pp. 1-20

Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler and Bumsoo Han

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions pp. 1-19

Anne Richelle, Austin W T Chiang, Chih-Chung Kuo and Nathan E Lewis

Ten simple rules for organizing a webinar series pp. 1-7

Faisal M Fadlelmola, Sumir Panji, Azza E Ahmed, Amel Ghouila, Wisdom A Akurugu, Jean-Baka Domelevo Entfellner, Oussema Souiai, Nicola Mulder and H3ABioNet Research working group as members of the H3Africa Consortium

Network motifs and their origins pp. 1-7

Lewi Stone, Daniel Simberloff and Yael Artzy-Randrup

Ten simple rules for providing a meaningful research experience to high school students pp. 1-7

Emily A Lescak, Kate M O’Neill, Giovanna M Collu and Subhamoy Das

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms pp. 1-21

Kyriaki Kalimeri, Matteo Delfino, Ciro Cattuto, Daniela Perrotta, Vittoria Colizza, Caroline Guerrisi, Clement Turbelin, Jim Duggan, John Edmunds, Chinelo Obi, Richard Pebody, Ana O Franco, Yamir Moreno, Sandro Meloni, Carl Koppeschaar, Charlotte Kjelsø, Ricardo Mexia and Daniela Paolotti

Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length pp. 1-21

Kai Liu, Brian Chu, Jay Newby, Elizabeth L Read, John Lowengrub and Jun Allard

Chemical features mining provides new descriptive structure-odor relationships pp. 1-21

Carmen C Licon, Guillaume Bosc, Mohammed Sabri, Marylou Mantel, Arnaud Fournel, Caroline Bushdid, Jerome Golebiowski, Celine Robardet, Marc Plantevit, Mehdi Kaytoue and Moustafa Bensafi

Approximate Bayesian estimation of coevolutionary arms races pp. 1-21

Scott L Nuismer and Bob Week

Neural crest streaming as an emergent property of tissue interactions during morphogenesis pp. 1-21

András Szabó, Eric Theveneau, Melissa Turan and Roberto Mayor

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) pp. 1-10

Hailong Meng, Gur Yaari, Christopher R Bolen, Stefan Avey and Steven H Kleinstein

A Bayesian framework for the analysis of systems biology models of the brain pp. 1-29

Joshua Russell-Buckland, Christopher P Barnes and Ilias Tachtsidis

A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism pp. 1-29

Oveis Jamialahmadi, Sameereh Hashemi-Najafabadi, Ehsan Motamedian, Stefano Romeo and Fatemeh Bagheri

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size pp. 1-24

Daniel I S Rosenbloom, Peter Bacchetti, Mars Stone, Xutao Deng, Ronald J Bosch, Douglas D Richman, Janet D Siliciano, John W Mellors, Steven G Deeks, Roger G Ptak, Rebecca Hoh, Sheila M Keating, Melanie Dimapasoc, Marta Massanella, Jun Lai, Michele D Sobolewski, Deanna A Kulpa, Michael P Busch and for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group

Confidence resets reveal hierarchical adaptive learning in humans pp. 1-24

Micha Heilbron and Florent Meyniel

Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits pp. 1-34

Yifan Gu, Yang Qi and Pulin Gong

Isolating and quantifying the role of developmental noise in generating phenotypic variation pp. 1-31

Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble and Ylenia Chiari

Evolutionary multiplayer games on graphs with edge diversity pp. 1-22

Qi Su, Lei Zhou and Long Wang

Ten simple rules towards healthier research labs pp. 1-8

Fernando T Maestre

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation pp. 1-25

Marko Järvenpää, Mohamad R Abdul Sater, Georgia K Lagoudas, Paul C Blainey, Loren G Miller, James A McKinnell, Susan S Huang, Yonatan H Grad and Pekka Marttinen

Competing evolutionary paths in growing populations with applications to multidrug resistance pp. 1-25

Michael D Nicholson and Tibor Antal

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks pp. 1-25

Graeme Benstead-Hume, Xiangrong Chen, Suzanna R Hopkins, Karen A Lane, Jessica A Downs and Frances M G Pearl

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder pp. 1-25

Abrar E Al-Shaer, George R Flentke, Mark E Berres, Ana Garic and Susan M Smith

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity pp. 1-25

Lex E Flagel, Benjamin K Blackman, Lila Fishman, Patrick J Monnahan, Andrea Sweigart and John K Kelly

Inferring neural circuit structure from datasets of heterogeneous tuning curves pp. 1-38

Takafumi Arakaki, G Barello and Yashar Ahmadian

Bet-hedging strategies in expanding populations pp. 1-17

Paula Villa Martín, Miguel A Muñoz and Simone Pigolotti

Model diagnostics and refinement for phylodynamic models pp. 1-17

Max S Y Lau, Bryan T Grenfell, Colin J Worby and Gavin J Gibson

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features pp. 1-35

Craig A Magaret, David C Benkeser, Brian D Williamson, Bhavesh R Borate, Lindsay N Carpp, Ivelin S Georgiev, Ian Setliff, Adam S Dingens, Noah Simon, Marco Carone, Christopher Simpkins, David Montefiori, Galit Alter, Wen-Han Yu, Michal Juraska, Paul T Edlefsen, Shelly Karuna, Nyaradzo M Mgodi, Srilatha Edugupanti and Peter B Gilbert

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis pp. 1-28

Remco Bouckaert, Timothy G Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K Mendes, Nicola F Müller, Huw A Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler and Alexei J Drummond

TASmania: A bacterial Toxin-Antitoxin Systems database pp. 1-28

Hatice Akarsu, Patricia Bordes, Moise Mansour, Donna-Joe Bigot, Pierre Genevaux and Laurent Falquet

I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment pp. 1-23

Stelios Pavlidis, Calixte Monast, Matthew J Loza, Patrick Branigan, Kiang F Chung, Ian M Adcock, Yike Guo, Anthony Rowe and Frédéric Baribaud

Imperfect Bayesian inference in visual perception pp. 1-27

Elina Stengård and Ronald van den Berg

A multiscale model of epigenetic heterogeneity-driven cell fate decision-making pp. 1-27

Núria Folguera-Blasco, Rubén Pérez-Carrasco, Elisabet Cuyàs, Javier A Menendez and Tomás Alarcón

The relative contribution of color and material in object selection pp. 1-27

Ana Radonjić, Nicolas P Cottaris and David H Brainard

Contextual influence on confidence judgments in human reinforcement learning pp. 1-27

Mael Lebreton, Karin Bacily, Stefano Palminteri and Jan Engelmann

Learning and forgetting using reinforced Bayesian change detection pp. 1-41

Vincent Moens and Alexandre Zénon

Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs pp. 1-18

Cheng Liang, Shengpeng Yu and Jiawei Luo

Volume 15, issue 3, 2019

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows pp. 1-19

Pei-Chi Yang, Shweta Purawat, Pek U Ieong, Mao-Tsuen Jeng, Kevin R DeMarco, Igor Vorobyov, Andrew D McCulloch, Ilkay Altintas, Rommie E Amaro and Colleen E Clancy

Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations pp. 1-19

Ramu Anandakrishnan, Robin T Varghese, Nicholas A Kinney and Harold R Garner

Spatial clustering and common regulatory elements correlate with coordinated gene expression pp. 1-16

Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A Taft, Guang Yao, Fan Bai and Jianhua Xing

A dynamic power-law sexual network model of gonorrhoea outbreaks pp. 1-20

Lilith K Whittles, Peter J White and Xavier Didelot

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data pp. 1-20

Finlay Campbell, Anne Cori, Neil Ferguson and Thibaut Jombart

Agent-based modeling of morphogenetic systems: Advantages and challenges pp. 1-31

Chad M Glen, Melissa L Kemp and Eberhard O Voit

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome pp. 1-31

Bernardo P de Almeida, André F Vieira, Joana Paredes, Mónica Bettencourt-Dias and Nuno L Barbosa-Morais

Soma-axon coupling configurations that enhance neuronal coincidence detection pp. 1-34

Joshua H Goldwyn, Michiel W H Remme and John Rinzel

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models pp. 1-29

Sungho Shin, Ophelia S Venturelli and Victor M Zavala

A spectrum of routing strategies for brain networks pp. 1-24

Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P van den Heuvel, Patric Hagmann and Olaf Sporns

Myopic control of neural dynamics pp. 1-24

David Hocker and Il Memming Park

A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus pp. 1-24

Sifat A Moon, Lee W Cohnstaedt, D Scott McVey and Caterina M Scoglio

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory pp. 1-26

Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel Christiaen, David Gresham and Daniel Tranchina

Building a mechanistic mathematical model of hepatitis C virus entry pp. 1-26

Mphatso Kalemera, Dilyana Mincheva, Joe Grove and Christopher J R Illingworth

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence pp. 1-21

Manh Cuong Ngô, Mads Peter Heide-Jørgensen and Susanne Ditlevsen

A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations pp. 1-21

Weiling Li, Lin Lin, Raunaq Malhotra, Lei Yang, Raj Acharya and Mary Poss

Optimizing the depth and the direction of prospective planning using information values pp. 1-21

Can Eren Sezener, Amir Dezfouli and Mehdi Keramati

Latent goal models for dynamic strategic interaction pp. 1-21

Shariq N Iqbal, Lun Yin, Caroline B Drucker, Qian Kuang, Jean-François Gariépy, Michael L Platt and John M Pearson

An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections pp. 1-32

T Alex Perkins, Robert C Reiner, Guido España, Quirine A ten Bosch, Amit Verma, Kelly A Liebman, Valerie A Paz-Soldan, John P Elder, Amy C Morrison, Steven T Stoddard, Uriel Kitron, Gonzalo M Vazquez-Prokopec, Thomas W Scott and David L Smith

ChIPulate: A comprehensive ChIP-seq simulation pipeline pp. 1-32

Vishaka Datta, Sridhar Hannenhalli and Rahul Siddharthan

Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability pp. 1-1

Vasileios Vavourakis, Triantafyllos Stylianopoulos and Peter A Wijeratne

Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines pp. 1-40

Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Kevin Alessandri, Pierre Nassoy and Dirk Drasdo

Humans use multi-objective control to regulate lateral foot placement when walking pp. 1-28

Jonathan B Dingwell and Joseph P Cusumano

Determination of effective synaptic conductances using somatic voltage clamp pp. 1-28

Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou and David Cai

Evolutionary model for the unequal segregation of high copy plasmids pp. 1-17

Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn and Johannes Müller

Bacterial surface colonization, preferential attachment and fitness under periodic stress pp. 1-17

Maor Grinberg, Tomer Orevi and Nadav Kashtan

Bayes-optimal estimation of overlap between populations of fixed size pp. 1-17

Daniel B Larremore

Methods for computing the maximum performance of computational models of fMRI responses pp. 1-25

Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano and Federico De Martino

A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell pp. 1-25

Robert John Holash and Brian R MacIntosh

Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas pp. 1-25

Lawrence W Sheppard, Emma J Defriez, Philip C Reid and Daniel C Reuman

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling pp. 1-25

Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D Price, Chenguang Liu and Zhuo Wang

Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks pp. 1-33

Manuel Beiran and Srdjan Ostojic

Ten principles for machine-actionable data management plans pp. 1-15

Tomasz Miksa, Stephanie Simms, Daniel Mietchen and Sarah Jones

Computational geometry for modeling neural populations: From visualization to simulation pp. 1-41

Marc de Kamps, Mikkel Lepperød and Yi Ming Lai

In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics pp. 1-18

David R Berg, Chetan P Offord, Iris Kemler, Matthew K Ennis, Lawrence Chang, George Paulik, Zeljko Bajzer, Claudia Neuhauser and David Dingli

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities pp. 1-18

Lei Wang, Zhu-Hong You, Xing Chen, Yang-Ming Li, Ya-Nan Dong, Li-Ping Li and Kai Zheng

Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits pp. 1-23

Florian Eberhardt, Andreas V M Herz and Stefan Häusler

Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition pp. 1-27

Marieke Rohde, Kenichi Narioka, Jochen J Steil, Lina K Klein and Marc O Ernst

The gradient of the reinforcement landscape influences sensorimotor learning pp. 1-27

Joshua G A Cashaback, Christopher K Lao, Dimitrios J Palidis, Susan K Coltman, Heather R McGregor and Paul L Gribble

Rapid interpretation of small-angle X-ray scattering data pp. 1-27

Marie Weiel, Ines Reinartz and Alexander Schug

Volume 15, issue 2, 2019

Learning the payoffs and costs of actions pp. 1-32

Moritz Möller and Rafal Bogacz

Maps of variability in cell lineage trees pp. 1-32

Damien G Hicks, Terence P Speed, Mohammed Yassin and Sarah M Russell

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction pp. 1-21

Amin Allahyar, Joske Ubels and Jeroen de Ridder

Phylogenies from dynamic networks pp. 1-21

Cornelia Metzig, Oliver Ratmann, Daniela Bezemer and Caroline Colijn

Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components pp. 1-21

Nicholas Rogers, John Hermiz, Mehran Ganji, Erik Kaestner, Kıvılcım Kılıç, Lorraine Hossain, Martin Thunemann, Daniel R Cleary, Bob S Carter, David Barba, Anna Devor, Eric Halgren, Shadi A Dayeh and Vikash Gilja

A local measure of symmetry and orientation for individual spikes of grid cells pp. 1-21

Simon N Weber and Henning Sprekeler

Information integration in large brain networks pp. 1-26

Daniel Toker and Friedrich T Sommer

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics pp. 1-26

Moritz Hoffmann, Christoph Fröhner and Frank Noé

Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos pp. 1-27

Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui and Philippe Andrey

Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors pp. 1-29

Lior Tiroshi and Joshua A Goldberg

Identifying individual risk rare variants using protein structure guided local tests (POINT) pp. 1-24

Rachel Marceau West, Wenbin Lu, Daniel M Rotroff, Melaine A Kuenemann, Sheng-Mao Chang, Michael C Wu, Michael J Wagner, John B Buse, Alison A Motsinger-Reif, Denis Fourches and Jung-Ying Tzeng

A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks pp. 1-24

Koichiro Uriu and Hajime Tei

Identifying the mechanism for superdiffusivity in mouse fibroblast motility pp. 1-15

Giuseppe Passucci, Megan E Brasch, James H Henderson, Vasily Zaburdaev and M Lisa Manning

A numerical approach for a discrete Markov model for progressing drug resistance of cancer pp. 1-15

Masayuki Maeda and Hideaki Yamashita

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis pp. 1-15

Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell and Qin Ma

Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions pp. 1-22

Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora and Udo Reichl

Efficient neural decoding of self-location with a deep recurrent network pp. 1-22

Ardi Tampuu, Tambet Matiisen, H Freyja Ólafsdóttir, Caswell Barry and Raul Vicente

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion pp. 1-36

Nico M Franz, Lukas J Musher, Joseph W Brown, Shizhuo Yu and Bertram Ludäscher

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses pp. 1-25

Stephen Woloszynek, Zhengqiao Zhao, Jian Chen and Gail L Rosen

Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana pp. 1-25

Shayne M Plourde, Prativa Amom, Michelle Tan, Adriana T Dawes and Anna A Dobritsa

Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling pp. 1-25

Nitzan Shahar, Tobias U Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, Consortium Nspn and Raymond J Dolan

Independent working memory resources for egocentric and allocentric spatial information pp. 1-20

David Aagten-Murphy and Paul M Bays

Development and validation of influenza forecasting for 64 temperate and tropical countries pp. 1-20

Sarah C Kramer and Jeffrey Shaman

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks pp. 1-16

Ahmed A Metwally, Philip S Yu, Derek Reiman, Yang Dai, Patricia W Finn and David L Perkins

Social evolution under demographic stochasticity pp. 1-13

David V McLeod and Troy Day

How good are pathogenicity predictors in detecting benign variants? pp. 1-17

Abhishek Niroula and Mauno Vihinen

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications pp. 1-17

He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov and Feixiong Cheng

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15 pp. 1-17

Sebastian Funk, Anton Camacho, Adam J Kucharski, Rachel Lowe, Rosalind M Eggo and W John Edmunds

Structure and variability of delay activity in premotor cortex pp. 1-17

Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I Ryu and Krishna V Shenoy

Script of Scripts: A pragmatic workflow system for daily computational research pp. 1-14

Gao Wang and Bo Peng

Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited pp. 1-19

Dave Osthus, Ashlynn R Daughton and Reid Priedhorsky

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis pp. 1-19

Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk and Mark R Chance

Predictability in process-based ensemble forecast of influenza pp. 1-19

Sen Pei, Mark A Cane and Jeffrey Shaman

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas pp. 1-19

David G P van IJzendoorn, Karoly Szuhai, Inge H Briaire- de Bruijn, Marie Kostine, Marieke L Kuijjer and Judith V M G Bovée

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis pp. 1-28

Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D Zoltowski and Peng Tao

Correction: Epistasis in genomic and survival data of cancer patients pp. 1-1

Dariusz Matlak and Ewa Szczurek

Volume 15, issue 1, 2019

Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects pp. 1-1

The PLOS Computational Biology Staff

Computational translation of genomic responses from experimental model systems to humans pp. 1-19

Douglas K Brubaker, Elizabeth A Proctor, Kevin M Haigis and Douglas A Lauffenburger

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis pp. 1-19

Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W Pasternak and Marta Filizola

Calcium phosphate precipitation inhibits mitochondrial energy metabolism pp. 1-19

Sathyavani Malyala, Yizhu Zhang, Jasiel O Strubbe and Jason N Bazil

Designing and running an advanced Bioinformatics and genome analyses course in Tunisia pp. 1-13

Fatma Z Guerfali, Dhafer Laouini, Abdellatif Boudabous and Fredj Tekaia

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens pp. 1-13

Joel Ostblom, Emanuel J P Nazareth, Mukul Tewary and Peter W Zandstra

Protein—protein binding supersites pp. 1-17

Raji Viswanathan, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller and Andras Fiser

Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization pp. 1-20

Timothy D Majarian, Robert F Murphy and Seema S Lakdawala

A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex pp. 1-20

Margot C Bjoring and C Daniel Meliza

On identifying collective displacements in apo-proteins that reveal eventual binding pathways pp. 1-18

Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal and Surajit Sengupta

OpenCASA: A new open-source and scalable tool for sperm quality analysis pp. 1-18

Carlos Alquézar-Baeta, Silvia Gimeno-Martos, Sara Miguel-Jiménez, Pilar Santolaria, Jesús Yániz, Inmaculada Palacín, Adriana Casao, José Álvaro Cebrián-Pérez, Teresa Muiño-Blanco and Rosaura Pérez-Pé

Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model pp. 1-24

Anna C Sales, Karl J Friston, Matthew W Jones, Anthony E Pickering and Rosalyn J Moran

Sour grapes and sweet victories: How actions shape preferences pp. 1-24

Fabien Vinckier, Lionel Rigoux, Irma T Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau and Mathias Pessiglione

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor pp. 1-29

Keesha E Erickson, Oleksii S Rukhlenko, Md Shahinuzzaman, Kalina P Slavkova, Yen Ting Lin, Ryan Suderman, Edward C Stites, Marian Anghel, Richard G Posner, Dipak Barua, Boris N Kholodenko and William S Hlavacek

The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments pp. 1-23

Zachary R Fox and Brian Munsky

STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds pp. 1-23

Abdul-Saboor Sheikh, Nicol S Harper, Jakob Drefs, Yosef Singer, Zhenwen Dai, Richard E Turner and Jörg Lücke

Deep image reconstruction from human brain activity pp. 1-23

Guohua Shen, Tomoyasu Horikawa, Kei Majima and Yukiyasu Kamitani

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems pp. 1-4

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel and Anders Wallqvist

Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli pp. 1-26

David Hodgson, Andrew D Rowan, Francesco Falciani and Carole J Proctor

PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data pp. 1-26

Yu-Han H Hsu, Claire Churchhouse, Tune H Pers, Josep M Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K Morgen, Clicerio Gonzalez, Maria E Gonzalez, Tonu Esko and Joel N Hirschhorn

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures pp. 1-21

Jordan J Clark, Mark L Benson, Richard D Smith and Heather A Carlson

Predicting change: Approximate inference under explicit representation of temporal structure in changing environments pp. 1-31

Dimitrije Marković, Andrea M F Reiter and Stefan J Kiebel

Prediction of ultra-high-order antibiotic combinations based on pairwise interactions pp. 1-15

Itay Katzir, Murat Cokol, Bree B Aldridge and Uri Alon

Spatial synchronization codes from coupled rate-phase neurons pp. 1-42

Joseph D Monaco, Rose M De Guzman, Hugh T Blair and Kechen Zhang