PLOS Computational Biology

2005 - 2022

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Volume 13, issue 12, 2017

Feature reliability determines specificity and transfer of perceptual learning in orientation search pp. 1-18

Amit Yashar and Rachel N Denison

Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems pp. 1-29

Tsvetomira Radeva, Anna Dornhaus, Nancy Lynch, Radhika Nagpal and Hsin-Hao Su

System identification of signaling dependent gene expression with different time-scale data pp. 1-29

Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi and Shinya Kuroda

Complete hazard ranking to analyze right-censored data: An ALS survival study pp. 1-21

Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A Goutman, Bhramar Mukherjee, Ivo D Dinov, Yuanfang Guan and for the Pooled Resource Open-Access ALS Clinical Trials Consortium

Non-linear auto-regressive models for cross-frequency coupling in neural time series pp. 1-32

Tom Dupré la Tour, Lucille Tallot, Laetitia Grabot, Valérie Doyère, Virginie van Wassenhove, Yves Grenier and Alexandre Gramfort

Genetic drift and selection in many-allele range expansions pp. 1-31

Bryan T Weinstein, Maxim O Lavrentovich, Wolfram Möbius, Andrew W Murray and David R Nelson

Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks pp. 1-37

Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P Nolan and Wing Hung Wong

pSSAlib: The partial-propensity stochastic chemical network simulator pp. 1-15

Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch and Ivo F Sbalzarini

Correction: Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions pp. 1-3

The PLOS Computational Biology Staff

Ten simple rules for writing a career development award proposal pp. 1-6

Crystal M Botham, Joshua A Arribere, Sky W Brubaker and Kevin T Beier

Physiological models of the lateral superior olive pp. 1-50

Go Ashida, Daniel J Tollin and Jutta Kretzberg

Ten simple rules for international short-term research stays pp. 1-5

Diego A Forero, Sandra Lopez-Leon and George P Patrinos

Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP pp. 1-8

Sanjay Sonney, Jeremy Leipzig, Marie T Lott, Shiping Zhang, Vincent Procaccio, Douglas C Wallace and Neal Sondheimer

Correction: Signatures of criticality arise from random subsampling in simple population models pp. 1-1

The PLOS Computational Biology Staff

LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction pp. 1-28

Xing Chen and Li Huang

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design pp. 1-13

Rebecca F Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L Dolan and Jeffrey J Gray

Stabilizing patterns in time: Neural network approach pp. 1-16

Nadav Ben-Shushan and Misha Tsodyks

MAGPIE: Simplifying access and execution of computational models in the life sciences pp. 1-11

Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder and Ingmar Glauche

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock pp. 1-20

Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A Porter, Dima Kozakov and Ora Schueler-Furman

MPLasso: Inferring microbial association networks using prior microbial knowledge pp. 1-20

Chieh Lo and Radu Marculescu

Volume 13, issue 11, 2017

Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue pp. 1-30

Mark A Walker, Viatcheslav Gurev, John J Rice, Joseph L Greenstein and Raimond L Winslow

fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks pp. 1-12

Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody and Marc Baguelin

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq pp. 1-25

Ruolin Liu and Julie Dickerson

A hierarchical stochastic model for bistable perception pp. 1-38

Stefan Albert, Katharina Schmack, Philipp Sterzer and Gaby Schneider

Correction: A Unifying Probabilistic View of Associative Learning pp. 1-1

The PLOS Computational Biology Staff

mixOmics: An R package for ‘omics feature selection and multiple data integration pp. 1-19

Florian Rohart, Benoît Gautier, Amrit Singh and Kim-Anh Lê Cao

Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems pp. 1-19

Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro and Carlo Piermarocchi

Improving virtual screening of G protein-coupled receptors via ligand-directed modeling pp. 1-40

Thomas Coudrat, John Simms, Arthur Christopoulos, Denise Wootten and Patrick M Sexton

Tracking urban human activity from mobile phone calling patterns pp. 1-16

Daniel Monsivais, Asim Ghosh, Kunal Bhattacharya, Robin I M Dunbar and Kimmo Kaski

The use of ambient humidity conditions to improve influenza forecast pp. 1-16

Jeffrey Shaman, Sasikiran Kandula, Wan Yang and Alicia Karspeck

Metabolic dynamics restricted by conserved carriers: Jamming and feedback pp. 1-16

Tetsuhiro S Hatakeyama and Chikara Furusawa

Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States pp. 1-17

Teresa K Yamana, Sasikiran Kandula and Jeffrey Shaman

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation pp. 1-17

Rosemary M McCloskey and Art F Y Poon

Multivariate pattern dependence pp. 1-20

Stefano Anzellotti, Alfonso Caramazza and Rebecca Saxe

Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception pp. 1-29

Alexis T Baria, Brian Maniscalco and Biyu J He

Are there physicochemical differences between allosteric and competitive ligands? pp. 1-18

Richard D Smith, Jing Lu and Heather A Carlson

Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks pp. 1-18

Alizée Lopez-Persem, Lionel Rigoux, Sacha Bourgeois-Gironde, Jean Daunizeau and Mathias Pessiglione

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation pp. 1-18

Alejandro F Villaverde and Julio R Banga

Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins pp. 1-26

Daniel R Romano, Matthew C Pharris, Neal M Patel and Tamara L Kinzer-Ursem

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil pp. 1-26

Shaima Hashem, Matteo Tiberti and Arianna Fornili

A Bayesian method for detecting pairwise associations in compositional data pp. 1-21

Emma Schwager, Himel Mallick, Steffen Ventz and Curtis Huttenhower

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs pp. 1-23

Michael F Sloma and David H Mathews

A modeling study of budding yeast colony formation and its relationship to budding pattern and aging pp. 1-23

Yanli Wang, Wing-Cheong Lo and Ching-Shan Chou

An efficient moments-based inference method for within-host bacterial infection dynamics pp. 1-27

David J Price, Alexandre Breuzé, Richard Dybowski, Piero Mastroeni and Olivier Restif

Identifying influential neighbors in animal flocking pp. 1-32

Li Jiang, Luca Giuggioli, Andrea Perna, Ramón Escobedo, Valentin Lecheval, Clément Sire, Zhangang Han and Guy Theraulaz

Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays pp. 1-33

Gonzalo E Mena, Lauren E Grosberg, Sasidhar Madugula, Paweł Hottowy, Alan Litke, John Cunningham, E J Chichilnisky and Liam Paninski

A free-boundary model of a motile cell explains turning behavior pp. 1-22

Masoud Nickaeen, Igor L Novak, Stephanie Pulford, Aaron Rumack, Jamie Brandon, Boris M Slepchenko and Alex Mogilner

The effect of spatial randomness on the average fixation time of mutants pp. 1-22

Suzan Farhang-Sardroodi, Amir H Darooneh, Moladad Nikbakht, Natalia L Komarova and Mohammad Kohandel

A Rescorla-Wagner drift-diffusion model of conditioning and timing pp. 1-50

André Luzardo, Eduardo Alonso and Esther Mondragón

Volume 13, issue 10, 2017

Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition pp. 1-24

Timothy N Rubin, Oluwasanmi Koyejo, Krzysztof J Gorgolewski, Michael N Jones, Russell A Poldrack and Tal Yarkoni

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action pp. 1-24

Shiran Abadi, Winston X Yan, David Amar and Itay Mayrose

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets pp. 1-29

Evelina Gabasova, John Reid and Lorenz Wernisch

Dynamics and heterogeneity of brain damage in multiple sclerosis pp. 1-26

Ekaterina Kotelnikova, Narsis A Kiani, Elena Abad, Elena H Martinez-Lapiscina, Magi Andorra, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi Garcia-Ojalvo and Pablo Villoslada

Ten simple rules for writing a response to reviewers pp. 1-4

William Stafford Noble

Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery pp. 1-21

Andrew J K Phillips, Elizabeth B Klerman and James P Butler

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization pp. 1-21

Claire N Bedbrook, Kevin K Yang, Austin J Rice, Viviana Gradinaru and Frances H Arnold

Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI pp. 1-32

Jaron T Colas, Wolfgang M Pauli, Tobias Larsen, J Michael Tyszka and John P O’Doherty

Inferring oscillatory modulation in neural spike trains pp. 1-31

Kensuke Arai and Robert E Kass

The evolutionary origins of Lévy walk foraging pp. 1-31

Marina E Wosniack, Marcos C Santos, Ernesto P Raposo, Gandhi M Viswanathan and Marcos G E da Luz

The structured ‘low temperature’ phase of the retinal population code pp. 1-31

Mark L Ioffe and Michael J Berry

Systematic, network-based characterization of therapeutic target inhibitors pp. 1-22

Yao Shen, Mariano J Alvarez, Brygida Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan and Andrea Califano

Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster pp. 1-22

Cen Wan, Jonathan G Lees, Federico Minneci, Christine A Orengo and David T Jones

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology pp. 1-12

Kevin S Bonham and Melanie I Stefan

Neural field model to reconcile structure with function in primary visual cortex pp. 1-30

James Rankin and Frédéric Chavane

Identification of immune signatures predictive of clinical protection from malaria pp. 1-14

John Joseph Valletta and Mario Recker

General principles of binding between cell surface receptors and multi-specific ligands: A computational study pp. 1-19

Jiawen Chen, Steven C Almo and Yinghao Wu

Learning infectious disease epidemiology in a modern framework pp. 1-11

Andreas Handel

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience pp. 1-11

Kim T Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L Fernandes, David P Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola Mulder and H3ABioNet Consortium's Education Training and Working Group as members of the H3Africa Consortium

A single-cell spiking model for the origin of grid-cell patterns pp. 1-41

Tiziano D’Albis and Richard Kempter

Network propagation in the cytoscape cyberinfrastructure pp. 1-9

Daniel E Carlin, Barry Demchak, Dexter Pratt, Eric Sage and Trey Ideker

Vicus: Exploiting local structures to improve network-based analysis of biological data pp. 1-18

Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou and Anna Goldenberg

A mechanistic spatio-temporal framework for modelling individual-to-individual transmission—With an application to the 2014-2015 West Africa Ebola outbreak pp. 1-18

Max S Y Lau, Gavin J Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, Jessica Metcalf, Benjamin D Dalziel and Bryan T Grenfell

Signatures of criticality arise from random subsampling in simple population models pp. 1-23

Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge and Jakob H Macke

Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time pp. 1-23

Anna Hake and Nico Pfeifer

A deep convolutional neural network for classification of red blood cells in sickle cell anemia pp. 1-27

Mengjia Xu, Dimitrios P Papageorgiou, Sabia Z Abidi, Ming Dao, Hong Zhao and George Em Karniadakis

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics pp. 1-27

Roman Shevchuk and Jochen S Hub

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models pp. 1-44

Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün and Moritz Helias

A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system pp. 1-37

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

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data pp. 1-33

Nan Lin, Yun Zhu, Ruzong Fan and Momiao Xiong

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing pp. 1-15

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir and Carl Kingsford

Ten simple rules in considering a career in academia versus government pp. 1-5

Philip E Bourne

Learning causal networks with latent variables from multivariate information in genomic data pp. 1-25

Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh and Hervé Isambert

Point process analysis of noise in early invertebrate vision pp. 1-25

Kris V Parag and Glenn Vinnicombe

Identifying parameter regions for multistationarity pp. 1-25

Carsten Conradi, Elisenda Feliu, Maya Mincheva and Carsten Wiuf

A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation pp. 1-25

Thomas Heidlauf, Thomas Klotz, Christian Rode, Tobias Siebert and Oliver Röhrle

Image-based model of the spectrin cytoskeleton for red blood cell simulation pp. 1-25

Thomas G Fai, Alejandra Leo-Macias, David L Stokes and Charles S Peskin

A Bayesian approach to modelling heterogeneous calcium responses in cell populations pp. 1-25

Agne Tilūnaitė, Wayne Croft, Noah Russell, Tomas C Bellamy and Rüdiger Thul

Correction: Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model pp. 1-1

The PLOS Computational Biology Staff

Object detection through search with a foveated visual system pp. 1-28

Emre Akbas and Miguel P Eckstein

A unifying Bayesian account of contextual effects in value-based choice pp. 1-28

Francesco Rigoli, Christoph Mathys, Karl J Friston and Raymond J Dolan

Volume 13, issue 9, 2017

Ten simple rules for structuring papers pp. 1-9

Brett Mensh and Konrad Kording

Cost-efficient vaccination protocols for network epidemiology pp. 1-18

Petter Holme and Nelly Litvak

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations pp. 1-27

Shintaroh Kubo, Wenfei Li and Shoji Takada

Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties pp. 1-23

Harang Ju, Costa M Colbert and William B Levy

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency pp. 1-37

Yuhan Chen, Shengjun Wang, Claus C Hilgetag and Changsong Zhou

Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans pp. 1-15

Julie J Lee and Mehdi Keramati

How can computation advance microbiome research? pp. 1-3

Ruth Nussinov and Jason A Papin

Ten simple rules for successfully completing a graduate degree in Latin America pp. 1-8

Ernesto Ruelas Inzunza, Gabriela I Salazar-Rivera, Magdiel Láinez, María Guadalupe Ruiz-Gómez, Carlo A Domínguez-Eusebio, Griselda Cristóbal-Sánchez, Issaac A Teodosio Faustino, Edel Pérez-López, Meagan L Campbell, Marcus Vinicius Merfa, Ivonne Tatiana Latorre Beltrán, Fernanda Armas and Claudio Mota-Vargas

Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem pp. 1-25

Cai Wingfield, Li Su, Xunying Liu, Chao Zhang, Phil Woodland, Andrew Thwaites, Elisabeth Fonteneau and William D Marslen-Wilson

Correction: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites pp. 1-1

The PLOS Computational Biology Staff

Correction: Dose-response relationships for environmentally mediated infectious disease transmission models pp. 1-1

The PLOS Computational Biology Staff

Correction: Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble pp. 1-1

The PLOS Computational Biology Staff

Predictive representations can link model-based reinforcement learning to model-free mechanisms pp. 1-35

Evan M Russek, Ida Momennejad, Matthew M Botvinick, Samuel J Gershman and Nathaniel D Daw

DeepPep: Deep proteome inference from peptide profiles pp. 1-17

Minseung Kim, Ameen Eetemadi and Ilias Tagkopoulos

Exploiting ecology in drug pulse sequences in favour of population reduction pp. 1-17

Marianne Bauer, Isabella R Graf, Vudtiwat Ngampruetikorn, Greg J Stephens and Erwin Frey

Reconstructing promoter activity from Lux bioluminescent reporters pp. 1-13

Mudassar Iqbal, Neil Doherty, Anna M L Page, Saara N A Qazi, Ishan Ajmera, Peter A Lund, Theodore Kypraios, David J Scott, Philip J Hill and Dov J Stekel

A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells pp. 1-24

Richard B Greaves, Sabine Dietmann, Austin Smith, Susan Stepney and Julianne D Halley

A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms pp. 1-29

Pietro Balbi, Paolo Massobrio and Jeanette Hellgren Kotaleski

Ten simple rules for developing a mentor–mentee expectations document pp. 1-4

Kristyn S Masters and Pamela K Kreeger

Probabilistic models for neural populations that naturally capture global coupling and criticality pp. 1-26

Jan Humplik and Gašper Tkačik

Probing eukaryotic cell mechanics via mesoscopic simulations pp. 1-22

Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim and Igor V Pivkin

Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies pp. 1-22

Burcu Tepekule, Hildegard Uecker, Isabel Derungs, Antoine Frenoy and Sebastian Bonhoeffer

Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle pp. 1-31

Xiaosheng Luo, Liufang Xu, Bo Han and Jin Wang

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics pp. 1-19

Jaideep Joshi, Iain D Couzin, Simon A Levin and Vishwesha Guttal

Stochastic principles governing alternative splicing of RNA pp. 1-20

Jianfei Hu, Eli Boritz, William Wylie and Daniel C Douek

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis pp. 1-20

Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, eQTLGen Consortium, Kai Kisand, Zoltán Kutalik, Pärt Peterson and Hedi Peterson

Volume 13, issue 8, 2017

The application of project-based learning in bioinformatics training pp. 1-8

Laura R Emery and Sarah L Morgan

Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels pp. 1-25

Alexander V Maltsev, Victor A Maltsev and Michael D Stern

Mouth-clicks used by blind expert human echolocators – signal description and model based signal synthesis pp. 1-17

Lore Thaler, Galen M Reich, Xinyu Zhang, Dinghe Wang, Graeme E Smith, Zeng Tao, Raja Syamsul Azmir Bin Raja Abdullah, Mikhail Cherniakov, Christopher J Baker, Daniel Kish and Michail Antoniou

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing pp. 1-20

Mohamed Ali Ghadie, Luke Lambourne, Marc Vidal and Yu Xia

Measuring distance through dense weighted networks: The case of hospital-associated pathogens pp. 1-19

Tjibbe Donker, Timo Smieszek, Katherine L Henderson, Alan P Johnson, A Sarah Walker and Julie V Robotham

Host population structure impedes reversion to drug sensitivity after discontinuation of treatment pp. 1-19

Jonas I Liechti, Gabriel E Leventhal and Sebastian Bonhoeffer

Robust averaging protects decisions from noise in neural computations pp. 1-19

Vickie Li, Santiago Herce Castañón, Joshua A Solomon, Hildward Vandormael and Christopher Summerfield

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors pp. 1-28

Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu and Tero Aittokallio

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity pp. 1-28

Michal Bassani-Sternberg, Chloé Chong, Philippe Guillaume, Marthe Solleder, HuiSong Pak, Philippe O Gannon, Lana E Kandalaft, George Coukos and David Gfeller

Ten simple rules for getting the most out of a summer laboratory internship pp. 1-7

Toby P Aicher, Dániel L Barabási, Benjamin D Harris, Ajay Nadig and Kaitlin L Williams

Ten simple rules to initiate and run a postdoctoral association pp. 1-7

Chiara Bruckmann and Endre Sebestyén

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data pp. 1-26

Lingfei Wang and Tom Michoel

Rearrangement moves on rooted phylogenetic networks pp. 1-21

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca

Noise correlations in the human brain and their impact on pattern classification pp. 1-23

Vikranth R Bejjanki, Rava Azeredo da Silveira, Jonathan D Cohen and Nicholas B Turk-Browne

A method of determining where to target surveillance efforts in heterogeneous epidemiological systems pp. 1-23

Alexander J Mastin, Frank van den Bosch, Timothy R Gottwald, Vasthi Alonso Chavez and Stephen R Parnell

Multi-scale approaches for high-speed imaging and analysis of large neural populations pp. 1-24

Johannes Friedrich, Weijian Yang, Daniel Soudry, Yu Mu, Misha B Ahrens, Rafael Yuste, Darcy S Peterka and Liam Paninski

Neuron’s eye view: Inferring features of complex stimuli from neural responses pp. 1-18

Xin Chen, Jeffrey M Beck and John M Pearson

A stochastic-field description of finite-size spiking neural networks pp. 1-34

Grégory Dumont, Alexandre Payeur and André Longtin

A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions pp. 1-34

Michael A Colman, Christian Pinali, Andrew W Trafford, Henggui Zhang and Ashraf Kitmitto

The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades pp. 1-36

Eduardo A Aponte, Dario Schöbi, Klaas E Stephan and Jakob Heinzle

Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation pp. 1-22

Christopher B Massa, Angela M Groves, Smita U Jaggernauth, Debra L Laskin and Andrew J Gow

Spread of hospital-acquired infections: A comparison of healthcare networks pp. 1-22

Narimane Nekkab, Pascal Astagneau, Laura Temime and Pascal Crépey

Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing pp. 1-22

Stefano Palminteri, Germain Lefebvre, Emma J Kilford and Sarah-Jayne Blakemore

Spatial dynamics of synthetic microbial mutualists and their parasites pp. 1-22

Daniel R Amor, Raúl Montañez, Salva Duran-Nebreda and Ricard Solé

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate pp. 1-22

David Amar, Ron Shamir and Daniel Yekutieli

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock pp. 1-22

Wesley M Botello-Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jerome J Lacroix, Jijun Hao and Yun Luo

Volume 13, issue 7, 2017

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales pp. 1-16

Lukas Bartonek and Bojan Zagrovic

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics pp. 1-17

Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks and Vijay S Pande

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape pp. 1-20

William Gilpin and Marcus W Feldman

Hybrid modeling and prediction of dynamical systems pp. 1-20

Franz Hamilton, Alun L Lloyd and Kevin B Flores

Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance pp. 1-14

Kamran Kaveh, Yutaka Takahashi, Michael A Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Z Leder and Susanta K Hui

Growth of bacteria in 3-d colonies pp. 1-19

Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R Levin and Ilya Nemenman

Correction: Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis pp. 1-7

Andrew F Brouwer, Rafael Meza and Marisa C Eisenberg

PCSF: An R-package for network-based interpretation of high-throughput data pp. 1-7

Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel and Ivo Kwee

Dissociating error-based and reinforcement-based loss functions during sensorimotor learning pp. 1-28

Joshua G A Cashaback, Heather R McGregor, Ayman Mohatarem and Paul L Gribble

Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits pp. 1-23

John Palmer, Adam Keane and Pulin Gong

Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference pp. 1-23

Giorgos Minas and David A Rand

A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium pp. 1-23

Oliver J Maclaren, Aimée Parker, Carmen Pin, Simon R Carding, Alastair J M Watson, Alexander G Fletcher, Helen M Byrne and Philip K Maini

Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models pp. 1-27

Laurent Mackay, Hana Zemkova, Stanko S Stojilkovic, Arthur Sherman and Anmar Khadra

A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing pp. 1-27

Haruo Hosoya and Aapo Hyvärinen

Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks pp. 1-27

Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini and Thierry Nieus

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions pp. 1-27

Zixuan Cang and Guo-Wei Wei

CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets pp. 1-29

Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu and Vamsi K Mootha

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics pp. 1-24

Aseel Shomar, Lukas Geyrhofer, Noam E Ziv and Naama Brenner

Temporal specificity of the initial adaptive response in motor adaptation pp. 1-18

Wilsaan M Joiner, Gary C Sing and Maurice A Smith

Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective pp. 1-18

James R H Cooke, Arjan C ter Horst, Robert J van Beers and W Pieter Medendorp

Inherent limitations of probabilistic models for protein-DNA binding specificity pp. 1-15

Shuxiang Ruan and Gary D Stormo

Speciation trajectories in recombining bacterial species pp. 1-15

Pekka Marttinen and William P Hanage

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors pp. 1-22

Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger and Erik van Nimwegen

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions pp. 1-22

Koon-Kiu Yan, Shaoke Lou and Mark Gerstein

Volume 13, issue 6, 2017

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle pp. 1-19

David L Gibbs and Ilya Shmulevich

An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules pp. 1-19

Noga Mosheiff, Haggai Agmon, Avraham Moriel and Yoram Burak

LASSIM—A network inference toolbox for genome-wide mechanistic modeling pp. 1-19

Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E M Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg and Mika Gustafsson

GINOM: A statistical framework for assessing interval overlap of multiple genomic features pp. 1-16

Darshan Bryner, Stephen Criscione, Andrew Leith, Quyen Huynh, Fred Huffer and Nicola Neretti

Leveraging functional annotations in genetic risk prediction for human complex diseases pp. 1-16

Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu and Hongyu Zhao

Good enough practices in scientific computing pp. 1-20

Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt and Tracy K Teal

A motor unit-based model of muscle fatigue pp. 1-30

Jim R Potvin and Andrew J Fuglevand

High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE pp. 1-12

Stefano Castellana, Caterina Fusilli, Gianluigi Mazzoccoli, Tommaso Biagini, Daniele Capocefalo, Massimo Carella, Angelo Luigi Vescovi and Tommaso Mazza

Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions pp. 1-25

Nargesalsadat Dorratoltaj, Achla Marathe, Bryan L Lewis, Samarth Swarup, Stephen G Eubank and Kaja M Abbas

Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice pp. 1-25

Samira Abbasi, Amber E Hudson, Selva K Maran, Ying Cao, Ataollah Abbasi, Detlef H Heck and Dieter Jaeger

A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements pp. 1-33

Daniel Durstewitz

Optimal structure of metaplasticity for adaptive learning pp. 1-22

Peyman Khorsand and Alireza Soltani

Active Vertex Model for cell-resolution description of epithelial tissue mechanics pp. 1-34

Daniel L Barton, Silke Henkes, Cornelis J Weijer and Rastko Sknepnek

Linking structure and activity in nonlinear spiking networks pp. 1-47

Gabriel Koch Ocker, Krešimir Josić, Eric Shea-Brown and Michael A Buice

Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation pp. 1-46

Moritz Augustin, Josef Ladenbauer, Fabian Baumann and Klaus Obermayer

Detecting similar binding pockets to enable systems polypharmacology pp. 1-18

Miquel Duran-Frigola, Lydia Siragusa, Eytan Ruppin, Xavier Barril, Gabriele Cruciani and Patrick Aloy

Fast and general tests of genetic interaction for genome-wide association studies pp. 1-29

Mattias Frånberg, Rona J Strawbridge, Anders Hamsten, Consortium Procardis, Ulf de Faire, Jens Lagergren and Bengt Sennblad

A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data pp. 1-29

En-Yu Lai, Yi-Hau Chen and Kun-Pin Wu

Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation pp. 1-24

Jae Kyoung Kim and Eduardo D Sontag

Rosetta:MSF: a modular framework for multi-state computational protein design pp. 1-24

Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner and Rainer Merkl

MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory pp. 1-24

Aliza B Rubenstein, Manasi A Pethe and Sagar D Khare

Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression pp. 1-23

Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin and Gabriella Juhasz

Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study pp. 1-23

Sonia Cortassa, Steven J Sollott and Miguel A Aon

A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images pp. 1-23

Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre and Marc Germain

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome pp. 1-21

Jens Christian Claussen, Jurgita Skiecevičienė, Jun Wang, Philipp Rausch, Tom H Karlsen, Wolfgang Lieb, John F Baines, Andre Franke and Marc-Thorsten Hütt

A review of active learning approaches to experimental design for uncovering biological networks pp. 1-26

Yuriy Sverchkov and Mark Craven

2017 ISCB Overton Prize awarded to Christoph Bock pp. 1-4

Christiana N Fogg, Diane E Kovats and Bonnie Berger

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network pp. 1-10

C Victor Jongeneel, Ovokeraye Achinike-Oduaran, Ezekiel Adebiyi, Marion Adebiyi, Seun Adeyemi, Bola Akanle, Shaun Aron, Efejiro Ashano, Hocine Bendou, Gerrit Botha, Emile Chimusa, Ananyo Choudhury, Ravikiran Donthu, Jenny Drnevich, Oluwadamila Falola, Christopher J Fields, Scott Hazelhurst, Liesl Hendry, Itunuoluwa Isewon, Radhika S Khetani, Judit Kumuthini, Magambo Phillip Kimuda, Lerato Magosi, Liudmila Sergeevna Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Danny Mugutso, Phelelani Mpangase, Richard Munthali, Victoria Nembaware, Andrew Ndhlovu, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Sumir Panji, Venesa Pillay, Gloria Rendon, Dhriti Sengupta and Nicola Mulder

Locking of correlated neural activity to ongoing oscillations pp. 1-32

Tobias Kühn and Moritz Helias

Volume 13, issue 5, 2017

Post-transcriptional regulation across human tissues pp. 1-20

Alexander Franks, Edoardo Airoldi and Nikolai Slavov

phyC: Clustering cancer evolutionary trees pp. 1-17

Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano and Teppei Shimamura

Short-term activity cycles impede information transmission in ant colonies pp. 1-17

Thomas O Richardson, Jonas I Liechti, Nathalie Stroeymeyt, Sebastian Bonhoeffer and Laurent Keller

Ten simple rules to make the most out of your undergraduate research career pp. 1-7

Megan Yu and Yu-Min Kuo

Ten simple rules for surviving an interdisciplinary PhD pp. 1-7

Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J Gavaghan, Charlotte M Deane and Bernhard Knapp

Automatically tracking neurons in a moving and deforming brain pp. 1-19

Jeffrey P Nguyen, Ashley N Linder, George S Plummer, Joshua W Shaevitz and Andrew M Leifer

Correction: Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches pp. 1-1

The PLOS Computational Biology Staff

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates pp. 1-25

Andreas Tuerk, Gregor Wiktorin and Serhat Güler

Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes pp. 1-30

Nick E Phillips, Cerys Manning, Nancy Papalopulu and Magnus Rattray

Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms pp. 1-30

Florian Berger and A J Hudspeth

FIMTrack: An open source tracking and locomotion analysis software for small animals pp. 1-15

Benjamin Risse, Dimitri Berh, Nils Otto, Christian Klämbt and Xiaoyi Jiang

Predicting cryptic links in host-parasite networks pp. 1-15

Tad Dallas, Andrew W Park and John M Drake

Ten simple rules to consider regarding preprint submission pp. 1-6

Philip E Bourne, Jessica K Polka, Ronald D Vale and Robert Kiley

Mechanisms underlying different onset patterns of focal seizures pp. 1-22

Yujiang Wang, Andrew J Trevelyan, Antonio Valentin, Gonzalo Alarcon, Peter N Taylor and Marcus Kaiser

Nucleotide-time alignment for molecular recorders pp. 1-22

Thaddeus R Cybulski, Edward S Boyden, George M Church, Keith E J Tyo and Konrad P Kording

Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia pp. 1-22

Ali Nematbakhsh, Wenzhao Sun, Pavel A Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J Zartman and Mark Alber

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities pp. 1-22

Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele and Christoph Kaleta

Dynamic decomposition of spatiotemporal neural signals pp. 1-37

Luca Ambrogioni, Marcel A J van Gerven and Eric Maris

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers pp. 1-10

Björn A Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor and Anton Nekrutenko

ROTS: An R package for reproducibility-optimized statistical testing pp. 1-10

Tomi Suomi, Fatemeh Seyednasrollah, Maria K Jaakkola, Thomas Faux and Laura L Elo

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks pp. 1-32

Don Klinkenberg, Jantien A Backer, Xavier Didelot, Caroline Colijn and Jacco Wallinga

Co-occurring protein phosphorylation are functionally associated pp. 1-23

Ying Li, Xueya Zhou, Zichao Zhai and Tingting Li

Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans pp. 1-21

Nicolás Tomasini, Paula Gabriela Ragone, Sébastien Gourbière, Juan Pablo Aparicio and Patricio Diosque

A predictive coding account of bistable perception - a model-based fMRI study pp. 1-21

Veith Weilnhammer, Heiner Stuke, Guido Hesselmann, Philipp Sterzer and Katharina Schmack

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci pp. 1-26

Jin Hyun Ju, Sushila A Shenoy, Ronald G Crystal and Jason G Mezey

The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning pp. 1-29

Eghbal A Hosseini, Katrina P Nguyen and Wilsaan M Joiner

Volume 13, issue 4, 2017

Computation and measurement of cell decision making errors using single cell data pp. 1-17

Iman Habibi, Raymond Cheong, Tomasz Lipniacki, Andre Levchenko, Effat S Emamian and Ali Abdi

Dynamic compensation, parameter identifiability, and equivariances pp. 1-17

Eduardo D Sontag

Dynamics of adaptive immunity against phage in bacterial populations pp. 1-16

Serena Bradde, Marija Vucelja, Tiberiu Teşileanu and Vijay Balasubramanian

ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time pp. 1-16

Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao and Yijun Sun

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data pp. 1-20

Ofir Shukron and David Holcman

Robust information propagation through noisy neural circuits pp. 1-35

Joel Zylberberg, Alexandre Pouget, Peter E Latham and Eric Shea-Brown

Correction: Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression pp. 1-1

The PLOS Computational Biology Staff

Correction: The missing link: Predicting connectomes from noisy and partially observed tract tracing data pp. 1-1

Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H E Tiesinga, Morten Mørup and Marcel A J van Gerven

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling pp. 1-28

Irene Otero-Muras, Pencho Yordanov and Joerg Stelling

Intrinsically-generated fluctuating activity in excitatory-inhibitory networks pp. 1-40

Francesca Mastrogiuseppe and Srdjan Ostojic

Human behavioral complexity peaks at age 25 pp. 1-14

Nicolas Gauvrit, Hector Zenil, Fernando Soler-Toscano, Jean-Paul Delahaye and Peter Brugger

Personalized glucose forecasting for type 2 diabetes using data assimilation pp. 1-38

David J Albers, Matthew Levine, Bruce Gluckman, Henry Ginsberg, George Hripcsak and Lena Mamykina

When do correlations increase with firing rates in recurrent networks? pp. 1-30

Andrea K Barreiro and Cheng Ly

Predicting explorative motor learning using decision-making and motor noise pp. 1-33

Xiuli Chen, Kieran Mohr and Joseph M Galea

Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis pp. 1-33

Jörn Diedrichsen and Nikolaus Kriegeskorte

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints pp. 1-22

Steffen Klamt, Georg Regensburger, Matthias P Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini and Stefan Müller

Sequence dependency of canonical base pair opening in the DNA double helix pp. 1-22

Viveca Lindahl, Alessandra Villa and Berk Hess

Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL) pp. 1-27

Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis and George Kollias

Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons pp. 1-27

Yann Zerlaut and Alain Destexhe

Geospatial characteristics of measles transmission in China during 2005−2014 pp. 1-21

Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-Yi Zhang and Jeffrey Shaman

Polarization and migration in the zebrafish posterior lateral line system pp. 1-26

Hildur Knutsdottir, Cole Zmurchok, Dhananjay Bhaskar, Eirikur Palsson, Damian Dalle Nogare, Ajay B Chitnis and Leah Edelstein-Keshet

Ten simple rules for making research software more robust pp. 1-10

Morgan Taschuk and Greg Wilson

Variable habitat conditions drive species covariation in the human microbiota pp. 1-18

Charles K Fisher, Thierry Mora and Aleksandra M Walczak

Probabilistic fluorescence-based synapse detection pp. 1-24

Anish K Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T Vogelstein, Kristina D Micheva, Richard J Weinberg, Stephen J Smith and Guillermo Sapiro

Volume 13, issue 3, 2017

Ten simple rules for responsible big data research pp. 1-10

Matthew Zook, Solon Barocas, Danah Boyd, Kate Crawford, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara A Koenig, Jacob Metcalf, Arvind Narayanan, Alondra Nelson and Frank Pasquale

Fast online deconvolution of calcium imaging data pp. 1-26

Johannes Friedrich, Pengcheng Zhou and Liam Paninski

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration pp. 1-26

Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn and Thomas F Miller

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells pp. 1-27

Aurélien Naldi, Romain M Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J Coopman and Ovidiu Radulescu

Phylodynamics on local sexual contact networks pp. 1-23

David A Rasmussen, Roger Kouyos, Huldrych F Günthard and Tanja Stadler

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells pp. 1-9

James T Yurkovich, Laurence Yang and Bernhard O Palsson

Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis pp. 1-18

Andrew F Brouwer, Rafael Meza and Marisa C Eisenberg

Ten simple rules for short and swift presentations pp. 1-6

Christopher J Lortie

Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N pp. 1-22

Polydefkis Diamantis, Oliver T Unke and Markus Meuwly

PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction pp. 1-22

Zhu-Hong You, Zhi-An Huang, Zexuan Zhu, Gui-Ying Yan, Zheng-Wei Li, Zhenkun Wen and Xing Chen

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study pp. 1-31

Emma Saulnier, Olivier Gascuel and Samuel Alizon

Ten simple rules for forming a scientific professional society pp. 1-8

Bruno A Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola Mulder, Paolo Romano and Lonnie Welch

Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation pp. 1-25

Junjiajia Long, Steven W Zucker and Thierry Emonet

A critical analysis of computational protein design with sparse residue interaction graphs pp. 1-30

Swati Jain, Jonathan D Jou, Ivelin S Georgiev and Bruce R Donald

Geometry can provide long-range mechanical guidance for embryogenesis pp. 1-30

Mahamar Dicko, Pierre Saramito, Guy B Blanchard, Claire M Lye, Bénédicte Sanson and Jocelyn Étienne

Multiregional integration in the brain during resting-state fMRI activity pp. 1-20

Etay Hay, Petra Ritter, Nancy J Lobaugh and Anthony R McIntosh

Systematic identification of phosphorylation-mediated protein interaction switches pp. 1-20

Matthew J Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P Roth, Anne-Claude Gavin, Peer Bork and Robert B Russell

Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study pp. 1-16

Erick A Perez Alday, Michael A Colman, Philip Langley and Henggui Zhang

Fidelity of the representation of value in decision-making pp. 1-16

Paul M Bays and Ben A Dowding

Dynamics robustness of cascading systems pp. 1-17

Jonathan T Young, Tetsuhiro S Hatakeyama and Kunihiko Kaneko

A human judgment approach to epidemiological forecasting pp. 1-19

David C Farrow, Logan C Brooks, Sangwon Hyun, Ryan J Tibshirani, Donald S Burke and Roni Rosenfeld

Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions pp. 1-19

Rashmi Priya, Guillermo A Gomez, Srikanth Budnar, Bipul R Acharya, Andras Czirok, Alpha S Yap and Zoltan Neufeld

A model for brain life history evolution pp. 1-28

Mauricio González-Forero, Timm Faulwasser and Laurent Lehmann

Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment pp. 1-28

Marie Devaine and Jean Daunizeau

Correction: A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus pp. 1-1

The PLOS Computational Biology Staff

Volume 13, issue 2, 2017

A mathematical model of calcium dynamics in HSY cells pp. 1-29

Jung Min Han, Akihiko Tanimura, Vivien Kirk and James Sneyd

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression pp. 1-26

William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A Knijnenburg and Brady Bernard

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression pp. 1-23

Berta Verd, Anton Crombach and Johannes Jaeger

Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees pp. 1-23

Mark Roper, Chrisantha Fernando and Lars Chittka

Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise pp. 1-32

Johannes Burge and Priyank Jaini

On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs pp. 1-31

Felipe Gerhard, Moritz Deger and Wilson Truccolo

Ten Simple Rules for Developing a Successful Research Proposal in Brazil pp. 1-6

Dyoni M de Oliveira, Marcos S Buckeridge and Wanderley D dos Santos

Elucidation of molecular kinetic schemes from macroscopic traces using system identification pp. 1-34

Miguel Fribourg, Diomedes E Logothetis, Javier González-Maeso, Stuart C Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés and Vladimir Brezina

Comparing individual-based approaches to modelling the self-organization of multicellular tissues pp. 1-34

James M Osborne, Alexander G Fletcher, Joe M Pitt-Francis, Philip K Maini and David J Gavaghan

Testing the limits of gradient sensing pp. 1-30

Vinal Lakhani and Timothy C Elston

Ten Simple Rules on How to Organize a Scientific Retreat pp. 1-8

Julia Ponomarenko, Romina Garrido and Roderic Guigó

Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome pp. 1-25

Jannis Schuecker, Maximilian Schmidt, Sacha J van Albada, Markus Diesmann and Moritz Helias

A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons pp. 1-25

Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S Yen and Chen-Hsiang Yeang

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models pp. 1-25

David Henriques, Alejandro F Villaverde, Miguel Rocha, Julio Saez-Rodriguez and Julio R Banga

Correction: Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning pp. 1-1

Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer and Katharina Schmack

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour pp. 1-14

Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C Coles, Marika C Kullberg and Jon Timmis

Mindboggling morphometry of human brains pp. 1-40

Arno Klein, Satrajit S Ghosh, Forrest S Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto and Anisha Keshavan

The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt pp. 1-28

Sophie K Kay, Heather A Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M Osborne, David J Gavaghan and Helen M Byrne

Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema pp. 1-17

Jarred R Mondoñedo and Béla Suki

Early and Real-Time Detection of Seasonal Influenza Onset pp. 1-20

Miguel Won, Manuel Marques-Pita, Carlota Louro and Joana Gonçalves-Sá

Two dynamic regimes in the human gut microbiome pp. 1-20

Sean M Gibbons, Sean M Kearney, Chris S Smillie and Eric J Alm

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture pp. 1-20

Dongjun Chung, Hang J Kim and Hongyu Zhao

The genotype-phenotype map of an evolving digital organism pp. 1-20

Miguel A Fortuna, Luis Zaman, Charles Ofria and Andreas Wagner

Volume 13, issue 1, 2017

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing pp. 1-12

Mary Regina Boland, Konrad J Karczewski and Nicholas P Tatonetti

Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model pp. 1-30

Chen Zhao, Jeffrey S Isenberg and Aleksander S Popel

Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses pp. 1-19

Ignacio A Rodriguez-Brenes, Andrew Hofacre, Hung Fan and Dominik Wodarz

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility pp. 1-19

David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann and Zoltán Kutalik

Structure-Function Network Mapping and Its Assessment via Persistent Homology pp. 1-19

Hualou Liang and Hongbin Wang

Efficient Switches in Biology and Computer Science pp. 1-16

Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau and Attila Csikász-Nagy

Coevolutionary dynamics of phenotypic diversity and contingent cooperation pp. 1-16

Te Wu, Long Wang and Feng Fu

Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome pp. 1-20

Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng and Chao Cheng

Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies pp. 1-20

Cox Lwaka Tamba, Yuan-Li Ni and Yuan-Ming Zhang

Could a Neuroscientist Understand a Microprocessor? pp. 1-24

Eric Jonas and Konrad Paul Kording

Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients pp. 1-24

Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta and Holger Stark

Multiple Choice Neurodynamical Model of the Uncertain Option Task pp. 1-29

Andrea Insabato, Mario Pannunzi and Gustavo Deco

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent? pp. 1-26

Christopher M Siwy, Christopher Lockhart and Dmitri K Klimov

Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies pp. 1-26

Tanmay A Gokhale, Jong M Kim, Robert D Kirkton, Nenad Bursac and Craig S Henriquez

Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans pp. 1-26

Ho-Yon Hwang and Jiou Wang

A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models pp. 1-21

Christoph Zimmer, Reza Yaesoubi and Ted Cohen

A Looping-Based Model for Quenching Repression pp. 1-21

Yaroslav Pollak, Sarah Goldberg and Roee Amit

A New Approach to Model Pitch Perception Using Sparse Coding pp. 1-36

Oded Barzelay, Miriam Furst and Omri Barak

The Flash-Lag Effect as a Motion-Based Predictive Shift pp. 1-31

Mina A Khoei, Guillaume S Masson and Laurent U Perrinet

Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons pp. 1-31

Iris Reuveni, Sourav Ghosh and Edi Barkai

Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling pp. 1-22

Stuart P Wilson

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model pp. 1-34

Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang and Jinbo Xu

Ten Simple Rules for Developing Usable Software in Computational Biology pp. 1-5

Markus List, Peter Ebert and Felipe Albrecht

Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing pp. 1-25

Edward S Lee, Paul G Thomas, Jeff E Mold and Andrew J Yates

Suboptimal Criterion Learning in Static and Dynamic Environments pp. 1-28

Elyse H Norton, Stephen M Fleming, Nathaniel D Daw and Michael S Landy

Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation pp. 1-13

Stewart Heitmann, Michael Rule, Wilson Truccolo and Bard Ermentrout

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks pp. 1-18

Fabian Fröhlich, Barbara Kaltenbacher, Fabian J Theis and Jan Hasenauer

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites pp. 1-18

Hsiao-Han Chang, Colin J Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R Kamya, Sarah G Staedke, Grant Dorsey, Maxwell Murphy, Daniel E Neafsey, Anna E Jeffreys, Christina Hubbart, Kirk A Rockett, Roberto Amato, Dominic P Kwiatkowski, Caroline O Buckee and Bryan Greenhouse

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