PLOS Computational Biology

2005 - 2025

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Volume 13, issue 12, 2017

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

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

Nadav Ben-Shushan and Misha Tsodyks

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

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

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

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

Xing Chen and Li Huang

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

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

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

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

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

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

Volume 13, issue 11, 2017

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

Emma Schwager, Himel Mallick, Steffen Ventz and Curtis Huttenhower

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

Alexis T Baria, Brian Maniscalco and Biyu J He

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

Teresa K Yamana, Sasikiran Kandula and Jeffrey Shaman

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

Ruolin Liu and Julie Dickerson

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

Shaima Hashem, Matteo Tiberti and Arianna Fornili

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

Stefan Albert, Katharina Schmack, Philipp Sterzer and Gaby Schneider

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

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

Multivariate pattern dependence pp. 1-20

Stefano Anzellotti, Alfonso Caramazza and Rebecca Saxe

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

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

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

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

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

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

Michael F Sloma and David H Mathews

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

Volume 13, issue 10, 2017

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

Philip E Bourne

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

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

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

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

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

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

Evelina Gabasova, John Reid and Lorenz Wernisch

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

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

Network propagation in the cytoscape cyberinfrastructure pp. 1-9

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

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

John Joseph Valletta and Mario Recker

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

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

James Rankin and Frédéric Chavane

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

Tiziano D’Albis and Richard Kempter

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

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

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

Anna Hake and Nico Pfeifer

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

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

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

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

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

Volume 13, issue 9, 2017

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

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

Ruth Nussinov and Jason A Papin

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

Jan Humplik and Gašper Tkačik

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

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

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

Ten simple rules for structuring papers pp. 1-9

Brett Mensh and Konrad Kording

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

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

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

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

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

Kristyn S Masters and Pamela K Kreeger

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

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

Petter Holme and Nelly Litvak

Volume 13, issue 8, 2017

Rearrangement moves on rooted phylogenetic networks pp. 1-21

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

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

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

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

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

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

Lingfei Wang and Tom Michoel

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

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

Xin Chen, Jeffrey M Beck and John M Pearson

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

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

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 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

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

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

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

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

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

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

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

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

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

Franz Hamilton, Alun L Lloyd and Kevin B Flores

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

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

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

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

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

Lukas Bartonek and Bojan Zagrovic

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

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

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

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

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

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

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

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

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

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

Christiana N Fogg, Diane E Kovats and Bonnie Berger

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

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

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

Peyman Khorsand and Alireza Soltani

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

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

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

Daniel Durstewitz

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

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

Tobias Kühn and Moritz Helias

Volume 13, issue 5, 2017

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

Tad Dallas, Andrew W Park and John M Drake

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

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

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

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

Ying Li, Xueya Zhou, Zichao Zhai and Tingting Li

Dynamic decomposition of spatiotemporal neural signals pp. 1-37

Luca Ambrogioni, Marcel A J van Gerven and Eric Maris

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

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

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

Volume 13, issue 4, 2017

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

Andrea K Barreiro and Cheng Ly

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

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

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

Ofir Shukron and David Holcman

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

Charles K Fisher, Thierry Mora and Aleksandra M Walczak

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

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

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

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

Francesca Mastrogiuseppe and Srdjan Ostojic

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

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

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

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

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

Irene Otero-Muras, Pencho Yordanov and Joerg Stelling

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

Volume 13, issue 3, 2017

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

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

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

Polydefkis Diamantis, Oliver T Unke and Markus Meuwly

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

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

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

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

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

Johannes Friedrich, Pengcheng Zhou and Liam Paninski

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

Emma Saulnier, Olivier Gascuel and Samuel Alizon

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 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

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

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

Volume 13, issue 2, 2017

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

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

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

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

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

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

Julia Ponomarenko, Romina Garrido and Roderic Guigó

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

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

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

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

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

Christoph Zimmer, Reza Yaesoubi and Ted Cohen

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

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

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

Oded Barzelay, Miriam Furst and Omri Barak

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

Andrea Insabato, Mario Pannunzi and Gustavo Deco

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

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

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

Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations pp. 1-27

Christian Donner, Klaus Obermayer and Hideaki Shimazaki

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

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

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

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

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

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

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

The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection pp. 1-15

Luc E Coffeng, Cornelus C Hermsen, Robert W Sauerwein and Sake J de Vlas