PLOS Computational Biology

2005 - 2025

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Volume 10, issue 12, 2014

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity pp. 1-12

Axel Kammerer and Christian Leibold

Ten Simple Rules for Finishing Your PhD pp. 1-4

Jacopo Marino, Melanie I Stefan and Sarah Blackford

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration pp. 1-15

Alexandra Gavryushkina, David Welch, Tanja Stadler and Alexei J Drummond

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences pp. 1-15

Alex N Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L Weiss, Christian R Landry and Alan M Moses

Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development pp. 1-16

Mayu Sugiyama, Takashi Saitou, Hiroshi Kurokawa, Asako Sakaue-Sawano, Takeshi Imamura, Atsushi Miyawaki and Tadahiro Iimura

Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons pp. 1-16

Jean-Pierre Rospars, Alexandre Grémiaux, David Jarriault, Antoine Chaffiol, Christelle Monsempes, Nina Deisig, Sylvia Anton, Philippe Lucas and Dominique Martinez

Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments pp. 1-9

Christoph Zechner and Heinz Koeppl

Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation pp. 1-14

Lin Chen, Javad Noorbakhsh, Rhys M Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta and Gábor Balázsi

The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn? pp. 1-14

Marie Devaine, Guillaume Hollard and Jean Daunizeau

Protein-Protein Docking with Dynamic Residue Protonation States pp. 1-14

Krishna Praneeth Kilambi, Kavan Reddy and Jeffrey J Gray

Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure pp. 1-10

Ritwik K Niyogi, Peter Shizgal and Peter Dayan

Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception pp. 1-10

Ofri Raviv, Itay Lieder, Yonatan Loewenstein and Merav Ahissar

Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models pp. 1-10

Xiaolin Tang, Mourad Bendjennat and Saveez Saffarian

Symmetry Restoring Bifurcation in Collective Decision-Making pp. 1-11

Natalia Zabzina, Audrey Dussutour, Richard P Mann, David J T Sumpter and Stamatios C Nicolis

The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets pp. 1-20

Evandro Ferrada

Volume 10, issue 11, 2014

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns pp. 1-14

Marcin J Skwark, Daniele Raimondi, Mirco Michel and Arne Elofsson

Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens pp. 1-12

Luca Ferreri, Mario Giacobini, Paolo Bajardi, Luigi Bertolotti, Luca Bolzoni, Valentina Tagliapietra, Annapaola Rizzoli and Roberto Rosà

Statistical Computations Underlying the Dynamics of Memory Updating pp. 1-13

Samuel J Gershman, Angela Radulescu, Kenneth A Norman and Yael Niv

Global Disease Monitoring and Forecasting with Wikipedia pp. 1-16

Nicholas Generous, Geoffrey Fairchild, Alina Deshpande, Sara Y Del Valle and Reid Priedhorsky

Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons pp. 1-16

Varsha Dhankani, J Nathan Kutz and Joshua T Schiffer

High-Fidelity Coding with Correlated Neurons pp. 1-25

Rava Azeredo da Silveira and Michael J Berry

Computational Thinking in Life Science Education pp. 1-5

Amir Rubinstein and Benny Chor

Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas pp. 1-5

Flávio Pinheiro, Vítor V Vasconcelos, Francisco C Santos and Jorge M Pacheco

Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG pp. 1-26

Klas H Pettersen, Henrik Lindén, Tom Tetzlaff and Gaute T Einevoll

Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart pp. 1-15

Ivan V Kazbanov, Richard H Clayton, Martyn P Nash, Chris P Bradley, David J Paterson, Martin P Hayward, Peter Taggart and Alexander V Panfilov

Ten Simple Rules to Achieve Conference Speaker Gender Balance pp. 1-3

Jennifer L Martin

Volume 10, issue 10, 2014

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells pp. 1-11

Christian L Althaus, Beda Joos, Alan S Perelson and Huldrych F Günthard

Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics pp. 1-19

Michael J Prerau, Katie E Hartnack, Gabriel Obregon-Henao, Aaron Sampson, Margaret Merlino, Karen Gannon, Matt T Bianchi, Jeffrey M Ellenbogen and Patrick L Purdon

Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment pp. 1-27

Robert Legenstein and Wolfgang Maass

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article pp. 1-5

Harriet Dashnow, Andrew Lonsdale and Philip E Bourne

Improving Contact Prediction along Three Dimensions pp. 1-13

Christoph Feinauer, Marcin J Skwark, Andrea Pagnani and Erik Aurell

Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery pp. 1-13

Jose A Seoane, Colin Campbell, Ian N M Day, Juan P Casas and Tom R Gaunt

The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion pp. 1-12

Nicole Dölker, Maria W Górna, Ludovico Sutto, Antonio S Torralba, Giulio Superti-Furga and Francesco L Gervasio

Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups pp. 1-10

Amos Korman, Efrat Greenwald and Ofer Feinerman

FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units pp. 1-6

Gang Peng, Yu Fan and Wenyi Wang

Synaptic Size Dynamics as an Effectively Stochastic Process pp. 1-17

Adiel Statman, Maya Kaufman, Amir Minerbi, Noam E Ziv and Naama Brenner

Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro pp. 1-17

Sophia Rudorf, Michael Thommen, Marina V Rodnina and Reinhard Lipowsky

Predicting Chemical Environments of Bacteria from Receptor Signaling pp. 1-14

Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik and Robert G Endres

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models pp. 1-14

Matthew N Benedict, Michael B Mundy, Christopher S Henry, Nicholas Chia and Nathan D Price

Volume 10, issue 9, 2014

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy pp. 1-17

David R Blair, Kanix Wang, Svetlozar Nestorov, James A Evans and Andrey Rzhetsky

Multi-state Modeling of Biomolecules pp. 1-9

Melanie I Stefan, Thomas M Bartol, Terrence J Sejnowski and Mary B Kennedy

Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies pp. 1-14

Diana Chang and Alon Keinan

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform pp. 1-10

N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith and Sergei L Kosakovsky Pond

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis pp. 1-10

Hong Yang, Elias W Krumholz, Evan D Brutinel, Nagendra P Palani, Michael J Sadowsky, Andrew M Odlyzko, Jeffrey A Gralnick and Igor G L Libourel

Pupil-Linked Arousal Determines Variability in Perceptual Decision Making pp. 1-13

Peter R Murphy, Joachim Vandekerckhove and Sander Nieuwenhuis

Environmental Statistics and Optimal Regulation pp. 1-12

David A Sivak and Matt Thomson

The Time Scale of Evolutionary Innovation pp. 1-7

Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam and Martin A Nowak

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing pp. 1-11

Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva-Guthrie, Hannah Carter, Peter D Stenson, David N Cooper, Biao Li, Sean Mooney and Rachel Karchin

NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles pp. 1-11

Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi and Satoshi Tabata

Inferring on the Intentions of Others by Hierarchical Bayesian Learning pp. 1-19

Andreea O Diaconescu, Christoph Mathys, Lilian A E Weber, Jean Daunizeau, Lars Kasper, Ekaterina I Lomakina, Ernst Fehr and Klaas E Stephan

eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models pp. 1-15

Michal Brylinski

Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method pp. 1-16

Simone Vincenzi, Marc Mangel, Alain J Crivelli, Stephan Munch and Hans J Skaug

Volume 10, issue 8, 2014

Phenotypic Signatures Arising from Unbalanced Bacterial Growth pp. 1-10

Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz and Lingchong You

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism pp. 1-11

Rui Xia, Selina Vattathil and Paul Scheet

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis pp. 1-11

Shuo Gu, Daniel-Adriano Silva, Luming Meng, Alexander Yue and Xuhui Huang

Sparsity and Compressed Coding in Sensory Systems pp. 1-11

Victor J Barranca, Gregor Kovačič, Douglas Zhou and David Cai

Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque pp. 1-19

Fang-Chieh Chou, Jan Lipfert and Rhiju Das

Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth pp. 1-19

Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M L Ebos, Lynn Hlatky and Philip Hahnfeldt

Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens pp. 1-9

Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S Lopes, Bruno Ceña, Cláudia T Codeço and M Gabriela M Gomes

Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus pp. 1-14

Nik J Cunniffe, Francisco F Laranjeira, Franco M Neri, R Erik DeSimone and Christopher A Gilligan

Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro pp. 1-14

René F M van Oers, Elisabeth G Rens, Danielle J LaValley, Cynthia A Reinhart-King and Roeland M H Merks

Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection pp. 1-14

Miri Adler, Avi Mayo and Uri Alon

Memory Capacity of Networks with Stochastic Binary Synapses pp. 1-15

Alexis M Dubreuil, Yali Amit and Nicolas Brunel

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes pp. 1-15

Anne-Florence Bitbol and David J Schwab

A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells pp. 1-15

Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J Sanderson and James Sneyd

The Upside of Failure: How Regional Student Groups Learn from Their Mistakes pp. 1-3

Tarun Mishra, R Gonzalo Parra and Thomas Abeel

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data pp. 1-16

Yuan Zhang, Yanni Sun and James R Cole

Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment pp. 1-16

Johannes Textor, Sarah E Henrickson, Judith N Mandl, Ulrich H von Andrian, Jürgen Westermann, Rob J de Boer and Joost B Beltman

Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment pp. 1-13

Eric L Haseltine, Sandra De Meyer, Inge Dierynck, Doug J Bartels, Anne Ghys, Andrew Davis, Eileen Z Zhang, Ann M Tigges, Joan Spanks, Gaston Picchio, Tara L Kieffer and James C Sullivan

Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images pp. 1-12

Umut Güçlü and Marcel A J van Gerven

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis pp. 1-12

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa and Raphael Gottardo

Volume 10, issue 7, 2014

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication" pp. 1-2

Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort and Peer Bork

A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges pp. 1-10

James Kaufman, Justin Lessler, April Harry, Stefan Edlund, Kun Hu, Judith Douglas, Christian Thoens, Bernd Appel, Annemarie Käsbohrer and Matthias Filter

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells pp. 1-10

Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem and Raphael Gottardo

CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells pp. 1-14

Benedict Anchang, Mary T Do, Xi Zhao and Sylvia K Plevritis

Brain and Behavior in Decision-Making pp. 1-8

Peter Cassey, Andrew Heathcote and Scott D Brown

Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling pp. 1-17

Tom Serge Weber, Irene Jaehnert, Christian Schichor, Michal Or-Guil and Jorge Carneiro

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics pp. 1-17

Jan Hasenauer, Christine Hasenauer, Tim Hucho and Fabian J Theis

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity pp. 1-25

Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Elodie Laine, Alain Trouvé, Patrice Dubreuil and Luba Tchertanov

Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities pp. 1-3

Jeroen de Ridder, Pieter Meysman, Olugbenga Oluwagbemi and Thomas Abeel

Modeling Higher-Order Correlations within Cortical Microcolumns pp. 1-12

Urs Köster, Jascha Sohl-Dickstein, Charles M Gray and Bruno A Olshausen

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion pp. 1-12

Christophe Restif, Carolina Ibáñez-Ventoso, Mehul M Vora, Suzhen Guo, Dimitris Metaxas and Monica Driscoll

Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex pp. 1-12

Suchin S Gururangan, Alexander J Sadovsky and Jason N MacLean

Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation pp. 1-13

Aniket Magarkar, Nawel Mele, Noha Abdel-Rahman, Sarah Butcher, Mika Torkkeli, Ritva Serimaa, Arja Paananen, Markus Linder and Alex Bunker

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics pp. 1-19

Salim Akhter Chowdhury, Stanley E Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A Schäffer and Russell Schwartz

Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials pp. 1-11

Fabrizio Pucci and Marianne Rooman

Correlated Inter-Domain Motions in Adenylate Kinase pp. 1-7

Santiago Esteban-Martín, Robert Bryn Fenwick, Jörgen Ådén, Benjamin Cossins, Carlos W Bertoncini, Victor Guallar, Magnus Wolf-Watz and Xavier Salvatella

Enhanced Regulatory Sequence Prediction Using Gapped k -mer Features pp. 1-15

Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad-Noori and Michael A Beer

Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior pp. 1-15

Adam M Gifford, Yale E Cohen and Alan A Stocker

Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks pp. 1-15

Robert Ton, Gustavo Deco and Andreas Daffertshofer

Volume 10, issue 6, 2014

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes pp. 1-13

Kevin J Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H Kohn and Luay Nakhleh

Unsupervised Learning of Cone Spectral Classes from Natural Images pp. 1-13

Noah C Benson, Jeremy R Manning and David H Brainard

Negative Example Selection for Protein Function Prediction: The NoGO Database pp. 1-12

Noah Youngs, Duncan Penfold-Brown, Richard Bonneau and Dennis Shasha

Ten Simple Rules for Approaching a New Job pp. 1-3

Philip E Bourne

A New Online Computational Biology Curriculum pp. 1-3

David B Searls

International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014 pp. 1-3

Christiana N Fogg and Diane E Kovats

AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects pp. 1-14

Qingrun Zhang, Quan Long and Jurg Ott

Model Selection in Systems Biology Depends on Experimental Design pp. 1-14

Daniel Silk, Paul D W Kirk, Chris P Barnes, Tina Toni and Michael P H Stumpf

The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map pp. 1-14

Mamiko Arai, Vicky Brandt and Yuri Dabaghian

Place Cell Rate Remapping by CA3 Recurrent Collaterals pp. 1-10

Trygve Solstad, Hosam N Yousif and Terrence J Sejnowski

An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation pp. 1-21

Jerry S Chen, Abygail M Gumbayan, Robert W Zeller and Joseph M Mahaffy

On the Origins of Suboptimality in Human Probabilistic Inference pp. 1-23

Luigi Acerbi, Sethu Vijayakumar and Daniel M Wolpert

Identifying Crucial Parameter Correlations Maintaining Bursting Activity pp. 1-23

Anca Doloc-Mihu and Ronald L Calabrese

A Novel Cell Traction Force Microscopy to Study Multi-Cellular System pp. 1-15

Xin Tang, Alireza Tofangchi, Sandeep V Anand and Taher A Saif

The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation pp. 1-16

Junjie Wang, Lisa Tucker-Kellogg, Inn Chuan Ng, Ruirui Jia, P S Thiagarajan, Jacob K White and Hanry Yu

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference pp. 1-16

Guocai Chen, Michael J Cairelli, Halil Kilicoglu, Dongwook Shin and Thomas C Rindflesch

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks pp. 1-16

Ankit Gupta, Corentin Briat and Mustafa Khammash

Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization pp. 1-16

Narjes Javaheri, Roland Dries and Jaap Kaandorp

CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data pp. 1-7

Michael J McGeachie, Hsun-Hsien Chang and Scott T Weiss

Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses pp. 1-11

Nadine Töpfer, Federico Scossa, Alisdair Fernie and Zoran Nikoloski

Volume 10, issue 5, 2014

Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism pp. 1-15

Vitaly V Ganusov and Jeremy Auerbach

A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus pp. 1-15

César Rennó-Costa, John E Lisman and Paul F M J Verschure

Inferring Host Gene Subnetworks Involved in Viral Replication pp. 1-22

Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist and Mark Craven

Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks pp. 1-21

Umeshkanta S Thounaojam, Jianxia Cui, Sharon E Norman, Robert J Butera and Carmen C Canavier

Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse pp. 1-8

Marko Jusup, Tadasu Matsuo and Yoh Iwasa

Spatial Generalization in Operant Learning: Lessons from Professional Basketball pp. 1-8

Tal Neiman and Yonatan Loewenstein

Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions pp. 1-9

Daphna Rothschild, Erez Dekel, Jean Hausser, Anat Bren, Guy Aidelberg, Pablo Szekely and Uri Alon

Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data pp. 1-17

Ciira wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G Stunnenberg, George Reid, Neil D Lawrence and Magnus Rattray

Predicting the Responses of Repetitively Firing Neurons to Current Noise pp. 1-17

Charles J Wilson, David Barraza, Todd Troyer and Michael A Farries

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones pp. 1-17

Ignacio J General, Ying Liu, Mandy E Blackburn, Wenzhi Mao, Lila M Gierasch and Ivet Bahar

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks pp. 1-14

Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo and Diego di Bernardo

Paving the Way Towards a Successful and Fulfilling Career in Computational Biology pp. 1-3

Olugbenga Oluwagbemi, Marion Adebiyi, Segun Fatumo and Geoff Macintyre

Ten Simple Rules for Internship in a Pharmaceutical Company pp. 1-3

Bin Chen

2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers pp. 1-3

Christiana N Fogg and Diane E Kovats

Learn from the Best pp. 1-3

Virginie Bernard, Sebastian J Schultheiss and Magali Michaut

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0 pp. 1-25

Masafumi Oizumi, Larissa Albantakis and Giulio Tononi

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells pp. 1-13

Sven Dähne, Niko Wilbert and Laurenz Wiskott

A Computational Framework for Analyzing Stochasticity in Gene Expression pp. 1-13

Marc S Sherman and Barak A Cohen

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation pp. 1-13

Marcus J Tindall and Angela Clerk

Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection pp. 1-12

Rodolphe Thiébaut, Julia Drylewicz, Mélanie Prague, Christine Lacabaratz, Stéphanie Beq, Ana Jarne, Thérèse Croughs, Rafick-Pierre Sekaly, Michael M Lederman, Irini Sereti, Daniel Commenges and Yves Lévy

Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks pp. 1-12

Eric A Yen, Aaron Tsay, Jerome Waldispuhl and Jackie Vogel

Volume 10, issue 4, 2014

Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment pp. 1-14

Kirill Serkh and Daniel B Forger

Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis pp. 1-9

Thomas Walenda, Thomas Stiehl, Hanna Braun, Julia Fröbel, Anthony D Ho, Thomas Schroeder, Tamme W Goecke, Björn Rath, Ulrich Germing, Anna Marciniak-Czochra and Wolfgang Wagner

Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model pp. 1-21

Matteo Farinella, Daniel T Ruedt, Padraig Gleeson, Frederic Lanore and R Angus Silver

ISMB 2014—The Premier Conference for the World's Computational Biologists pp. 1-2

Christiana N Fogg and Diane E Kovats

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible pp. 1-12

Paul J McMurdie and Susan Holmes

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin pp. 1-13

Qing-Miao Nie, Akio Togashi, Takeshi N Sasaki, Mitsunori Takano, Masaki Sasai and Tomoki P Terada

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids pp. 1-7

Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E Hubbard and S David Morley

Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity pp. 1-24

David Samu, Anil K Seth and Thomas Nowotny

Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells pp. 1-18

Bailu Si, Sandro Romani and Misha Tsodyks

The Evolution of Multivariate Maternal Effects pp. 1-11

Bram Kuijper, Rufus A Johnstone and Stuart Townley

A Toolbox for Representational Similarity Analysis pp. 1-11

Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William Marslen-Wilson and Nikolaus Kriegeskorte

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method pp. 1-16

Ke Tang, Jinfeng Zhang and Jie Liang

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems pp. 1-16

Justin S Hogg, Leonard A Harris, Lori J Stover, Niketh S Nair and James R Faeder

Evolutionary Game Dynamics in Populations with Heterogenous Structures pp. 1-16

Wes Maciejewski, Feng Fu and Christoph Hauert

Phylodynamic Inference for Structured Epidemiological Models pp. 1-16

David A Rasmussen, Erik M Volz and Katia Koelle

Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics pp. 1-15

Jeffrey P Perley, Judith Mikolajczak, Marietta L Harrison, Gregery T Buzzard and Ann E Rundell

Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics pp. 1-15

Wan Yang, Alicia Karspeck and Jeffrey Shaman

Volume 10, issue 3, 2014

Ten Simple Rules for Effective Computational Research pp. 1-3

James M Osborne, Miguel O Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J McInerny, Gary R Mirams, Joe Pitt-Francis, Biswa Sengupta, David W Wright, Christian A Yates, David J Gavaghan, Stephen Emmott and Charlotte Deane

Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars pp. 1-13

Partha S Bhagavatula, Charles Claudianos, Michael R Ibbotson and Mandyam V Srinivasan

Global Quantitative Modeling of Chromatin Factor Interactions pp. 1-13

Jian Zhou and Olga G Troyanskaya

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields pp. 1-12

Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu

Modeling Mutual Exclusivity of Cancer Mutations pp. 1-12

Ewa Szczurek and Niko Beerenwinkel

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies pp. 1-10

Lonnie Welch, Fran Lewitter, Russell Schwartz, Cath Brooksbank, Predrag Radivojac, Bruno Gaeta and Maria Victoria Schneider

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases pp. 1-10

Teresa Szczepińska, Jan Kutner, Michał Kopczyński, Krzysztof Pawłowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski and Maga Rowicka

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins pp. 1-17

Lit-Hsin Loo, Danai Laksameethanasan and Yi-Ling Tung

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding pp. 1-14

Shaun Mahony, Matthew D Edwards, Esteban O Mazzoni, Richard I Sherwood, Akshay Kakumanu, Carolyn A Morrison, Hynek Wichterle and David K Gifford

Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach pp. 1-14

Fabian Konrath, Johannes Witt, Thomas Sauter and Dagmar Kulms

If You Can't Measure It, You Can't Manage It pp. 1-4

Jean Peccoud

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems pp. 1-16

Samanthe M Lyons, Wenlong Xu, June Medford and Ashok Prasad

STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning pp. 1-22

David Kappel, Bernhard Nessler and Wolfgang Maass

Slowness and Sparseness Have Diverging Effects on Complex Cell Learning pp. 1-11

Jörn-Philipp Lies, Ralf M Häfner and Matthias Bethge

Universal Count Correction for High-Throughput Sequencing pp. 1-11

Tatsunori B Hashimoto, Matthew D Edwards and David K Gifford

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation pp. 1-18

Michael Pargett, Ann E Rundell, Gregery T Buzzard and David M Umulis

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains pp. 1-19

Vladimir Kazeev, Mustafa Khammash, Michael Nip and Christoph Schwab

Dynamic Alignment Models for Neural Coding pp. 1-19

Sepp Kollmorgen and Richard H R Hahnloser

Volume 10, issue 2, 2014

A Network Characteristic That Correlates Environmental and Genetic Robustness pp. 1-23

Zeina Shreif and Vipul Periwal

The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes pp. 1-22

Yu Hu, Joel Zylberberg and Eric Shea-Brown

Learning Gene Networks under SNP Perturbations Using eQTL Datasets pp. 1-20

Lingxue Zhang and Seyoung Kim

GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans pp. 1-11

Oscar Lao, Fan Liu, Andreas Wollstein and Manfred Kayser

Workshops: A Great Way to Enhance and Supplement a Degree pp. 1-3

Segun Fatumo, Sayane Shome and Geoff Macintyre

A Unified View of “How Allostery Works” pp. 1-12

Chung-Jung Tsai and Ruth Nussinov

Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint pp. 1-12

Germán Enciso, Douglas R Kellogg and Arturo Vargas

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species pp. 1-12

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu and Mikko Arvas

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes pp. 1-12

Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino and Michele Caselle

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics pp. 1-13

Pascal Carrivain, Maria Barbi and Jean-Marc Victor

Mathematical Modeling of the Phoenix Rising Pathway pp. 1-10

Chad Liu, Chuan-Yuan Li and Fan Yuan

A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses pp. 1-14

Frederick A Matsen Iv, Christopher T Small, Khanh Soliven, Gregory A Engel, Mostafa M Feeroz, Xiaoxing Wang, Karen L Craig, M Kamrul Hasan, Michael Emerman, Maxine L Linial and Lisa Jones-Engel

Combining Experiments and Simulations Using the Maximum Entropy Principle pp. 1-9

Wouter Boomsma, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen

Volume 10, issue 1, 2014

Fast Reconstruction of Compact Context-Specific Metabolic Network Models pp. 1-10

Nikos Vlassis, Maria Pires Pacheco and Thomas Sauter

The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics pp. 1-21

Moritz Helias, Tom Tetzlaff and Markus Diesmann

Machine Learning Estimates of Natural Product Conformational Energies pp. 1-8

Matthias Rupp, Matthias R Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M Boeckler and Gisbert Schneider

Ten Simple Rules for Writing Research Papers pp. 1-3

Weixiong Zhang

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks pp. 1-13

Axel von Kamp and Steffen Klamt

Stress and Strain Provide Positional and Directional Cues in Development pp. 1-13

Behruz Bozorg, Pawel Krupinski and Henrik Jönsson

Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants pp. 1-13

Gesham Magombedze, Shigetoshi Eda and Vitaly V Ganusov

The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity pp. 1-13

Sean T Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso and Garrett B Stanley

Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures pp. 1-12

Yi-Fei Huang and G Brian Golding

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations pp. 1-11

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D Wieben, Jaroslav Zendulka, Jan Brezovsky and Jiri Damborsky

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency pp. 1-18

Biswa Sengupta, Simon Barry Laughlin and Jeremy Edward Niven

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function pp. 1-18

Areum Han, Peter Stoilov, Anthony J Linares, Yu Zhou, Xiang-Dong Fu and Douglas L Black

Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching pp. 1-15

Garrett Jenkinson and John Goutsias

Task-Specific Response Strategy Selection on the Basis of Recent Training Experience pp. 1-16

Jacqueline M Fulvio, C Shawn Green and Paul R Schrater

Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data pp. 1-16

Nicole Bohme Carnegie, Rui Wang, Vladimir Novitsky and Victor De Gruttola

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data pp. 1-16

Jean Daunizeau, Vincent Adam and Lionel Rigoux

Searching for Collective Behavior in a Large Network of Sensory Neurons pp. 1-23

Gašper Tkačik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek and Michael J Berry