PLOS Computational Biology
2005 - 2025
From Public Library of Science Bibliographic data for series maintained by ploscompbiol (). Access Statistics for this journal.
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Volume 10, issue 12, 2014
- 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
- Hippocampal Remapping Is Constrained by Sparseness rather than Capacity pp. 1-12

- Axel Kammerer and Christian Leibold
- 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
- Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments pp. 1-9

- Christoph Zechner and Heinz Koeppl
- 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
- Ten Simple Rules for Finishing Your PhD pp. 1-4

- Jacopo Marino, Melanie I Stefan and Sarah Blackford
- 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
- The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets pp. 1-20

- Evandro Ferrada
- 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
Volume 10, issue 11, 2014
- 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
- 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
- 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
- Statistical Computations Underlying the Dynamics of Memory Updating pp. 1-13

- Samuel J Gershman, Angela Radulescu, Kenneth A Norman and Yael Niv
- 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
- Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns pp. 1-14

- Marcin J Skwark, Daniele Raimondi, Mirco Michel and Arne Elofsson
- 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
- High-Fidelity Coding with Correlated Neurons pp. 1-25

- Rava Azeredo da Silveira and Michael J Berry
Volume 10, issue 10, 2014
- 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
- 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
- Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment pp. 1-27

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

- Gang Peng, Yu Fan and Wenyi Wang
- 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
- Ten Simple Rules for Writing a PLOS Ten Simple Rules Article pp. 1-5

- Harriet Dashnow, Andrew Lonsdale and Philip E Bourne
- 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
- 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
- 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
- Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups pp. 1-10

- Amos Korman, Efrat Greenwald and Ofer Feinerman
Volume 10, issue 9, 2014
- The Time Scale of Evolutionary Innovation pp. 1-7

- Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam and Martin A Nowak
- 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
- Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies pp. 1-14

- Diana Chang and Alon Keinan
- Pupil-Linked Arousal Determines Variability in Perceptual Decision Making pp. 1-13

- Peter R Murphy, Joachim Vandekerckhove and Sander Nieuwenhuis
- eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models pp. 1-15

- Michal Brylinski
- Multi-state Modeling of Biomolecules pp. 1-9

- Melanie I Stefan, Thomas M Bartol, Terrence J Sejnowski and Mary B Kennedy
- 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
- 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
- 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
- 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
- Environmental Statistics and Optimal Regulation pp. 1-12

- David A Sivak and Matt Thomson
Volume 10, issue 8, 2014
- 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
- 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
- Phenotypic Signatures Arising from Unbalanced Bacterial Growth pp. 1-10

- Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz and Lingchong You
- 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
- 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
- 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
- The Upside of Failure: How Regional Student Groups Learn from Their Mistakes pp. 1-3

- Tarun Mishra, R Gonzalo Parra and Thomas Abeel
Volume 10, issue 7, 2014
- Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials pp. 1-11

- Fabrizio Pucci and Marianne Rooman
- 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
- 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
- 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
- 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
- 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
- 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
- Brain and Behavior in Decision-Making pp. 1-8

- Peter Cassey, Andrew Heathcote and Scott D Brown
- 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
- 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
- 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
- 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
- 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
Volume 10, issue 6, 2014
- 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
- 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
- Negative Example Selection for Protein Function Prediction: The NoGO Database pp. 1-12

- Noah Youngs, Duncan Penfold-Brown, Richard Bonneau and Dennis Shasha
- Place Cell Rate Remapping by CA3 Recurrent Collaterals pp. 1-10

- Trygve Solstad, Hosam N Yousif and Terrence J Sejnowski
- 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
- 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
- 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
- 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
- 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
- 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
Volume 10, issue 5, 2014
- 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
- 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
- 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
- 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
- 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
- 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
- Inferring Host Gene Subnetworks Involved in Viral Replication pp. 1-22

- Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist and Mark Craven
- From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0 pp. 1-25

- Masafumi Oizumi, Larissa Albantakis and Giulio Tononi
- 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
Volume 10, issue 4, 2014
- Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity pp. 1-24

- David Samu, Anil K Seth and Thomas Nowotny
- ISMB 2014—The Premier Conference for the World's Computational Biologists pp. 1-2

- Christiana N Fogg and Diane E Kovats
- 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
- Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment pp. 1-14

- Kirill Serkh and Daniel B Forger
- Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells pp. 1-18

- Bailu Si, Sandro Romani and Misha Tsodyks
- 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
- 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
- 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
- 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
- Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible pp. 1-12

- Paul J McMurdie and Susan Holmes
- 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
- 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
Volume 10, issue 3, 2014
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems pp. 1-16

- Samanthe M Lyons, Wenlong Xu, June Medford and Ashok Prasad
- If You Can't Measure It, You Can't Manage It pp. 1-4

- Jean Peccoud
- 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
- 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
Volume 10, issue 2, 2014
- 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
- Workshops: A Great Way to Enhance and Supplement a Degree pp. 1-3

- Segun Fatumo, Sayane Shome and Geoff Macintyre
- 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
- A Network Characteristic That Correlates Environmental and Genetic Robustness pp. 1-23

- Zeina Shreif and Vipul Periwal
- 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
- 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
- Mathematical Modeling of the Phoenix Rising Pathway pp. 1-10

- Chad Liu, Chuan-Yuan Li and Fan Yuan
- Combining Experiments and Simulations Using the Maximum Entropy Principle pp. 1-9

- Wouter Boomsma, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen
- In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics pp. 1-13

- Pascal Carrivain, Maria Barbi and Jean-Marc Victor
Volume 10, issue 1, 2014
- 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
- Ten Simple Rules for Writing Research Papers pp. 1-3

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

- Nikos Vlassis, Maria Pires Pacheco and Thomas Sauter
- 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
- 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
- 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
- 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
- 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
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