PLOS Computational Biology

2005 - 2022

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Volume 9, issue 12, 2013

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information pp. 1-18

Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty and Alessandra Carbone

Modeling the Afferent Dynamics of the Baroreflex Control System pp. 1-18

Adam Mahdi, Jacob Sturdy, Johnny T Ottesen and Mette S Olufsen

A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions pp. 1-9

Roger Guimerà and Marta Sales-Pardo

Education in Computational Biology Today and Tomorrow pp. 1-2

Joanne A Fox and B F Francis Ouellette

Sharpness of Spike Initiation in Neurons Explained by Compartmentalization pp. 1-10

Romain Brette

Epidemic Spread on Weighted Networks pp. 1-10

Christel Kamp, Mathieu Moslonka-Lefebvre and Samuel Alizon

Flow Cytometry Bioinformatics pp. 1-10

Kieran O'Neill, Nima Aghaeepour, Josef Špidlen and Ryan Brinkman

A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda pp. 1-10

Artemis Koukounari, Christl A Donnelly, Irini Moustaki, Edridah M Tukahebwa, Narcis B Kabatereine, Shona Wilson, Joanne P Webster, André M Deelder, Birgitte J Vennervald and Govert J van Dam

Perturbation Biology: Inferring Signaling Networks in Cellular Systems pp. 1-23

Evan J Molinelli, Anil Korkut, Weiqing Wang, Martin L Miller, Nicholas P Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B Solit, Christine A Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina and Chris Sander

Forward and Backward Inference in Spatial Cognition pp. 1-22

Will D Penny, Peter Zeidman and Neil Burgess

A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca2+-Dependent Priming Catalyst Effectively Explains Ca2+-Dependent Properties of Neurosecretion pp. 1-15

Alexander M Walter, Paulo S Pinheiro, Matthijs Verhage and Jakob B Sørensen

Extrapolating Weak Selection in Evolutionary Games pp. 1-7

Bin Wu, Julián García, Christoph Hauert and Arne Traulsen

Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized pp. 1-14

Amir Dezfouli and Bernard W Balleine

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei pp. 1-14

Eduard J Kerkhoven, Fiona Achcar, Vincent P Alibu, Richard J Burchmore, Ian H Gilbert, Maciej Trybiło, Nicole N Driessen, David Gilbert, Rainer Breitling, Barbara M Bakker and Michael P Barrett

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs pp. 1-13

Patrick G Blachly, César A F de Oliveira, Sarah L Williams and J Andrew McCammon

Inferring the Source of Transmission with Phylogenetic Data pp. 1-13

Erik M Volz and Simon D W Frost

Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission pp. 1-16

T Alex Perkins, Thomas W Scott, Arnaud Le Menach and David L Smith

Volume 9, issue 11, 2013

About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium pp. 1-3

Lennart Martens

Leading a Statistical Bioinformatics Lab: It's All About Finding Balance pp. 1-3

Olga Vitek

Breaking the Ice and Forging Links: The Importance of Socializing in Research pp. 1-3

Miranda Stobbe, Tarun Mishra and Geoff Macintyre

Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells pp. 1-15

Kazunari Mouri and Yasushi Sako

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos pp. 1-15

Julian E Fuchs, Susanne von Grafenstein, Roland G Huber, Christian Kramer and Klaus R Liedl

Communication and Common Interest pp. 1-6

Peter Godfrey-Smith and Manolo Martínez

Dread and the Disvalue of Future Pain pp. 1-18

Giles W Story, Ivaylo Vlaev, Ben Seymour, Joel S Winston, Ara Darzi and Raymond J Dolan

Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity pp. 1-9

Kejian Wang, Jiazhi Sun, Shufeng Zhou, Chunling Wan, Shengying Qin, Can Li, Lin He and Lun Yang

Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification pp. 1-9

Lucas Theis, Andrè Maia Chagas, Daniel Arnstein, Cornelius Schwarz and Matthias Bethge

Learning How to Run a Lab: Interviews with Principal Investigators pp. 1-2

Theodore Alexandrov and Philip E Bourne

Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations pp. 1-10

Jakob J Metzger and Stephan Eule

MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms pp. 1-10

Rotem Ben-Hamo and Sol Efroni

Ten Simple Rules for Starting a Regional Student Group pp. 1-4

Avinash Kumar Shanmugam, Geoff Macintyre, Magali Michaut and Thomas Abeel

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013 pp. 1-4

Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P Satagopam, Manuel Corpas, Geoff Macintyre and Theodore Alexandrov

Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code pp. 1-7

Christophe Micheyl, Paul R Schrater and Andrew J Oxenham

Stochastic Computations in Cortical Microcircuit Models pp. 1-28

Stefan Habenschuss, Zeno Jonke and Wolfgang Maass

A Neurocomputational Model of the Mismatch Negativity pp. 1-14

Falk Lieder, Klaas E Stephan, Jean Daunizeau, Marta I Garrido and Karl J Friston

A Computational Model of Liver Iron Metabolism pp. 1-14

Simon Mitchell and Pedro Mendes

Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon pp. 1-14

Denis Valle and James Clark

Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance pp. 1-14

Biyu J He and John M Zempel

Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations pp. 1-17

Noa Chapal-Ilani, Yosef E Maruvka, Adam Spiro, Yitzhak Reizel, Rivka Adar, Liran I Shlush and Ehud Shapiro

A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions pp. 1-13

Xiaoxia Wang, Sarada Panchanathan and Gerardo Chowell

Mapping the Structural and Dynamical Features of Kinesin Motor Domains pp. 1-13

Guido Scarabelli and Barry J Grant

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data pp. 1-11

Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G Christodoulou, Kalaimathy Singaravelu and Andreas Beyer

Predictive Coding of Dynamical Variables in Balanced Spiking Networks pp. 1-16

Martin Boerlin, Christian K Machens and Sophie Denève

Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers pp. 1-16

Oliwia M Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F Sbalzarini and Helge Ewers

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data pp. 1-16

Ridvan Eksi, Hong-Dong Li, Rajasree Menon, Yuchen Wen, Gilbert S Omenn, Matthias Kretzler and Yuanfang Guan

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks pp. 1-16

Takeshi Hase, Samik Ghosh, Ryota Yamanaka and Hiroaki Kitano

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins pp. 1-12

Debabani Ganguly, Weihong Zhang and Jianhan Chen

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction pp. 1-8

Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes and David G Miguez

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data pp. 1-8

Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim and Jie Zhang

Volume 9, issue 10, 2013

Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin pp. 1-9

Lennart Hilbert, Genevieve Bates, Horia N Roman, Jenna L Blumenthal, Nedjma B Zitouni, Apolinary Sobieszek, Michael C Mackey and Anne-Marie Lauzon

Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides pp. 1-18

Gabriel Rosser, Alexander G Fletcher, David A Wilkinson, Jennifer A de Beyer, Christian A Yates, Judith P Armitage, Philip K Maini and Ruth E Baker

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis pp. 1-18

Pralay Mitra, David Shultis, Jeffrey R Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki and Yang Zhang

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data pp. 1-10

André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias and Alan Mitchell Durham

Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses pp. 1-10

Ricardo Aguas and Neil M Ferguson

Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening pp. 1-10

Arnab Bhattacherjee and Stefan Wallin

Ten Simple Rules for Reproducible Computational Research pp. 1-4

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor and Eivind Hovig

GINI: From ISH Images to Gene Interaction Networks pp. 1-15

Kriti Puniyani and Eric P Xing

Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise pp. 1-15

Qiang Luo, Tian Ge, Fabian Grabenhorst, Jianfeng Feng and Edmund T Rolls

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision pp. 1-15

Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès and Denis Thieffry

Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments pp. 1-15

Francesca Falcetta, Monica Lupi, Valentina Colombo and Paolo Ubezio

Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice pp. 1-15

Sebastian Gluth, Jörg Rieskamp and Christian Büchel

Explain Bioinformatics to Your Grandmother! pp. 1-3

Virginie Bernard and Magali Michaut

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region pp. 1-3

Asif M Khan, Tin Wee Tan, Christian Schönbach and Shoba Ranganathan

The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity pp. 1-12

Thomas Hannagan and Jonathan Grainger

The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters pp. 1-12

Chunfeng Zhao and Sergei Yu Noskov

Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways pp. 1-14

Farzad Farkhooi, Anja Froese, Eilif Muller, Randolf Menzel and Martin P Nawrot

Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model pp. 1-14

Tim Odenthal, Bart Smeets, Paul Van Liedekerke, Engelbert Tijskens, Hans Van Oosterwyck and Herman Ramon

Comprehensive Repertoire of Foldable Regions within Whole Genomes pp. 1-14

Guilhem Faure and Isabelle Callebaut

How Can PLOS Computational Biology Help the Biological Sciences? pp. 1-1

Ruth Nussinov

The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics pp. 1-16

Ramakrishnan Iyer, Vilas Menon, Michael Buice, Christof Koch and Stefan Mihalas

The Convallis Rule for Unsupervised Learning in Cortical Networks pp. 1-16

Pierre Yger and Kenneth D Harris

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster pp. 1-16

Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R Banga and Johannes Jaeger

Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins pp. 1-11

Fan Jin, Chen Yu, Luhua Lai and Zhirong Liu

Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes pp. 1-11

Ryan Suderman and Eric J Deeds

A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks pp. 1-11

Evan S Schaffer, Srdjan Ostojic and L F Abbott

A Brain-Machine Interface for Control of Medically-Induced Coma pp. 1-17

Maryam M Shanechi, Jessica J Chemali, Max Liberman, Ken Solt and Emery N Brown

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data pp. 1-13

Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley, Robert Landick and Sündüz Keleş

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data pp. 1-13

Joshua G Schraiber, Yulia Mostovoy, Tiffany Y Hsu and Rachel B Brem

Volume 9, issue 9, 2013

From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells pp. 1-10

Julián Candia, Ryan Maunu, Meghan Driscoll, Angélique Biancotto, Pradeep Dagur, J Philip McCoy, H Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B Nussenblatt, Jayanth R Banavar and Wolfgang Losert

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization pp. 1-27

Rudi Agius, Mieczyslaw Torchala, Iain H Moal, Juan Fernández-Recio and Paul A Bates

The Regional Student Group Program of the ISCB Student Council: Stories from the Road pp. 1-4

Geoff Macintyre, Magali Michaut and Thomas Abeel

Ten Simple Rules for Cultivating Open Science and Collaborative R&D pp. 1-4

Hassan Masum, Aarthi Rao, Benjamin M Good, Matthew H Todd, Aled M Edwards, Leslie Chan, Barry A Bunin, Andrew I Su, Zakir Thomas and Philip E Bourne

The Next Generation of Transcription Factor Binding Site Prediction pp. 1-18

Anthony Mathelier and Wyeth W Wasserman

Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer pp. 1-9

James J Lee, Justin Huang, Christopher G England, Lacey R McNally and Hermann B Frieboes

ISCB Computational Biology Wikipedia Competition pp. 1-2

Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff Macintyre, Tomás Di Domenico, Thomas Abeel, Darren W Logan, Predrag Radivojac and Burkhard Rost

Frequency Response of a Protein to Local Conformational Perturbations pp. 1-15

Dilek Eren and Burak Alakent

Collective Dynamics Underlying Allosteric Transitions in Hemoglobin pp. 1-8

Martin D Vesper and Bert L de Groot

Predicting Odor Perceptual Similarity from Odor Structure pp. 1-12

Kobi Snitz, Adi Yablonka, Tali Weiss, Idan Frumin, Rehan M Khan and Noam Sobel

Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules pp. 1-12

Jing Chen, Zhen Hu, Mukta Phatak, John Reichard, Johannes M Freudenberg, Siva Sivaganesan and Mario Medvedovic

Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli pp. 1-12

Johnatan Aljadeff, Ronen Segev, Michael J Berry and Tatyana O Sharpee

Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization pp. 1-12

Giuseppe Maccari, Mariagrazia Di Luca, Riccardo Nifosí, Francesco Cardarelli, Giovanni Signore, Claudia Boccardi and Angelo Bifone

Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus pp. 1-12

Kartik Subramanian, Mark R Paul and John J Tyson

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family pp. 1-12

Jianhui Song, Sheung Chun Ng, Peter Tompa, Kevin A W Lee and Hue Sun Chan

Using Biological Pathway Data with Paxtools pp. 1-5

Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken I Fukuda, Benjamin Gross, Onur Selçuk Sümer, Gary D Bader and Chris Sander

Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors pp. 1-20

Linhui Hao, Qiuling He, Zhishi Wang, Mark Craven, Michael A Newton and Paul Ahlquist

Adaptation Dynamics in Densely Clustered Chemoreceptors pp. 1-13

William Pontius, Michael W Sneddon and Thierry Emonet

Task-Based Core-Periphery Organization of Human Brain Dynamics pp. 1-16

Danielle S Bassett, Nicholas F Wymbs, M Puck Rombach, Mason A Porter, Peter J Mucha and Scott T Grafton

Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum pp. 1-16

Eddy J Bautista, Joseph Zinski, Steven M Szczepanek, Erik L Johnson, Edan R Tulman, Wei-Mei Ching, Steven J Geary and Ranjan Srivastava

From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems pp. 1-16

Izzet B Yildiz, Katharina von Kriegstein and Stefan J Kiebel

Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation pp. 1-16

Yun M Zhao and Anthony R French

Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways pp. 1-16

Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg and Tero Aittokallio

Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis pp. 1-14

Tristan Ursell, Rosanna Man Wah Chau, Susanne Wisen, Devaki Bhaya and Kerwyn Casey Huang

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs pp. 1-19

Ioannis N Melas, Regina Samaga, Leonidas G Alexopoulos and Steffen Klamt

Volume 9, issue 8, 2013

A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays pp. 1-12

Neta S Zuckerman, Yair Noam, Andrea J Goldsmith and Peter P Lee

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths pp. 1-14

Chunhe Li and Jin Wang

Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation pp. 1-14

Frédéric Crevecoeur and Stephen H Scott

Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis pp. 1-14

Jordi Heijman, Antonio Zaza, Daniel M Johnson, Yoram Rudy, Ralf L M Peeters, Paul G A Volders and Ronald L Westra

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases pp. 1-14

Simona Mariani, Daniele Dell'Orco, Angelo Felline, Francesco Raimondi and Francesca Fanelli

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction pp. 1-17

Simona Cocco, Remi Monasson and Martin Weigt

Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data pp. 1-16

Christoph Bauermeister, Tilo Schwalger, David F Russell, Alexander B Neiman and Benjamin Lindner

Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization pp. 1-11

Guillermo Rodrigo, Thomas E Landrain, Eszter Majer, José-Antonio Daròs and Alfonso Jaramillo

Sensory Information and Encounter Rates of Interacting Species pp. 1-11

Andrew M Hein and Scott A McKinley

Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons pp. 1-20

Carlo Baldassi, Alireza Alemi-Neissi, Marino Pagan, James J DiCarlo, Riccardo Zecchina and Davide Zoccolan

Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model pp. 1-23

Jung H Lee, Miles A Whittington and Nancy J Kopell

Software for Computing and Annotating Genomic Ranges pp. 1-10

Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan and Vincent J Carey

Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms pp. 1-10

Ohad Manor and Eran Segal

Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions pp. 1-15

Christian A Tiemann, Joep Vanlier, Maaike H Oosterveer, Albert K Groen, Peter A J Hilbers and Natal A W van Riel

Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System pp. 1-15

Mengchen Zhu and Christopher J Rozell

Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3 pp. 1-15

Harish Shankaran, Yi Zhang, Yunbing Tan and Haluk Resat

International Society for Computational Biology Welcomes Its Newest Class of Fellows pp. 1-3

Christiana N Fogg and Diane E Kovats

Volume 9, issue 7, 2013

Spatial Stochastic Dynamics Enable Robust Cell Polarization pp. 1-12

Michael J Lawson, Brian Drawert, Mustafa Khammash, Linda Petzold and Tau-Mu Yi

Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs pp. 1-18

James M McFarland, Yuwei Cui and Daniel A Butts

A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems pp. 1-18

Robert C Wilson, Matthew R Nassar and Joshua I Gold

Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential pp. 1-23

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

Ten Simple Rules for Writing a Literature Review pp. 1-4

Marco Pautasso

The Minimal Complexity of Adapting Agents Increases with Fitness pp. 1-10

Nikhil J Joshi, Giulio Tononi and Christof Koch

Co-expression Profiling of Autism Genes in the Mouse Brain pp. 1-10

Idan Menashe, Pascal Grange, Eric C Larsen, Sharmila Banerjee-Basu and Partha P Mitra

Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations pp. 1-10

Denis Bucher, Yuan-Hao Hsu, Varnavas D Mouchlis, Edward A Dennis and J Andrew McCammon

Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples pp. 1-14

Andrew Cron, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder K Singh, Cedrik M Britten, Marij J P Welters, Sjoerd H van der Burg, Mike West and Cliburn Chan

Statistical Analysis of Molecular Signal Recording pp. 1-14

Joshua I Glaser, Bradley M Zamft, Adam H Marblestone, Jeffrey R Moffitt, Keith Tyo, Edward S Boyden, George Church and Konrad P Kording

Gain Control Network Conditions in Early Sensory Coding pp. 1-13

Eduardo Serrano, Thomas Nowotny, Rafael Levi, Brian H Smith and Ramón Huerta

Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein pp. 1-13

Burcu Aykaç Fas, Yusuf Tutar and Türkan Haliloğlu

A Family of Algorithms for Computing Consensus about Node State from Network Data pp. 1-17

Eleanor R Brush, David C Krakauer and Jessica C Flack

Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells pp. 1-17

Changji Shi, Chuan-Hsiang Huang, Peter N Devreotes and Pablo A Iglesias

Consistent Estimation of Gibbs Energy Using Component Contributions pp. 1-11

Elad Noor, Hulda S Haraldsdóttir, Ron Milo and Ronan M T Fleming

Volume 9, issue 6, 2013

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation pp. 1-9

Christian P Koch, Anna M Perna, Max Pillong, Nickolay K Todoroff, Paul Wrede, Gerd Folkers, Jan A Hiss and Gisbert Schneider

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins pp. 1-19

Louis-François Handfield, Yolanda T Chong, Jibril Simmons, Brenda J Andrews and Alan M Moses

PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data pp. 1-19

Gabriel E Hoffman, Benjamin A Logsdon and Jason G Mezey

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach pp. 1-14

Meagan C Small, Pedro Lopes, Rodrigo B Andrade and Alexander D MacKerell

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1 pp. 1-17

Lyudmyla Dorosh, Olesya A Kharenko, Nandhakishore Rajagopalan, Michele C Loewen and Maria Stepanova

Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution pp. 1-15

Rui Zhao and Franziska Michor

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer pp. 1-13

Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G Stunnenberg and Sampsa Hautaniemi

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum pp. 1-11

William R Harcombe, Nigel F Delaney, Nicholas Leiby, Niels Klitgord and Christopher J Marx

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression pp. 1-11

Nanye Long, Samuel P Dickson, Jessica M Maia, Hee Shin Kim, Qianqian Zhu and Andrew S Allen

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study pp. 1-16

Jörg Bornschein, Marc Henniges and Jörg Lücke

Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making pp. 1-20

Ritwik K Niyogi and KongFatt Wong-Lin

Volume 9, issue 5, 2013

The Emergence of Environmental Homeostasis in Complex Ecosystems pp. 1-9

James G Dyke and Iain S Weaver

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA pp. 1-9

Tobias Linder, Bert L de Groot and Anna Stary-Weinzinger

Long-range Order in Canary Song pp. 1-12

Jeffrey E Markowitz, Elizabeth Ivie, Laura Kligler and Timothy J Gardner

Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability pp. 1-12

Yunpeng Wang, Jon Olav Vik, Stig W Omholt and Arne B Gjuvsland

Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus pp. 1-10

Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre and Carine Brouat

A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli pp. 1-1

Jonathan L Robinson and Mark P Brynildsen

STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification pp. 1-14

Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler and Gregory Batt

Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation pp. 1-14

Haipeng Li and Thomas Wiehe

Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment pp. 1-11

Gouri Shankar Pandey, Chen Yanover, Tom E Howard and Zuben E Sauna

Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury pp. 1-11

Alexey Solovyev, Qi Mi, Yi-Ting Tzen, David Brienza and Yoram Vodovotz

Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task pp. 1-11

Hang Zhang, Nathaniel D Daw and Laurence T Maloney

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling pp. 1-16

Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A Logsdon, Gaurav Pandey, Benjamin A Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H Mecham, Oscar M Rueda, Jorg Tost, Christina Curtis, Mariano J Alvarez, Vessela N Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H Friend, Trey Ideker, Eric E Schadt, Gustavo A Stolovitzky and Adam A Margolin

Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains pp. 1-17

Seth Blumberg and James O Lloyd-Smith

Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input pp. 1-17

Jonathan J Hunt, Peter Dayan and Geoffrey J Goodhill

Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups pp. 1-13

Can Guven, Erin Rericha, Edward Ott and Wolfgang Losert

Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations pp. 1-13

Xiaodong Cai, Juan Andrés Bazerque and Georgios B Giannakis

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch pp. 1-13

Wei Huang, Joohyun Kim, Shantenu Jha and Fareed Aboul-ela

Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia pp. 1-13

Ayako Watanabe, Daisuke Hosino, Naohiko Koshikawa, Motoharu Seiki, Takashi Suzuki and Kazuhisa Ichikawa

Volume 9, issue 4, 2013

A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience pp. 1-6

Matthew R Nassar and Joshua I Gold

Noise Suppression and Surplus Synchrony by Coincidence Detection pp. 1-15

Matthias Schultze-Kraft, Markus Diesmann, Sonja Grün and Moritz Helias

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation pp. 1-15

Gabriela V Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen K Y Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, Janet Wilson-McManus, Robert Balshaw, Paul A Keown, Christoph H Borchers, Bruce McManus, Raymond T Ng, W Robert McMaster and for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams

Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion pp. 1-15

Hans B Sieburg, Giulio Cattarossi and Christa E Muller-Sieburg

Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization pp. 1-15

Annabelle Ballesta, Jonathan Lopez, Nikolay Popgeorgiev, Philippe Gonzalo, Marie Doumic and Germain Gillet

Optimal Balance of the Striatal Medium Spiny Neuron Network pp. 1-21

Adam Ponzi and Jeffery R Wickens

Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria pp. 1-10

Juho Rousu, Daniel D Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor and Delmiro Fernandez-Reyes

Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations pp. 1-10

Daniel L Parton, Alex Tek, Marc Baaden and Mark S P Sansom

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase pp. 1-9

Lin-Tai Da, Fátima Pardo Avila, Dong Wang and Xuhui Huang

Learning Multisensory Integration and Coordinate Transformation via Density Estimation pp. 1-17

Joseph G Makin, Matthew R Fellows and Philip N Sabes

Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure pp. 1-13

Xiaobo Wan, Yue Ma, Christopher L McClendon, Lily Jun-shen Huang and Niu Huang

Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect pp. 1-14

Anne-Sophie Coquel, Jean-Pascal Jacob, Mael Primet, Alice Demarez, Mariella Dimiccoli, Thomas Julou, Lionel Moisan, Ariel B Lindner and Hugues Berry

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies pp. 1-14

Jordan R Willis, Bryan S Briney, Samuel L DeLuca, James E Crowe and Jens Meiler

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps pp. 1-12

Andrei Zinovyev, Inna Kuperstein, Emmanuel Barillot and Wolf-Dietrich Heyer

Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition pp. 1-12

Joseph L Baker, Nicolas Biais and Florence Tama

Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity pp. 1-30

Bernhard Nessler, Michael Pfeiffer, Lars Buesing and Wolfgang Maass

Volume 9, issue 3, 2013

Stimulus-dependent Maximum Entropy Models of Neural Population Codes pp. 1-14

Einat Granot-Atedgi, Gašper Tkačik, Ronen Segev and Elad Schneidman

Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise pp. 1-14

R Channing Moore, Tyler Lee and Frédéric E Theunissen

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes pp. 1-14

Christopher Y Park, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca D Burdine and Olga G Troyanskaya

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State pp. 1-14

Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John Stamatoyannopoulos, Jason Ernst, Manolis Kellis and Bing Ren

Automated Analysis of a Diverse Synapse Population pp. 1-14

Brad Busse and Stephen Smith

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection pp. 1-13

Richard P Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E Herbert-Read, David J T Sumpter and Ashley J W Ward

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage pp. 1-13

Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser and Francisco S Domingues

Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis pp. 1-13

Anton Spanne and Henrik Jörntell

An Integrated Computational/Experimental Model of Lymphoma Growth pp. 1-13

Hermann B Frieboes, Bryan R Smith, Yao-Li Chuang, Ken Ito, Allison M Roettgers, Sanjiv S Gambhir and Vittorio Cristini

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology pp. 1-17

Tina Toni and Bruce Tidor

Differential Expression Analysis for Pathways pp. 1-17

Winston A Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins and Eugene Kolker

Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity pp. 1-16

BoHung Kim, Sarah L Hawes, Fawad Gillani, Lane J Wallace and Kim T Blackwell

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment pp. 1-16

Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu and Rui Kuang

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum pp. 1-16

Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew and Jens Nielsen

A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana pp. 1-16

Christoph Schmal, Peter Reimann and Dorothee Staiger

Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases pp. 1-11

Alane Izu, Ted Cohen and Victor DeGruttola

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences pp. 1-11

Dazhi Jiao, Yuzhen Ye and Haixu Tang

Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model pp. 1-12

Néstor Sepúlveda, Laurence Petitjean, Olivier Cochet, Erwan Grasland-Mongrain, Pascal Silberzan and Vincent Hakim

Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks pp. 1-12

Munia Amin, Steven L Porter and Orkun S Soyer

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model pp. 1-12

Libin Rong, Jeremie Guedj, Harel Dahari, Daniel J Coffield, Micha Levi, Patrick Smith and Alan S Perelson

Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action pp. 1-12

James B Gilmore, Anthony D Kelleher, David A Cooper and John M Murray

A Model of Binocular Rivalry and Cross-orientation Suppression pp. 1-12

Christopher P Said and David J Heeger

Chaste: An Open Source C++ Library for Computational Physiology and Biology pp. 1-8

Gary R Mirams, Christopher J Arthurs, Miguel O Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G Fletcher, Daniel G Harvey, Megan E Marsh, James M Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi and David J Gavaghan

Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning pp. 1-15

Tomoki Kurikawa and Kunihiko Kaneko

Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza pp. 1-15

Laura Matrajt, M Elizabeth Halloran and Ira M Longini

Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds pp. 1-18

Michael A Carlin and Mounya Elhilali

Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza pp. 1-9

Chad R Wells, Eili Y Klein and Chris T Bauch

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models pp. 1-9

Per Larsson and Peter M Kasson

The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks pp. 1-9

Clive Bowsher, Margaritis Voliotis and Peter S Swain

Bursts of Vertex Activation and Epidemics in Evolving Networks pp. 1-9

Luis Rocha and Vincent D Blondel

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network pp. 1-9

Jialiang Huang, Chaoqun Niu, Christopher D Green, Lun Yang, Hongkang Mei and Jing-Dong J Han

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field pp. 1-9

Silvio a Beccara, Tatjana Škrbić, Roberto Covino, Cristian Micheletti and Pietro Faccioli

Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface pp. 1-10

David K Johnson and John Karanicolas

Stability and Responsiveness in a Self-Organized Living Architecture pp. 1-10

Simon Garnier, Tucker Murphy, Matthew Lutz, Edward Hurme, Simon Leblanc and Iain D Couzin

Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming pp. 1-21

Robert W Mill, Tamás M Bőhm, Alexandra Bendixen, István Winkler and Susan L Denham

Volume 9, issue 2, 2013

Optimal Properties of Analog Perceptrons with Excitatory Weights pp. 1-6

Claudia Clopath and Nicolas Brunel

Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions pp. 1-15

Romain Daniel Cazé, Mark Humphries and Boris Gutkin

An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules pp. 1-9

Michael Thomas, Dylan Jayatilaka and Ben Corry

Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems pp. 1-9

Kieran Alden, Mark Read, Jon Timmis, Paul S Andrews, Henrique Veiga-Fernandes and Mark Coles

No Evidence for an Item Limit in Change Detection pp. 1-9

Shaiyan Keshvari, Ronald van den Berg and Wei Ji Ma

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data pp. 1-18

Gerard J P van Westen, Alwin Hendriks, Jörg K Wegner, Adriaan P IJzerman, Herman W T van Vlijmen and Andreas Bender

Let's Make Those Book Chapters Open Too! pp. 1-2

Philip E Bourne

Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package pp. 1-10

David C Sterratt, Daniel Lyngholm, David J Willshaw and Ian D Thompson

Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs pp. 1-19

Robert R Kerr, Anthony N Burkitt, Doreen A Thomas, Matthieu Gilson and David B Grayden

Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models pp. 1-19

Paul Michael Loriaux, Glenn Tesler and Alexander Hoffmann

Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila pp. 1-14

Andrea Censi, Andrew D Straw, Rosalyn W Sayaman, Richard M Murray and Michael H Dickinson

Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model pp. 1-14

Thomas Stockner, Therese R Montgomery, Oliver Kudlacek, Rene Weissensteiner, Gerhard F Ecker, Michael Freissmuth and Harald H Sitte

Biomolecular Events in Cancer Revealed by Attractor Metagenes pp. 1-14

Wei-Yi Cheng, Tai-Hsien Ou Yang and Dimitris Anastassiou

Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus pp. 1-11

Tanya Gurieva, Martin C J Bootsma and Marc J M Bonten

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves pp. 1-11

Carsten Magnus

Collective States, Multistability and Transitional Behavior in Schooling Fish pp. 1-11

Kolbjørn Tunstrøm, Yael Katz, Christos C Ioannou, Cristián Huepe, Matthew J Lutz and Iain D Couzin

Multi-Population Classical HLA Type Imputation pp. 1-13

Alexander Dilthey, Stephen Leslie, Loukas Moutsianas, Judong Shen, Charles Cox, Matthew R Nelson and Gil McVean

Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning pp. 1-13

Charlotte Prévost, Daniel McNamee, Ryan K Jessup, Peter Bossaerts and John P O'Doherty

Volume 9, issue 1, 2013

The Effects of City Streets on an Urban Disease Vector pp. 1-9

Corentin M Barbu, Andrew Hong, Jennifer M Manne, Dylan S Small, Javier E Quintanilla Calderón, Karthik Sethuraman, Víctor Quispe-Machaca, Jenny Ancca-Juárez, Juan G Cornejo del Carpio, Fernando S Málaga Chavez, César Náquira and Michael Z Levy

Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation pp. 1-9

Linan Xu, Naushaba Hasin, Manli Shen, Jianwei He, Youlin Xue, Xiaohong Zhou, Sarah Perrett, Youtao Song and Gary W Jones

Dynamic Finite Size Effects in Spiking Neural Networks pp. 1-21

Michael A Buice and Carson C Chow

Approximate Bayesian Computation pp. 1-10

Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll and Christophe Dessimoz

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin pp. 1-10

Giovanni Settanni, David Serquera, Piotr E Marszalek, Emanuele Paci and Laura S Itzhaki

Reward from Punishment Does Not Emerge at All Costs pp. 1-6

Jeromos Vukov, Flávio Pinheiro, Francisco C Santos and Jorge M Pacheco

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator pp. 1-3

Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P Satagopam and Nils Gehlenborg

Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties? pp. 1-15

Cornelis van de Kamp, Peter J Gawthrop, Henrik Gollee and Ian D Loram

Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics pp. 1-15

Nol Chindapol, Jaap A Kaandorp, Carolina Cronemberger, Tali Mass and Amatzia Genin

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective pp. 1-15

Graham Rockwell, Nicholas J Guido and George M Church

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations pp. 1-15

Hang Yu and Klaus Schulten

The Effects of Temperature on the Stability of a Neuronal Oscillator pp. 1-12

Anatoly Rinberg, Adam L Taylor and Eve Marder

How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns pp. 1-14

Yann Le Cunff, Annette Baudisch and Khashayar Pakdaman

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships pp. 1-14

Nives Škunca, Matko Bošnjak, Anita Kriško, Panče Panov, Sašo Džeroski, Tomislav Šmuc and Fran Supek

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations pp. 1-11

Thomas Lemmin, Cinque S Soto, Graham Clinthorne, William F DeGrado and Matteo Dal Peraro

The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack pp. 1-11

Karen E Joyce, Satoru Hayasaka and Paul J Laurienti

Significance Analysis of Prognostic Signatures pp. 1-17

Andrew H Beck, Nicholas W Knoblauch, Marco M Hefti, Jennifer Kaplan, Stuart J Schnitt, Aedin C Culhane, Markus S Schroeder, Thomas Risch, John Quackenbush and Benjamin Haibe-Kains

Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy pp. 1-13

Niklas Wilming, Simon Harst, Nico Schmidt and Peter König

Maximizing the Information Content of Experiments in Systems Biology pp. 1-13

Juliane Liepe, Sarah Filippi, Michał Komorowski and Michael P H Stumpf

Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images pp. 1-13

Fabian Sinz and Matthias Bethge