PLOS Computational Biology

2005 - 2025

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Volume 9, issue 12, 2013

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

Extrapolating Weak Selection in Evolutionary Games pp. 1-7

Bin Wu, Julián García, Christoph Hauert and Arne Traulsen

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

Will D Penny, Peter Zeidman and Neil Burgess

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

Epidemic Spread on Weighted Networks pp. 1-10

Christel Kamp, Mathieu Moslonka-Lefebvre and Samuel Alizon

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

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

Roger Guimerà and Marta Sales-Pardo

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

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

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

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

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

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

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

Christophe Micheyl, Paul R Schrater and Andrew J Oxenham

Communication and Common Interest pp. 1-6

Peter Godfrey-Smith and Manolo Martínez

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

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

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

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

Miranda Stobbe, Tarun Mishra and Geoff Macintyre

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

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

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

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

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

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

Volume 9, issue 10, 2013

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

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

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

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

Guilhem Faure and Isabelle Callebaut

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

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

Sebastian Gluth, Jörg Rieskamp and Christian Büchel

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

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

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

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

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

Volume 9, issue 9, 2013

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

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

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

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

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

Dilek Eren and Burak Alakent

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

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

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

Anthony Mathelier and Wyeth W Wasserman

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

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

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

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

Volume 9, issue 8, 2013

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

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

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

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

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

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

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

Volume 9, issue 7, 2013

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

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

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

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

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

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

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

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

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

Volume 9, issue 5, 2013

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

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

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

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

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

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

Jonathan L Robinson and Mark P Brynildsen

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

Volume 9, issue 4, 2013

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

Joseph G Makin, Matthew R Fellows and Philip N Sabes

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

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

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

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

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

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

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

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

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

Christoph Schmal, Peter Reimann and Dorothee Staiger

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

Dazhi Jiao, Yuzhen Ye and Haixu Tang

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

Laura Matrajt, M Elizabeth Halloran and Ira M Longini

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

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

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

Brad Busse and Stephen Smith

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

Tina Toni and Bruce Tidor

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

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

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

Volume 9, issue 2, 2013

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

Carsten Magnus

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

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

Romain Daniel Cazé, Mark Humphries and Boris Gutkin

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

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

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

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

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

Claudia Clopath and Nicolas Brunel

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

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

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

Volume 9, issue 1, 2013

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

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

Graham Rockwell, Nicholas J Guido and George M Church

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

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

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

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

Approximate Bayesian Computation pp. 1-10

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

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

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

Michael A Buice and Carson C Chow

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