PLOS Computational Biology

2005 - 2022

From Public Library of Science
Bibliographic data for series maintained by ploscompbiol ().

Access Statistics for this journal.
Is something missing from the series or not right? See the RePEc data check for the archive and series.

Volume 8, issue 12, 2012

Chapter 2: Data-Driven View of Disease Biology pp. 1-8

Casey S Greene and Olga G Troyanskaya

Chapter 9: Analyses Using Disease Ontologies pp. 1-12

Nigam H Shah, Tyler Cole and Mark A Musen

Chapter 8: Biological Knowledge Assembly and Interpretation pp. 1-12

Ju Han Kim

Mechanics of Undulatory Swimming in a Frictional Fluid pp. 1-13

Yang Ding, Sarah S Sharpe, Andrew Masse and Daniel I Goldman

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density pp. 1-13

Claudia Coronnello, Ryan Hartmaier, Arshi Arora, Luai Huleihel, Kusum V Pandit, Abha S Bais, Michael Butterworth, Naftali Kaminski, Gary D Stormo, Steffi Oesterreich and Panayiotis V Benos

A Comparison of Computational Models for Eukaryotic Cell Shape and Motility pp. 1-17

William R Holmes and Leah Edelstein-Keshet

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes pp. 1-14

Kishore R Mosaliganti, Ramil R Noche, Fengzhu Xiong, Ian A Swinburne and Sean G Megason

SnIPRE: Selection Inference Using a Poisson Random Effects Model pp. 1-14

Kirsten E Eilertson, James G Booth and Carlos D Bustamante

Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells pp. 1-14

Katja Rateitschak, Felix Winter, Falko Lange, Robert Jaster and Olaf Wolkenhauer

Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study pp. 1-14

Juexuan Long, Michael Junkin, Pak Kin Wong, James Hoying and Pierre Deymier

Interconnected Cavernous Structure of Bacterial Fruiting Bodies pp. 1-14

Cameron W Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor Aranson and Mark Alber

Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures pp. 1-10

Niels Röckendorf, Markus Borschbach and Andreas Frey

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking pp. 1-10

Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund and Morten Nielsen

Chapter 7: Pharmacogenomics pp. 1-18

Konrad J Karczewski, Roxana Daneshjou and Russ B Altman

Chapter 10: Mining Genome-Wide Genetic Markers pp. 1-9

Xiang Zhang, Shunping Huang, Zhaojun Zhang and Wei Wang

Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought pp. 1-9

Ting Xiang, Debajyoti Ray, Terry Lohrenz, Peter Dayan and P Read Montague

Ten Simple Rules for the Open Development of Scientific Software pp. 1-3

Andreas Prlić and James B Procter

Chapter 13: Mining Electronic Health Records in the Genomics Era pp. 1-15

Joshua C Denny

Volume 8, issue 11, 2012

Efficient “Communication through Coherence” Requires Oscillations Structured to Minimize Interference between Signals pp. 1-15

Thomas E Akam and Dimitri M Kullmann

Reconstructing Mammalian Sleep Dynamics with Data Assimilation pp. 1-15

Madineh Sedigh-Sarvestani, Steven J Schiff and Bruce J Gluckman

The PLOS Computational Biology Software Section pp. 1-2

Andreas Prlić and Hilmar Lapp

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 pp. 1-9

Natali V Di Russo, Dario A Estrin, Marcelo A Martí and Adrian E Roitberg

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis pp. 1-24

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C Crowley, Matthias Kaschube and Fred Wolf

Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies pp. 1-26

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C Crowley, Matthias Kaschube and Fred Wolf

Ten Simple Rules to Protect Your Intellectual Property pp. 1-4

Mark Jolly, Anthony C Fletcher and Philip E Bourne

Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing pp. 1-19

Luigi Acerbi, Daniel M Wolpert and Sethu Vijayakumar

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles pp. 1-14

Gergely Boza, Ádám Kun, István Scheuring and Ulf Dieckmann

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data pp. 1-14

Marco J Morelli, Gaël Thébaud, Joël Chadœuf, Donald P King, Daniel T Haydon and Samuel Soubeyrand

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay pp. 1-14

Filippo Cacace, Paola Paci, Valerio Cusimano, Alfredo Germani and Lorenzo Farina

A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles pp. 1-13

Robert Stojnic, Audrey Qiuyan Fu and Boris Adryan

Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens pp. 1-13

Renske M A Vroomans, Athanasius F M Marée, Rob J de Boer and Joost B Beltman

Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation pp. 1-17

Anupam Saxena, Hod Lipson and Francisco J Valero-Cuevas

The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains pp. 1-16

Márton Münz, Jotun Hein and Philip C Biggin

How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population pp. 1-11

Nicolas Perony, Claudio J Tessone, Barbara König and Frank Schweitzer

Mesoscopic Model of Actin-Based Propulsion pp. 1-12

Jie Zhu and Alex Mogilner

Volume 8, issue 10, 2012

Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories pp. 1-16

Iris I A Groen, Sennay Ghebreab, Victor A F Lamme and H Steven Scholte

Modeling Dynamic Regulatory Processes in Stroke pp. 1-17

Jason E McDermott, Kenneth Jarman, Ronald Taylor, Mary Lancaster, Harish Shankaran, Keri B Vartanian, Susan L Stevens, Mary P Stenzel-Poore and Antonio Sanfilippo

A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control pp. 1-13

Lionel Rigoux and Emmanuel Guigon

Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices pp. 1-13

Christoph Kayser, Robin A A Ince and Stefano Panzeri

Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics pp. 1-13

Valerii M Sukhorukov, Daniel Dikov, Andreas S Reichert and Michael Meyer-Hermann

How Entorhinal Grid Cells May Learn Multiple Spatial Scales from a Dorsoventral Gradient of Cell Response Rates in a Self-organizing Map pp. 1-31

Stephen Grossberg and Praveen K Pilly

Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram pp. 1-14

Richard Naud and Wulfram Gerstner

Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain pp. 1-14

Andrew J K Conlan, Trevelyan J McKinley, Katerina Karolemeas, Ellen Brooks Pollock, Anthony V Goodchild, Andrew P Mitchell, Colin P D Birch, Richard S Clifton-Hadley and James L N Wood

Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations pp. 1-10

Noah S Bieler, Tuomas P J Knowles, Daan Frenkel and Robert Vácha

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection pp. 1-10

Jan H Peters and Bert L de Groot

Probability Fluxes and Transition Paths in a Markovian Model Describing Complex Subunit Cooperativity in HCN2 Channels pp. 1-10

Klaus Benndorf, Jana Kusch and Eckhard Schulz

How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation pp. 1-10

Ofri Raviv, Merav Ahissar and Yonatan Loewenstein

Seven Years; It's Time for a Change pp. 1-2

Philip E Bourne

Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling pp. 1-12

James Truscott and Neil M Ferguson

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures pp. 1-12

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor and Jiri Damborsky

Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task pp. 1-12

Hang Zhang, Camille Morvan, Louis-Alexandre Etezad-Heydari and Laurence T Maloney

Predictive Dynamics of Human Pain Perception pp. 1-12

Guillermo A Cecchi, Lejian Huang, Javeria Ali Hashmi, Marwan Baliki, María V Centeno, Irina Rish and A Vania Apkarian

Volume 8, issue 9, 2012

The Spatial Structure of Stimuli Shapes the Timescale of Correlations in Population Spiking Activity pp. 1-15

Ashok Litwin-Kumar, Maurice J Chacron and Brent Doiron

Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations pp. 1-15

Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J Marrink and Ben Corry

Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models pp. 1-3

Antony J Williams, John Wilbanks and Sean Ekins

Ten Simple Rules To Commercialize Scientific Research pp. 1-3

Anthony C Fletcher and Philip E Bourne

Speeded Reaching Movements around Invisible Obstacles pp. 1-9

Todd E Hudson, Uta Wolfe and Laurence T Maloney

Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study pp. 1-9

Iskra Staneva, Yongqi Huang, Zhirong Liu and Stefan Wallin

Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles pp. 1-9

Benjamin A Hall, Judith P Armitage and Mark S P Sansom

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease pp. 1-10

Omar Haq, Michael Andrec, Alexandre V Morozov and Ronald M Levy

Analysis of Surface Protein Expression Reveals the Growth Pattern of the Gram-Negative Outer Membrane pp. 1-10

Tristan S Ursell, Eliane H Trepagnier, Kerwyn Casey Huang and Julie A Theriot

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks pp. 1-10

Oded Magger, Yedael Y Waldman, Eytan Ruppin and Roded Sharan

The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels pp. 1-10

Danielle E Chandler, François Penin, Klaus Schulten and Christophe Chipot

Risk-Sensitivity in Bayesian Sensorimotor Integration pp. 1-7

Jordi Grau-Moya, Pedro A Ortega and Daniel A Braun

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA pp. 1-13

Liran Carmel, Eugene V Koonin and Stella Dracheva

Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex pp. 1-13

Moritz Deger, Moritz Helias, Stefan Rotter and Markus Diesmann

The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation pp. 1-13

Haiyang Zhang, Zalman Vaksman, Douglas B Litwin, Peng Shi, Heidi B Kaplan and Oleg A Igoshin

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts pp. 1-17

Tobias Sikosek, Erich Bornberg-Bauer and Hue Sun Chan

Confidence-based Somatic Mutation Evaluation and Prioritization pp. 1-11

Martin Löwer, Bernhard Y Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Christoph Kneip, Özlem Türeci, Mustafa Diken, Cedrik Britten, Sebastian Kreiter, Michael Koslowski, John C Castle and Ugur Sahin

Predicting the Extension of Biomedical Ontologies pp. 1-16

Catia Pesquita and Francisco M Couto

Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis pp. 1-16

Vitaly A Selivanov, Marta Cascante, Mark Friedman, Mark F Schumaker, Massimo Trucco and Tatyana V Votyakova

An Online Bioinformatics Curriculum pp. 1-20

David B Searls

Spontaneous Excitation Patterns Computed for Axons with Injury-like Impairments of Sodium Channels and Na/K Pumps pp. 1-20

Na Yu, Catherine E Morris, Béla Joós and André Longtin

High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications pp. 1-12

Ping-Chang Lee, Chao-Chun Chuang, Ann-Shyn Chiang and Yu-Tai Ching

Spike-based Decision Learning of Nash Equilibria in Two-Player Games pp. 1-12

Johannes Friedrich and Walter Senn

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function pp. 1-8

Michael A Jamros, Leandro C Oliveira, Paul C Whitford, José N Onuchic, Joseph A Adams and Patricia A Jennings

Volume 8, issue 8, 2012

Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics pp. 1-15

Reuben H Kraft, Phillip Justin Mckee, Amy M Dagro and Scott T Grafton

A Canonical Model of Multistability and Scale-Invariance in Biological Systems pp. 1-15

Frank Freyer, James A Roberts, Petra Ritter and Michael Breakspear

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case pp. 1-15

Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho and Modesto Orozco

Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration pp. 1-22

Allen Cheung, David Ball, Michael Milford, Gordon Wyeth and Janet Wiles

The Roots of Bioinformatics in ISMB pp. 1-10

Todd A Gibson

Decorrelation of Neural-Network Activity by Inhibitory Feedback pp. 1-29

Tom Tetzlaff, Moritz Helias, Gaute T Einevoll and Markus Diesmann

A Network-based Approach for Predicting Missing Pathway Interactions pp. 1-13

Saket Navlakha, Anthony Gitter and Ziv Bar-Joseph

Locust Dynamics: Behavioral Phase Change and Swarming pp. 1-11

Chad M Topaz, Maria R D'Orsogna, Leah Edelstein-Keshet and Andrew J Bernoff

Unifying Time to Contact Estimation and Collision Avoidance across Species pp. 1-1

Matthias S Keil and Joan López-Moliner

Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students pp. 1-1

Jennifer McQueen, Jody J Wright and Joanne A Fox

Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma pp. 1-7

Maria Abou Chakra and Arne Traulsen

Performance Limitations of Relay Neurons pp. 1-19

Rahul Agarwal and Sridevi V Sarma

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology pp. 1-14

Y Dabaghian, F Mémoli, L Frank and G Carlsson

Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems pp. 1-14

Georg K Gerber, Andrew B Onderdonk and Lynn Bry

The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles pp. 1-14

Deena M A Gendoo and Paul M Harrison

Hybrid Models and Biological Model Reduction with PyDSTool pp. 1-8

Robert Clewley

Volume 8, issue 7, 2012

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation pp. 1-13

Jason Flannick, Joshua M Korn, Pierre Fontanillas, George B Grant, Eric Banks, Mark A Depristo and David Altshuler

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia pp. 1-11

Peilin Jia, Lily Wang, Ayman H Fanous, Carlos N Pato, Todd L Edwards, The International Schizophrenia Consortium and Zhongming Zhao

Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation pp. 1-11

Marieke Pluijmert, Wilco Kroon, Alessandro C Rossi, Peter H M Bovendeerd and Tammo Delhaas

Coding Conspecific Identity and Motion in the Electric Sense pp. 1-16

Na Yu, Ginette Hupé, Charles Garfinkle, John E Lewis and André Longtin

A Quick Guide to Software Licensing for the Scientist-Programmer pp. 1-7

Andrew Morin, Jennifer Urban and Piotr Sliz

Automated Tracking of Whiskers in Videos of Head Fixed Rodents pp. 1-8

Nathan G Clack, Daniel H O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda and Eugene W Myers

Adaptive Temperature Compensation in Circadian Oscillations pp. 1-12

Paul François, Nicolas Despierre and Eric D Siggia

Individual Rules for Trail Pattern Formation in Argentine Ants (Linepithema humile) pp. 1-12

Andrea Perna, Boris Granovskiy, Simon Garnier, Stamatios C Nicolis, Marjorie Labédan, Guy Theraulaz, Vincent Fourcassié and David J T Sumpter

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data pp. 1-12

Haipeng Xing, Yifan Mo, Will Liao and Michael Q Zhang

Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO) pp. 1-5

Yann Joly, Edward S Dove, Bartha M Knoppers, Martin Bobrow and Don Chalmers

Which of Our Modeling Predictions Are Robust? pp. 1-5

Rob J De Boer

Shaping the Dynamics of a Bidirectional Neural Interface pp. 1-15

Alessandro Vato, Marianna Semprini, Emma Maggiolini, Francois D Szymanski, Luciano Fadiga, Stefano Panzeri and Ferdinando A Mussa-Ivaldi

A Range-Normalization Model of Context-Dependent Choice: A New Model and Evidence pp. 1-15

Alireza Soltani, Benedetto De Martino and Colin Camerer

Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity pp. 1-22

Matthieu Gilson, Tomoki Fukai and Anthony N Burkitt

Assessing Drug Target Association Using Semantic Linked Data pp. 1-10

Bin Chen, Ying Ding and David J Wild

A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations pp. 1-10

Michael Knott and Robert B Best

Bioinformatics Meets User-Centred Design: A Perspective pp. 1-4

Katrina Pavelin, Jennifer A Cham, Paula de Matos, Cath Brooksbank, Graham Cameron and Christoph Steinbeck

Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity pp. 1-18

Miles Miller, Marc Hafner, Eduardo Sontag, Noah Davidsohn, Sairam Subramanian, Priscilla E M Purnick, Douglas Lauffenburger and Ron Weiss

Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation pp. 1-9

Diana Chang and Alon Keinan

Volume 8, issue 6, 2012

Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches pp. 1-15

Dominik Wodarz, Andrew Hofacre, John W Lau, Zhiying Sun, Hung Fan and Natalia L Komarova

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach pp. 1-15

Hector Garcia-Seisdedos, Beatriz Ibarra-Molero and Jose M Sanchez-Ruiz

MC EMiNEM Maps the Interaction Landscape of the Mediator pp. 1-10

Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin C Maier, Dietmar E Martin, Holger Fröhlich, Patrick Cramer and Achim Tresch

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems pp. 1-9

Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie and Germán Enciso

A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis pp. 1-9

R Zachariah Aandahl, Josephine F Reyes, Scott A Sisson and Mark M Tanaka

Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer pp. 1-18

Robert Rosenbaum, Jonathan Rubin and Brent Doiron

Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging pp. 1-18

Marc Thilo Figge, Andreas S Reichert, Michael Meyer-Hermann and Heinz D Osiewacz

What Can Systems Theory of Networks Offer to Biology? pp. 1-2

Indika Rajapakse, Mark Groudine and Mehran Mesbahi

A Report of the Curriculum Task Force of the ISCB Education Committee pp. 1-2

Lonnie R Welch, Russell Schwartz and Fran Lewitter

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation pp. 1-11

Crina-Maria Ionescu, Radka Svobodová Vařeková, Jochen H M Prehn, Heinrich J Huber and Jaroslav Koča

Fast Coding of Orientation in Primary Visual Cortex pp. 1-16

Oren Shriki, Adam Kohn and Maoz Shamir

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations pp. 1-16

Xin Wang, Mauro A Castro, Klaas W Mulder and Florian Markowetz

Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue pp. 1-17

Florian Raudies and Michael E Hasselmo

Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees pp. 1-17

Eftychios A Pnevmatikakis, Keith Kelleher, Rebecca Chen, Petter Saggau, Krešimir Josić and Liam Paninski

Complementarity of Spike- and Rate-Based Dynamics of Neural Systems pp. 1-1

M T Wilson, P A Robinson, B O'Neill and D A Steyn-Ross

The Role of Non-Native Interactions in the Folding of Knotted Proteins pp. 1-12

Tatjana Škrbić, Cristian Micheletti and Pietro Faccioli

Structural Drift: The Population Dynamics of Sequential Learning pp. 1-12

James P Crutchfield and Sean Whalen

A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts pp. 1-12

Arno Onken, Valentin Dragoi and Klaus Obermayer

A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks pp. 1-12

Daniele De Martino, Matteo Figliuzzi, Andrea De Martino and Enzo Marinari

Volume 8, issue 5, 2012

The Layer-Oriented Approach to Declarative Languages for Biological Modeling pp. 1-21

Ivan Raikov and Erik De Schutter

Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments pp. 1-10

Sepideh Bazazi, Frederic Bartumeus, Joseph J Hale and Iain D Couzin

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs pp. 1-10

Adrian M Altenhoff, Romain A Studer, Marc Robinson-Rechavi and Christophe Dessimoz

Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus pp. 1-18

H H L M Goossens and A J van Opstal

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes pp. 1-16

Christof Winter, Glen Kristiansen, Stephan Kersting, Janine Roy, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert, Marcus Bahra, Hans J Schlitt, Utz Settmacher, Helmut Friess, Markus Büchler, Hans-Detlev Saeger, Michael Schroeder, Christian Pilarsky and Robert Grützmann

Conformational Spread in the Flagellar Motor Switch: A Model Study pp. 1-16

Qi Ma, Dan V Nicolau, Philip K Maini, Richard M Berry and Fan Bai

Quality of Computationally Inferred Gene Ontology Annotations pp. 1-11

Nives Škunca, Adrian Altenhoff and Christophe Dessimoz

Optimality of Human Contour Integration pp. 1-17

Udo A Ernst, Sunita Mandon, Nadja Schinkel–Bielefeld, Simon D Neitzel, Andreas K Kreiter and Klaus R Pawelzik

Emergence of a Small-World Functional Network in Cultured Neurons pp. 1-17

Julia H Downes, Mark W Hammond, Dimitris Xydas, Matthew C Spencer, Victor M Becerra, Kevin Warwick, Ben J Whalley and Slawomir J Nasuto

Termination of Ca2+ Release for Clustered IP3R Channels pp. 1-13

Sten Rüdiger, Peter Jung and Jian-Wei Shuai

A Spatial Model of Mosquito Host-Seeking Behavior pp. 1-13

Bree Cummins, Ricardo Cortez, Ivo M Foppa, Justin Walbeck and James M Hyman

Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO pp. 1-14

Wei Tang, Steven L Bressler, Chad M Sylvester, Gordon L Shulman and Maurizio Corbetta

Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory pp. 1-14

Young-Ah Rho and Steven A Prescott

Simulation of Molecular Data under Diverse Evolutionary Scenarios pp. 1-8

Miguel Arenas

Crossing Over…Markov Meets Mendel pp. 1-12

Saad Mneimneh

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference pp. 1-12

Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Weixing Zhou, Jin Huang and Yun Tang

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package pp. 1-12

Alexander Favorov, Loris Mularoni, Leslie M Cope, Yulia Medvedeva, Andrey A Mironov, Vsevolod J Makeev and Sarah J Wheelan

Volume 8, issue 4, 2012

Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models pp. 1-10

Claudia Clopath, Jean-Pierre Nadal and Nicolas Brunel

The Impact of Imitation on Vaccination Behavior in Social Contact Networks pp. 1-10

Martial L Ndeffo Mbah, Jingzhou Liu, Chris T Bauch, Yonas I Tekel, Jan Medlock, Lauren Ancel Meyers and Alison P Galvani

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA pp. 1-21

Dina Zhabinskaya and Craig J Benham

Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold pp. 1-12

Chris T Bauch and Samit Bhattacharyya

What Can Causal Networks Tell Us about Metabolic Pathways? pp. 1-12

Rachael Hageman Blair, Daniel J Kliebenstein and Gary A Churchill

Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression pp. 1-12

Christopher C Poirier, Win Pin Ng, Douglas N Robinson and Pablo A Iglesias

Optimizing Provider Recruitment for Influenza Surveillance Networks pp. 1-12

Samuel V Scarpino, Nedialko B Dimitrov and Lauren Ancel Meyers

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity pp. 1-12

Kyle E Roberts, Patrick R Cushing, Prisca Boisguerin, Dean R Madden and Bruce R Donald

Tension and Robustness in Multitasking Cellular Networks pp. 1-12

Jeffrey V Wong, Bochong Li and Lingchong You

Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks pp. 1-9

Raoul-Martin Memmesheimer and Marc Timme

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability pp. 1-9

Yunpeng Wang, Arne B Gjuvsland, Jon Olav Vik, Nicolas P Smith, Peter J Hunter and Stig W Omholt

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein pp. 1-15

Yong Wang, Chun Tang, Erkang Wang and Jin Wang

Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis pp. 1-15

Suzanne Gaudet, Sabrina L Spencer, William W Chen and Peter K Sorger

Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons pp. 1-15

Kyriaki Sidiropoulou and Panayiota Poirazi

Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts pp. 1-17

J Lucas McKay and Lena H Ting

Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons pp. 1-11

Yasuhiro Tsubo, Yoshikazu Isomura and Tomoki Fukai

Determinants of Sexual Network Structure and Their Impact on Cumulative Network Measures pp. 1-11

Boris V Schmid and Mirjam Kretzschmar

Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat pp. 1-7

Yihwa Kim, Robert Sinclair, Nol Chindapol, Jaap A Kaandorp and Erik De Schutter

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases? pp. 1-1

Mahmoud Moradi, Volodymyr Babin, Christopher Roland and Celeste Sagui

Volume 8, issue 3, 2012

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB pp. 1-9

Elif Nihal Korkmaz, Ruth Nussinov and Türkan Haliloğlu

Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria pp. 1-9

David M Richards, Antje M Hempel, Klas Flärdh, Mark J Buttner and Martin Howard

Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics pp. 1-18

Ruben Coen-Cagli, Peter Dayan and Odelia Schwartz

Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction pp. 1-10

Gustavo Deco and Etienne Hugues

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data pp. 1-10

Alexander R Macalalad, Michael C Zody, Patrick Charlebois, Niall J Lennon, Ruchi M Newman, Christine M Malboeuf, Elizabeth M Ryan, Christian L Boutwell, Karen A Power, Doug E Brackney, Kendra N Pesko, Joshua Z Levin, Gregory D Ebel, Todd M Allen, Bruce W Birren and Matthew R Henn

Traffic Instabilities in Self-Organized Pedestrian Crowds pp. 1-10

Mehdi Moussaïd, Elsa G Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond and Guy Theraulaz

Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza pp. 1-8

Ken T D Eames, Natasha L Tilston, Ellen Brooks-Pollock and W John Edmunds

Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains pp. 1-8

Stefano Mostarda, David Gfeller and Francesco Rao

State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data pp. 1-27

Hideaki Shimazaki, Shun-ichi Amari, Emery N Brown and Sonja Grün

Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery pp. 1-14

András Lörincz, Zsolt Palotai and Gábor Szirtes

Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses pp. 1-14

Mathieu Lemay, Enno de Lange and Jan P Kucera

A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons pp. 1-1

Dimitrios V Vavoulis, Volko A Straub, John A D Aston and Jianfeng Feng

Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections pp. 1-16

Kendra S Burbank and Gabriel Kreiman

Ensemble Models of Neutrophil Trafficking in Severe Sepsis pp. 1-16

Sang O K Song, Justin Hogg, Zhi-Yong Peng, Robert Parker, John A Kellum and Gilles Clermont

Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations pp. 1-16

Giulia Morra, Raffaello Potestio, Cristian Micheletti and Giorgio Colombo

Impact of Network Structure and Cellular Response on Spike Time Correlations pp. 1-15

James Trousdale, Yu Hu, Eric Shea-Brown and Krešimir Josić

Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin? pp. 1-15

Christian Keck, Cristina Savin and Jörg Lücke

Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion pp. 1-15

Graciano Dieck Kattas, Xiao-Ke Xu and Michael Small

Ten Simple Rules for Starting a Company pp. 1-3

Anthony C Fletcher and Philip E Bourne

Volume 8, issue 2, 2012

Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets pp. 1-11

Camille Morvan and Laurence T Maloney

Joint Analysis of Multiple Metagenomic Samples pp. 1-11

Yael Baran and Eran Halperin

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1 pp. 1-11

Xueyang Feng, You Xu, Yixin Chen and Yinjie J Tang

Comparison of Insertional RNA Editing in Myxomycetes pp. 1-11

Cai Chen, David Frankhouser and Ralf Bundschuh

Early Warning Signals for Critical Transitions: A Generalized Modeling Approach pp. 1-6

Steven J Lade and Thilo Gross

Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke pp. 1-13

Yukikazu Hidaka, Cheol E Han, Steven L Wolf, Carolee J Winstein and Nicolas Schweighofer

Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina pp. 1-13

Pranidhi Sood, Robert J Johnston and Edo Kussell

Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy pp. 1-17

Iraj Hosseini and Feilim Mac Gabhann

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data pp. 1-15

Santiago Treviño, Yudong Sun, Tim F Cooper and Kevin E Bassler

Noise and Robustness in Phyllotaxis pp. 1-12

Vincent Mirabet, Fabrice Besnard, Teva Vernoux and Arezki Boudaoud

Paradoxical Evidence Integration in Rapid Decision Processes pp. 1-10

Johannes Rüter, Nicolas Marcille, Henning Sprekeler, Wulfram Gerstner and Michael H Herzog

Volume 8, issue 1, 2012

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection pp. 1-12

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

Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity pp. 1-12

Yotam Luz and Maoz Shamir

Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress pp. 1-12

Patrick D McMullen, Erin Z Aprison, Peter B Winter, Luis A N Amaral, Richard I Morimoto and Ilya Ruvinsky

Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks pp. 1-8

Christian Meisel, Alexander Storch, Susanne Hallmeyer-Elgner, Ed Bullmore and Thilo Gross

Adjusting Phenotypes by Noise Control pp. 1-14

Kyung H Kim and Herbert M Sauro

Prediction by Promoter Logic in Bacterial Quorum Sensing pp. 1-14

Navneet Rai, Rajat Anand, Krishna Ramkumar, Varun Sreenivasan, Sugat Dabholkar, K V Venkatesh and Mukund Thattai

Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells pp. 1-13

Caterina A M La Porta, Stefano Zapperi and James P Sethna

A Dynamic View of Domain-Motif Interactions pp. 1-13

Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki and Hanah Margalit

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding pp. 1-13

Iain H Moal and Paul A Bates

A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser pp. 1-11

Justin Hsia, William J Holtz, Daniel C Huang, Murat Arcak and Michel M Maharbiz

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism pp. 1-11

Fiona Achcar, Eduard J Kerkhoven, The SilicoTryp Consortium, Barbara M Bakker, Michael P Barrett and Rainer Breitling

Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition pp. 1-20

Michael N Economo and John A White

A Review of 2011 for PLoS Computational Biology pp. 1-2

Rosemary Dickin, Chris James Hall, Laura K Taylor, Andrew M Collings, Ruth Nussinov and Philip E Bourne

Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer pp. 1-18

Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y Seiwert, Ezra E W Cohen, H Rosie Xing and Yves A Lussier

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies pp. 1-9

Nicoló Fusi, Oliver Stegle and Neil D Lawrence

Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana pp. 1-15

Michael Seifert, André Gohr, Marc Strickert and Ivo Grosse

Protein Design Using Continuous Rotamers pp. 1-15

Pablo Gainza, Kyle E Roberts and Bruce R Donald

Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins pp. 1-15

Weihong Zhang, Debabani Ganguly and Jianhan Chen

Computational and Statistical Analysis of Protein Mass Spectrometry Data pp. 1-6

William Stafford Noble and Michael J MacCoss