July 2014

Electric images modeled on wave-type and pulse-type electric fishes, with electric organs of different complexity. Source distributions are calculated from experimental measurements; determined how the electric organ complexity shapes the electric field and consequently, electric images. Hypothesis are generalized that fishes explore objects using the perioral "fovea", while surrounding regions are suitable for detecting the presence and movement of surrounding objects. Due to the complexity of distributed electric organs American fishes show weaker fields than Africans. However, this endows American fishes to emit site-specific signals to be detected by conspecifics while developing encryption strategies to avoid predators. See Pedraja et al.

Image Credit: Federico Pedraja

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Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities

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

PLOS Computational Biology: published July 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003708

Education Articles

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

Benjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock III

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003719

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding

Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003738

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins

B. Scott Perrin Jr, Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock, Bernard R. Brooks, Toshiko Ichiye

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003739

Research Articles

Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003734

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study

Bernhard Knapp, James Dunbar, Charlotte M. Deane

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003748

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

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003664

Correlated Inter-Domain Motions in Adenylate Kinase

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003721

Antibody Responses during Hepatitis B Viral Infection

Stanca M. Ciupe, Ruy M. Ribeiro, Alan S. Perelson

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003730

Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks

Robert Ton, Gustavo Deco, Andreas Daffertshofer

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003736

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003740

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

Kathryn A. Loving, Andy Lin, Alan C. Cheng

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003741

No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag

Jean-Luc Schwartz, Christophe Savariaux

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003743

Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003745

Different Inward and Outward Conduction Mechanisms in Na_VMs Suggested by Molecular Dynamics Simulations

Song Ke, E. N. Timin, Anna Stary-Weinzinger

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003746

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003749

A Real-Time All-Atom Structural Search Engine for Proteins

Gabriel Gonzalez, Brett Hannigan, William F. DeGrado

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003750

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

Christopher J. R. Illingworth, Andrej Fischer, Ville Mustonen

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003755

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Sergey Hosid, Ilya Ioshikhes

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003760

Robustness and Evolvability of the Human Signaling Network

Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, Kwang-Hyun Cho

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003763

Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model

Athanasia Papoutsi, Kyriaki Sidiropoulou, Panayiota Poirazi

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003764

Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling

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

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003616

From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model

Hugo Gravato Marques, Arjun Bharadwaj, Fumiya Iida

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003653

Collective Behaviour without Collective Order in Wild Swarms of Midges

Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Stefania Melillo, Leonardo Parisi, Oliver Pohl, Bruno Rossaro, Edward Shen, Edmondo Silvestri, Massimiliano Viale

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003697

Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm

Ankur P. Parikh, Ross E. Curtis, Irene Kuhn, Sabine Becker-Weimann, Mina Bissell, Eric P. Xing, Wei Wu

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003713

Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations

Alessandro Barardi, Belen Sancristóbal, Jordi Garcia-Ojalvo

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003723

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, Stein Aerts

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003731

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor

Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003742

Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration

Assaf Zaritsky, Doron Kaplan, Inbal Hecht, Sari Natan, Lior Wolf, Nir S. Gov, Eshel Ben-Jacob, Ilan Tsarfaty

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003747

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes

Antonio Rausell, Pejman Mohammadi, Paul J. McLaren, Istvan Bartha, Ioannis Xenarios, Jacques Fellay, Amalio Telenti

PLOS Computational Biology: published July 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003757

Poisson-Like Spiking in Circuits with Probabilistic Synapses

Rubén Moreno-Bote

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003522

Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials

Fabrizio Pucci, Marianne Rooman

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003689

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

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

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003696

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

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

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003702

Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock

Karl Fogelmark, Carl Troein

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003705

Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase

Rocio Rebollido-Rios, Shyam Bandari, Christoph Wilms, Stanislav Jakuschev, Andrea Vortkamp, Kay Grobe, Daniel Hoffmann

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003707

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

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

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003711

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

Richard Lonsdale, Sarah L. Rouse, Mark S. P. Sansom, Adrian J. Mulholland

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003714

Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior

Adam M. Gifford, Yale E. Cohen, Alan A. Stocker

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003715

LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry

Jacob D. Durrant, Rommie E. Amaro

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003720

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis

Eder Zavala, Tatiana T. Marquez-Lago

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003725

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

Raphy Zarecki, Matthew A. Oberhardt, Leah Reshef, Uri Gophna, Eytan Ruppin

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003726

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang, Tingjun Hou

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003729

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

Alejandro Barrera, Ana Alastruey-Izquierdo, María J. Martín, Isabel Cuesta, Juan Antonio Vizcaíno

PLOS Computational Biology: published July 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003733

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

Allan Haldane, Michael Manhart, Alexandre V. Morozov

PLOS Computational Biology: published July 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003683

Inferring Clonal Composition from Multiple Sections of a Breast Cancer

Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau, William Stafford Noble

PLOS Computational Biology: published July 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003703

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen

PLOS Computational Biology: published July 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003706

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis

Andrew E. Teschendorff, Xiaoping Liu, Helena Caren, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen

PLOS Computational Biology: published July 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003709

Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex

Suchin S. Gururangan, Alexander J. Sadovsky, Jason N. MacLean

PLOS Computational Biology: published July 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003710

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

Daria A. Beshnova, Andrey G. Cherstvy, Yevhen Vainshtein, Vladimir B. Teif

PLOS Computational Biology: published July 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003698

Formal Comments

Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication

Param Priya Singh, Séverine Affeldt, Giulia Malaguti, Hervé Isambert

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003754

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"

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

PLOS Computational Biology: published July 31, 2014 | https://doi.org/10.1371/journal.pcbi.1003758

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Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences.

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