Advertisement

Table of Contents: 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

Messages from ISCB

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

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

Education Articles

Research Articles

Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

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

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

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

Antibody Responses during Hepatitis B Viral Infection

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

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

Robert Ton, Gustavo Deco, Andreas Daffertshofer

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

Related Articles

  1. New Methods Section in PLOS Computational Biology

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

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

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

Gabriel Gonzalez, Brett Hannigan, William F. DeGrado

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

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

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

Sergey Hosid, Ilya Ioshikhes

Robustness and Evolvability of the Human Signaling Network

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

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

From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model

Hugo Gravato Marques, Arjun Bharadwaj, Fumiya Iida

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

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

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

Alessandro Barardi, Belen Sancristóbal, Jordi Garcia-Ojalvo

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

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

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

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

Poisson-Like Spiking in Circuits with Probabilistic Synapses

Rubén Moreno-Bote

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

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

Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock

Karl Fogelmark, Carl Troein

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

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

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

Related Articles

  1. Correction: Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

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

Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior

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

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

Eder Zavala, Tatiana T. Marquez-Lago

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

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

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

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

Allan Haldane, Michael Manhart, Alexandre V. Morozov

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

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

Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen

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

On the Use of Human Mobility Proxies for Modeling Epidemics

Michele Tizzoni, Paolo Bajardi, Adeline Decuyper, Guillaume Kon Kam King, Christian M. Schneider, Vincent Blondel, Zbigniew Smoreda, Marta C. González, Vittoria Colizza

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

James Smadbeck, Kiat Hwa Chan, George A. Khoury, Bo Xue, Robert C. Robinson, Charlotte A. E. Hauser, Christodoulos A. Floudas

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

Federico Pedraja, Pedro Aguilera, Angel A. Caputi, Ruben Budelli

BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum

Marc Griesemer, Carissa Young, Anne S. Robinson, Linda Petzold

Modeling Higher-Order Correlations within Cortical Microcolumns

Urs Köster, Jascha Sohl-Dickstein, Charles M. Gray, Bruno A. Olshausen

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics

Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis

Related Articles

  1. New Methods Section in PLOS Computational Biology

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

Yong Wang, Chun Tang, Erkang Wang, Jin Wang

A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges

James Kaufman, Justin Lessler, April Harry, Stefan Edlund, Kun Hu, Judith Douglas, Christian Thoens, Bernd Appel, Annemarie Käsbohrer, Matthias Filter

Related Articles

  1. Correction: A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges

Emergent Biosynthetic Capacity in Simple Microbial Communities

Hsuan-Chao Chiu, Roie Levy, Elhanan Borenstein

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

Brain and Behavior in Decision-Making

Peter Cassey, Andrew Heathcote, Scott D. Brown

Computational Modeling and Analysis of Iron Release from Macrophages

Alka A. Potdar, Joydeep Sarkar, Nupur K. Das, Paroma Ghosh, Miklos Gratzl, Paul L. Fox, Gerald M. Saidel