Table of Contents: March 2015

Research by Valdano et al. analyses the livestock trade in Italy and sexual encounters in a Brazilian prostitution service to find a correlation between loyalty and infection risk.

Image Credit: Valdano et al.

Education Articles

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon, Sydne Record, Eelke Jongejans

Integrating Interactive Computational Modeling in Biology Curricula

Tomáš Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers

Research Articles

Improved Estimation and Interpretation of Correlations in Neural Circuits

Dimitri Yatsenko, Krešimir Josić, Alexander S. Ecker, Emmanouil Froudarakis, R. James Cotton, Andreas S. Tolias

The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels

Jérémie Sibille, Khanh Dao Duc, David Holcman, Nathalie Rouach

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association

Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola

Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments

Maxim Volgushev, Vladimir Ilin, Ian H. Stevenson

Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision

Adrian M. Haith, David M. Huberdeau, John W. Krakauer

Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model

Alistair M. Senior, Michael A. Charleston, Mathieu Lihoreau, Jerome Buhl, David Raubenheimer, Stephen J. Simpson

Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation

Miriam C. Klein-Flügge, Steven W. Kennerley, Ana C. Saraiva, Will D. Penny, Sven Bestmann

Kinetically-Defined Component Actions in Gene Repression

Carson C. Chow, Kelsey K. Finn, Geoffery B. Storchan, Xinping Lu, Xiaoyan Sheng, S. Stoney Simons Jr.

Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

Francisco Martínez-Jiménez, Marc A. Marti-Renom

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting

Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati

Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats

Luca Giuggioli, Thomas J. McKetterick, Marc Holderied

Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species

Amanda Miguel, Jen Hsin, Tianyun Liu, Grace Tang, Russ B. Altman, Kerwyn Casey Huang

Evolution of Bow-Tie Architectures in Biology

Tamar Friedlander, Avraham E. Mayo, Tsvi Tlusty, Uri Alon

Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief

Giles W. Story, Ivo Vlaev, Peter Dayan, Ben Seymour, Ara Darzi, Raymond J. Dolan

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner

Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells

Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass, Adelinde M. Uhrmacher

Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer

Christopher R. S. Banerji, Simone Severini, Carlos Caldas, Andrew E. Teschendorff

When Can Species Abundance Data Reveal Non-neutrality?

Omar Al Hammal, David Alonso, Rampal S. Etienne, Stephen J. Cornell

Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock

Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

Fan Yang, Evangelia Petsalaki, Thomas Rolland, David E. Hill, Marc Vidal, Frederick P. Roth

Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process

Cheng Lv, Xiaoguang Li, Fangting Li, Tiejun Li

Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy

Feng Fu, Martin A. Nowak, Sebastian Bonhoeffer

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals

Thomas Obadia, Romain Silhol, Lulla Opatowski, Laura Temime, Judith Legrand, Anne C. M. Thiébaut, Jean-Louis Herrmann, Éric Fleury, Didier Guillemot, Pierre-Yves Boëlle, on behalf of the I-Bird Study Group

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data

Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming Sound-Tsao, Igor Jurisica

Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants

Matthew Hartfield, Samuel Alizon

Proportionality: A Valid Alternative to Correlation for Relative Data

David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler

On the Firing Rate Dependency of the Phase Response Curve of Rat Purkinje Neurons In Vitro

João Couto, Daniele Linaro, E De Schutter, Michele Giugliano

Angiogenic Activity of Breast Cancer Patients’ Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches

Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene-Treboux, Eveline Faes-van’t Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, Francois Majo, Michäel Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnès Doucey

Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting

Adam S. Shai, Costas A. Anastassiou, Matthew E. Larkum, Christof Koch

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Rassenti, Christian L. Barrett, Kristen Jepsen, Catriona H. M. Jamieson, Dennis Carson, Thomas J. Kipps, Kelly A. Frazer

HPV Clearance and the Neglected Role of Stochasticity

Marc D. Ryser, Evan R. Myers, Rick Durrett

Predicting Epidemic Risk from Past Temporal Contact Data

Eugenio Valdano, Chiara Poletto, Armando Giovannini, Diana Palma, Lara Savini, Vittoria Colizza

Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles

Jérôme R. D. Soiné, Christoph A. Brand, Jonathan Stricker, Patrick W. Oakes, Margaret L. Gardel, Ulrich S. Schwarz

Evolution and Phenotypic Selection of Cancer Stem Cells

Jan Poleszczuk, Philip Hahnfeldt, Heiko Enderling

Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families

Lucas A. Defelipe, Esteban Lanzarotti, Diego Gauto, Marcelo A. Marti, Adrián G. Turjanski

How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks

Jaldert O. Rombouts, Sander M. Bohte, Pieter R. Roelfsema

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

Vesna Memišević, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist

PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population

Oren E. Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober, Dan L. Nicolae