Table of Contents

May 2012

Fluorescently stained wholemount of mouse small intestine. A single confocal optical section at the base of the crypts is stained to show nuclei (blue), F-actin (red), and intestinal stem cells (green). Actin-rich smooth muscle fibres forming the muscular mucosae appear as a meshwork around the crypt bases. Lgr5 positive stem cells labelled with green fluorescent protein are found only in the crypt bases. See Dunn, et al. (10.1371/journal.pcbi.1002515).

Image Credit: Paul Appleton, College of Life Sciences, University of Dundee.

Education Articles

Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators

Reed B. Jacob, Tim Andersen, Owen M. McDougal

Crossing Over…Markov Meets Mendel

Saad Mneimneh

Research Articles

Termination of Ca2+ Release for Clustered IP3R Channels

Sten Rüdiger, Peter Jung, Jian-Wei Shuai

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

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

General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity

David N. LeBard, Jérôme Hénin, Roderic G. Eckenhoff, Michael L. Klein, Grace Brannigan

Quality of Computationally Inferred Gene Ontology Annotations

Nives Škunca, Adrian Altenhoff, Christophe Dessimoz

Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution

Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Medigue, David Vallenet

Structure and Age Jointly Influence Rates of Protein Evolution

Macarena Toll-Riera, David Bostick, M. Mar Albà, Joshua B. Plotkin

Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO

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

A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath

Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Näthke, David J. Gavaghan, James M. Osborne

Optimality of Human Contour Integration

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

Conformational Spread in the Flagellar Motor Switch: A Model Study

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

Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase

Rafal Mostowy, Roger D. Kouyos, Ilka Hoof, Trevor Hinkley, Mojgan Haddad, Jeannette M. Whitcomb, Christos J. Petropoulos, Can Keşmir, Sebastian Bonhoeffer

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly

Brittany Burton, Michael T. Zimmermann, Robert L. Jernigan, Yongmei Wang

A Spatial Model of Mosquito Host-Seeking Behavior

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

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

M. S. Vijayabaskar, Saraswathi Vishveshwara

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

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, Robert Grützmann

Mechanical Stress Inference for Two Dimensional Cell Arrays

Kevin K. Chiou, Lars Hufnagel, Boris I. Shraiman

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

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

Proteome Sampling by the HLA Class I Antigen Processing Pathway

Ilka Hoof, Debbie van Baarle, William H. Hildebrand, Can Keşmir

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen

The Layer-Oriented Approach to Declarative Languages for Biological Modeling

Ivan Raikov, Erik De Schutter

Emergence of a Small-World Functional Network in Cultured Neurons

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

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

Yan Fu, Trevor Glaros, Meng Zhu, Ping Wang, Zhanghan Wu, John J. Tyson, Liwu Li, Jianhua Xing

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Yekaterina Shpanskaya, Jill Banfield, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova

Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments

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

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

Daniel S. D. Larsson, Lars Liljas, David van der Spoel

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

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

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler, on behalf of the Southern African Treatment and Resistance Network (SATuRN) Consortium

Dynamic Prestress in a Globular Protein

Scott A. Edwards, Johannes Wagner, Frauke Gräter

Challenges and New Approaches to Proving the Existence of Muscle Synergies of Neural Origin

Jason J. Kutch, Francisco J. Valero-Cuevas

Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study

Abbas Shirinifard, James Alexander Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus

Homeostatic Scaling of Excitability in Recurrent Neural Networks

Michiel W. H. Remme, Wytse J. Wadman

Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition

Christopher A. Penfold, Paul E. Brown, Neil D. Lawrence, Alastair S. H. Goldman