Table of Contents

December 2011

Simulation of malaria-infected blood in a cylindrical vessel. Shown in red are healthy red blood cells, and in orange are Plasmodium falciparum-parasitized red blood cells. Blood hematocrit is 30% and the parasitemia level (percentage of infected RBCs with respect to the total number of cells in a unit volume) is 20%. The small particles in the background are markers of the plasma flow. (See Fedosov et al., 10.1371/journal.pcbi.1002270)

Image Credit: Joseph A. Insley and Michael E. Papka (Argonne National Laboratories, Argonne, IL, USA) and Leopold Grinberg (Brown University, Providence, RI, USA).

Education Articles

Integrating Bioinformatics Tools to Handle Glycosylation

Yuliet Mazola, Glay Chinea, Alexis Musacchio

BeadArray Expression Analysis Using Bioconductor

Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch

Computational Mass Spectrometry–Based Proteomics

Lukas Käll, Olga Vitek

Research Articles

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes

Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy J. Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

Edward B. Baskerville, Andy P. Dobson, Trevor Bedford, Stefano Allesina, T. Michael Anderson, Mercedes Pascual

Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome

Guillaume Guilbaud, Aurélien Rappailles, Antoine Baker, Chun-Long Chen, Alain Arneodo, Arach Goldar, Yves d'Aubenton-Carafa, Claude Thermes, Benjamin Audit, Olivier Hyrien

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort, Peer Bork

The Rates of Protein Synthesis and Degradation Account for the Differential Response of Neurons to Spaced and Massed Training Protocols

Faisal Naqib, Carole A. Farah, Christopher C. Pack, Wayne S. Sossin

Radial and Spiral Stream Formation in Proteus mirabilis Colonies

Chuan Xue, Elena O. Budrene, Hans G. Othmer

Genetic Co-Occurrence Network across Sequenced Microbes

Pan-Jun Kim, Nathan D. Price

Modeling Brain Resonance Phenomena Using a Neural Mass Model

Andreas Spiegler, Thomas R. Knösche, Karin Schwab, Jens Haueisen, Fatihcan M. Atay

Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

Rui Chang, Robert Shoemaker, Wei Wang

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

Jonathan Göke, Marc Jung, Sarah Behrens, Lukas Chavez, Sean O'Keeffe, Bernd Timmermann, Hans Lehrach, James Adjaye, Martin Vingron

Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains

Ashok Litwin-Kumar, Anne-Marie M. Oswald, Nathaniel N. Urban, Brent Doiron

Two Birds with One Stone? Possible Dual-Targeting H1N1 Inhibitors from Traditional Chinese Medicine

Su-Sen Chang, Hung-Jin Huang, Calvin Yu-Chian Chen

The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities

Ying Zhang, Olga Zagnitko, Irina Rodionova, Andrei Osterman, Adam Godzik

Joint Ancestry and Association Testing in Admixed Individuals

Daniel Shriner, Adebowale Adeyemo, Charles N. Rotimi

Role of Histone Tails in Structural Stability of the Nucleosome

Mithun Biswas, Karine Voltz, Jeremy C. Smith, Jörg Langowski

Predictability of Evolutionary Trajectories in Fitness Landscapes

Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin

A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs

Izzet B. Yildiz, Stefan J. Kiebel

Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops

Angela Relógio, Pal O. Westermark, Thomas Wallach, Katja Schellenberg, Achim Kramer, Hanspeter Herzel

Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps)

Zhichao Liu, Qiang Shi, Don Ding, Reagan Kelly, Hong Fang, Weida Tong

Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome

Ismail Adeniran, Mark J. McPate, Harry J. Witchel, Jules C. Hancox, Henggui Zhang

Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System

Lan K. Nguyen, Javier Muñoz-García, Helene Maccario, Aaron Ciechanover, Walter Kolch, Boris N. Kholodenko

Structural Insights into the Inhibition of Cytosolic 5′-Nucleotidase II (cN-II) by Ribonucleoside 5′-Monophosphate Analogues

Franck Gallier, Perrine Lallemand, Maïa Meurillon, Lars P. Jordheim, Charles Dumontet, Christian Périgaud, Corinne Lionne, Suzanne Peyrottes, Laurent Chaloin

Information Routing Driven by Background Chatter in a Signaling Network

Núria Domedel-Puig, Pau Rué, Antonio J. Pons, Jordi García-Ojalvo

Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication

Simon Mitternacht, Igor N. Berezovsky

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers

Andrew T. Kwon, Alice Yi Chou, David J. Arenillas, Wyeth W. Wasserman

Dominant Glint Based Prey Localization in Horseshoe Bats: A Possible Strategy for Noise Rejection

Dieter Vanderelst, Jonas Reijniers, Uwe Firzlaff, Herbert Peremans

Identifying Single Copy Orthologs in Metazoa

Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork

Multiscale Modeling of Red Blood Cell Mechanics and Blood Flow in Malaria

Dmitry A. Fedosov, Huan Lei, Bruce Caswell, Subra Suresh, George E. Karniadakis

A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis

Ke Xu, Kevin T. Morgan, Abby Todd Gehris, Timothy C. Elston, Shawn M. Gomez

Chemotaxis when Bacteria Remember: Drift versus Diffusion

Sakuntala Chatterjee, Rava Azeredo da Silveira, Yariv Kafri

Modelling the Spread of HIV Immune Escape Mutants in a Vaccinated Population

Helen R. Fryer, Angela R. McLean

Dynamics of Mutant Cells in Hierarchical Organized Tissues

Benjamin Werner, David Dingli, Tom Lenaerts, Jorge M. Pacheco, Arne Traulsen

Estimated Comparative Integration Hotspots Identify Different Behaviors of Retroviral Gene Transfer Vectors

Alessandro Ambrosi, Ingrid K. Glad, Danilo Pellin, Claudia Cattoglio, Fulvio Mavilio, Clelia Di Serio, Arnoldo Frigessi

A Tale of Two Stories: Astrocyte Regulation of Synaptic Depression and Facilitation

Maurizio De Pittà, Vladislav Volman, Hugues Berry, Eshel Ben-Jacob