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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002285

BeadArray Expression Analysis Using Bioconductor

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

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002276

Computational Mass Spectrometry–Based Proteomics

Lukas Käll, Olga Vitek

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002277

Reviews

Of Toasters and Molecular Ticker Tapes

Konrad P. Kording

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002291

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field

Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002278

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002319

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002321

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002322

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002323

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002324

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

Tianyun Liu, Russ B. Altman

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002326

Radial and Spiral Stream Formation in Proteus mirabilis Colonies

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

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002332

Genetic Co-Occurrence Network across Sequenced Microbes

Pan-Jun Kim, Nathan D. Price

PLOS Computational Biology: published December 29, 2011 | https://doi.org/10.1371/journal.pcbi.1002340

Modeling Brain Resonance Phenomena Using a Neural Mass Model

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

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002298

Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

Rui Chang, Robert Shoemaker, Wei Wang

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002300

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

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002304

Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains

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

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002305

Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments

Yang Jiao, Salvatore Torquato

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002314

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

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

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002315

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

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

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002318

Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease

Christian Frech, Nansheng Chen

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002320

Joint Ancestry and Association Testing in Admixed Individuals

Daniel Shriner, Adebowale Adeyemo, Charles N. Rotimi

PLOS Computational Biology: published December 22, 2011 | https://doi.org/10.1371/journal.pcbi.1002325

Role of Histone Tails in Structural Stability of the Nucleosome

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002279

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons

Dejan Pecevski, Lars Buesing, Wolfgang Maass

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002294

Predictability of Evolutionary Trajectories in Fitness Landscapes

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002302

A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs

Izzet B. Yildiz, Stefan J. Kiebel

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002303

Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002309

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002310

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002313

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

PLOS Computational Biology: published December 15, 2011 | https://doi.org/10.1371/journal.pcbi.1002317

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

PLOS Computational Biology: published December 8, 2011 | https://doi.org/10.1371/journal.pcbi.1002295

Information Routing Driven by Background Chatter in a Signaling Network

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

PLOS Computational Biology: published December 8, 2011 | https://doi.org/10.1371/journal.pcbi.1002297

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

Simon Mitternacht, Igor N. Berezovsky

PLOS Computational Biology: published December 8, 2011 | https://doi.org/10.1371/journal.pcbi.1002301

Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry

Pranesh Padmanabhan, Narendra M. Dixit

PLOS Computational Biology: published December 8, 2011 | https://doi.org/10.1371/journal.pcbi.1002307

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

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

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002228

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

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002256

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

PLOS Computational Biology: published December 1, 2011 | https://doi.org/10.1371/journal.pcbi.1002272

Cover

Modeling blood flow in malaria.

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