Table of Contents: August 2009


Map of Europe showing a lactose molecule, Linearbandkeramik pottery, and the inferred origin location of lactase persistence/dairying coevolution.

Image Credit: Yael Pinchevsky, Yuval Itan, Joachim Burger, and Mark G. Thomas. Photograph credit: Sabine Schade-Lindig.
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Lactase persistence, the genetic trait that enables adult humans to digest the milk sugar lactose, is thought to have coevolved with the culturally transmitted practice of dairying. In this work the authors use computer simulations, conditioned on archaeological and genetic data, to infer that this coevolution process began about 7,500 years ago in a region between the northern Balkans and Central Europe, probably in association with the Neolithic Linearbandkeramik culture (see Itan et al., doi:10.1371/journal.pcbi.1000491).



Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges

Azura M. H. Zeti, Mohd S. Shamsir, Khairina Tajul-Arifin, Amir F. Merican, Rahmah Mohamed, Sheila Nathan, Nor Muhammad Mahadi, Suhaimi Napis, Tin W. Tan

Strong Inference for Systems Biology

Daniel A. Beard, Martin J. Kushmerick

Research Articles

Evolutionary Triplet Models of Structured RNA

Robert K. Bradley, Ian Holmes

Computation of Conformational Coupling in Allosteric Proteins

Brian A. Kidd, David Baker, Wendy E. Thomas

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

Oliver C. Redfern, Benoît H. Dessailly, Timothy J. Dallman, Ian Sillitoe, Christine A. Orengo

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan

The Origins of Lactase Persistence in Europe

Yuval Itan, Adam Powell, Mark A. Beaumont, Joachim Burger, Mark G. Thomas

Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong

Anne Cori, Pierre-Yves Boëlle, Guy Thomas, Gabriel M. Leung, Alain-Jacques Valleron

On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network

Wilfred Ndifon, Joshua B. Plotkin, Jonathan Dushoff

Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens

Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E. Hedley, Paul R. J. Birch, Ian K. Toth

A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism

James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

Joost Van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz

A Self-Organizing Algorithm for Modeling Protein Loops

Pu Liu, Fangqiang Zhu, Dmitrii N. Rassokhin, Dimitris K. Agrafiotis

Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus

Shenghua Li, Paul Brazhnik, Bruno Sobral, John J. Tyson

Recognizing Sequences of Sequences

Stefan J. Kiebel, Katharina von Kriegstein, Jean Daunizeau, Karl J. Friston

Nash Equilibria in Multi-Agent Motor Interactions

Daniel A. Braun, Pedro A. Ortega, Daniel M. Wolpert

Red Queen Dynamics with Non-Standard Fitness Interactions

Jan Engelstädter, Sebastian Bonhoeffer

How Thioredoxin Dissociates Its Mixed Disulfide

Goedele Roos, Nicolas Foloppe, Koen Van Laer, Lode Wyns, Lennart Nilsson, Paul Geerlings, Joris Messens

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana

Geometric De-noising of Protein-Protein Interaction Networks

Oleksii Kuchaiev, Marija Rašajski, Desmond J. Higham, Nataša Pržulj

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander

Towards Reproducible Descriptions of Neuronal Network Models

Eilen Nordlie, Marc-Oliver Gewaltig, Hans Ekkehard Plesser