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Table of Contents: January 2013

COVER

Local regions of natural images.

Image Credit: Holly E. Gerhard, Werner Reichardt Centre for Integrative Neuroscience
Issue Image

Local regions of natural images contain rich information about form and texture. Psychophysical experiments show that human observers are remarkably sensitive to these natural image regularities. Indeed, the visual system seems to know much more about the regularities in natural images than any current probabilistic model, even at very fine scales. These fail to capture contrast fluctuations and local contour information—features to which human observers are highly sensitive. See Gerhard et al.

Message from ISCB

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator

Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg

Education

Visual Data Mining of Biological Networks: One Size Does Not Fit All

Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize Shirdel, Igor Jurisica

Topic Page

Approximate Bayesian Computation

Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz

Research Articles

Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics

Gkikas Magiorkinis, Vana Sypsa, Emmanouil Magiorkinis, Dimitrios Paraskevis, Antigoni Katsoulidou, Robert Belshaw, Christophe Fraser, Oliver George Pybus, Angelos Hatzakis

Maximizing the Information Content of Experiments in Systems Biology

Juliane Liepe, Sarah Filippi, Michał Komorowski, Michael P. H. Stumpf

Bayesian Inference of Spatial Organizations of Chromosomes

Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu

Starling Flock Networks Manage Uncertainty in Consensus at Low Cost

George F. Young, Luca Scardovi, Andrea Cavagna, Irene Giardina, Naomi E. Leonard

Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation

Linan Xu, Naushaba Hasin, Manli Shen, Jianwei He, Youlin Xue, Xiaohong Zhou, Sarah Perrett, Youtao Song, Gary W. Jones

Significance Analysis of Prognostic Signatures

Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedin C. Culhane, Markus S. Schroeder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains

Important miRs of Pathways in Different Tumor Types

Stefan Wuchty, Dolores Arjona, Peter O. Bauer

The Effects of City Streets on an Urban Disease Vector

Corentin M. Barbu, Andrew Hong, Jennifer M. Manne, Dylan S. Small, Javier E. Quintanilla Calderón, Karthik Sethuraman, Víctor Quispe-Machaca, Jenny Ancca-Juárez, Juan G. Cornejo del Carpio, Fernando S. Málaga Chavez, César Náquira, Michael Z. Levy

ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information

A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Ozsoyoglu

Evolutionary Optimization of Protein Folding

Cédric Debès, Minglei Wang, Gustavo Caetano-Anollés, Frauke Gräter

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin

Giovanni Settanni, David Serquera, Piotr E. Marszalek, Emanuele Paci, Laura S. Itzhaki

Reward from Punishment Does Not Emerge at All Costs

Jeromos Vukov, Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco

Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore

Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xiaohan Dai, Jianfeng Wang, Hongen Li, Xin Wang, Wei Tan, Mingjing Luo, Xiaodi Niu, Xuming Deng

An Integrative Model of Ion Regulation in Yeast

Ruian Ke, Piers J. Ingram, Ken Haynes

Metallochaperones Regulate Intracellular Copper Levels

W. Lee Pang, Amardeep Kaur, Alexander V. Ratushny, Aleksandar Cvetkovic, Sunil Kumar, Min Pan, Adam P. Arkin, John D. Aitchison, Michael W. W. Adams, Nitin S. Baliga

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

Kristy Nowak-Lovato, Ludmil B. Alexandrov, Afsheen Banisadr, Amy L. Bauer, Alan R. Bishop, Anny Usheva, Fangping Mu, Elizabeth Hong-Geller, Kim Ø. Rasmussen, William S. Hlavacek, Boian S. Alexandrov

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective

Graham Rockwell, Nicholas J. Guido, George M. Church

Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures

Sandra V. Bennun, Kevin J. Yarema, Michael J. Betenbaugh, Frederick J. Krambeck

Computational Analysis of Rho GTPase Cycling

Cibele Vieira Falkenberg, Leslie M. Loew

Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

Stefka Tyanova, Jürgen Cox, Jesper Olsen, Matthias Mann, Dmitrij Frishman

Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics

Nol Chindapol, Jaap A. Kaandorp, Carolina Cronemberger, Tali Mass, Amatzia Genin

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

Nives Škunca, Matko Bošnjak, Anita Kriško, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Fran Supek

Identification of a Functional Connectome for Long-Term Fear Memory in Mice

Anne L. Wheeler, Cátia M. Teixeira, Afra H. Wang, Xuejian Xiong, Natasa Kovacevic, Jason P. Lerch, Anthony R. McIntosh, John Parkinson, Paul W. Frankland

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

Martin H. Schaefer, Tiago J. S. Lopes, Nancy Mah, Jason E. Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Caroline Louis-Jeune, Amie J. Eisfeld, Gabriele Neumann, Carol Perez-Iratxeta, Yoshihiro Kawaoka, Hiroaki Kitano, Miguel A. Andrade-Navarro