Table of Contents: June 2013


Bioinformatics – exploring new dimensions in biology

Image Credit: Dr. Philipp Gebhardt, European Molecular Biology Laboratory
Issue Image

This image is an artistic representation of different elements related to bioinformatics. It shows a section of an illustration of the tree of life (upper left), part of a multiple sequence alignment of different hemoglobin DNA sequences (bottom), and the flow of biological information between DNA, RNA, and protein molecules (middle). See Wood and Gebhardt.

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Cooperative Binding

Melanie I. Stefan, Nicolas Le Novère

Research Articles

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer

PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data

Gabriel E. Hoffman, Benjamin A. Logsdon, Jason G. Mezey

Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module

Diane M. Longo, Jangir Selimkhanov, Jeffrey D. Kearns, Jeff Hasty, Alexander Hoffmann, Lev S. Tsimring

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

Lyudmyla Dorosh, Olesya A. Kharenko, Nandhakishore Rajagopalan, Michele C. Loewen, Maria Stepanova

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus

Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

William R. Harcombe, Nigel F. Delaney, Nicholas Leiby, Niels Klitgord, Christopher J. Marx

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer

Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi

How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies

Katy Robinson, Nick Fyson, Ted Cohen, Christophe Fraser, Caroline Colijn

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples

David R. Riley, Karsten B. Sieber, Kelly M. Robinson, James Robert White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp

Mate Choice and the Origin of Menopause

Richard A. Morton, Jonathan R. Stone, Rama S. Singh

Emotional Valence and the Free-Energy Principle

Mateus Joffily, Giorgio Coricelli

Fibrin Networks Regulate Protein Transport during Thrombus Development

Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber

Modelling Co-Infection with Malaria and Lymphatic Filariasis

Hannah C. Slater, Manoj Gambhir, Paul E. Parham, Edwin Michael

Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities

Antonio G. Zippo, Riccardo Storchi, Sara Nencini, Gian Carlo Caramenti, Maurizio Valente, Gabriele Eliseo M. Biella

Theta Coordinated Error-Driven Learning in the Hippocampus

Nicholas Ketz, Srinimisha G. Morkonda, Randall C. O'Reilly

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

Elzbieta Petelenz-Kurdziel, Clemens Kuehn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation

Christian P. Koch, Anna M. Perna, Max Pillong, Nickolay K. Todoroff, Paul Wrede, Gerd Folkers, Jan A. Hiss, Gisbert Schneider

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression

Nanye Long, Samuel P. Dickson, Jessica M. Maia, Hee Shin Kim, Qianqian Zhu, Andrew S. Allen

Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach

Balázs Könnyű, S. Kashif Sadiq, Tamás Turányi, Rita Hírmondó, Barbara Müller, Hans-Georg Kräusslich, Peter V. Coveney, Viktor Müller