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Table of Contents

June 2013

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.

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


Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Louisa Wood, Philipp Gebhardt

Topic Page

Cooperative Binding

Melanie I. Stefan, Nicolas Le Novère

Research Articles

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

Yan Zhang, Hye Kyong Kweon, Christian Shively, Anuj Kumar, Philip C. Andrews

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

A Design Principle of Group-level Decision Making in Cell Populations

Koichi Fujimoto, Satoshi Sawai

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

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses

Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation

S. G. Raju, Annika F. Barber, David N. LeBard, Michael L. Klein, Vincenzo Carnevale

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

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

Jörg Bornschein, Marc Henniges, Jörg Lücke

Theta Coordinated Error-Driven Learning in the Hippocampus

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

Constraint and Contingency in Multifunctional Gene Regulatory Circuits

Joshua L. Payne, Andreas Wagner

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

Related Articles

Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome

Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki

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

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

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