Advertisement
Table of Contents

January 2015

The image represents a signal in a three-dimensional NMR spectrum being assigned to a specific nucleus of the protein backbone. The multi-platform software COMPASS, as presented by Niklasson et al., was developed for this purpose. COMPASS was designed to be suitable for resonance assignments of small-to-large proteins from complete or limited data sets. User friendliness was also a priority when designing the software. Advantages over competing software include increased user control of the entire backbone assignment process and instant feedback on assignments in the form of a graphical representation of the calculated secondary structure.

Image Credit: Markus Niklasson

Editorials

Ten Simple Rules for Organizing an Unconference

Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood

Advancements and Challenges in Computational Biology

Ruth Nussinov

Message from ISCB

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus

Peter D. Karp, Bonnie Berger, Diane Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost

Perspective

150 Years of the Mass Action Law

Eberhard O. Voit, Harald A. Martens, Stig W. Omholt

Research Articles

GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells

Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein

Computation in Dynamically Bounded Asymmetric Systems

Ueli Rutishauser, Jean-Jacques Slotine, Rodney Douglas

Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

Helen L. Ramsden, Gülşen Sürmeli, Steven G. McDonagh, Matthew F. Nolan

A Probabilistic Palimpsest Model of Visual Short-term Memory

Loic Matthey, Paul M. Bays, Peter Dayan

A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso

Erick A. Perez Alday, Michael A. Colman, Philip Langley, Timothy D. Butters, Jonathan Higham, Antony J. Workman, Jules C. Hancox, Henggui Zhang

A Computational Approach to Identifying Gene-microRNA Modules in Cancer

Daeyong Jin, Hyunju Lee

Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions

Massimo Lai, Denis Brun, Stuart J. Edelstein, Nicolas Le Novère

Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data

Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann, Hidde de Jong

Related Articles

Synaptic Plasticity Enables Adaptive Self-Tuning Critical Networks

Nigel Stepp, Dietmar Plenz, Narayan Srinivasa

System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance

Emilie Montastier, Nathalie Villa-Vialaneix, Sylvie Caspar-Bauguil, Petr Hlavaty, Eva Tvrzicka, Ignacio Gonzalez, Wim H. M. Saris, Dominique Langin, Marie Kunesova, Nathalie Viguerie

A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution

Frédéric Boudon, Jérôme Chopard, Olivier Ali, Benjamin Gilles, Olivier Hamant, Arezki Boudaoud, Jan Traas, Christophe Godin

Related Articles

Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model

Martin Rückl, Ian Parker, Jonathan S. Marchant, Chamakuri Nagaiah, Friedrich W. Johenning, Sten Rüdiger

Simulating the Complex Cell Design of Trypanosoma brucei and Its Motility

Davod Alizadehrad, Timothy Krüger, Markus Engstler, Holger Stark

Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda

Ioannis Andrianakis, Ian R. Vernon, Nicky McCreesh, Trevelyan J. McKinley, Jeremy E. Oakley, Rebecca N. Nsubuga, Michael Goldstein, Richard G. White

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms

J. Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield

Related Articles

A RESTful API for Accessing Microbial Community Data for MG-RAST

Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer

What Makes a Protein Sequence a Prion?

Raimon Sabate, Frederic Rousseau, Joost Schymkowitz, Salvador Ventura

Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells

Lu Chen, Lei Du-Cuny, Sylvestor Moses, Sabrina Dumas, Zuohe Song, Abdol Hossein Rezaeian, Hui-Kuan Lin, Emmanuelle J. Meuillet, Shuxing Zhang

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph A. Marsh, Patrik Lundström

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel

Brain Network Adaptability across Task States

Elizabeth N. Davison, Kimberly J. Schlesinger, Danielle S. Bassett, Mary-Ellen Lynall, Michael B. Miller, Scott T. Grafton, Jean M. Carlson