Table of Contents: March 2014


Using mathematical models to design better anti-arrhythmic drugs.

Image Credit: Megan Cummins, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai
Issue Image

Many cardiac drugs fail because they exhibit reverse rate dependence, prolonging ventricular action potentials at slow heart rates, where this is pro-arrhythmic, while failing to prolong action potentials at fast heart rates. The colored squares in the image show predictions that were obtained by testing the effects of multiple ion channel perturbations in multiple mathematical models. Through this analysis we identified perturbations that act with forward rate dependence, prolonging the cardiac action potential at fast heart rates (top traces) but not at slow rates (bottom traces). See Cummins et al.


Ten Simple Rules for Effective Computational Research

James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David J. Gavaghan, Stephen Emmott, Charlotte Deane

Messages from ISCB

Crossing Borders for Science

Sebastian J. Schultheiss, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, Magali Michaut

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies

Lonnie Welch, Fran Lewitter, Russell Schwartz, Cath Brooksbank, Predrag Radivojac, Bruno Gaeta, Maria Victoria Schneider



The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling

Nico J. D. Nagelkerke, Paul Arora, Prabhat Jha, Brian Williams, Lyle McKinnon, Sake J. de Vlas

Research Articles

Resolving Structural Variability in Network Models and the Brain

Florian Klimm, Danielle S. Bassett, Jean M. Carlson, Peter J. Mucha

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford

A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects

Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya

Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain

Alexandros Goulas, Matteo Bastiani, Gleb Bezgin, Harry B. M. Uylings, Alard Roebroeck, Peter Stiers

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad

Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence

Megan A. Cummins, Pavan J. Dalal, Marco Bugana, Stefano Severi, Eric A. Sobie

Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map

Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yu-Fang Jin

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases

Teresa Szczepińska, Jan Kutner, Michał Kopczyński, Krzysztof Pawłowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski, Maga Rowicka

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing

Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq

Computational Analyses of Synergism in Small Molecular Network Motifs

Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

Vladimir Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab

Modular Composition of Gene Transcription Networks

Andras Gyorgy, Domitilla Del Vecchio

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating

Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten

Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence

Mingming Chen, Daqing Guo, Tiebin Wang, Wei Jing, Yang Xia, Peng Xu, Cheng Luo, Pedro A. Valdes-Sosa, Dezhong Yao

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation

Michael Pargett, Ann E. Rundell, Gregery T. Buzzard, David M. Umulis

Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver

Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser, Lars Kuepfer

Dynamic Alignment Models for Neural Coding

Sepp Kollmorgen, Richard H. R. Hahnloser

Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability

Andrey Rzhetsky, Steven C. Bagley, Kanix Wang, Christopher S. Lyttle, Edwin H. Cook Jr, Russ B. Altman, Robert D. Gibbons

Slowness and Sparseness Have Diverging Effects on Complex Cell Learning

Jörn-Philipp Lies, Ralf M. Häfner, Matthias Bethge

Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars

Partha S. Bhagavatula, Charles Claudianos, Michael R. Ibbotson, Mandyam V. Srinivasan

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

Navneet Bung, Meenakshi Pradhan, Harini Srinivasan, Gopalakrishnan Bulusu

Universal Count Correction for High-Throughput Sequencing

Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford