Table of Contents: July 2016

Scientists use mathematical modeling to simulate human mesenchymal stem cell delivery to a damaged heart and found that using one subtype of these stem cells minimises the risks associated with this therapy. Costa et al.

Image Credit: Jerry Reyes


Ten Simple Rules for Writing a Postdoctoral Fellowship

Ke Yuan, Lei Cai, Siu Ping Ngok, Li Ma, Crystal M. Botham

Ten Simple Rules for Taking Advantage of Git and GitHub

Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno

Computing Biology

Ruth Nussinov, Jason A. Papin

Messages from ISCB

2016 ISCB Innovator Award: Serafim Batzoglou

Christiana N. Fogg, Diane E. Kovats

Topic Pages

Ancestral Reconstruction

Jeffrey B. Joy, Richard H. Liang, Rosemary M. McCloskey, T. Nguyen, Art F. Y. Poon

Research Articles

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

Juliana Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone

The Differential Response of Proteins to Macromolecular Crowding

Michela Candotti, Modesto Orozco

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering

Chuan Gao, Ian C. McDowell, Shiwen Zhao, Christopher D. Brown, Barbara E. Engelhardt

Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages

Julia Rex, Ute Albrecht, Christian Ehlting, Maria Thomas, Ulrich M. Zanger, Oliver Sawodny, Dieter Häussinger, Michael Ederer, Ronny Feuer, Johannes G. Bode

Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes

Joshua Mayourian, Ruben M. Savizky, Eric A. Sobie, Kevin D. Costa

Modeling of Kidney Hemodynamics: Probability-Based Topology of an Arterial Network

Dmitry D. Postnov, Donald J. Marsh, Dmitry E. Postnov, Thomas H. Braunstein, Niels-Henrik Holstein-Rathlou, Erik A. Martens, Olga Sosnovtseva

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J. Theis, Ramon Grima, Jan Hasenauer

Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling

Manikandan Narayanan, Andrew J. Martins, John S. Tsang

Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin

Takahiro Ezaki, Yutaka Horita, Masanori Takezawa, Naoki Masuda

Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage

Zheng Sun, Maksim V. Plikus, Natalia L. Komarova

The Integrated Role of Wnt/β-Catenin, N-Glycosylation, and E-Cadherin-Mediated Adhesion in Network Dynamics

Diego A. Vargas, Meng Sun, Khikmet Sadykov, Maria A. Kukuruzinska, Muhammad H. Zaman

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains

Emiliano Torre, Carlos Canova, Michael Denker, George Gerstein, Moritz Helias, Sonja Grün

Disease Surveillance on Complex Social Networks

Jose L. Herrera, Ravi Srinivasan, John S. Brownstein, Alison P. Galvani, Lauren Ancel Meyers

NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning

Xing Chen, Biao Ren, Ming Chen, Quanxin Wang, Lixin Zhang, Guiying Yan

Phasic Burst Stimulation: A Closed-Loop Approach to Tuning Deep Brain Stimulation Parameters for Parkinson’s Disease

Abbey B. Holt, Dan Wilson, Max Shinn, Jeff Moehlis, Theoden I. Netoff

Intrinsic Valuation of Information in Decision Making under Uncertainty

Daniel Bennett, Stefan Bode, Maja Brydevall, Hayley Warren, Carsten Murawski

A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation

Pei-Chi Yang, Britton W. Boras, Mao-Tsuen Jeng, Steffen S. Docken, Timothy J. Lewis, Andrew D. McCulloch, Robert D. Harvey, Colleen E. Clancy

Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions

Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens

Deborah Chasman, Kevin B. Walters, Tiago J. S. Lopes, Amie J. Eisfeld, Yoshihiro Kawaoka, Sushmita Roy

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph

Dynamic Reweighting of Auditory Modulation Filters

Eva R. M. Joosten, Shihab A. Shamma, Christian Lorenzi, Peter Neri

Properties of Neurons in External Globus Pallidus Can Support Optimal Action Selection

Rafal Bogacz, Eduardo Martin Moraud, Azzedine Abdi, Peter J. Magill, Jérôme Baufreton

Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data

Gustaf Rydevik, Giles T. Innocent, Glenn Marion, Ross S. Davidson, Piran C. L. White, Charalambos Billinis, Paul Barrow, Peter P. C. Mertens, Dolores Gavier-Widén, Michael R. Hutchings

The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation

Julian Weichsel, Phillip L. Geissler

Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling

Javier Estrada, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad, Jeremy Gunawardena

Collective Signal Processing in Cluster Chemotaxis: Roles of Adaptation, Amplification, and Co-attraction in Collective Guidance

Brian A. Camley, Juliane Zimmermann, Herbert Levine, Wouter-Jan Rappel