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May 2015

The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Babaei et al.

Image Credit: Ms. Annelies te Selle


Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, DREAM8 Parameter Estimation Challenge Consortium, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer

Topic Page

Inferring Horizontal Gene Transfer

Matt Ravenhall, Nives Škunca, Florent Lassalle, Christophe Dessimoz

Research Articles

Maintaining Homeostasis by Decision-Making

Christoph W. Korn, Dominik R. Bach

Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response

Augustin Luna, Geoffrey B. McFadden, Mirit I. Aladjem, Kurt W. Kohn

Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle

Wilfredo Blanco, Catia M. Pereira, Vinicius R. Cota, Annie C. Souza, César Rennó-Costa, Sharlene Santos, Gabriella Dias, Ana M. G. Guerreiro, Adriano B. L. Tort, Adrião D. Neto, Sidarta Ribeiro

Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling

David W. P. Dolan, Anze Zupanic, Glyn Nelson, Philip Hall, Satomi Miwa, Thomas B. L. Kirkwood, Daryl P. Shanley

Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network

Bader Al-Anzi, Patrick Arpp, Sherif Gerges, Christopher Ormerod, Noah Olsman, Kai Zinn

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma

Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand

Geometrical and Mechanical Properties Control Actin Filament Organization

Gaëlle Letort, Antonio Z. Politi, Hajer Ennomani, Manuel Théry, Francois Nedelec, Laurent Blanchoin

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis

A Multiscale Model Evaluates Screening for Neoplasia in Barrett’s Esophagus

Kit Curtius, William D. Hazelton, Jihyoun Jeon, E. Georg Luebeck

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

Erik van Dijk, Arlo Hoogeveen, Sanne Abeln

Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations

Zhi Yang Tam, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan

Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer

Matthew H. Ung, Frederick S. Varn, Shaoke Lou, Chao Cheng

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

Christopher A. Lavender, Robert J. Gorelick, Kevin M. Weeks

Metapopulation Persistence in Random Fragmented Landscapes

Jacopo Grilli, György Barabás, Stefano Allesina

Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron

Cengiz Günay, Fred H. Sieling, Logesh Dharmar, Wei-Hsiang Lin, Verena Wolfram, Richard Marley, Richard A. Baines, Astrid A. Prinz

Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer

Gianluca Ascolani, Annalisa Occhipinti, Pietro Liò

The Effect of Incentives and Meta-incentives on the Evolution of Cooperation

Isamu Okada, Hitoshi Yamamoto, Fujio Toriumi, Tatsuya Sasaki

Forecasting the 2013–2014 Influenza Season Using Wikipedia

Kyle S. Hickmann, Geoffrey Fairchild, Reid Priedhorsky, Nicholas Generous, James M. Hyman, Alina Deshpande, Sara Y. Del Valle

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

Emma Pierson, the GTEx Consortium, Daphne Koller, Alexis Battle, Sara Mostafavi

Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View

Yaroslav I. Molkov, Bartholomew J. Bacak, Adolfo E. Talpalar, Ilya A. Rybak

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P. F. Lelieveldt, Jeroen de Ridder, Marcel Reinders

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Gary K. Chen, Eric C. Chi, John Michael O. Ranola, Kenneth Lange

Optimal Census by Quorum Sensing

Thibaud Taillefumier, Ned S. Wingreen

Extensive Decoupling of Metabolic Genes in Cancer

Ed Reznik, Chris Sander

Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity

Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts

Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics

Torsten Neher, Sen Cheng, Laurenz Wiskott

Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level

Wanling Song, Harsha Bajaj, Chady Nasrallah, Hualiang Jiang, Mathias Winterhalter, Jacques-Philippe Colletier, Yechun Xu

Accurate Computation of Survival Statistics in Genome-Wide Studies

Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal

A Dynamical Phyllotaxis Model to Determine Floral Organ Number

Miho S. Kitazawa, Koichi Fujimoto

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau

An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse

Daniel Keller, Norbert Babai, Olexiy Kochubey, Yunyun Han, Henry Markram, Felix Schürmann, Ralf Schneggenburger

Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses

Kiana Toufighi, Jae-Seong Yang, Nuno Miguel Luis, Salvador Aznar Benitah, Ben Lehner, Luis Serrano, Christina Kiel

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale

T. Scott Chen, Donald Petrey, Jose Ignacio Garzon, Barry Honig

Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities

Victor Garcia, Kirsten Richter, Frederik Graw, Annette Oxenius, Roland R. Regoes

Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering

Thomas P. Prescott, Moritz Lang, Antonis Papachristodoulou