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Table of Contents

February 2015

The level of inosine 5'-monophosphate (IMP), an intermediate metabolite in de novo purine synthesis, showed significant circadian oscillation in larval zebrafish. We focused on IMP dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis, with three circadian oscillating gene homologs: impdh1a, impdh1b and impdh2. Functional analysis revealed that impdh2 contributes to the daily rhythm of S phase in the cell cycle while impdh1a contributes to ocular development and pigment synthesis. The three zebrafish homologs of impdh are likely regulated by different circadian transcription factors. Li et al.

Image Credit: Ying Li and Guang Li

Education

A Quick Guide for Building a Successful Bioinformatics Community

Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

Research Articles

Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells

David G. García Münzer, Margaritis Kostoglou, Michael C. Georgiadis, Efstratios N. Pistikopoulos, Athanasios Mantalaris

Protein Sectors: Statistical Coupling Analysis versus Conservation

Tiberiu Teşileanu, Lucy J. Colwell, Stanislas Leibler

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

Saheed Imam, Daniel R. Noguera, Timothy J. Donohue

Protein Complexes in Bacteria

J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz

A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning

Mei Yan Lee, Scott L. Diamond

Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information

Daniel M. Keenan, Amy W. Quinkert, Donald W. Pfaff

Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble

Renaud Jolivet, Jay S. Coggan, Igor Allaman, Pierre J. Magistretti

Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies

Benjamin J. Binder, Joanna F. Sundstrom, Jennifer M. Gardner, Vladimir Jiranek, Stephen G. Oliver

The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure

Benjamin Allen, Christine Sample, Yulia Dementieva, Ruben C. Medeiros, Christopher Paoletti, Martin A. Nowak

Correlations and Functional Connections in a Population of Grid Cells

Benjamin Dunn, Maria Mørreaunet, Yasser Roudi

A Theoretical Justification for Single Molecule Peptide Sequencing

Jagannath Swaminathan, Alexander A. Boulgakov, Edward M. Marcotte

Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle

Ying Li, Guang Li, Benjamin Görling, Burkhard Luy, Jiulin Du, Jun Yan

Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds

Yonatan Schweitzer, Michael M. Kozlov

PathVisio 3: An Extendable Pathway Analysis Toolbox

Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. Evelo

Segment-Specific Adhesion as a Driver of Convergent Extension

Renske M. A. Vroomans, Paulien Hogeweg, Kirsten H. W. J. ten Tusscher

Critical Slowing Down Governs the Transition to Neuron Spiking

Christian Meisel, Andreas Klaus, Christian Kuehn, Dietmar Plenz

Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum

Jorge M. Pacheco, Vítor V. Vasconcelos, Francisco C. Santos, Brian Skyrms

Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis

Andrew J. K. Conlan, Ellen Brooks Pollock, Trevelyan J. McKinley, Andrew P. Mitchell, Gareth J. Jones, Martin Vordermeier, James L. N. Wood

Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli

Elisa M. Tartaglia, Nicolas Brunel, Gianluigi Mongillo

Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion

Johannes Eckstein, Nikolaus Berndt, Hermann-Georg Holzhütter

A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception

Renaud Bastien, Stéphane Douady, Bruno Moulia

Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis

Edward J. Banigan, Tajie H. Harris, David A. Christian, Christopher A. Hunter, Andrea J. Liu

Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage

Ishutesh Jain, Mandar M. Inamdar, Ranjith Padinhateeri

Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity

Adrián Ponce-Alvarez, Gustavo Deco, Patric Hagmann, Gian Luca Romani, Dante Mantini, Maurizio Corbetta

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination

Laura R. González-Ramírez, Omar J. Ahmed, Sydney S. Cash, C. Eugene Wayne, Mark A. Kramer

Integrative Multi-omics Module Network Inference with Lemon-Tree

Eric Bonnet, Laurence Calzone, Tom Michoel

Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding

Eric Lowet, Mark Roberts, Avgis Hadjipapas, Alina Peter, Jan van der Eerden, Peter De Weerd

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Xavier Didelot, Daniel J. Wilson

Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model

Daniel Malagarriga, Alessandro E. P. Villa, Jordi Garcia-Ojalvo, Antonio J. Pons

Developing a Molecular Roadmap of Drug-Food Interactions

Kasper Jensen, Yueqiong Ni, Gianni Panagiotou, Irene Kouskoumvekaki

Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency

Hanna Julienne, Benjamin Audit, Alain Arneodo

Cell Cycle Control by a Minimal Cdk Network

Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák

HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects

Bence Ferdinandy, Enys Mones, Tamás Vicsek, Viktor Müller

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

Paul T. Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, RV144 Sequencing Team, Miguel A. Arroyo, Robert J. O’Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin S. Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson L. Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert

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