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Table of Contents: August 2016

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. Kirsch et al.

Image Credit: Lior Kirsch

Perspectives

The Virtuous Cycle of a Data Ecosystem

Bradley Voytek

Research Articles

On Expression Patterns and Developmental Origin of Human Brain Regions

Lior Kirsch, Gal Chechik

Efficient Reconstruction of Predictive Consensus Metabolic Network Models

Ruben G. A. van Heck, Mathias Ganter, Vitor A. P. Martins dos Santos, Joerg Stelling

When Does Model-Based Control Pay Off?

Wouter Kool, Fiery A. Cushman, Samuel J. Gershman

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

Jose Lugo-Martinez, Vikas Pejaver, Kymberleigh A. Pagel, Shantanu Jain, Matthew Mort, David N. Cooper, Sean D. Mooney, Predrag Radivojac

Leveraging Hypoxia-Activated Prodrugs to Prevent Drug Resistance in Solid Tumors

Danika Lindsay, Colleen M. Garvey, Shannon M. Mumenthaler, Jasmine Foo

Noncommutative Biology: Sequential Regulation of Complex Networks

William Letsou, Long Cai

A Robust Actin Filaments Image Analysis Framework

Mitchel Alioscha-Perez, Carine Benadiba, Katty Goossens, Sandor Kasas, Giovanni Dietler, Ronnie Willaert, Hichem Sahli

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

Daphne Ezer, Victoria Moignard, Berthold Göttgens, Boris Adryan

Cortico-Cortical Interactions during Acquisition and Use of a Neuroprosthetic Skill

Jeremiah D. Wander, Devapratim Sarma, Lise A. Johnson, Eberhard E. Fetz, Rajesh P. N. Rao, Jeffrey G. Ojemann, Felix Darvas

Inverse Stochastic Resonance in Cerebellar Purkinje Cells

Anatoly Buchin, Sarah Rieubland, Michael Häusser, Boris S. Gutkin, Arnd Roth

Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks

Brendan Chambers, Jason N. MacLean

Vulnerability-Based Critical Neurons, Synapses, and Pathways in the Caenorhabditis elegans Connectome

Seongkyun Kim, Hyoungkyu Kim, Jerald D. Kralik, Jaeseung Jeong

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns

Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit

Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes

Mohammad Soltani, Cesar A. Vargas-Garcia, Duarte Antunes, Abhyudai Singh

Inference of Ancestral Recombination Graphs through Topological Data Analysis

Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán

Defining the Product Chemical Space of Monoterpenoid Synthases

Boxue Tian, C. Dale Poulter, Matthew P. Jacobson

Shaping Neural Circuits by High Order Synaptic Interactions

Neta Ravid Tannenbaum, Yoram Burak

A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases

Tamra Heberling, Lisa Davis, Jakub Gedeon, Charles Morgan, Tomáš Gedeon

Evolutionary Games of Multiplayer Cooperation on Graphs

Jorge Peña, Bin Wu, Jordi Arranz, Arne Traulsen

The Impact of Cortical Lesions on Thalamo-Cortical Network Dynamics after Acute Ischaemic Stroke: A Combined Experimental and Theoretical Study

Joeri B. G. van Wijngaarden, Riccardo Zucca, Simon Finnigan, Paul F. M. J. Verschure

Autonomous Optimization of Targeted Stimulation of Neuronal Networks

Sreedhar S. Kumar, Jan Wülfing, Samora Okujeni, Joschka Boedecker, Martin Riedmiller, Ulrich Egert

Malaria Incidence Rates from Time Series of 2-Wave Panel Surveys

Marcia C. Castro, Mathieu Maheu-Giroux, Christinah Chiyaka, Burton H. Singer

Modeling of Large-Scale Functional Brain Networks Based on Structural Connectivity from DTI: Comparison with EEG Derived Phase Coupling Networks and Evaluation of Alternative Methods along the Modeling Path

Holger Finger, Marlene Bönstrup, Bastian Cheng, Arnaud Messé, Claus Hilgetag, Götz Thomalla, Christian Gerloff, Peter König

Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures – Part I: Idealized Axisymmetric Swirling Flow

Paula A. Vasquez, Yuan Jin, Erik Palmer, David Hill, M. Gregory Forest

The Complexity of Dynamics in Small Neural Circuits

Diego Fasoli, Anna Cattani, Stefano Panzeri

Structure Prediction of RNA Loops with a Probabilistic Approach

Jun Li, Jian Zhang, Jun Wang, Wenfei Li, Wei Wang

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells

Ruth Merkle, Bernhard Steiert, Florian Salopiata, Sofia Depner, Andreas Raue, Nao Iwamoto, Max Schelker, Helge Hass, Marvin Wäsch, Martin E. Böhm, Oliver Mücke, Daniel B. Lipka, Christoph Plass, Wolf D. Lehmann, Clemens Kreutz, Jens Timmer, Marcel Schilling, Ursula Klingmüller

Flow-Based Network Analysis of the Caenorhabditis elegans Connectome

Karol A. Bacik, Michael T. Schaub, Mariano Beguerisse-Díaz, Yazan N. Billeh, Mauricio Barahona

Comparison of Detailed and Simplified Models of Human Atrial Myocytes to Recapitulate Patient Specific Properties

Daniel M. Lombardo, Flavio H. Fenton, Sanjiv M. Narayan, Wouter-Jan Rappel

Neuromotor Noise Is Malleable by Amplifying Perceived Errors

Christopher J. Hasson, Zhaoran Zhang, Masaki O. Abe, Dagmar Sternad

The Representation of Prediction Error in Auditory Cortex

Jonathan Rubin, Nachum Ulanovsky, Israel Nelken, Naftali Tishby

Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy

Ganna Rozhnova, Maarten F. Schim van der Loeff, Janneke C. M. Heijne, Mirjam E. Kretzschmar

Inference of Gene Regulatory Network Based on Local Bayesian Networks

Fei Liu, Shao-Wu Zhang, Wei-Feng Guo, Ze-Gang Wei, Luonan Chen