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

Editorial

Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation

Rachel Karchin, Ruth Nussinov

PLOS Computational Biology: published August 18, 2016 | https://doi.org/10.1371/journal.pcbi.1005043

Perspective

The Virtuous Cycle of a Data Ecosystem

Bradley Voytek

PLOS Computational Biology: published August 4, 2016 | https://doi.org/10.1371/journal.pcbi.1005037

Research Articles

On Expression Patterns and Developmental Origin of Human Brain Regions

Lior Kirsch, Gal Chechik

PLOS Computational Biology: published August 26, 2016 | https://doi.org/10.1371/journal.pcbi.1005064

Efficient Reconstruction of Predictive Consensus Metabolic Network Models

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

PLOS Computational Biology: published August 26, 2016 | https://doi.org/10.1371/journal.pcbi.1005085

When Does Model-Based Control Pay Off?

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

PLOS Computational Biology: published August 26, 2016 | https://doi.org/10.1371/journal.pcbi.1005090

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

PLOS Computational Biology: published August 26, 2016 | https://doi.org/10.1371/journal.pcbi.1005091

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design

Wanli You, Yu-ming M. Huang, Smitha Kizhake, Amarnath Natarajan, Chia-en A. Chang

PLOS Computational Biology: published August 25, 2016 | https://doi.org/10.1371/journal.pcbi.1005057

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

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

PLOS Computational Biology: published August 25, 2016 | https://doi.org/10.1371/journal.pcbi.1005077

Noncommutative Biology: Sequential Regulation of Complex Networks

William Letsou, Long Cai

PLOS Computational Biology: published August 25, 2016 | https://doi.org/10.1371/journal.pcbi.1005089

A Robust Actin Filaments Image Analysis Framework

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

PLOS Computational Biology: published August 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005063

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

Daphne Ezer, Victoria Moignard, Berthold Göttgens, Boris Adryan

PLOS Computational Biology: published August 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005072

Conflict Resolution as Near-Threshold Decision-Making: A Spiking Neural Circuit Model with Two-Stage Competition for Antisaccadic Task

Chung-Chuan Lo, Xiao-Jing Wang

PLOS Computational Biology: published August 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005081

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

PLOS Computational Biology: published August 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004931

Inverse Stochastic Resonance in Cerebellar Purkinje Cells

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

PLOS Computational Biology: published August 19, 2016 | https://doi.org/10.1371/journal.pcbi.1005000

Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks

Brendan Chambers, Jason N. MacLean

PLOS Computational Biology: published August 19, 2016 | https://doi.org/10.1371/journal.pcbi.1005078

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

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

PLOS Computational Biology: published August 19, 2016 | https://doi.org/10.1371/journal.pcbi.1005084

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

PLOS Computational Biology: published August 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004751

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

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

PLOS Computational Biology: published August 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004972

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease

Jonas Reeb, Maximilian Hecht, Yannick Mahlich, Yana Bromberg, Burkhard Rost

PLOS Computational Biology: published August 18, 2016 | https://doi.org/10.1371/journal.pcbi.1005047

Inference of Ancestral Recombination Graphs through Topological Data Analysis

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

PLOS Computational Biology: published August 17, 2016 | https://doi.org/10.1371/journal.pcbi.1005071

Defining the Product Chemical Space of Monoterpenoid Synthases

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

PLOS Computational Biology: published August 12, 2016 | https://doi.org/10.1371/journal.pcbi.1005053

Shaping Neural Circuits by High Order Synaptic Interactions

Neta Ravid Tannenbaum, Yoram Burak

PLOS Computational Biology: published August 12, 2016 | https://doi.org/10.1371/journal.pcbi.1005056

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

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

PLOS Computational Biology: published August 12, 2016 | https://doi.org/10.1371/journal.pcbi.1005069

Evolutionary Games of Multiplayer Cooperation on Graphs

Jorge Peña, Bin Wu, Jordi Arranz, Arne Traulsen

PLOS Computational Biology: published August 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005059

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

PLOS Computational Biology: published August 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005048

Autonomous Optimization of Targeted Stimulation of Neuronal Networks

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

PLOS Computational Biology: published August 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005054

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

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

PLOS Computational Biology: published August 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005065

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

PLOS Computational Biology: published August 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005025

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

PLOS Computational Biology: published August 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004872

The Complexity of Dynamics in Small Neural Circuits

Diego Fasoli, Anna Cattani, Stefano Panzeri

PLOS Computational Biology: published August 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004992

Structure Prediction of RNA Loops with a Probabilistic Approach

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

PLOS Computational Biology: published August 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005032

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity

Biman Jana, José N. Onuchic

PLOS Computational Biology: published August 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005035

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

PLOS Computational Biology: published August 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005049

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

Daniel Hartleb, Florian Jarre, Martin J. Lercher

PLOS Computational Biology: published August 2, 2016 | https://doi.org/10.1371/journal.pcbi.1005036

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

PLOS Computational Biology: published August 1, 2016 | https://doi.org/10.1371/journal.pcbi.1005012

Inference of Gene Regulatory Network Based on Local Bayesian Networks

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

PLOS Computational Biology: published August 1, 2016 | https://doi.org/10.1371/journal.pcbi.1005024

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On Expression Patterns and Developmental Origin of Human Brain Regions

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