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Table of Contents: January 2017

Complex brain networks are mainly estimated from empirical measurements. As a result, filtering procedures are typically adopted to prune the weakest connections. The structural properties of the thresholded networks depend on the number of remaining links and how to objectively fix such threshold is still an open issue. We propose a possible criterion to filter connectivity based on the optimization of fundamental properties in complex systems, such as efficiency and economy, and we show that a general law can be derived. Given its generality, ECO can advance the ability to analyze biological networks inferred from experimentally obtained data. De Vico Fallani et al.

Image Credit: Fabrizio De Vico Fallani

Editorials

Computing the Dynamic Supramolecular Structural Proteome

Ruth Nussinov, Jason A. Papin, Ilya Vakser

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing

Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti

Ten Simple Rules for Developing Usable Software in Computational Biology

Markus List, Peter Ebert, Felipe Albrecht

Perspective

Efficient Switches in Biology and Computer Science

Luca Cardelli, Rosa D. Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikász-Nagy

Review

Pain: A Statistical Account

Abby Tabor, Michael A. Thacker, G. Lorimer Moseley, Konrad P. Körding

Research Articles

The missing link: Predicting connectomes from noisy and partially observed tract tracing data

Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H. E. Tiesinga, Morten Mørup, Marcel A. J. van Gerven

Coevolutionary dynamics of phenotypic diversity and contingent cooperation

Te Wu, Long Wang, Feng Fu

Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure

Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das, Ranjith Padinhateeri

Memory replay in balanced recurrent networks

Nikolay Chenkov, Henning Sprekeler, Richard Kempter

Exploring the inhibitory effect of membrane tension on cell polarization

Weikang Wang, Kuan Tao, Jing Wang, Gen Yang, Qi Ouyang, Yugang Wang, Lei Zhang, Feng Liu

Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains

Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas Schilling, Qing Nie

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

Ilan Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger-Lotem

Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs

Austin W. T. Chiang, Walt Y. L. Wu, Ting Wang, Ming-Jing Hwang

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

Hsiao-Han Chang, Colin J. Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R. Kamya, Sarah G. Staedke, Grant Dorsey, Maxwell Murphy, Daniel E. Neafsey, Anna E. Jeffreys, Christina Hubbart, Kirk A. Rockett, Roberto Amato, Dominic P. Kwiatkowski, Caroline O. Buckee, Bryan Greenhouse

The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks

Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Luca Zarenghi, Matteo Ricchi, Luca Bolzoni

The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers

Marie Amalric, Liping Wang, Pierre Pica, Santiago Figueira, Mariano Sigman, Stanislas Dehaene

A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth

Vasileios Vavourakis, Peter A. Wijeratne, Rebecca Shipley, Marilena Loizidou, Triantafyllos Stylianopoulos, David J. Hawkes

The Flash-Lag Effect as a Motion-Based Predictive Shift

Mina A. Khoei, Guillaume S. Masson, Laurent U. Perrinet

Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation

Stewart Heitmann, Michael Rule, Wilson Truccolo, Bard Ermentrout

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility

David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann, Zoltán Kutalik

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann

Computational Account of Spontaneous Activity as a Signature of Predictive Coding

Veronika Koren, Sophie Denève

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer

Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients

Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta, Holger Stark

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

William R. Holmes, Nabora Soledad Reyes de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie

Morphological Transformation and Force Generation of Active Cytoskeletal Networks

Tamara Carla Bidone, Wonyeong Jung, Daniel Maruri, Carlos Borau, Roger D. Kamm, Taeyoon Kim

Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies

Tanmay A. Gokhale, Jong M. Kim, Robert D. Kirkton, Nenad Bursac, Craig S. Henriquez

Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses

Ignacio A. Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz

Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome

Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng

Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing

Edward S. Lee, Paul G. Thomas, Jeff E. Mold, Andrew J. Yates

Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels

Hilje M. Doekes, Christophe Fraser, Katrina A. Lythgoe

A New Approach to Model Pitch Perception Using Sparse Coding

Oded Barzelay, Miriam Furst, Omri Barak

Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations

Christian Donner, Klaus Obermayer, Hideaki Shimazaki

A General Shear-Dependent Model for Thrombus Formation

Alireza Yazdani, He Li, Jay D. Humphrey, George Em Karniadakis

A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models

Christoph Zimmer, Reza Yaesoubi, Ted Cohen

A Looping-Based Model for Quenching Repression

Yaroslav Pollak, Sarah Goldberg, Roee Amit

Inference of Transmission Network Structure from HIV Phylogenetic Trees

Federica Giardina, Ethan Obie Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

Christopher M. Siwy, Christopher Lockhart, Dmitri K. Klimov

A Computational Approach for Identifying Synergistic Drug Combinations

Kaitlyn M. Gayvert, Omar Aly, James Platt, Marcus W. Bosenberg, David F. Stern, Olivier Elemento

Could a Neuroscientist Understand a Microprocessor?

Eric Jonas, Konrad Paul Kording

The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection

Luc E. Coffeng, Cornelus C. Hermsen, Robert W. Sauerwein, Sake J. de Vlas

Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion

James M. Kunert, Joshua L. Proctor, Steven L. Brunton, J. Nathan Kutz

Multiple Choice Neurodynamical Model of the Uncertain Option Task

Andrea Insabato, Mario Pannunzi, Gustavo Deco

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez

Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms

Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes Bode, Martina U. Muckenthaler, Stefan Legewie

Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma

Martina Michalikova, Michiel W. H. Remme, Richard Kempter

Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies

Pia Abel zur Wiesch, Fabrizio Clarelli, Ted Cohen

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher

Structure-Function Network Mapping and Its Assessment via Persistent Homology

Hualou Liang, Hongbin Wang

Suboptimal Criterion Learning in Static and Dynamic Environments

Elyse H. Norton, Stephen M. Fleming, Nathaniel D. Daw, Michael S. Landy

Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model

Chen Zhao, Jeffrey S. Isenberg, Aleksander S. Popel