Advertisement

Table of Contents: November 2016

Asian citrus psyllids (Diaphorina citri), pictured, feed on citrus and can transmit the pathogen causing citrus greening. We connected psyllids to electrical circuits to monitor their feeding then used machine learning algorithms to classify insect feeding, detect new feeding states, and investigate resistance mechanisms. Willett et al.

Image Credit: Jeffrey Weston Lotz

Editorial

Ten Simple Rules for Developing Public Biological Databases

Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader

Research Articles

Network Receptive Field Modeling Reveals Extensive Integration and Multi-feature Selectivity in Auditory Cortical Neurons

Nicol S. Harper, Oliver Schoppe, Ben D. B. Willmore, Zhanfeng Cui, Jan W. H. Schnupp, Andrew J. King

Real-Time Control of an Articulatory-Based Speech Synthesizer for Brain Computer Interfaces

Florent Bocquelet, Thomas Hueber, Laurent Girin, Christophe Savariaux, Blaise Yvert

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion

Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R. Petzold

Improved Measures of Integrated Information

Max Tegmark

Error-Robust Modes of the Retinal Population Code

Jason S. Prentice, Olivier Marre, Mark L. Ioffe, Adrianna R. Loback, Gašper Tkačik, Michael J. Berry II

Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach

Shreyas Bhaban, Donatello Materassi, Mingang Li, Thomas Hays, Murti Salapaka

Machine Learning for Characterization of Insect Vector Feeding

Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012

William J. Love, Kelson A. Zawack, James G. Booth, Yrjo T. Grӧhn, Cristina Lanzas

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

Ye Eun Kim, Paul G. Higgs

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1

Jeffrey S. Seely, Matthew T. Kaufman, Stephen I. Ryu, Krishna V. Shenoy, John P. Cunningham, Mark M. Churchland

High-Frequency Resonance in the Gerbil Medial Superior Olive

Jason Mikiel-Hunter, Vibhakar Kotak, John Rinzel

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Elad Noor, Avi Flamholz, Arren Bar-Even, Dan Davidi, Ron Milo, Wolfram Liebermeister

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4

Kristyna Pluhackova, Stefan Gahbauer, Franziska Kranz, Tsjerk A. Wassenaar, Rainer A. Böckmann

Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning

Jonathan A. Michaels, Benjamin Dann, Hansjörg Scherberger

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

David A. Van Valen, Takamasa Kudo, Keara M. Lane, Derek N. Macklin, Nicolas T. Quach, Mialy M. DeFelice, Inbal Maayan, Yu Tanouchi, Euan A. Ashley, Markus W. Covert

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan

Elizabeth N. Davison, Benjamin O. Turner, Kimberly J. Schlesinger, Michael B. Miller, Scott T. Grafton, Danielle S. Bassett, Jean M. Carlson

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

George L. Sutphin, J. Matthew Mahoney, Keith Sheppard, David O. Walton, Ron Korstanje

A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging

Sagi Snir, Bridgett M. vonHoldt, Matteo Pellegrini

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents

Sophia S. Liu, Adam J. Hockenberry, Andrea Lancichinetti, Michael C. Jewett, Luís A. N. Amaral

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias

Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

Adam F. Prasanphanich, Douglas E. White, Margaret A. Gran, Melissa L. Kemp

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

Arno Onken, Jian K. Liu, P. P. Chamanthi R. Karunasekara, Ioannis Delis, Tim Gollisch, Stefano Panzeri

Malaria Elimination Campaigns in the Lake Kariba Region of Zambia: A Spatial Dynamical Model

Milen Nikolov, Caitlin A. Bever, Alexander Upfill-Brown, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger, Jaline Gerardin

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue

Geir Halnes, Tuomo Mäki-Marttunen, Daniel Keller, Klas H. Pettersen, Ole A. Andreassen, Gaute T. Einevoll

Drivers of Inter-individual Variation in Dengue Viral Load Dynamics

Rotem Ben-Shachar, Scott Schmidler, Katia Koelle

PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases

Marzieh Ayati, Mehmet Koyutürk

The Environment Shapes the Inner Vestibule of LeuT

Azmat Sohail, Kumaresan Jayaraman, Santhoshkannan Venkatesan, Kamil Gotfryd, Markus Daerr, Ulrik Gether, Claus J. Loland, Klaus T. Wanner, Michael Freissmuth, Harald H. Sitte, Walter Sandtner, Thomas Stockner

Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City

Wan Yang, Donald R. Olson, Jeffrey Shaman

Induced Fit in Protein Multimerization: The HFBI Case

Laura Riccardi, Paolo Mereghetti

Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

Fang-Cheng Yeh, Jean M. Vettel, Aarti Singh, Barnabas Poczos, Scott T. Grafton, Kirk I. Erickson, Wen-Yih I. Tseng, Timothy D. Verstynen

An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production

Adaoha E. C. Ihekwaba, Ivan Mura, John Walshaw, Michael W. Peck, Gary C. Barker

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

Aleksandr V. Zhuravlev, Gennady A. Zakharov, Boris F. Shchegolev, Elena V. Savvateeva-Popova

Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle

Peter Rashkov, Ian P. Barrett, Robert E. Beardmore, Claus Bendtsen, Ivana Gudelj

Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM

André F. Pereira, Daniel J. Hageman, Tomasz Garbowski, Christof Riedesel, Ulf Knothe, Dirk Zeidler, Melissa L. Knothe Tate

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction

Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira

Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway

Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi

Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?

Elif Tekin, David Hunt, Mitchell G. Newberry, Van M. Savage