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Table of Contents: October 2017

A large number of species from primates to shrimps do not see the visual world with uniform spatial detail. An area with heightened sensitivity to spatial detail, known as the fovea in mammals is oriented through eye and head movements to scrutinize regions of interest in the visual environment. Akbas and Eckstein showed using a computer vision object detection model, that the foveated version of the model can attain similar search performance to its non-foveated version while bringing significant computational savings. The image shows the spatial pooling regions of the foveated model.

Image Credit: Emre Akbas

Editorials

Network approaches and applications in biology

Trey Ideker, Ruth Nussinov

Ten simple rules for writing a response to reviewers

William Stafford Noble

Education Articles

Learning infectious disease epidemiology in a modern framework

Andreas Handel

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola Mulder, H3ABioNet Consortium's Education Training and Working Group as members of the H3Africa Consortium

Review

Structural host-microbiota interaction networks

Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov

Research Articles

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin

Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen

A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling

Vijay Vedula, Juhyun Lee, Hao Xu, C.-C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden

A mechanistic spatio-temporal framework for modelling individual-to-individual transmission—With an application to the 2014-2015 West Africa Ebola outbreak

Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, Jessica Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell

The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective

Ryan T. Philips, Mriganka Sur, V. Srinivasa Chakravarthy

Point process analysis of noise in early invertebrate vision

Kris V. Parag, Glenn Vinnicombe

Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation

Guoshi Li, Craig S. Henriquez, Flavio Fröhlich

Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery

Andrew J. K. Phillips, Elizabeth B. Klerman, James P. Butler

Dynamics and heterogeneity of brain damage in multiple sclerosis

Ekaterina Kotelnikova, Narsis A. Kiani, Elena Abad, Elena H. Martinez-Lapiscina, Magi Andorra, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G. Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi Garcia-Ojalvo, Pablo Villoslada

Transcriptomic correlates of neuron electrophysiological diversity

Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis

Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics

Nicolas E Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini

Neural field model to reconcile structure with function in primary visual cortex

James Rankin, Frédéric Chavane

Scaffolding the cup-shaped double membrane in autophagy

Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, James H. Hurley, Gerhard Hummer

Identification of immune signatures predictive of clinical protection from malaria

John Joseph Valletta, Mario Recker

Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network

Cynthia Sandor, Nicola L. Beer, Caleb Webber

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

Theodore Roman, Lu Xie, Russell Schwartz

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold

Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition

Timothy N. Rubin, Oluwasanmi Koyejo, Krzysztof J. Gorgolewski, Michael N. Jones, Russell A. Poldrack, Tal Yarkoni

Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI

Jaron T. Colas, Wolfgang M. Pauli, Tobias Larsen, J. Michael Tyszka, John P. O’Doherty

Quantifying the strength of quorum sensing crosstalk within microbial communities

Kalinga Pavan T. Silva, Prithiviraj Chellamuthu, James Q. Boedicker

Deconvolving sequence features that discriminate between overlapping regulatory annotations

Akshay Kakumanu, Silvia Velasco, Esteban Mazzoni, Shaun Mahony

Seasonality in risk of pandemic influenza emergence

Spencer J. Fox, Joel C. Miller, Lauren Ancel Meyers

A deep convolutional neural network for classification of red blood cells in sickle cell anemia

Mengjia Xu, Dimitrios P. Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George Em Karniadakis

Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster

Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

Evelina Gabasova, John Reid, Lorenz Wernisch

The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization

Niklas Hübel, Mahshid S. Hosseini-Zare, Jokūbas Žiburkus, Ghanim Ullah

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte

Vicus: Exploiting local structures to improve network-based analysis of biological data

Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg

Systematic, network-based characterization of therapeutic target inhibitors

Yao Shen, Mariano J. Alvarez, Brygida Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano

Network propagation in the cytoscape cyberinfrastructure

Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker

The structured ‘low temperature’ phase of the retinal population code

Mark L. Ioffe, Michael J. Berry II

Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?

Alex D. M. Dewar, Antoine Wystrach, Andrew Philippides, Paul Graham

Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments

Peter Ashcroft, Markus G. Manz, Sebastian Bonhoeffer

Image-based model of the spectrin cytoskeleton for red blood cell simulation

Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin

Object detection through search with a foveated visual system

Emre Akbas, Miguel P. Eckstein

A Bayesian approach to modelling heterogeneous calcium responses in cell populations

Agne Tilūnaitė, Wayne Croft, Noah Russell, Tomas C. Bellamy, Rüdiger Thul

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths

Gudrun Gygli, Maria Fátima Lucas, Victor Guallar, Willem J. H. van Berkel

Inferring oscillatory modulation in neural spike trains

Kensuke Arai, Robert E. Kass

A unifying Bayesian account of contextual effects in value-based choice

Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan

Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling

Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda

The evolutionary origins of Lévy walk foraging

Marina E. Wosniack, Marcos C. Santos, Ernesto P. Raposo, Gandhi M. Viswanathan, Marcos G. E. da Luz

Identifying parameter regions for multistationarity

Carsten Conradi, Elisenda Feliu, Maya Mincheva, Carsten Wiuf

Signatures of criticality arise from random subsampling in simple population models

Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge, Jakob H. Macke

A single-cell spiking model for the origin of grid-cell patterns

Tiziano D’Albis, Richard Kempter

A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system

Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

Estimating time of HIV-1 infection from next-generation sequence diversity

Vadim Puller, Richard Neher, Jan Albert

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models

Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün, Moritz Helias

Learning causal networks with latent variables from multivariate information in genomic data

Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh, Hervé Isambert