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Table of Contents

January 2019

In influenza virus infected cells, eight viral genomic RNPs are assembled into progeny virions, which predominantly contain one copy of each. Using sets of fluorescence microscope images of four vRNPs, the likelihood that the subcellular distribution of one vRNP can be predicted from the distribution of another was estimated for all pairs of vRNPs with significant relationships. The thick base of the bands indicates the vRNP whose location can be used to predict the location of the vRNP indicated by the thin base. These pairwise and higher order relationships were used to infer the assembly network for all eight vRNPs.

Image Credit: Timothy D. Majarian, Robert F. Murphy and Seema S. Lakdawala. © 2018, Carnegie Mellon University

Editorials

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist

Ten Simple Rules for avoiding and resolving conflicts with your colleagues

Fran Lewitter, Philip E. Bourne, Teresa K. Attwood

Ten simple rules for writing statistical book reviews

Christopher J. Lortie

Education

Designing and running an advanced Bioinformatics and genome analyses course in Tunisia

Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia

Research Articles

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens

Joel Ostblom, Emanuel J. P. Nazareth, Mukul Tewary, Peter W. Zandstra

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

Song-Yao Zhang, Shao-Wu Zhang, Xiao-Nan Fan, Jia Meng, Yidong Chen, Shou-Jiang Gao, Yufei Huang

Short-term synaptic depression can increase the rate of information transfer at a release site

Mehrdad Salmasi, Alex Loebel, Stefan Glasauer, Martin Stemmler

Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model

Anna C. Sales, Karl J. Friston, Matthew W. Jones, Anthony E. Pickering, Rosalyn J. Moran

A computational model to understand mouse iron physiology and disease

Jignesh H. Parmar, Pedro Mendes

Sour grapes and sweet victories: How actions shape preferences

Fabien Vinckier, Lionel Rigoux, Irma T. Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione

Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia

Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko, Rosemary Braun, Seth J. Corey, Marek Kimmel

Protein—protein binding supersites

Raji Viswanathan, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, Andras Fiser

Calcium phosphate precipitation inhibits mitochondrial energy metabolism

Sathyavani Malyala, Yizhu Zhang, Jasiel O. Strubbe, Jason N. Bazil

Using the drug-protein interactome to identify anti-ageing compounds for humans

Matías Fuentealba, Handan Melike Dönertaş, Rhianna Williams, Johnathan Labbadia, Janet M. Thornton, Linda Partridge

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson

Computational translation of genomic responses from experimental model systems to humans

Douglas K. Brubaker, Elizabeth A. Proctor, Kevin M. Haigis, Douglas A. Lauffenburger

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer

Deena M. A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Ping-Jiang Cao, Lincoln D. Stein, Julie M. Wilson, John M. S. Bartlett, Ming-Sound Tsao, Neesha Dhani, David Hedley, Steven Gallinger, Benjamin Haibe-Kains

Deep image reconstruction from human brain activity

Guohua Shen, Tomoyasu Horikawa, Kei Majima, Yukiyasu Kamitani

PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data

Yu-Han H. Hsu, Claire Churchhouse, Tune H. Pers, Josep M. Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K. Morgen, Clicerio Gonzalez, Maria E. Gonzalez, Tonu Esko, Joel N. Hirschhorn

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta

Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection

Ada W. C. Yan, Sophie G. Zaloumis, Julie A. Simpson, James M. McCaw

STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds

Abdul-Saboor Sheikh, Nicol S. Harper, Jakob Drefs, Yosef Singer, Zhenwen Dai, Richard E. Turner, Jörg Lücke

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

Keesha E. Erickson, Oleksii S. Rukhlenko, Md Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek

Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila

Alejandra González, Shadi Jafari, Alberto Zenere, Mattias Alenius, Claudio Altafini

OpenCASA: A new open-source and scalable tool for sperm quality analysis

Carlos Alquézar-Baeta, Silvia Gimeno-Martos, Sara Miguel-Jiménez, Pilar Santolaria, Jesús Yániz, Inmaculada Palacín, Adriana Casao, José Álvaro Cebrián-Pérez, Teresa Muiño-Blanco, Rosaura Pérez-Pé

Differential mobility and local variation in infection attack rate

David J. Haw, Derek A. T. Cummings, Justin Lessler, Henrik Salje, Jonathan M. Read, Steven Riley

Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction

Wayne Adams, James N. Graham, Xuchen Han, Hermann Riecke

Generalizing clusters of similar species as a signature of coexistence under competition

Rafael D’Andrea, Maria Riolo, Annette M. Ostling

A Gestalt inference model for auditory scene segregation

Debmalya Chakrabarty, Mounya Elhilali

Epithelial stratification shapes infection dynamics

Carmen Lía Murall, Robert Jackson, Ingeborg Zehbe, Nathalie Boulle, Michel Segondy, Samuel Alizon

Multi-study inference of regulatory networks for more accurate models of gene regulation

Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau

Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli

David Hodgson, Andrew D. Rowan, Francesco Falciani, Carole J. Proctor

Cellular determinants of metabolite concentration ranges

Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis

Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W. Pasternak, Marta Filizola

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism

Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas

Spatial synchronization codes from coupled rate-phase neurons

Joseph D. Monaco, Rose M. De Guzman, Hugh T. Blair, Kechen Zhang

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures

Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson

Social dynamics modeling of chrono-nutrition

Alessandro Di Stefano, Marialisa Scatà, Supreeta Vijayakumar, Claudio Angione, Aurelio La Corte, Pietro Liò

Prediction of ultra-high-order antibiotic combinations based on pairwise interactions

Itay Katzir, Murat Cokol, Bree B. Aldridge, Uri Alon

Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator

Laurent Mombaerts, Alberto Carignano, Fiona C. Robertson, Timothy J. Hearn, Jin Junyang, David Hayden, Zoe Rutterford, Carlos T. Hotta, Katherine E. Hubbard, Marti Ruiz C. Maria, Ye Yuan, Matthew A. Hannah, Jorge Goncalves, Alex A. R. Webb

Predicting change: Approximate inference under explicit representation of temporal structure in changing environments

Dimitrije Marković, Andrea M. F. Reiter, Stefan J. Kiebel