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Table of Contents: June 2017

Repeat-proteins fold cooperatively into elongated arrays of similar structural elements. The image represents the structure of the I-kappa-B-alpha protein as modeled from x-ray crystallography (bottom) and as a biological object (top). Physical folding energetics is fundamentally linked to protein evolution. Espada et al.

Image Credit: May-K (@proteinart)

Messages from ISCB

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner

Christiana N. Fogg, Diane E. Kovats, Bonnie Berger

2017 Outstanding Contributions to ISCB Award: Fran Lewitter

Christiana N. Fogg, Diane E. Kovats, Bonnie Berger

2017 ISCB Overton Prize awarded to Christoph Bock

Christiana N. Fogg, Diane E. Kovats, Bonnie Berger

2017 ISCB Innovator Award: Aviv Regev

Christiana N. Fogg, Diane E. Kovats, Bonnie Berger

Education

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

C. Victor Jongeneel, Ovokeraye Achinike-Oduaran, Ezekiel Adebiyi, Marion Adebiyi, Seun Adeyemi, Bola Akanle, Shaun Aron, Efejiro Ashano, Hocine Bendou, Gerrit Botha, Emile Chimusa, Ananyo Choudhury, Ravikiran Donthu, Jenny Drnevich, Oluwadamila Falola, Christopher J. Fields, Scott Hazelhurst, Liesl Hendry, Itunuoluwa Isewon, Radhika S. Khetani, Judit Kumuthini, Magambo Phillip Kimuda, Lerato Magosi, Liudmila Sergeevna Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Danny Mugutso, Phelelani Mpangase, Richard Munthali, Victoria Nembaware, Andrew Ndhlovu, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Sumir Panji, Venesa Pillay, Gloria Rendon, Dhriti Sengupta, Nicola Mulder

Perspective

Good enough practices in scientific computing

Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K. Teal

Reviews

A comprehensive overview and evaluation of circular RNA detection tools

Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou

Research Articles

Independent regulation of gene expression level and noise by histone modifications

Shaohuan Wu, Ke Li, Yingshu Li, Tong Zhao, Ting Li, Yu-Fei Yang, Wenfeng Qian

Active Vertex Model for cell-resolution description of epithelial tissue mechanics

Daniel L. Barton, Silke Henkes, Cornelis J. Weijer, Rastko Sknepnek

Landscape and variation of novel retroduplications in 26 human populations

Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein

Detecting similar binding pockets to enable systems polypharmacology

Miquel Duran-Frigola, Lydia Siragusa, Eytan Ruppin, Xavier Barril, Gabriele Cruciani, Patrick Aloy

Optimal structure of metaplasticity for adaptive learning

Peyman Khorsand, Alireza Soltani

Linking structure and activity in nonlinear spiking networks

Gabriel Koch Ocker, Krešimir Josić, Eric Shea-Brown, Michael A. Buice

Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation

Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer

Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression

Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin, Gabriella Juhasz

High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE

Stefano Castellana, Caterina Fusilli, Gianluigi Mazzoccoli, Tommaso Biagini, Daniele Capocefalo, Massimo Carella, Angelo Luigi Vescovi, Tommaso Mazza

A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images

Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre, Marc Germain

LASSIM—A network inference toolbox for genome-wide mechanistic modeling

Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R. Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E. M. Nordling, Elin Nyman, Sylvie Schulze, Colm E. Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson

Transmembrane helical interactions in the CFTR channel pore

Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan

Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease

Maxwell B. Wang, Julia P. Owen, Pratik Mukherjee, Ashish Raj

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome

Jens Christian Claussen, Jurgita Skiecevičienė, Jun Wang, Philipp Rausch, Tom H. Karlsen, Wolfgang Lieb, John F. Baines, Andre Franke, Marc-Thorsten Hütt

An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules

Noga Mosheiff, Haggai Agmon, Avraham Moriel, Yoram Burak

In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis

Michael A. Colman, Haibo Ni, Bo Liang, Nicole Schmitt, Henggui Zhang

Sensory noise predicts divisive reshaping of receptive fields

Matthew Chalk, Paul Masset, Sophie Deneve, Boris Gutkin

Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE

Meng Ke, Yafei Yuan, Xin Jiang, Nieng Yan, Haipeng Gong

GINOM: A statistical framework for assessing interval overlap of multiple genomic features

Darshan Bryner, Stephen Criscione, Andrew Leith, Quyen Huynh, Fred Huffer, Nicola Neretti

Inferring repeat-protein energetics from evolutionary information

Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro

Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice

Samira Abbasi, Amber E. Hudson, Selva K. Maran, Ying Cao, Ataollah Abbasi, Detlef H. Heck, Dieter Jaeger

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain

Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller

Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria

Dominic G. Whittaker, Haibo Ni, Aziza El Harchi, Jules C. Hancox, Henggui Zhang

Rosetta:MSF: a modular framework for multi-state computational protein design

Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner, Rainer Merkl

Locking of correlated neural activity to ongoing oscillations

Tobias Kühn, Moritz Helias

Ribosome reinitiation can explain length-dependent translation of messenger RNA

David W. Rogers, Marvin A. Böttcher, Arne Traulsen, Duncan Greig

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt

Leveraging functional annotations in genetic risk prediction for human complex diseases

Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu, Hongyu Zhao

Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders

Raony G. C. C. L. Cardenas, Natália D. Linhares, Raquel L. Ferreira, Sérgio D. J. Pena

Temperature–amplitude coupling for stable biological rhythms at different temperatures

Gen Kurosawa, Atsuko Fujioka, Satoshi Koinuma, Atsushi Mochizuki, Yasufumi Shigeyoshi

Mechanisms underlying a thalamocortical transformation during active tactile sensation

Diego Adrian Gutnisky, Jianing Yu, Samuel Andrew Hires, Minh-Son To, Michael Ross Bale, Karel Svoboda, David Golomb

An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

Sebastián A. Romano, Verónica Pérez-Schuster, Adrien Jouary, Jonathan Boulanger-Weill, Alessia Candeo, Thomas Pietri, Germán Sumbre

Fast and general tests of genetic interaction for genome-wide association studies

Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad

Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes

Caroline Baroukh, Violette Turon, Olivier Bernard

Mechanisms of generation of membrane potential resonance in a neuron with multiple resonant ionic currents

David M. Fox, Hua-an Tseng, Tomasz G. Smolinski, Horacio G. Rotstein, Farzan Nadim

A motor unit-based model of muscle fatigue

Jim R. Potvin, Andrew J. Fuglevand

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlić, Peter W. Rose

Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions

Nargesalsadat Dorratoltaj, Achla Marathe, Bryan L. Lewis, Samarth Swarup, Stephen G. Eubank, Kaja M. Abbas

Breakdown of local information processing may underlie isoflurane anesthesia effects

Patricia Wollstadt, Kristin K. Sellers, Lucas Rudelt, Viola Priesemann, Axel Hutt, Flavio Fröhlich, Michael Wibral