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

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005561

2017 Outstanding Contributions to ISCB Award: Fran Lewitter

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005560

2017 ISCB Overton Prize awarded to Christoph Bock

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005559

2017 ISCB Innovator Award: Aviv Regev

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005558

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

PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005419

Good enough practices in scientific computing

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005510

A comprehensive overview and evaluation of circular RNA detection tools

Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou

PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005420

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A review of active learning approaches to experimental design for uncovering biological networks

Yuriy Sverchkov, Mark Craven

PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005466

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005585

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

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

PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005569

Landscape and variation of novel retroduplications in 26 human populations

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

PLOS Computational Biology: published June 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005567

Detecting similar binding pockets to enable systems polypharmacology

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

PLOS Computational Biology: published June 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005522

Optimal structure of metaplasticity for adaptive learning

Peyman Khorsand, Alireza Soltani

PLOS Computational Biology: published June 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005630

MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory

Aliza B. Rubenstein, Manasi A. Pethe, Sagar D. Khare

PLOS Computational Biology: published June 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005614

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

Marine Le Morvan, Andrei Zinovyev, Jean-Philippe Vert

PLOS Computational Biology: published June 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005573

Linking structure and activity in nonlinear spiking networks

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

PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005583

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

PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005545

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

PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005487

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005628

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005612

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005608

Transmembrane helical interactions in the CFTR channel pore

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005594

Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities

HaDi MaBouDi, Hideaki Shimazaki, Martin Giurfa, Lars Chittka

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005551

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005550

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

PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005361

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

PLOS Computational Biology: published June 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005597

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle

David L. Gibbs, Ilya Shmulevich

PLOS Computational Biology: published June 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005591

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A knowledge-based T²-statistic to perform pathway analysis for quantitative proteomic data

En-Yu Lai, Yi-Hau Chen, Kun-Pin Wu

PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005601

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

PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005587

Sensory noise predicts divisive reshaping of receptive fields

Matthew Chalk, Paul Masset, Sophie Deneve, Boris Gutkin

PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005582

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

PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005603

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

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

PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005586

Inferring repeat-protein energetics from evolutionary information

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

PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005584

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

PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005578

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain

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

PLOS Computational Biology: published June 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005602

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

PLOS Computational Biology: published June 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005593

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

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

PLOS Computational Biology: published June 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005600

Locking of correlated neural activity to ongoing oscillations

Tobias Kühn, Moritz Helias

PLOS Computational Biology: published June 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005534

Ribosome reinitiation can explain length-dependent translation of messenger RNA

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

PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005592

Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study

Sonia Cortassa, Steven J. Sollott, Miguel A. Aon

PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005588

Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data

Andreas Kuehne, Urs Mayr, Daniel C. Sévin, Manfred Claassen, Nicola Zamboni

PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005577

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

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

PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005595

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

PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005589

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

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Temperature–amplitude coupling for stable biological rhythms at different temperatures

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PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005501

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

PLOS Computational Biology: published June 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005576

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

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PLOS Computational Biology: published June 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005526

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

PLOS Computational Biology: published June 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005556

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

Caroline Baroukh, Violette Turon, Olivier Bernard

PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005590

Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation

Jae Kyoung Kim, Eduardo D. Sontag

PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005571

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

PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005565

A motor unit-based model of muscle fatigue

Jim R. Potvin, Andrew J. Fuglevand

PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005581

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

PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005575

Network-assisted target identification for haploinsufficiency and homozygous profiling screens

Sheng Wang, Jian Peng

PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005553

A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements

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PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005542

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

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PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005521

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

PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005511