PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006885

Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools

Ana Julia Velez Rueda, Guillermo I. Benítez, Julia Marchetti, Marcia Anahí Hasenahuer, María Silvina Fornasari, Nicolas Palopoli, Gustavo Parisi

PLOS Computational Biology: published February 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006473

Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited

Dave Osthus, Ashlynn R. Daughton, Reid Priedhorsky

PLOS Computational Biology: published February 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006599

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RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt

PLOS Computational Biology: published February 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006759

Mapping DNA sequence to transcription factor binding energy in vivo

Stephanie L. Barnes, Nathan M. Belliveau, William T. Ireland, Justin B. Kinney, Rob Phillips

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006226

Noise-resistant developmental reproducibility in vertebrate somite formation

Honda Naoki, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii, Yasumasa Bessho, Takaaki Matsui

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006579

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks

Ahmed A. Metwally, Philip S. Yu, Derek Reiman, Yang Dai, Patricia W. Finn, David L. Perkins

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006693

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006718

Social evolution under demographic stochasticity

David V. McLeod, Troy Day

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006739

Characteristics of measles epidemics in China (1951-2004) and implications for elimination: A case study of three key locations

Wan Yang, Juan Li, Jeffrey Shaman

PLOS Computational Biology: published February 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006806

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

Robert Marsland III, Wenping Cui, Joshua Goldford, Alvaro Sanchez, Kirill Korolev, Pankaj Mehta

PLOS Computational Biology: published February 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006793

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction

Amin Allahyar, Joske Ubels, Jeroen de Ridder

PLOS Computational Biology: published February 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006657

Apollo: Democratizing genome annotation

Nathan A. Dunn, Deepak R. Unni, Colin Diesh, Monica Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis

PLOS Computational Biology: published February 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006790

Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors

Lior Tiroshi, Joshua A. Goldberg

PLOS Computational Biology: published February 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006782

A local measure of symmetry and orientation for individual spikes of grid cells

Simon N. Weber, Henning Sprekeler

PLOS Computational Biology: published February 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006804

Information integration in large brain networks

Daniel Toker, Friedrich T. Sommer

PLOS Computational Biology: published February 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006807

BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte

PLOS Computational Biology: published February 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006791

How good are pathogenicity predictors in detecting benign variants?

Abhishek Niroula, Mauno Vihinen

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006481

Network-guided prediction of aromatase inhibitor response in breast cancer

Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006730

A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex

Qingtian Zhang, Xiaolin Hu, Bo Hong, Bo Zhang

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006766

Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components

Nicholas Rogers, John Hermiz, Mehran Ganji, Erik Kaestner, Kıvılcım Kılıç, Lorraine Hossain, Martin Thunemann, Daniel R. Cleary, Bob S. Carter, David Barba, Anna Devor, Eric Halgren, Shadi A. Dayeh, Vikash Gilja

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006769

Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos

Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui, Philippe Andrey

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006771

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15

Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds

PLOS Computational Biology: published February 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006785

Maps of variability in cell lineage trees

Damien G. Hicks, Terence P. Speed, Mohammed Yassin, Sarah M. Russell

PLOS Computational Biology: published February 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006745

Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes

Yangchun Frank Chen, Yu Xia

PLOS Computational Biology: published February 13, 2019 | https://doi.org/10.1371/journal.pcbi.1006762

Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling

Nitzan Shahar, Tobias U. Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, NSPN consortium, Raymond J. Dolan

PLOS Computational Biology: published February 13, 2019 | https://doi.org/10.1371/journal.pcbi.1006803

Identifying the mechanism for superdiffusivity in mouse fibroblast motility

Giuseppe Passucci, Megan E. Brasch, James H. Henderson, Vasily Zaburdaev, M. Lisa Manning

PLOS Computational Biology: published February 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006732

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma

PLOS Computational Biology: published February 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006792

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher

PLOS Computational Biology: published February 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006493

Efficient neural decoding of self-location with a deep recurrent network

Ardi Tampuu, Tambet Matiisen, H. Freyja Ólafsdóttir, Caswell Barry, Raul Vicente

PLOS Computational Biology: published February 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006822

Identifying individual risk rare variants using protein structure guided local tests (POINT)

Rachel Marceau West, Wenbin Lu, Daniel M. Rotroff, Melaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches, Jung-Ying Tzeng

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006722

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad, Geir K. Sandve

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006731

A numerical approach for a discrete Markov model for progressing drug resistance of cancer

Masayuki Maeda, Hideaki Yamashita

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006770

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006772

Multi-modality in gene regulatory networks with slow promoter kinetics

M. Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006784

A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks

Koichiro Uriu, Hajime Tei

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006787

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006801

Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions

Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora, Udo Reichl

PLOS Computational Biology: published February 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006819

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas

David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée

PLOS Computational Biology: published February 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006826

Independent working memory resources for egocentric and allocentric spatial information

David Aagten-Murphy, Paul M. Bays

PLOS Computational Biology: published February 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006563

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models

Tyler Funnell, Allen W. Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah

PLOS Computational Biology: published February 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006799

Structure and variability of delay activity in premotor cortex

Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I. Ryu, Krishna V. Shenoy

PLOS Computational Biology: published February 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006808

A computational model of epithelial solute and water transport along a human nephron

Anita T. Layton, Harold E. Layton

PLOS Computational Biology: published February 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006108

Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits

Tuan Pham, Julie S. Haas

PLOS Computational Biology: published February 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006440

Controlling seizure propagation in large-scale brain networks

Simona Olmi, Spase Petkoski, Maxime Guye, Fabrice Bartolomei, Viktor Jirsa

PLOS Computational Biology: published February 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006805

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses

Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, Gail L. Rosen

PLOS Computational Biology: published February 26, 2019 | https://doi.org/10.1371/journal.pcbi.1006721

Phylogenies from dynamic networks

Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn

PLOS Computational Biology: published February 26, 2019 | https://doi.org/10.1371/journal.pcbi.1006761

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis

Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006678

Development and validation of influenza forecasting for 64 temperate and tropical countries

Sarah C. Kramer, Jeffrey Shaman

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006742

Maximum entropy and population heterogeneity in continuous cell cultures

Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006823

Script of Scripts: A pragmatic workflow system for daily computational research

Gao Wang, Bo Peng

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006843

Learning the payoffs and costs of actions

Moritz Möller, Rafal Bogacz

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006285

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans Victor Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006733

Predictability in process-based ensemble forecast of influenza

Sen Pei, Mark A. Cane, Jeffrey Shaman

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006783

Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana

Shayne M. Plourde, Prativa Amom, Michelle Tan, Adriana T. Dawes, Anna A. Dobritsa

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006800

Modeling and MEG evidence of early consonance processing in auditory cortex

Alejandro Tabas, Martin Andermann, Valeria Schuberth, Helmut Riedel, Emili Balaguer-Ballester, André Rupp

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006820

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1. Correction: Modeling and MEG evidence of early consonance processing in auditory cortex

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

Moritz Hoffmann, Christoph Fröhner, Frank Noé

PLOS Computational Biology: published February 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006830

Correction: Epistasis in genomic and survival data of cancer patients

Dariusz Matlak, Ewa Szczurek

PLOS Computational Biology: published February 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006887

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