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PLoS Computational Biology, Volume 15
Volume 15, Number 1, January 2019
- Arne Elofsson
, Berk Hess
, Erik Lindahl
, Alexey Onufriev
, David van der Spoel
, Anders Wallqvist
:
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Fran Lewitter
, Philip E. Bourne, Teresa K. Attwood:
Ten Simple Rules for avoiding and resolving conflicts with your colleagues. - Christopher J. Lortie
:
Ten simple rules for writing statistical book reviews.
- Fatma Z. Guerfali
, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia
:
Designing and running an advanced Bioinformatics and genome analyses course in Tunisia.
- Joel Ostblom
, Emanuel J. P. Nazareth, Mukul Tewary
, Peter W. Zandstra:
Context-explorer: Analysis of spatially organized protein expression in high-throughput screens. - Song-Yao Zhang
, Shaowu Zhang
, Xiaonan Fan, Jia Meng
, Yidong Chen, Shou-Jiang Gao
, Yufei Huang
:
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Mehrdad Salmasi
, Alex Loebel, Stefan Glasauer
, Martin Stemmler
:
Short-term synaptic depression can increase the rate of information transfer at a release site. - Anna C. Sales
, Karl J. Friston
, Matthew W. Jones
, Anthony E. Pickering
, Rosalyn J. Moran
:
Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model. - Jignesh H. Parmar, Pedro Mendes
:
A computational model to understand mouse iron physiology and disease. - Fabien Vinckier
, Lionel Rigoux
, Irma T. Kurniawan, Chen Hu
, Sacha Bourgeois-Gironde
, Jean Daunizeau, Mathias Pessiglione:
Sour grapes and sweet victories: How actions shape preferences. - Tomasz Wojdyla, Hrishikesh Mehta
, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko, Rosemary Braun
, Seth J. Corey, Marek Kimmel:
Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. - Raji Viswanathan, J. Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, András Fiser
:
Protein - protein binding supersites. - Sathyavani Malyala
, Yizhu Zhang, Jasiel O. Strubbe
, Jason N. Bazil
:
Calcium phosphate precipitation inhibits mitochondrial energy metabolism. - Matías Fuentealba
, Handan Melike Dönertas
, Rhianna Williams, Johnathan Labbadia
, Janet M. Thornton
, Linda Partridge
:
Using the drug-protein interactome to identify anti-ageing compounds for humans. - Yara Seif, Jonathan M. Monk
, Nathan Mih
, Hannah Tsunemoto
, Saugat Poudel
, Cristal Zuñiga
, Jared Broddrick
, Karsten Zengler, Bernhard O. Palsson
:
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. - Douglas K. Brubaker
, Elizabeth A. Proctor
, Kevin M. Haigis, Douglas A. Lauffenburger
:
Computational translation of genomic responses from experimental model systems to humans. - 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
:
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. - Guohua Shen
, Tomoyasu Horikawa
, Kei Majima
, Yukiyasu Kamitani
:
Deep image reconstruction from human brain activity. - Yuan-Hao Hsu
, Claire Churchhouse, Tune H. Pers
, Josep M. Mercader
, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K. Morgen, Clicerio Gonzalez
, Maria E. Gonzalez
, Tõnu Esko, Joel Hirschhorn
:
PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data. - Zachary R. Fox
, Brian Munsky
:
The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments. - Dheeraj Dube, Navjeet Ahalawat
, Himanshu Khandelia
, Jagannath Mondal
, Surajit Sengupta
:
On identifying collective displacements in apo-proteins that reveal eventual binding pathways. - Ada W. C. Yan
, Sophie G. Zaloumis
, Julie A. Simpson
, James M. McCaw
:
Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection. - Abdul-Saboor Sheikh, Nicol S. Harper
, Jakob Drefs, Yosef Singer
, Zhenwen Dai, Richard E. Turner, Jörg Lücke
:
STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds. - 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
:
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. - Alejandra Gonzalez, Shadi Jafari
, Alberto Zenere, Mattias Alenius, Claudio Altafini
:
Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila. - Carlos Alquezar-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
:
OpenCASA: A new open-source and scalable tool for sperm quality analysis. - David J. Haw
, Derek A. T. Cummings
, Justin Lessler
, Henrik Salje
, Jonathan M. Read
, Steven Riley
:
Differential mobility and local variation in infection attack rate. - Wayne Adams, James N. Graham, Xuchen Han, Hermann Riecke:
Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction. - Rafael D'Andrea
, Maria A. Riolo, Annette Ostling
:
Generalizing clusters of similar species as a signature of coexistence under competition. - Debmalya Chakrabarty, Mounya Elhilali
:
A Gestalt inference model for auditory scene segregation. - Carmen Lía Murall
, Robert Jackson
, Ingeborg Zehbe, Nathalie Boulle, Michel Segondy
, Samuel Alizon
:
Epithelial stratification shapes infection dynamics. - Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau
:
Multi-study inference of regulatory networks for more accurate models of gene regulation. - David Hodgson
, Andrew D. Rowan, Francesco Falciani, Carole J. Proctor
:
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. - Anika Küken
, Jeanne M. O. Eloundou-Mbebi
, Georg Basler, Zoran Nikoloski
:
Cellular determinants of metabolite concentration ranges. - Xiaohu Hu, Yibo Wang
, Amanda Hunkele
, Davide Provasi, Gavril W. Pasternak, Marta Filizola
:
Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. - Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas
:
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. - Joseph D. Monaco
, Rose M. De Guzman
, Hugh T. Blair, Kechen Zhang:
Spatial synchronization codes from coupled rate-phase neurons. - Timothy Majarian, Robert F. Murphy
, Seema S. Lakdawala
:
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. - Margot C. Bjoring
, C. Daniel Meliza
:
A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex. - Jordan J. Clark
, Mark L. Benson
, Richard D. Smith
, Heather A. Carlson
:
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. - Alessandro Di Stefano
, Marialisa Scatà
, Supreeta Vijayakumar
, Claudio Angione
, Aurelio La Corte
, Pietro Liò
:
Social dynamics modeling of chrono-nutrition. - Sulav Duwal
, Laura Dickinson
, Saye Khoo
, Max von Kleist
:
Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis. - Itay Katzir
, Murat Cokol, Bree B. Aldridge
, Uri Alon
:
Prediction of ultra-high-order antibiotic combinations based on pairwise interactions. - Laurent Mombaerts
, Alberto Carignano, Fiona C. Robertson, Timothy J. Hearn, Jin Junyang, David P. Hayden, Zoe Rutterford, Carlos T. Hotta
, Katherine E. Hubbard, Marti Ruiz C. Maria, Ye Yuan, Matthew A. Hannah
, Jorge M. Gonçalves
, Alex Webb:
Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. - Dimitrije Markovic
, Andrea M. F. Reiter, Stefan J. Kiebel
:
Predicting change: Approximate inference under explicit representation of temporal structure in changing environments.
- Correction: clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.
- Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects.
Volume 15, Number 2, February 2019
- PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You.
- Ana Julia Velez Rueda
, Guillermo I. Benítez, Julia Marchetti
, Marcia Anahi Hasenahuer
, María Silvina Fornasari
, Nicolas Palopoli
, Gustavo D. Parisi
:
Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.
- Dave Osthus
, Ashlynn R. Daughton
, Reid Priedhorsky
:
Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited. - Sabine Koch
, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger
, Stefan Wendschuh, Dirk Benndorf
, Udo Reichl, Steffen Klamt
:
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. - Stephanie L. Barnes
, Nathan M. Belliveau
, William T. Ireland, Justin B. Kinney
, Rob Phillips
:
Mapping DNA sequence to transcription factor binding energy in vivo. - Honda Naoki
, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii
, Yasumasa Bessho, Takaaki Matsui:
Noise-resistant developmental reproducibility in vertebrate somite formation. - Ahmed A. Metwally
, Philip S. Yu
, Derek Reiman
, Yang Dai, Patricia W. Finn, David L. Perkins
:
Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks. - Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine
, Hsiao-Chun Wu, Michal Brylinski
:
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. - David V. McLeod
, Troy Day:
Social evolution under demographic stochasticity. - Wan Yang
, Juan Li, Jeffrey Shaman
:
Characteristics of measles epidemics in China (1951-2004) and implications for elimination: A case study of three key locations. - Robert Marsland III
, Cui Wenping
, Joshua Goldford
, Alvaro Sanchez
, Kirill S. Korolev, Pankaj Mehta:
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities. - Amin Allahyar
, Joske Ubels
, Jeroen de Ridder
:
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. - Nathan A. Dunn
, Deepak R. Unni
, Colin M. Diesh, Monica C. Munoz-Torres
, Nomi L. Harris
, Eric Yao
, Helena Rasche
, Ian H. Holmes
, Christine G. Elsik
, Suzanna E. Lewis:
Apollo: Democratizing genome annotation. - Lior Tiroshi
, Joshua A. Goldberg
:
Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors. - Simon N. Weber
, Henning Sprekeler
:
A local measure of symmetry and orientation for individual spikes of grid cells. - Daniel Toker
, Friedrich T. Sommer:
Information integration in large brain networks. - Aleix Lafita
, Spencer Bliven
, Andreas Prlic, Dmytro Guzenko, Peter W. Rose
, Anthony R. Bradley
, Paolo Pavan, Douglas Myers-Turnbull
, Yana Valasatava
, Michael L. Heuer
, Matt Larson
, Stephen K. Burley, Jose M. Duarte
:
BioJava 5: A community driven open-source bioinformatics library. - Abhishek Niroula
, Mauno Vihinen
:
How good are pathogenicity predictors in detecting benign variants? - Matthew Ruffalo
, Roby Thomas
, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph
:
Network-guided prediction of aromatase inhibitor response in breast cancer. - Qingtian Zhang, Xiaolin Hu
, Bo Hong, Bo Zhang:
A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex. - Nicholas Rogers
, John Hermiz
, Mehran Ganji, Erik J. Kaestner
, Kivilcim Kiliç
, Lorraine Hossain
, Martin Thunemann
, Daniel R. Cleary, Bob S. Carter, David Barba, Anna Devor
, Eric Halgren
, Shadi A. Dayeh
, Vikash Gilja
:
Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components. - Julien Moukhtar, Alain Trubuil
, Katia Belcram, David Legland
, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui, Philippe Andrey
:
Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos. - Sebastian Funk
, Anton Camacho
, Adam J. Kucharski, Rachel Lowe
, Rosalind M. Eggo
, W. John Edmunds:
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15. - Damien G. Hicks
, Terence P. Speed
, Mohammed Yassin, Sarah M. Russell
:
Maps of variability in cell lineage trees. - Yangchun Frank Chen
, Yu Xia
:
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. - Nitzan Shahar
, Tobias U. Hauser
, Michael Moutoussis
, Rani Moran
, Mehdi Keramati, Raymond J. Dolan
:
Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling. - Giuseppe Passucci
, Megan E. Brasch
, James H. Henderson
, Vasily Zaburdaev
, M. Lisa Manning
:
Identifying the mechanism for superdiffusivity in mouse fibroblast motility. - Brandon Monier, Adam McDermaid, Cankun Wang
, Jing Zhao, Allison J. Miller
, Anne Fennell
, Qin Ma
:
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. - Nico M. Franz
, Lukas J. Musher
, Joseph W. Brown
, Shizhuo Yu, Bertram Ludäscher:
Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. - Ardi Tampuu, Tambet Matiisen, H. Freyja Ólafsdóttir, Caswell Barry
, Raul Vicente
:
Efficient neural decoding of self-location with a deep recurrent network. - Rachel Marceau West, Wenbin Lu, Daniel M. Rotroff
, Mélaine A. Kuenemann
, Sheng-Mao Chang
, Michael C. Wu
, Michael J. Wagner, John B. Buse
, Alison A. Motsinger-Reif
, Denis Fourches, Jung-Ying Tzeng
:
Identifying individual risk rare variants using protein structure guided local tests (POINT). - Ivar Grytten
, Knut D. Rand, Alexander Johan Nederbragt
, Geir Storvik
, Ingrid Kristine Glad, Geir Kjetil Sandve:
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. - Masayuki Maeda
, Hideaki Yamashita:
A numerical approach for a discrete Markov model for progressing drug resistance of cancer. - He Peng
, Xiangxiang Zeng
, Yadi Zhou
, Defu Zhang, Ruth Nussinov
, Feixiong Cheng
:
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. - Muhammad Ali Al-Radhawi
, Domitilla Del Vecchio, Eduardo D. Sontag
:
Multi-modality in gene regulatory networks with slow promoter kinetics. - Koichiro Uriu
, Hajime Tei
:
A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks. - Hongyu Zhou, Zheng Dong
, Gennady Verkhivker
, Brian D. Zoltowski
, Peng Tao
:
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. - Daniel Rüdiger
, Sascha Young Kupke
, Tanja Laske
, Pawel Zmora
, Udo Reichl:
Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions. - David G. P. van IJzendoorn
, Karoly Szuhai
, Inge H. Briaire-de Bruijn
, Marie Kostine, Marieke L. Kuijjer
, Judith V. M. G. Bovée
:
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. - David Aagten-Murphy
, Paul M. Bays
:
Independent working memory resources for egocentric and allocentric spatial information. - Tyler Funnell
, Allen W. Zhang
, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah:
Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. - Nir Even-Chen
, Blue Sheffer
, Saurabh Vyas, Stephen I. Ryu
, Krishna V. Shenoy:
Structure and variability of delay activity in premotor cortex. - Anita T. Layton
, Harold E. Layton:
A computational model of epithelial solute and water transport along a human nephron. - Tuan Pham
, Julie S. Haas
:
Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits. - Simona Olmi
, Spase Petkoski
, Maxime Guye
, Fabrice Bartolomei, Viktor K. Jirsa
:
Controlling seizure propagation in large-scale brain networks. - Stephen Woloszynek
, Zhengqiao Zhao
, Jian Chen
, Gail L. Rosen
:
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses. - Cornelia Metzig
, Oliver Ratmann
, Daniela Bezemer, Caroline Colijn
:
Phylogenies from dynamic networks. - Marzieh Ayati
, Danica Wiredja, Daniela Schlatzer, Sean Maxwell
, Ming Li
, Mehmet Koyutürk, Mark R. Chance:
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. - Sarah C. Kramer
, Jeffrey Shaman
:
Development and validation of influenza forecasting for 64 temperate and tropical countries. - Jorge Fernandez-de-Cossío-Diaz
, Roberto Mulet
:
Maximum entropy and population heterogeneity in continuous cell cultures. - Gao Wang
, Bo Peng
:
Script of Scripts: A pragmatic workflow system for daily computational research. - Moritz Möller
, Rafal Bogacz
:
Learning the payoffs and costs of actions. - Chiara Damiani
, Davide Maspero
, Marzia Di Filippo
, Riccardo Colombo
, Dario Pescini
, Alex Graudenzi
, Hans V. Westerhoff
, Lilia Alberghina
, Marco Vanoni, Giancarlo Mauri
:
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Sen Pei
, Mark A. Cane, Jeffrey Shaman
:
Predictability in process-based ensemble forecast of influenza. - Shayne M. Plourde
, Prativa Amom, Michelle Tan, Adriana T. Dawes
, Anna A. Dobritsa
:
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. - Alejandro Tabas
, Martin Andermann, Valeria Schuberth, Helmut Riedel
, Emili Balaguer-Ballester
, André Rupp
:
Modeling and MEG evidence of early consonance processing in auditory cortex. - Moritz Hoffmann
, Christoph Fröhner
, Frank Noé
:
ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.
- Dariusz Matlak, Ewa Szczurek:
Correction: Epistasis in genomic and survival data of cancer patients.
Volume 15, Number 3, March 2019
- Tomasz Miksa
, Stephanie Renee Simms
, Daniel Mietchen
, Sarah Jones:
Ten principles for machine-actionable data management plans.
- Chad M. Glen, Melissa L. Kemp
, Eberhard O. Voit
:
Agent-based modeling of morphogenetic systems: Advantages and challenges. - Ruth Nussinov
, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
:
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
- Colton J. Lloyd
, Zachary A. King
, Troy E. Sandberg, Ying Hefner, Connor A. Olson
, Patrick V. Phaneuf
, Edward J. O'Brien, Jon G. Sanders
, Rodolfo A. Salido
, Karenina Sanders
, Caitriona Brennan
, Gregory Humphrey, Rob Knight
, Adam M. Feist
:
The genetic basis for adaptation of model-designed syntrophic co-cultures. - Jingyu Zhang
, Hengyu Chen, Ruoyan Li
, David A. Taft
, Guang Yao, Fan Bai
, Jianhua Xing
:
Spatial clustering and common regulatory elements correlate with coordinated gene expression.