


default search action
PLoS Computational Biology, Volume 17
Volume 17, Number 1, January 2021
- Korryn Bodner
, Chris Brimacombe
, Emily S. Chenery, Ariel Greiner
, Anne M. McLeod, Stephanie R. Penk
, Juan S. Vargas Soto
:
Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students.
- Mehmet Aziz Yirik
, Christoph Steinbeck
:
Chemical graph generators.
- Graham Casey Gibson, Kelly R. Moran
, Nicholas G. Reich
, Dave Osthus:
Improving probabilistic infectious disease forecasting through coherence. - Antonino Casile
, Rose T. Faghih
, Emery N. Brown:
Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains. - Claudio Tomi-Andrino
, Rupert Norman
, Thomas Millat
, Philippe Soucaille
, Klaus Winzer, David A. Barrett, John R. King
, Dong-Hyun Kim
:
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. - Tristan Ursell:
Structured environments foster competitor coexistence by manipulating interspecies interfaces. - Pedro Manuel Martínez García
, Miguel García-Torres
, Federico Divina
, José Terrón-Bautista
, Irene Delgado-Sainz, Francisco Gómez-Vela
, Felipe Cortés-Ledesma
:
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility. - Jonas Béal
, Lorenzo Pantolini, Vincent Noël
, Emmanuel Barillot
, Laurence Calzone
:
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. - Muneki Ikeda
, Hirotaka Matsumoto
, Eduardo J. Izquierdo:
Persistent thermal input controls steering behavior in Caenorhabditis elegans. - James Giammona
, Otger Campàs
:
Physical constraints on early blastomere packings. - Daria Stepanova
, Helen M. Byrne
, Philip K. Maini, Tomás Alarcón:
A multiscale model of complex endothelial cell dynamics in early angiogenesis. - Evanthia Koukouli
, Dennis Wang
, Frank Dondelinger
, Juhyun Park
:
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response. - Sára Sáray
, Christian A. Rössert
, Shailesh Appukuttan
, Rosanna Migliore
, Paola Vitale, Carmen Alina Lupascu, Luca Leonardo Bologna
, Werner Van Geit
, Armando Romani
, Andrew P. Davison
, Eilif Müller, Tamás F. Freund, Szabolcs Káli:
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. - Satyajit D. Rao
, Oleg A. Igoshin
:
Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system. - Hamed Khakzad
, Lotta Happonen
, Yasaman Karami
, Sounak Chowdhury, Gizem Ertürk Bergdahl
, Michael Nilges
, Guy Tran Van Nhieu, Johan Malmström
, Lars Malmström
:
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. - Zachary B. Haiman
, Daniel C. Zielinski
, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
:
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. - Yohsuke Murase
, Seung Ki Baek
:
Friendly-rivalry solution to the iterated n-person public-goods game. - Jonathan Lu
, Bianca Dumitrascu
, Ian C. McDowell
, Brian Jo
, Alejandro Barrera
, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
:
Causal network inference from gene transcriptional time-series response to glucocorticoids. - Jan Rombouts
, Lendert Gelens
:
Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions. - Adil Alsiyabi, Ariadna Gonzalez Solis
, Edgar B. Cahoon
, Rajib Saha
:
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants. - Marco Aqil
, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks
:
Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome. - Vinícius R. Carvalho
, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo Mazoni Andrade Marçal Mendes:
Active probing to highlight approaching transitions to ictal states in coupled neural mass models. - Linda K. Sundermann
, Jeff Wintersinger
, Gunnar Rätsch, Jens Stoye
, Quaid Morris:
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. - Rachael L. Sumner
, Meg J. Spriggs
, Alexander D. Shaw
:
Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex. - David W. Eyre
, Mirjam Laager, A. Sarah Walker, Ben S. Cooper
, Daniel J. Wilson
:
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. - Viacheslav N. Kachalov
, Huyen Nguyen, Suraj Balakrishna, Luisa Salazar-Vizcaya
, Rami Sommerstein
, Stefan P. Kuster
, Anthony Hauser
, Pia Abel zur Wiesch
, Eili Y. Klein
, Roger D. Kouyos
:
Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level. - Bruce Y. Lee, Sarah M. Bartsch
, Marie C. Ferguson
, Patrick T. Wedlock, Kelly J. O'Shea, Sheryl S. Siegmund, Sarah N. Cox, James A. McKinnell:
The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. - N. Suhas Jagannathan
, Christopher W. V. Hogue, Lisa Tucker-Kellogg
:
Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2. - Miri Gordin, Hagit Philip, Alona Zilberberg, Moriah Gidoni, Raanan Margalit, Christopher Clouser
, Kristofor Adams, Francois Vigneault
, Irun R. Cohen, Gur Yaari
, Sol Efroni
:
Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. - Preecha Patumcharoenpol
, Massalin Nakphaichit
, Gianni Panagiotou
, Anchalee Senavonge
, Narissara Suratannon, Wanwipa Vongsangnak:
MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. - Maral Budak, Karl Grosh
, Aritra Sasmal
, Gabriel Corfas, Michal Zochowski
, Victoria Booth
:
Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects. - Oleksandr Sorochynskyi
, Stéphane Deny, Olivier Marre
, Ulisse Ferrari
:
Predicting synchronous firing of large neural populations from sequential recordings. - Marzia Antonella Scelsi
, Valerio Napolioni
, Michael D. Greicius, André Altmann
, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's Disease Sequencing Project:
Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities. - Bor Kavcic
, Gasper Tkacik
, Tobias Bollenbach
:
Minimal biophysical model of combined antibiotic action. - Ronald E. Crump
, Ching-I Huang, Edward S. Knock
, Simon E. F. Spencer, Paul E. Brown
, Erick Mwamba Miaka, Chansy Shampa, Matt J. Keeling
, Kat S. Rock
:
Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo. - Guillaume Lingas, Kyle Rosenke, David Safronetz, Jérémie Guedj:
Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin. - Jun Li, Juliane Manitz, Enrico Bertuzzo
, Eric D. Kolaczyk:
Sensor-based localization of epidemic sources on human mobility networks. - Beatriz Seoane
, Alessandra Carbone
:
The complexity of protein interactions unravelled from structural disorder. - Albertas Janulevicius
, G. Sander van Doorn:
Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance. - Lillian R. Thistlethwaite, Varduhi Petrosyan, Xiqi Li
, Marcus J. Miller, Sarah H. Elsea
, Aleksandar Milosavljevic
:
CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. - Giulio Tesei
, João M. Martins
, Micha B. A. Kunze
, Yong Wang, Ramon Crehuet, Kresten Lindorff-Larsen
:
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. - Rani Moran
, Mehdi Keramati, Raymond J. Dolan
:
Model based planners reflect on their model-free propensities. - Vikki Neville
, Peter Dayan, Iain D. Gilchrist
, Elizabeth S. Paul, Michael Mendl
:
Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach. - Zhongling Jiang
, Bin Zhang
:
On the role of transcription in positioning nucleosomes. - Hungyo Kharerin, Lu Bai:
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. - Antanas Kalkauskas
, Umberto Perron
, Yuxuan Sun
, Nick Goldman
, Guy Baele, Stéphane Guindon, Nicola De Maio
:
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk. - Katharine Best, Dan H. Barouch
, Jérémie Guedj, Ruy M. Ribeiro
, Alan S. Perelson:
Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. - Johannes Friedrich
, Andrea Giovannucci
, Eftychios A. Pnevmatikakis:
Online analysis of microendoscopic 1-photon calcium imaging data streams. - Michael C. Tackenberg, Jacob J. Hughey
:
The risks of using the chi-square periodogram to estimate the period of biological rhythms. - Samuel Schmitz
, Moritz Ertelt, Rainer Merkl
, Jens Meiler
:
Rosetta design with co-evolutionary information retains protein function. - Andreas Tjärnberg
, Omar Mahmood
, Christopher A. Jackson
, Giuseppe-Antonio Saldi
, Kyunghyun Cho, Lionel A. Christiaen
, Richard A. Bonneau
:
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. - Muir Morrison
, Manuel Razo-Mejia
, Rob Phillips:
Reconciling kinetic and thermodynamic models of bacterial transcription. - Aniello Lombardi
, Peter Jedlicka, Heiko J. Luhmann
, Werner Kilb
:
Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons. - Grant Hartung
, Shoale Badr, Mohammad Moeini
, Frédéric Lesage, David Kleinfeld, Ali Alaraj
, Andreas A. Linninger:
Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex. - Charlotte Soneson
, Avi Srivastava
, Rob Patro
, Michael B. Stadler:
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. - Son Hoang Nguyen
, Minh Duc Cao
, Lachlan J. M. Coin
:
Real-time resolution of short-read assembly graph using ONT long reads. - Filipe Tostevin
, Manon Wigbers, Lotte Søgaard-Andersen
, Ulrich Gerland:
Four different mechanisms for switching cell polarity. - Ke Chen
, Amitesh Anand
, Connor A. Olson
, Troy E. Sandberg
, Ye Gao
, Nathan Mih
, Bernhard O. Palsson
:
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. - Bansho Masutani
, Shin-ichi Arimura
, Shinichi Morishita
:
Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing. - Samuel Planton
, Timo van Kerkoerle
, Leïla Abbih, Maxime Maheu
, Florent Meyniel
, Mariano Sigman, Liping Wang, Santiago Figueira, Sergio Romano, Stanislas Dehaene:
A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans. - Yushuf Sharker, Eben Kenah
:
Estimating and interpreting secondary attack risk: Binomial considered biased. - Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar
, Sahar Arbabi Moghadam, Jack A. Tuszynski
, Michael T. Woodside:
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. - Michelangelo Bin, Peter Y. K. Cheung, Emanuele Crisostomi
, Pietro Ferraro
, Hugo Lhachemi
, Roderick Murray-Smith
, Connor Myant
, Thomas Parisini, Robert Shorten
, Sebastian Stein
, Lewi Stone
:
Post-lockdown abatement of COVID-19 by fast periodic switching. - Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang
, Daniel Worstell
, Christopher A. Cassa
, Richard I. Sherwood
, David K. Gifford
:
Machine learning based CRISPR gRNA design for therapeutic exon skipping. - Oren Avram
, Aya Kigel, Anna Vaisman-Mentesh
, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko
, Yariv Wine
:
PASA: Proteomic analysis of serum antibodies web server. - Burcu Tepekule, Anthony Hauser
, Viacheslav N. Kachalov
, Sara Andresen
, Thomas Scheier, Peter W. Schreiber
, Huldrych F. Günthard
, Roger D. Kouyos
:
Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19. - Leonardo Miele
, Silvia De Monte:
Aggregative cycles evolve as a solution to conflicts in social investment. - Matt J. Keeling
, Edward M. Hill
, Erin E. Gorsich
, Bridget S. Penman
, Glen Guyver-Fletcher
, Alex Holmes
, Trystan Leng
, Hector McKimm
, Massimiliano Tamborrino
, Louise Dyson
, Michael J. Tildesley
:
Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies. - Seth Talyansky
, Braden A. W. Brinkman
:
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex. - Vikas Pandey, Lai-Hua Xie, Zhilin Qu
, Zhen Song
:
Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model. - Stephanie C. Hicks
, Ruoxi Liu
, Yuwei Ni
, Elizabeth Purdom
, Davide Risso
:
mbkmeans: Fast clustering for single cell data using mini-batch k-means. - Kathryn L. Schaber
, T. Alex Perkins, Alun L. Lloyd
, Lance A. Waller
, Uriel Kitron
, Valerie A. Paz-Soldan
, John P. Elder, Alan L. Rothman
, David J. Civitello, William H. Elson
, Amy C. Morrison
, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec:
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics. - Victor Boutin
, Angelo Franciosini
, Frédéric Chavane
, Franck Ruffier
, Laurent Perrinet
:
Sparse deep predictive coding captures contour integration capabilities of the early visual system. - Martina Conte
, Sergio Casas-Tintò
, Juan Soler
:
Modeling invasion patterns in the glioblastoma battlefield. - Dániel Vörös, Balázs Könnyü, Tamás Czárán
:
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism. - Steven Phillips
:
A reconstruction theory of relational schema induction. - Helen M. Kurkjian
, M. Javad Akbari, Babak Momeni
:
The impact of interactions on invasion and colonization resistance in microbial communities. - Daniel A. Burbano L.
, Maurizio Porfiri
:
Modeling multi-sensory feedback control of zebrafish in a flow. - Leonard Schmiester
, Yannik Schälte
, Frank T. Bergmann
, Tacio Camba, Erika Dudkin
, Janine Egert, Fabian Fröhlich
, Lara Fuhrmann
, Adrian L. Hauber
, Svenja Kemmer
, Polina A. Lakrisenko
, Carolin Loos
, Simon Merkt
, Wolfgang Müller
, Dilan Pathirana
, Elba Raimúndez-Álvarez
, Lukas Refisch
, Marcus Rosenblatt
, Paul Stapor
, Philipp Städter
, Dantong Wang
, Franz-Georg Wieland
, Julio R. Banga
, Jens Timmer, Alejandro F. Villaverde
, Sven Sahle, Clemens Kreutz
, Jan Hasenauer
, Daniel Weindl
:
PEtab - Interoperable specification of parameter estimation problems in systems biology. - Gabriel Studer
, Gerardo Tauriello
, Stefan Bienert
, Marco Biasini, Niklaus Johner
, Torsten Schwede
:
ProMod3 - A versatile homology modelling toolbox. - Alessandro Toso
, Arash Fassihi, Luciano Paz, Francesca Pulecchi, Mathew E. Diamond:
A sensory integration account for time perception. - Carlos Valiente-Mullor, Beatriz Beamud
, Iván Ansari, Carlos Francés-Cuesta
, Neris García-González
, Lorena Mejía
, Paula Ruiz-Hueso
, Fernando González-Candelas
:
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. - Shinsuke Koyama, Taiki Horie, Shigeru Shinomoto
:
Estimating the time-varying reproduction number of COVID-19 with a state-space method.
Volume 17, Number 2, February 2021
- Avni Malik, Paranjay Patel, Lubaina Ehsan
, Shan Guleria
, Thomas Hartka
, Sodiq Adewole
, Sana Syed:
Ten simple rules for engaging with artificial intelligence in biomedicine. - Sabrina Islam
, Christine A. Wells
:
Ten simple rules for navigating the computational aspect of an interdisciplinary PhD. - Johannes Werner
, Debora Jeske:
Ten simple rules for running and managing virtual internships. - Micaela S. Parker
, Arlyn E. Burgess, Philip E. Bourne
:
Ten simple rules for starting (and sustaining) an academic data science initiative. - Parice A. Brandies
, Carolyn J. Hogg:
Ten simple rules for getting started with command-line bioinformatics. - Jennifer H. Kong
, Latishya J. Steele
, Crystal M. Botham
:
Ten simple rules for writing compelling recommendation letters. - Matthias C. Rillig
, Karine Bonneval
, Christian de Lutz, Johannes Lehmann
, India Mansour
, Regine Rapp
, Sasa Spacal, Vera Meyer
:
Ten simple rules for hosting artists in a scientific lab. - Mathieu Boudreau
, Jean-Baptiste Poline, Pierre Bellec, Nikola Stikov
:
On the open-source landscape of PLOS Computational Biology.
- Michael Jackson
, Kostas Kavoussanakis
, Edward W. J. Wallace
:
Using prototyping to choose a bioinformatics workflow management system. - Verena Ras
, Gerrit Botha
, Shaun Aron
, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz
, Kilaza Samson Mwaikono, Dane Kennedy
, Jessica R. Holmes
, Gloria Rendon, Sumir Panji, Christopher J. Fields
, Nicola J. Mulder
:
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. - Kimberly A. Dill-McFarland, Stephan G. König
, Florent Mazel
, David C. Oliver, Lisa M. McEwen
, Kris Y. Hong, Steven J. Hallam
:
An integrated, modular approach to data science education in microbiology.
- Johannes Bracher
, Evan L. Ray, Tilmann Gneiting
, Nicholas G. Reich
:
Evaluating epidemic forecasts in an interval format.
- Lowell T. Edgar
, Claudio A. Franco
, Holger Gerhardt
, Miguel O. Bernabeu
:
On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling. - Hana Susak
, Laura Serra-Saurina
, German Demidov
, Raquel Rabionet
, Laura Domènech
, Mattia Bosio
, Francesc Muyas
, Xavier Estivill
, Geòrgia Escaramís, Stephan Ossowski
:
Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. - Mathew Titus
, George Hagstrom
, James R. Watson
:
Unsupervised manifold learning of collective behavior. - Davide Bernardi
, Guy Doron
, Michael Brecht
, Benjamin Lindner
:
A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation. - Marc A. Dämgen
, Philip C. Biggin
:
State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. - Helmut Schmidt
, Gerald Hahn, Gustavo Deco
, Thomas R. Knösche:
Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays. - George G. Vega Yon
, Duncan C. Thomas
, John Morrison
, Huaiyu Mi, Paul D. Thomas
, Paul Marjoram:
Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees. - Casey A. Cole
, Nourhan S. Daigham, Gaohua Liu
, Gaetano T. Montelione
, Homayoun Valafar:
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. - Sam Gijsen, Miro Grundei
, Robert T. Lange, Dirk Ostwald
, Felix Blankenburg:
Neural surprise in somatosensory Bayesian learning. - Karoline Horgmo Jæger
, Samuel Wall, Aslak Tveito
:
Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes. - Boris I. Ratnikov
, Piotr Cieplak
, Albert G. Remacle
, Elise Nguyen
, Jeffrey W. Smith:
Quantitative profiling of protease specificity.