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PLoS Computational Biology, Volume 18
Volume 18, Number 1, January 2022
- Stevie A. Bain
, Heleen Plaisier
, Felicity Anderson
, Nicola Cook
, Kathryn Crouch
, Thomas R. Meagher, Michael G. Ritchie
, Edward W. J. Wallace
, Daniel Barker
:
Bringing bioinformatics to schools with the 4273pi project. - Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco:
Project-based learning course on metabolic network modelling in computational systems biology.
- Elizabeth Dupre
, Chris Holdgraf
, Agah Karakuzu
, Loïc Tetrel, Pierre Bellec
, Nikola Stikov
, Jean-Baptiste Poline
:
Beyond advertising: New infrastructures for publishing integrated research objects. - Sheila M. Saia
, Natalie G. Nelson
, Sierra N. Young
, Stanton Parham
, Micah Vandegrift
:
Ten simple rules for researchers who want to develop web apps.
- George Courcoubetis
, Manasi S. Gangan
, Sean Lim
, Xiaokan Guo
, Stephan Haas
, James Q. Boedicker
:
Formation, collective motion, and merging of macroscopic bacterial aggregates. - István Z. Reguly
, Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, Bence Keömley-Horváth, Tamás Kós, György Cserey
, Kristóf Iván, Sándor Pongor, Gábor Szederkényi, Gergely Röst, Attila Csikász-Nagy
:
Microsimulation based quantitative analysis of COVID-19 management strategies. - He Li, Yixiang Deng, Konstantina Sampani, Shengze Cai, Zhen Li, Jennifer K. Sun, George E. Karniadakis:
Computational investigation of blood cell transport in retinal microaneurysms. - Raga Krishnakumar
, Anne M. Ruffing
:
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. - Nathan C. L. Kong
, Eshed Margalit
, Justin L. Gardner
, Anthony M. Norcia
:
Increasing neural network robustness improves match to macaque V1 eigenspectrum, spatial frequency preference and predictivity. - Gautam Reddy
, Laura Desban
, Hidenori Tanaka, Julian Roussel
, Olivier Mirat
, Claire Wyart
:
A lexical approach for identifying behavioural action sequences. - Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood
, Andrew D. Rutenberg
:
Interpretable machine learning for high-dimensional trajectories of aging health. - Benjamin Martin
, Pablo D. Dans
, Milosz Wieczór
, Núria Villegas
, Isabelle Brun-Heath
, Federica Battistini
, Montserrat Terrazas
, Modesto Orozco:
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. - Yan Wu
, Lingfeng Xue
, Wen Huang
, Minghua Deng, Yihan Lin
:
Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data. - Eline R. Kupers
, Noah C. Benson
, Marisa Carrasco
, Jonathan Winawer
:
Asymmetries around the visual field: From retina to cortex to behavior. - Marina Papadopoulou
, Hanno Hildenbrandt
, Daniel W. E. Sankey
, Steven J. Portugal
, Charlotte K. Hemelrijk
:
Self-organization of collective escape in pigeon flocks. - Jennifer Yihong Tan
, Ana Claudia Marques
:
The activity of human enhancers is modulated by the splicing of their associated lncRNAs. - Arno Strouwen
, Bart M. Nicolaï
, Peter Goos
:
Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables. - Georgy Antonov
, Christopher Gagne
, Eran Eldar
, Peter Dayan
:
Optimism and pessimism in optimised replay. - Le Khanh Ngan Nguyen
, Itamar Megiddo
, Susan Howick
:
Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff. - Yushi Yang
, Francesco Turci
, Erika Kague
, Chrissy L. Hammond
, John Russo
, C. Patrick Royall:
Dominating lengthscales of zebrafish collective behaviour. - Zhi Ming Xu
, Sina Rüeger
, Michaela Zwyer, Daniela Brites
, Hellen Hiza
, Miriam Reinhard, Liliana K. Rutaihwa
, Sonia Borrell
, Faima Isihaka
, Hosiana Temba, Thomas Maroa, Rastard Naftari, Jerry Hella
, Mohamed Sasamalo, Klaus Reither, Damien Portevin
, Sebastien Gagneux
, Jacques Fellay:
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. - William F. Turner
, Daniel Feuerriegel
, Robert Hester, Stefan Bode
:
An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind. - Ulrike Münzner
, Tomoya Mori
, Marcus Krantz
, Edda Klipp
, Tatsuya Akutsu
:
Identification of periodic attractors in Boolean networks using a priori information. - Jann Paul Mattern
, Kristof Glauninger
, Gregory L. Britten
, John R. Casey
, Sangwon Hyun
, Zhen Wu
, E. Virginia Armbrust
, Zaïd Harchaoui, Francois Ribalet
:
A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series. - Xiangyu Kuang
, Guoye Guan
, Ming-Kin Wong
, Lu-Yan Chan, Zhongying Zhao
, Chao Tang
, Lei Zhang
:
Computable early Caenorhabditis elegans embryo with a phase field model. - Joanna E. Handzlik
, Manu
:
Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. - Rory M. Donovan-Maiye
, Eva Maxfield Brown
, K. Caleb Chan
, Liya Ding
, Calysta Yan, Nathalie Gaudreault
, Julie A. Theriot
, Mary M. Maleckar
, Theo A. Knijnenburg
, Gregory R. Johnson
:
A deep generative model of 3D single-cell organization. - Winston Campeau
, Andrew M. Simons
, Brett Stevens
:
The evolutionary maintenance of Lévy flight foraging. - Md Zulfikar Ali
, Robert C. Brewster
:
Controlling gene expression timing through gene regulatory architecture. - Marcell Miski
, Bence Márk Keömley-Horváth
, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy
, Zoltán Gáspári:
Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach. - Chenfei Zhang, David Hofmann
, Andreas Neef
, Fred Wolf
:
Ultrafast population coding and axo-somatic compartmentalization. - Gorka Lasso
, Saad Khan
, Stephanie A. Allen, Margarette Mariano
, Catalina Florez
, Erika P. Orner
, Jose A. Quiroz
, Gregory Quevedo
, Aldo Massimi
, Aditi Hegde, Ariel S. Wirchnianski
, Robert H. Bortz III
, Ryan J. Malonis
, George I. Georgiev
, Karen Tong
, Natalia G. Herrera
, Nicholas C. Morano, Scott J. Garforth
, Avinash Malaviya, Ahmed Khokhar
, Ethan Laudermilch
, M. Eugenia Dieterle
, J. Maximilian Fels
, Denise Haslwanter
, Rohit K. Jangra
, Jason Barnhill
, Steven C. Almo, Kartik Chandran
, Jonathan R. Lai
, Libusha Kelly
, Johanna P. Daily, Olivia Vergnolle
:
Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes. - Alexander J. Bryer
, Tyler Reddy
, Edward Lyman, Juan R. Perilla
:
Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. - Anton V. Chizhov
, Dmitry V. Amakhin
, Elena Yu. Smirnova
, Aleksey V. Zaitsev
:
Ictal wavefront propagation in slices and simulations with conductance-based refractory density model. - Maggie Wisniewska
, Ivan Puga-Gonzalez
, Phyllis Lee
, Cynthia Moss
, Gareth Russell
, Simon Garnier
, Cédric Sueur
:
Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants - An exemplar of how human disturbance impacts group-living species. - Chen Jia, Abhyudai Singh
, Ramon Grima
:
Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach. - Owen M. O'Connor
, Razan N. Alnahhas
, Jean-Baptiste Lugagne
, Mary J. Dunlop
:
DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics. - Tadamune Kaneko
, Macoto Kikuchi
:
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution. - Shun Sakuraba
, Qilin Xie, Kota Kasahara
, Junichi Iwakiri
, Hidetoshi Kono
:
Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. - Vladimír Palivec
, Christian Johannessen
, Jakub Kaminský
, Hector Martinez-Seara
:
Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution. - Janet Ong
, Stacy Soh
, Soon Hoe Ho, Annabel Seah
, Borame Sue Dickens
, Ken Wei Tan, Joel Ruihan Koo
, Alex R. Cook, Daniel Rex Richards
, Leon Yan-Feng Gaw
, Ng Lee Ching, Jue Tao Lim
:
Fine-scale estimation of effective reproduction numbers for dengue surveillance. - Mengting Niu
, Quan Zou
, Chen Lin:
CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach. - Arish Alreja
, Ilya Nemenman
, Christopher J. Rozell
:
Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices. - Priyan Bhattacharya
, Karthik Raman
, Arun K. Tangirala
:
Discovering adaptation-capable biological network structures using control-theoretic approaches. - Fabien Laporte
, Alain Charcosset
, Tristan Mary-Huard
:
Efficient ReML inference in variance component mixed models using a Min-Max algorithm. - André Bogdanowski
, Thomas Banitz
, Linea Katharina Muhsal
, Christian Kost
, Karin Frank
:
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems. - Ryan R. Wick
, Kathryn E. Holt
:
Polypolish: Short-read polishing of long-read bacterial genome assemblies. - Alasdair D. F. Clarke, Amelia R. Hunt
, Anna E. Hughes
:
Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection. - Eduard Porta-Pardo
, Victoria Ruiz-Serra
, Samuel Valentini
, Alfonso Valencia
:
The structural coverage of the human proteome before and after AlphaFold. - Qi Jiang, Shuo Zhang, Lin Wan
:
Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data. - Alexander Byers Brummer
, Xin Yang, Eric Ma, Margarita Gutova
, Christine E. Brown
, Russell C. Rockne
:
Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy. - Elodie Goldwaser
, Catherine Laurent
, Nathalie Lagarde
, Sylvie Fabrega
, Laure Nay, Bruno O. Villoutreix
, Christian Jelsch
, Arnaud B. Nicot, Marie-Anne Loriot, Maria A. Miteva
:
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. - Tianwei Yu
:
AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments. - Quinn Dickinson
, Jesse G. Meyer
:
Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences. - Nina Kudryashova
, Theoklitos Amvrosiadis
, Nathalie Dupuy
, Nathalie Rochefort
, Arno Onken
:
Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships. - Alexander Nestor-Bergmann
, Guy B. Blanchard
, Nathan Hervieux
, Alexander G. Fletcher
, Jocelyn Étienne
, Bénédicte Sanson
:
Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model. - Chloé Dequeker
, Yasser Mohseni Behbahani
, Laurent David, Elodie Laine
, Alessandra Carbone
:
From complete cross-docking to partners identification and binding sites predictions. - Sayak Bhattacharya, Scott L. Brincat
, Mikael Lundqvist
, Earl K. Miller:
Traveling waves in the prefrontal cortex during working memory. - Chunrui Xu
, Henry Hollis
, Michelle Dai
, Xiangyu Yao
, Layne T. Watson, Yang Cao
, Minghan Chen
:
Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle. - Kaushik N. Shankar
, Yiyuan Zhang
, Talid Sinno
, Scott L. Diamond
:
A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution. - Dave Osthus
:
Fast and accurate influenza forecasting in the United States with Inferno. - Tomiko Oskotsky
, Ruchika Bajaj
, Jillian Burchard, Taylor Cavazos
, Ina Chen
, William T. Connell, Stephanie Eaneff
, Tianna Grant
, Ishan Kanungo
, Karla Lindquist
, Douglas Myers-Turnbull
, Zun Zar Chi Naing
, Alice Tang
, Bianca Vora
, Jon Wang
, Isha Karim, Claire Swadling
, Janice Yang, AI4ALL Student Cohort, Bill Lindstaedt, Marina Sirota
:
Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students. - Sina Tootoonian
, Andreas T. Schaefer
, Peter E. Latham
:
Sparse connectivity for MAP inference in linear models using sister mitral cells. - Vatsala Chauhan
, Mohamed N. M. Bahrudeen
, Cristina S. D. Palma
, Ines S. C. Baptista
, Bilena Almeida
, Suchintak Dash
, Vinodh Kandavalli
, Andre S. Ribeiro
:
Analytical kinetic model of native tandem promoters in E. coli. - Richard M. Jiang
, Prashant Singh
, Fredrik Wrede
, Andreas Hellander
, Linda R. Petzold
:
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods. - Junhao Liang
, Changsong Zhou
:
Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks. - Yuan Gao, Jeff Gaither
, Julia Chifman
, Laura Salter Kubatko:
A phylogenetic approach to inferring the order in which mutations arise during cancer progression. 1010560
- Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin:
Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data. - Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke
, Nathan E. Lewis:
Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models.
Volume 18, Number 2, February 2022
- Arkarachai Fungtammasan
, Alexandra Lee
, Jaclyn N. Taroni
, Kurt Wheeler
, Chen-Shan Chin
, Sean Davis
, Casey S. Greene
:
Ten simple rules for large-scale data processing. - Nicole Contaxis
, Jason A. Clark
, Anthony Dellureficio
, Sara Gonzales
, Sara Mannheimer
, Peter R. Oxley
, Melissa A. Ratajeski
, Alisa Surkis
, Amy M. Yarnell
, Michelle Yee
, Kristi L. Holmes
:
Ten simple rules for improving research data discovery. - Mark Baillie
, Saskia le Cessie, Carsten Oliver Schmidt
, Lara Lusa
, Marianne Huebner
:
Ten simple rules for initial data analysis.
- Camilo Fuentes-Beals
, Alejandro Valdés-Jiménez
, Gonzalo Riadi
:
Hidden Markov Modeling with HMMTeacher. - Greg Wilson
:
Twelve quick tips for software design.
- Jon Zelner
, Nina B. Masters
, Ramya Naraharisetti
, Sanyu A. Mojola
, Merlin Chowkwanyun, Ryan Malosh
:
There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.
- Mathieu Desroches
, John Rinzel
, Serafim Rodrigues
:
Classification of bursting patterns: A tale of two ducks.
- Stefan Müller
, Diana Széliová
, Jürgen Zanghellini
:
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. - Myo T. Naung
, Elijah Martin
, Jacob E. Munro
, Somya Mehra
, Andrew J. Guy
, Moses Laman
, G. L. Abby Harrison, Livingstone Tavul
, Manuel Hetzel
, Dominic Kwiatkowski
, Ivo Mueller
, Melanie Bahlo
, Alyssa E. Barry
:
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. - Ignacio Sanchez-Burgos
, Jorge R. Espinosa
, Jerelle A. Joseph
, Rosana Collepardo-Guevara
:
RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins. - Gabriela Canto-Encalada
, Diego Tec-Campos
, Juan D. Tibocha-Bonilla
, Karsten Zengler
, Alejandro Zepeda
, Cristal Zuñiga
:
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. - Cristian Buc Calderon
, Tom Verguts
, Michael J. Frank
:
Thunderstruck: The ACDC model of flexible sequences and rhythms in recurrent neural circuits. - Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler
, Julia Grajek
, Katerina Stanková
, Alexander T. Pearson
, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling
, Jan Poleszczuk
, Jakob Nikolas Kather
:
Classical mathematical models for prediction of response to chemotherapy and immunotherapy. - Daniel Kaiser
, Arthur M. Jacobs, Radoslaw Martin Cichy
:
Modelling brain representations of abstract concepts. - Anca R. Radulescu
, Gabrielle C. Todd
, Cassandra L. Williams, Benjamin A. Bennink
, Alex A. Lemus
, Haley E. Chesbro
, Justin R. Bourgeois
, Ashley M. Kopec
, Damian G. Zuloaga
, Annalisa Scimemi
:
Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes. - Benjamin J. Livesey
, Joseph A. Marsh
:
The properties of human disease mutations at protein interfaces. - Aleksey V. Zimin
, Steven L. Salzberg
:
The SAMBA tool uses long reads to improve the contiguity of genome assemblies. - Marzia Di Filippo
, Dario Pescini
, Bruno Giovanni Galuzzi
, Marcella Bonanomi
, Daniela Gaglio, Eleonora Mangano
, Clarissa Consolandi
, Lilia Alberghina, Marco Vanoni, Chiara Damiani
:
INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. - Thomas J. Moutinho Jr.
, Benjamin C. Neubert
, Matthew L. Jenior
, Jason A. Papin
:
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. - Leah Briscoe
, Brunilda Balliu
, Sriram Sankararaman
, Eran Halperin
, Nandita R. Garud
:
Evaluating supervised and unsupervised background noise correction in human gut microbiome data. - David E. Chen Kersen
, Gaia Tavoni
, Vijay Balasubramanian
:
Connectivity and dynamics in the olfactory bulb. - Haiting Chai
, Quan Gu
, Joseph Hughes
, David L. Robertson
:
In silico prediction of HIV-1-host molecular interactions and their directionality. - Lovemore Tenha
, Mingzhou Song
:
Inference of trajectory presence by tree dimension and subset specificity by subtree cover. - Ramin Khajeh
, Francesco Fumarola, L. F. Abbott:
Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights. - György Abrusán
, David B. Ascher
, Michael Inouye:
Known allosteric proteins have central roles in genetic disease. - Reza Yaesoubi
, Ted Cohen
, Katherine Hsu, Thomas L. Gift
, Sancta B. St. Cyr
, Joshua A. Salomon
, Yonatan H. Grad
:
Evaluating spatially adaptive guidelines for the treatment of gonorrhea to reduce the incidence of gonococcal infection and increase the effective lifespan of antibiotics. - Qi Sun
, Ali Nematbakhsh
, Prashant Kumar Kuntala
, Gretta Kellogg
, B. Franklin Pugh
, William K. M. Lai
:
STENCIL: A web templating engine for visualizing and sharing life science datasets. - Sevan K. Harootonian
, Arne D. Ekstrom, Robert C. Wilson
:
Combination and competition between path integration and landmark navigation in the estimation of heading direction. - Anna Foix
, Daniel López
, Francisco Diez-Fuertes
, Michael J. McConnell, Antonio J. Martin-Galiano
:
Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2. - Robert C. Mines
, Tomasz Lipniacki
, Xiling Shen
:
Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts. - Júlia V. Gallinaro
, Nebojsa Gasparovic
, Stefan Rotter
:
Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams. - Samuel Goldman
, Ria Das, Kevin K. Yang
, Connor W. Coley
:
Machine learning modeling of family wide enzyme-substrate specificity screens. - Siyu Wang, Stephanie M. Reeve
, Graham T. Holt
, Adegoke A. Ojewole
, Marcel S. Frenkel
, Pablo Gainza, Santosh Keshipeddy, Vance G. Fowler
, Dennis L. Wright
, Bruce Randall Donald
:
Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. - Alexander Eugene Zarebski
, Louis du Plessis
, Kris V. Parag
, Oliver George Pybus
:
A computationally tractable birth-death model that combines phylogenetic and epidemiological data. - Liron Sheintuch
, Alon Rubin, Ziv Yaniv
:
Bias-free estimation of information content in temporally sparse neuronal activity.