PLOS Computational Biology

2005 - 2022

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Volume 18, issue 4, 2022

Ten simple rules for using entrepreneurship skills to improve research careers and culture pp. 1-7

Matt Bawn, David Dent and Philip E Bourne

DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data pp. 1-22

Lijun Cheng, Pratik Karkhanis, Birkan Gokbag, Yueze Liu and Lang Li

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants pp. 1-22

Nicholas J Ose, Brandon M Butler, Avishek Kumar, I Can Kazan, Maxwell Sanderford, Sudhir Kumar and S Banu Ozkan

Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders pp. 1-31

Yuge Wang and Hongyu Zhao

Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy pp. 1-31

Noemi S Araújo, Selvin Z Reyes-Garcia, João A F Brogin, Douglas D Bueno, Esper A Cavalheiro, Carla A Scorza and Jean Faber

Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets pp. 1-33

Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutti, Christophe Godin and Jan Traas

Using topic modeling to detect cellular crosstalk in scRNA-seq pp. 1-20

Alexandrina Pancheva, Helen Wheadon, Simon Rogers and Thomas D Otto

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention pp. 1-20

Bryan T Mayer, Allan C deCamp, Yunda Huang, Joshua T Schiffer, Raphael Gottardo, Peter B Gilbert and Daniel B Reeves

RNA folding using quantum computers pp. 1-17

Dillion M Fox, Christopher M MacDermaid, Andrea M A Schreij, Magdalena Zwierzyna and Ross C Walker

Ten simple rules to ruin a collaborative environment pp. 1-11

Carolyn J Lawrence-Dill, Robyn L Allscheid, Albert Boaitey, Todd Bauman, Edward S Buckler Iv, Jennifer L Clarke, Christopher Cullis, Jack Dekkers, Cassandra J Dorius, Shawn F Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M Reecy, Patrick S Schnable, Nicole M Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K Tuggle, Alison Van Eenennaam and Rachael Voas

Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit pp. 1-9

Gautam Munglani, Hannes Vogler and Ueli Grossniklaus

Ten simple rules for building a successful science start-up pp. 1-10

Tobias Reichmuth and Collin Y Ewald

SUITOR: Selecting the number of mutational signatures through cross-validation pp. 1-27

Donghyuk Lee, Difei Wang, Xiaohong R Yang, Jianxin Shi, Maria Teresa Landi and Bin Zhu

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors pp. 1-27

Nicolas Sundqvist, Nina Grankvist, Jeramie Watrous, Jain Mohit, Roland Nilsson and Gunnar Cedersund

Microbiome-based disease prediction with multimodal variational information bottlenecks pp. 1-27

Filippo Grazioli, Raman Siarheyeu, Israa Alqassem, Andreas Henschel, Giampaolo Pileggi and Andrea Meiser

Volume 18, issue 3, 2022

Estimating genetic variance contributed by a quantitative trait locus: A random model approach pp. 1-30

Shibo Wang, Fangjie Xie and Shizhong Xu

Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task pp. 1-20

Oscar Portoles, Manuel Blesa, Marieke van Vugt, Ming Cao and Jelmer P Borst

Ten quick tips for deep learning in biology pp. 1-20

Benjamin D Lee, Anthony Gitter, Casey S Greene, Sebastian Raschka, Finlay Maguire, Alexander J Titus, Michael D Kessler, Alexandra J Lee, Marc G Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J Fertig, Alexandr A Kalinin, Brandon Signal, Benjamin J Lengerich, Timothy J Triche and Simina M Boca

Transcriptome diversity is a systematic source of variation in RNA-sequencing data pp. 1-20

Pablo E García-Nieto, Ban Wang and Hunter B Fraser

A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data pp. 1-16

Snehalika Lall, Sumanta Ray and Sanghamitra Bandyopadhyay

Constructing benchmark test sets for biological sequence analysis using independent set algorithms pp. 1-14

Samantha Petti and Sean R Eddy

Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms pp. 1-14

Noortje G Godijk, Martin C J Bootsma, Henri C van Werkhoven, Valentijn A Schweitzer, Sabine C de Greeff, Annelot F Schoffelen and Marc J M Bonten

Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data pp. 1-14

Pablo M De Salazar, Fred Lu, James A Hay, Diana Gómez-Barroso, Pablo Fernández-Navarro, Elena V Martínez, Jenaro Astray-Mochales, Rocío Amillategui, Ana García-Fulgueiras, Maria D Chirlaque, Alonso Sánchez-Migallón, Amparo Larrauri, María J Sierra, Marc Lipsitch, Fernando Simón, Mauricio Santillana and Miguel A Hernán

Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness pp. 1-26

Daniel J Lugar and Ganesh Sriram

Automatic wound detection and size estimation using deep learning algorithms pp. 1-26

Héctor Carrión, Mohammad Jafari, Michelle Dawn Bagood, Hsin-ya Yang, Roslyn Rivkah Isseroff and Marcella Gomez

Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches pp. 1-21

Timos Papadopoulos and Emilia Vynnycky

How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments pp. 1-21

Immanuel Meyer, Bnaya Steinmetz and Nadav M Shnerb

Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition pp. 1-24

Shin-ichi Koda and Shinji Saito

Encoding time in neural dynamic regimes with distinct computational tradeoffs pp. 1-29

Shanglin Zhou, Sotiris C Masmanidis and Dean V Buonomano

Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation pp. 1-29

Yingjing Feng, Caroline H Roney, Jason D Bayer, Steven A Niederer, Mélèze Hocini and Edward J Vigmond

Bayesian calibration, process modeling and uncertainty quantification in biotechnology pp. 1-47

Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres and Marco Oldiges

Task-induced neural covariability as a signature of approximate Bayesian learning and inference pp. 1-39

Richard D Lange and Ralf M Haefner

The ability to classify patients based on gene-expression data varies by algorithm and performance metric pp. 1-34

Stephen R Piccolo, Avery Mecham, Nathan P Golightly, Jérémie L Johnson and Dustin B Miller

The role of cell geometry and cell-cell communication in gradient sensing pp. 1-22

Jonathan Fiorentino and Antonio Scialdone

Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level pp. 1-22

Anđela Davidović, Remy Chait, Gregory Batt and Jakob Ruess

Performance of early warning signals for disease re-emergence: A case study on COVID-19 data pp. 1-22

Daniele Proverbio, Françoise Kemp, Stefano Magni and Jorge Gonçalves

Oscillator decomposition of infant fNIRS data pp. 1-31

Takeru Matsuda, Fumitaka Homae, Hama Watanabe, Gentaro Taga and Fumiyasu Komaki

Evolution of innate behavioral strategies through competitive population dynamics pp. 1-38

Tong Liang and Braden A W Brinkman

Ten simple rules for principled simulation modelling pp. 1-8

Laurel Fogarty, Madeleine Ammar, Thomas Holding, Adam Powell and Anne Kandler

Survival analysis of pathway activity as a prognostic determinant in breast cancer pp. 1-13

Gustavo S Jeuken, Nicholas P Tobin and Lukas Käll

Pooled testing of traced contacts under superspreading dynamics pp. 1-17

Stratis Tsirtsis, Abir De, Lars Lorch and Manuel Gomez-Rodriguez

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins pp. 1-27

Lei Wang, Jiangguo Zhang, Dali Wang and Chen Song

Deep inference of seabird dives from GPS-only records: Performance and generalization properties pp. 1-18

Amédée Roy, Sophie Lanco Bertrand and Ronan Fablet

SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included pp. 1-18

Jianle Sun, Ruiqi Lyu, Luojia Deng, Qianwen Li, Yang Zhao and Yue Zhang

Cortical oscillations support sampling-based computations in spiking neural networks pp. 1-41

Agnes Korcsak-Gorzo, Michael G Müller, Andreas Baumbach, Luziwei Leng, Oliver J Breitwieser, Sacha J van Albada, Walter Senn, Karlheinz Meier, Robert Legenstein and Mihai A Petrovici

Bayesian inference of ancestral recombination graphs pp. 1-15

Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan and David Balding

Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2 pp. 1-15

Leonardo Souto Ferreira, Otavio Canton, Rafael Lopes Paixão da Silva, Silas Poloni, Vítor Sudbrack, Marcelo Eduardo Borges, Caroline Franco, Flavia Maria Darcie Marquitti, José Cássio de Moraes, Maria Amélia de Sousa Mascena Veras, Roberto André Kraenkel and Renato Mendes Coutinho

Volume 18, issue 2, 2022

Learning as filtering: Implications for spike-based plasticity pp. 1-23

Jannes Jegminat, Simone Carlo Surace and Jean-Pascal Pfister

Meta-control of social learning strategies pp. 1-27

Anil Yaman, Nicolas Bredeche, Onur Çaylak, Joel Z Leibo and Sang Wan Lee

Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network pp. 1-27

R Krishnakumaran, Mohammed Raees and Supratim Ray

Combination and competition between path integration and landmark navigation in the estimation of heading direction pp. 1-26

Sevan K Harootonian, Arne D Ekstrom and Robert C Wilson

In silico prediction of HIV-1-host molecular interactions and their directionality pp. 1-26

Haiting Chai, Quan Gu, Joseph Hughes and David L Robertson

Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights pp. 1-21

Ramin Khajeh, Francesco Fumarola and Abbott Lf

Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19 pp. 1-21

Xian Yang, Shuo Wang, Yuting Xing, Ling Li, Richard Yi Da Xu, Karl J Friston and Yike Guo

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic pp. 1-21

Yuen Ler Chow, Shantanu Singh, Anne E Carpenter and Gregory P Way

Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning pp. 1-21

Indriani P Astono, James S Welsh, Christopher W Rowe and Phillip Jobling

Classical mathematical models for prediction of response to chemotherapy and immunotherapy pp. 1-18

Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler, Julia Grajek, Kateřina Staňková, Alexander T Pearson, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling, Jan Poleszczuk and Jakob Nikolas Kather

RNA-Seq is not required to determine stable reference genes for qPCR normalization pp. 1-24

Nirmal Kumar Sampathkumar, Venkat Krishnan Sundaram, Prakroothi S Danthi, Rasha Barakat, Shiden Solomon, Mrityunjoy Mondal, Ivo Carre, Tatiana El Jalkh, Aïda Padilla-Ferrer, Julien Grenier, Charbel Massaad and Jacqueline C Mitchell

Hidden Markov Modeling with HMMTeacher pp. 1-9

Camilo Fuentes-Beals, Alejandro Valdés-Jiménez and Gonzalo Riadi

A computationally tractable birth-death model that combines phylogenetic and epidemiological data pp. 1-22

Alexander Eugene Zarebski, Louis du Plessis, Kris Varun Parag and Oliver George Pybus

High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication pp. 1-22

Nithya Ramakrishnan, Sibi Raj B Pillai and Ranjith Padinhateeri

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates pp. 1-37

Alessandra Løchen, James E Truscott and Nicholas J Croucher

Evaluating supervised and unsupervised background noise correction in human gut microbiome data pp. 1-25

Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin and Nandita R Garud

Inference of trajectory presence by tree dimension and subset specificity by subtree cover pp. 1-20

Lovemore Tenha and Mingzhou Song

Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model pp. 1-20

Nicholas J Clark, Tatiana Proboste, Guyan Weerasinghe and Ricardo J Soares Magalhães

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk pp. 1-11

Jon Zelner, Nina B Masters, Ramya Naraharisetti, Sanyu A Mojola, Merlin Chowkwanyun and Ryan Malosh

Ten simple rules for initial data analysis pp. 1-7

Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner and for the Topic Group “Initial Data Analysis” of the STRATOS Initiative

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich pp. 1-14

Liam M Longo, Rachel Kolodny and Shawn E McGlynn

Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster pp. 1-19

Katherine E Overman, Daniel M Choi, Kawai Leung, Joshua W Shaevitz and Gordon J Berman

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts pp. 1-35

Robert C Mines, Tomasz Lipniacki and Xiling Shen

Volume 18, issue 1, 2022

Formation, collective motion, and merging of macroscopic bacterial aggregates pp. 1-24

George Courcoubetis, Manasi S Gangan, Sean Lim, Xiaokan Guo, Stephan Haas and James Q Boedicker

Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach pp. 1-24

Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy and Zoltán Gáspári

A lexical approach for identifying behavioural action sequences pp. 1-29

Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat and Claire Wyart

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data pp. 1-18

Raga Krishnakumar and Anne M Ruffing

The evolutionary maintenance of Lévy flight foraging pp. 1-26

Winston Campeau, Andrew M Simons and Brett Stevens

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach pp. 1-26

Chen Jia, Abhyudai Singh and Ramon Grima

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods pp. 1-21

Richard Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander and Linda Petzold

Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables pp. 1-23

Arno Strouwen, Bart M Nicolaï and Peter Goos

Analytical kinetic model of native tandem promoters in E. coli pp. 1-23

Vatsala Chauhan, Mohamed N M Bahrudeen, Cristina S D Palma, Ines S C Baptista, Bilena L B Almeida, Suchintak Dash, Vinodh Kandavalli and Andre S Ribeiro

Identification of periodic attractors in Boolean networks using a priori information pp. 1-27

Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp and Tatsuya Akutsu

Optimism and pessimism in optimised replay pp. 1-32

Georgy Antonov, Christopher Gagne, Eran Eldar and Peter Dayan

Fast and accurate influenza forecasting in the United States with Inferno pp. 1-22

Dave Osthus

Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy pp. 1-22

Alexander B Brummer, Xin Yang, Eric Ma, Margarita Gutova, Christine E Brown and Russell C Rockne

Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data pp. 1-22

Qi Jiang, Shuo Zhang and Lin Wan

Interpretable machine learning for high-dimensional trajectories of aging health pp. 1-30

Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood and Andrew D Rutenberg

Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships pp. 1-30

Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort and Arno Onken

Efficient ReML inference in variance component mixed models using a Min-Max algorithm pp. 1-19

Fabien Laporte, Alain Charcosset and Tristan Mary-Huard

Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection pp. 1-19

Alasdair D F Clarke, Amelia R Hunt and Anna E Hughes

Discovering adaptation-capable biological network structures using control-theoretic approaches pp. 1-28

Priyan Bhattacharya, Karthik Raman and Arun K Tangirala

An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind pp. 1-16

William Turner, Daniel Feuerriegel, Robert Hester and Stefan Bode

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach pp. 1-17

Mengting Niu, Quan Zou and Chen Lin

Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution pp. 1-20

Tadamune Kaneko and Macoto Kikuchi