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PLOS Computational Biology

2005 - 2022

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Volume 18, issue 4, 2022

RNA folding using quantum computers pp. 1-17 Downloads
Dillion M Fox, Christopher M MacDermaid, Andrea M A Schreij, Magdalena Zwierzyna and Ross C Walker
Using topic modeling to detect cellular crosstalk in scRNA-seq pp. 1-20 Downloads
Alexandrina Pancheva, Helen Wheadon, Simon Rogers and Thomas D Otto
Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention pp. 1-20 Downloads
Bryan T Mayer, Allan C deCamp, Yunda Huang, Joshua T Schiffer, Raphael Gottardo, Peter B Gilbert and Daniel B Reeves
Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets pp. 1-33 Downloads
Anuradha Kar, Manuel Petit, Yassin Refahi, Guillaume Cerutti, Christophe Godin and Jan Traas
Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit pp. 1-9 Downloads
Gautam Munglani, Hannes Vogler and Ueli Grossniklaus
Ten simple rules for using entrepreneurship skills to improve research careers and culture pp. 1-7 Downloads
Matt Bawn, David Dent and Philip E Bourne
Ten simple rules to ruin a collaborative environment pp. 1-11 Downloads
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
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders pp. 1-31 Downloads
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 Downloads
Noemi S Araújo, Selvin Z Reyes-Garcia, João A F Brogin, Douglas D Bueno, Esper A Cavalheiro, Carla A Scorza and Jean Faber
DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data pp. 1-22 Downloads
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 Downloads
Nicholas J Ose, Brandon M Butler, Avishek Kumar, I Can Kazan, Maxwell Sanderford, Sudhir Kumar and S Banu Ozkan
Ten simple rules for building a successful science start-up pp. 1-10 Downloads
Tobias Reichmuth and Collin Y Ewald
SUITOR: Selecting the number of mutational signatures through cross-validation pp. 1-27 Downloads
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 Downloads
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 Downloads
Filippo Grazioli, Raman Siarheyeu, Israa Alqassem, Andreas Henschel, Giampaolo Pileggi and Andrea Meiser

Volume 18, issue 3, 2022

Pooled testing of traced contacts under superspreading dynamics pp. 1-17 Downloads
Stratis Tsirtsis, Abir De, Lars Lorch and Manuel Gomez-Rodriguez
Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task pp. 1-20 Downloads
Oscar Portoles, Manuel Blesa, Marieke van Vugt, Ming Cao and Jelmer P Borst
Ten quick tips for deep learning in biology pp. 1-20 Downloads
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 Downloads
Pablo E García-Nieto, Ban Wang and Hunter B Fraser
Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches pp. 1-21 Downloads
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 Downloads
Immanuel Meyer, Bnaya Steinmetz and Nadav M Shnerb
Encoding time in neural dynamic regimes with distinct computational tradeoffs pp. 1-29 Downloads
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 Downloads
Yingjing Feng, Caroline H Roney, Jason D Bayer, Steven A Niederer, Mélèze Hocini and Edward J Vigmond
A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data pp. 1-16 Downloads
Snehalika Lall, Sumanta Ray and Sanghamitra Bandyopadhyay
Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition pp. 1-24 Downloads
Shin-ichi Koda and Shinji Saito
Ten simple rules for principled simulation modelling pp. 1-8 Downloads
Laurel Fogarty, Madeleine Ammar, Thomas Holding, Adam Powell and Anne Kandler
Cortical oscillations support sampling-based computations in spiking neural networks pp. 1-41 Downloads
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 calibration, process modeling and uncertainty quantification in biotechnology pp. 1-47 Downloads
Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres and Marco Oldiges
Survival analysis of pathway activity as a prognostic determinant in breast cancer pp. 1-13 Downloads
Gustavo S Jeuken, Nicholas P Tobin and Lukas Käll
Bayesian inference of ancestral recombination graphs pp. 1-15 Downloads
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 Downloads
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
Evolution of innate behavioral strategies through competitive population dynamics pp. 1-38 Downloads
Tong Liang and Braden A W Brinkman
The ability to classify patients based on gene-expression data varies by algorithm and performance metric pp. 1-34 Downloads
Stephen R Piccolo, Avery Mecham, Nathan P Golightly, Jérémie L Johnson and Dustin B Miller
Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness pp. 1-26 Downloads
Daniel J Lugar and Ganesh Sriram
Automatic wound detection and size estimation using deep learning algorithms pp. 1-26 Downloads
Héctor Carrión, Mohammad Jafari, Michelle Dawn Bagood, Hsin-ya Yang, Roslyn Rivkah Isseroff and Marcella Gomez
Deep inference of seabird dives from GPS-only records: Performance and generalization properties pp. 1-18 Downloads
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 Downloads
Jianle Sun, Ruiqi Lyu, Luojia Deng, Qianwen Li, Yang Zhao and Yue Zhang
Constructing benchmark test sets for biological sequence analysis using independent set algorithms pp. 1-14 Downloads
Samantha Petti and Sean R Eddy
Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms pp. 1-14 Downloads
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 Downloads
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
The role of cell geometry and cell-cell communication in gradient sensing pp. 1-22 Downloads
Jonathan Fiorentino and Antonio Scialdone
Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level pp. 1-22 Downloads
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 Downloads
Daniele Proverbio, Françoise Kemp, Stefano Magni and Jorge Gonçalves
Oscillator decomposition of infant fNIRS data pp. 1-31 Downloads
Takeru Matsuda, Fumitaka Homae, Hama Watanabe, Gentaro Taga and Fumiyasu Komaki
Task-induced neural covariability as a signature of approximate Bayesian learning and inference pp. 1-39 Downloads
Richard D Lange and Ralf M Haefner
Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins pp. 1-27 Downloads
Lei Wang, Jiangguo Zhang, Dali Wang and Chen Song
Estimating genetic variance contributed by a quantitative trait locus: A random model approach pp. 1-30 Downloads
Shibo Wang, Fangjie Xie and Shizhong Xu

Volume 18, issue 2, 2022

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk pp. 1-11 Downloads
Jon Zelner, Nina B Masters, Ramya Naraharisetti, Sanyu A Mojola, Merlin Chowkwanyun and Ryan Malosh
Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster pp. 1-19 Downloads
Katherine E Overman, Daniel M Choi, Kawai Leung, Joshua W Shaevitz and Gordon J Berman
Combination and competition between path integration and landmark navigation in the estimation of heading direction pp. 1-26 Downloads
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 Downloads
Haiting Chai, Quan Gu, Joseph Hughes and David L Robertson
Evaluating supervised and unsupervised background noise correction in human gut microbiome data pp. 1-25 Downloads
Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin and Nandita R Garud
Classical mathematical models for prediction of response to chemotherapy and immunotherapy pp. 1-18 Downloads
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
A computationally tractable birth-death model that combines phylogenetic and epidemiological data pp. 1-22 Downloads
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 Downloads
Nithya Ramakrishnan, Sibi Raj B Pillai and Ranjith Padinhateeri
Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich pp. 1-14 Downloads
Liam M Longo, Rachel Kolodny and Shawn E McGlynn
Learning as filtering: Implications for spike-based plasticity pp. 1-23 Downloads
Jannes Jegminat, Simone Carlo Surace and Jean-Pascal Pfister
Meta-control of social learning strategies pp. 1-27 Downloads
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 Downloads
R Krishnakumaran, Mohammed Raees and Supratim Ray
Inference of trajectory presence by tree dimension and subset specificity by subtree cover pp. 1-20 Downloads
Lovemore Tenha and Mingzhou Song
Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model pp. 1-20 Downloads
Nicholas J Clark, Tatiana Proboste, Guyan Weerasinghe and Ricardo J Soares Magalhães
Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates pp. 1-37 Downloads
Alessandra Løchen, James E Truscott and Nicholas J Croucher
Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts pp. 1-35 Downloads
Robert C Mines, Tomasz Lipniacki and Xiling Shen
Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights pp. 1-21 Downloads
Ramin Khajeh, Francesco Fumarola and Abbott Lf
Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19 pp. 1-21 Downloads
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 Downloads
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 Downloads
Indriani P Astono, James S Welsh, Christopher W Rowe and Phillip Jobling
Hidden Markov Modeling with HMMTeacher pp. 1-9 Downloads
Camilo Fuentes-Beals, Alejandro Valdés-Jiménez and Gonzalo Riadi
RNA-Seq is not required to determine stable reference genes for qPCR normalization pp. 1-24 Downloads
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
Ten simple rules for initial data analysis pp. 1-7 Downloads
Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner and for the Topic Group “Initial Data Analysis” of the STRATOS Initiative

Volume 18, issue 1, 2022

Identification of periodic attractors in Boolean networks using a priori information pp. 1-27 Downloads
Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp and Tatsuya Akutsu
Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables pp. 1-23 Downloads
Arno Strouwen, Bart M Nicolaï and Peter Goos
Analytical kinetic model of native tandem promoters in E. coli pp. 1-23 Downloads
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
Interpretable machine learning for high-dimensional trajectories of aging health pp. 1-30 Downloads
Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood and Andrew D Rutenberg
Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships pp. 1-30 Downloads
Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort and Arno Onken
The evolutionary maintenance of Lévy flight foraging pp. 1-26 Downloads
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 Downloads
Chen Jia, Abhyudai Singh and Ramon Grima
Efficient ReML inference in variance component mixed models using a Min-Max algorithm pp. 1-19 Downloads
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 Downloads
Alasdair D F Clarke, Amelia R Hunt and Anna E Hughes
Fast and accurate influenza forecasting in the United States with Inferno pp. 1-22 Downloads
Dave Osthus
Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy pp. 1-22 Downloads
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 Downloads
Qi Jiang, Shuo Zhang and Lin Wan
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data pp. 1-18 Downloads
Raga Krishnakumar and Anne M Ruffing
A lexical approach for identifying behavioural action sequences pp. 1-29 Downloads
Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat and Claire Wyart
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods pp. 1-21 Downloads
Richard Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander and Linda Petzold
Optimism and pessimism in optimised replay pp. 1-32 Downloads
Georgy Antonov, Christopher Gagne, Eran Eldar and Peter Dayan
An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind pp. 1-16 Downloads
William Turner, Daniel Feuerriegel, Robert Hester and Stefan Bode
Formation, collective motion, and merging of macroscopic bacterial aggregates pp. 1-24 Downloads
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 Downloads
Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy and Zoltán Gáspári
Discovering adaptation-capable biological network structures using control-theoretic approaches pp. 1-28 Downloads
Priyan Bhattacharya, Karthik Raman and Arun K Tangirala
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution pp. 1-20 Downloads
Tadamune Kaneko and Macoto Kikuchi
CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach pp. 1-17 Downloads
Mengting Niu, Quan Zou and Chen Lin
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