PLoS Comput. Biol.

Keyphrases

Publications

volume 19, number 3, 2023

Brennica Marlow, Georg Kuenze, Jens Meiler, Julia Koehler Leman
Docking cholesterol to integral membrane proteins with Rosetta. PLoS Comput. Biol. 19 (3) (2023)
Lorenzo Cappello, Jaehee Kim, Julia A. Palacios
adaPop: Bayesian inference of dependent population dynamics in coalescent models. PLoS Comput. Biol. 19 (3) (2023)
Arthur Bernard, Steffen Wischmann, Dario Floreano, Laurent Keller
The evolution of behavioral cues and signaling in displaced communication. PLoS Comput. Biol. 19 (3) (2023)
Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein
G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data. PLoS Comput. Biol. 19 (3) (2023)
Christian Malte Boßelmann, Ulrike B. S. Hedrich, Holger Lerche, Nico Pfeifer
Predicting functional effects of ion channel variants using new phenotypic machine learning methods. PLoS Comput. Biol. 19 (3) (2023)
Dohoon Lee, Bonil Koo, Jeewon Yang, Sun Kim
Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. PLoS Comput. Biol. 19 (3) (2023)
Joshua Adam Bull, Helen M. Byrne
Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions. PLoS Comput. Biol. 19 (3) (2023)
Sasikiran Kandula, Mark Olfson, Madelyn S. Gould, Katherine M. Keyes, Jeffrey Shaman
Hindcasts and forecasts of suicide mortality in US: A modeling study. PLoS Comput. Biol. 19 (3) (2023)
Neda Kaboodvand, Behzad Iravani, Martijn P. van den Heuvel, Jonas Persson, Robert Boden
Macroscopic resting state model predicts theta burst stimulation response: A randomized trial. PLoS Comput. Biol. 19 (3) (2023)
Sean B. King, Mona Singh
Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput. Biol. 19 (3) (2023)
Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells. PLoS Comput. Biol. 19 (3) (2023)
Mahmood Kalemati, Mojtaba Zamani Emani, Somayyeh Koohi
BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach. PLoS Comput. Biol. 19 (3) (2023)
Karen E. Ross, Guolin Zhang, Cuneyt Akcora, Yu Lin, Bin Fang, John M. Koomen, Eric B. Haura, Mark Grimes
Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer. PLoS Comput. Biol. 19 (3) (2023)
Myriah Haggard, Maurice J. Chacron
Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish. PLoS Comput. Biol. 19 (3) (2023)
Ruth Nanjala, Festus Nyasimi, Daniel Masiga, Caleb Kipkurui Kibet
A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya. PLoS Comput. Biol. 19 (3) (2023)
Sameer D'Costa, Emily C. Hinds, Chase R. Freschlin, Hyebin Song, Philip A. Romero
Inferring protein fitness landscapes from laboratory evolution experiments. PLoS Comput. Biol. 19 (3) (2023)
Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS Comput. Biol. 19 (3) (2023)
Marco Pensalfini, Adrian Buganza Tepole
Mechano-biological and bio-mechanical pathways in cutaneous wound healing. PLoS Comput. Biol. 19 (3) (2023)
Máté L. Telek, Elisenda Feliu
Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity. PLoS Comput. Biol. 19 (3) (2023)
Michael Lukowski, Andrew Prokhorenkov, Robert L. Grossman
Towards self-describing and FAIR bulk formats for biomedical data. PLoS Comput. Biol. 19 (3) (2023)
Delora Baptista, Pedro G. Ferreira, Miguel Rocha
A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer. PLoS Comput. Biol. 19 (3) (2023)
Paul Manuel Müller, Christian Meisel
Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load. PLoS Comput. Biol. 19 (3) (2023)
Nick P. Taylor, Nik J. Cunniffe
Modelling quantitative fungicide resistance and breakdown of resistant cultivars: Designing integrated disease management strategies for Septoria of winter wheat. PLoS Comput. Biol. 19 (3) (2023)
Zhe Li, Josue Ortega Caro, Evgenia Rusak, Wieland Brendel, Matthias Bethge, Fabio Anselmi, Ankit B. Patel, Andreas S. Tolias, Xaq Pitkow
Robust deep learning object recognition models rely on low frequency information in natural images. PLoS Comput. Biol. 19 (3) (2023)
Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes
Correction: Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection. PLoS Comput. Biol. 19 (3) (2023)
William T. Harvey, Vinny Davies, Rodney S. Daniels, Lynne Whittaker, Victoria Gregory, Alan J. Hay, Dirk Husmeier, John W. McCauley, Richard E. Reeve
A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses. PLoS Comput. Biol. 19 (3) (2023)
Hakim Benkirane, Yoann Pradat, Stefan Michiels, Paul-Henry Cournède
CustOmics: A versatile deep-learning based strategy for multi-omics integration. PLoS Comput. Biol. 19 (3) (2023)
Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L. Morgan
Correction: Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses. PLoS Comput. Biol. 19 (3) (2023)
Benjamin J. Heil, Jake Crawford, Casey S. Greene
The effect of non-linear signal in classification problems using gene expression. PLoS Comput. Biol. 19 (3) (2023)
Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol
Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression. PLoS Comput. Biol. 19 (3) (2023)
Luciana Melina Luque, Carlos Manuel Carlevaro, Camilo Julio Llamoza Torres, Enrique Lomba
Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence. PLoS Comput. Biol. 19 (3) (2023)
Carlos A. Gandarilla-Pérez, Sergio Pinilla, Anne-Florence Bitbol, Martin Weigt
Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. PLoS Comput. Biol. 19 (3) (2023)
Sean A. Rands, Christos C. Ioannou
Personality variation is eroded by simple social behaviours in collective foragers. PLoS Comput. Biol. 19 (3) (2023)
Cameron Mura, Philip E. Bourne
Ten simple rules for serving as an editor. PLoS Comput. Biol. 19 (3) (2023)
Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen
Correction: A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait. PLoS Comput. Biol. 19 (3) (2023)
Darya Pokutnaya, Bruce Childers, Alice E. Arcury-Quandt, Harry Hochheiser, Willem G. Van Panhuis
An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases. PLoS Comput. Biol. 19 (3) (2023)
Chenxi Dai, Dongsheng Zhou, Bo Gao, Kaifa Wang
A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics. PLoS Comput. Biol. 19 (3) (2023)
Elias Ventre, Ulysse Herbach, Thibault Espinasse, Gérard Benoit, Olivier Gandrillon
One model fits all: Combining inference and simulation of gene regulatory networks. PLoS Comput. Biol. 19 (3) (2023)
Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chrétien, Eric Rosenthal, Gérard Le Goff, David Moher, John P. A. Ioannidis, Florian Naudet
Ten (not so) simple rules for clinical trial data-sharing. PLoS Comput. Biol. 19 (3) (2023)
Ana Morán, Mathieu Lihoreau, Alfonso Pérez-Escudero, Jacques Gautrais
Modeling bee movement shows how a perceptual masking effect can influence flower discovery. PLoS Comput. Biol. 19 (3) (2023)
Christoffer Norn, Ingemar André
Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates. PLoS Comput. Biol. 19 (3) (2023)
Karina Arias-Calluari, Theotime Colin, Tanya Latty, Mary Myerscough, Eduardo G. Altmann
Modelling daily weight variation in honey bee hives. PLoS Comput. Biol. 19 (3) (2023)
Pål Vegard Johnsen, Inga Strümke, Mette Langaas, Andrew Thomas DeWan, Signe Riemer-Sørensen
Inferring feature importance with uncertainties with application to large genotype data. PLoS Comput. Biol. 19 (3) (2023)
Hui Peng, Limsoon Wong, Wilson Wen Bin Goh
ProInfer: An interpretable protein inference tool leveraging on biological networks. PLoS Comput. Biol. 19 (3) (2023)
Jacqueline A. May, Zeny Feng, Sarah J. Adamowicz
A real data-driven simulation strategy to select an imputation method for mixed-type trait data. PLoS Comput. Biol. 19 (3) (2023)
Robert C. Glastad, Iain G. Johnston
Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions. PLoS Comput. Biol. 19 (3) (2023)
Peng Zhang, Shikui Tu
MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders. PLoS Comput. Biol. 19 (3) (2023)
David Moreau, Kristina Wiebels
Ten simple rules for designing and conducting undergraduate replication projects. PLoS Comput. Biol. 19 (3) (2023)
Eliram Nof, Saurabh Bhardwaj, Pantelis Koullapis, Ron Bessler, Stavros Kassinos, Josué Sznitman
In vitro-in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model. PLoS Comput. Biol. 19 (3) (2023)
Weiqi Lu, José N. Onuchic, Michele Di Pierro
An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput. Biol. 19 (3) (2023)