Garwood, Indie C Chakravarty, Sourish Donoghue, Jacob Mahnke, Meredith Kahali, Pegah Chamadia, Shubham Akeju, Oluwaseun Miller, Earl K Brown, Emery N
Published in
PLoS computational biology
Ketamine is an NMDA receptor antagonist commonly used to maintain general anesthesia. At anesthetic doses, ketamine causes high power gamma (25-50 Hz) oscillations alternating with slow-delta (0.1-4 Hz) oscillations. These dynamics are readily observed in local field potentials (LFPs) of non-human primates (NHPs) and electroencephalogram (EEG) reco...
Durand, Marc
Published in
PLoS computational biology
Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be a possible driving source for cell sorting, no clear consensus has emerged on the kinetic law of cell sorting...
Li, Zhi-Wei Ma, Wei Ji
Published in
PLoS computational biology
When people view a consumable item for a longer amount of time, they choose it more frequently; this also seems to be the direction of causality. The leading model of this effect is a drift-diffusion model with a fixation-based attentional bias. Here, we propose an explicitly Bayesian account for the same data. This account is based on the notion t...
Mangold, Kathryn E Wang, Wei Johnson, Eric K Bhagavan, Druv Moreno, Jonathan D Nerbonne, Jeanne M Silva, Jonathan R
Published in
PLoS computational biology
Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for tw...
Qi, Jing Zhou, Yang Zhao, Zicen Jin, Shuilin
Published in
PLoS computational biology
The single-cell RNA sequencing (scRNA-seq) technologies obtain gene expression at single-cell resolution and provide a tool for exploring cell heterogeneity and cell types. As the low amount of extracted mRNA copies per cell, scRNA-seq data exhibit a large number of dropouts, which hinders the downstream analysis of the scRNA-seq data. We propose a...
Gardner, Billy J Kilpatrick, A Marm
Published in
PLoS computational biology
Simultaneously controlling COVID-19 epidemics and limiting economic and societal impacts presents a difficult challenge, especially with limited public health budgets. Testing, contact tracing, and isolating/quarantining is a key strategy that has been used to reduce transmission of SARS-CoV-2, the virus that causes COVID-19 and other pathogens. Ho...
Lu, Fred S Nguyen, Andre T Link, Nicholas B Molina, Mathieu Davis, Jessica T Chinazzi, Matteo Xiong, Xinyue Vespignani, Alessandro Lipsitch, Marc Santillana, Mauricio
...
Published in
PLoS computational biology
Effectively designing and evaluating public health responses to the ongoing COVID-19 pandemic requires accurate estimation of the prevalence of COVID-19 across the United States (US). Equipment shortages and varying testing capabilities have however hindered the usefulness of the official reported positive COVID-19 case counts. We introduce four co...
Kameda, Takeru Asano, Katsura Togashi, Yuichi
Published in
PLoS computational biology
Specific interaction between the start codon, 5'-AUG-3', and the anticodon, 5'-CAU-3', ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribo...
Aydin, Ali-Kemal Haselden, William D Dang, Julie Drew, Patrick J Charpak, Serge Boido, Davide
Published in
PLoS computational biology
Understanding the relationships between biological processes is paramount to unravel pathophysiological mechanisms. These relationships can be modeled with Transfer Functions (TFs), with no need of a priori hypotheses as to the shape of the transfer function. Here we present Iliski, a software dedicated to TFs computation between two signals. It in...
Sandhu, Simran K Bayliss, Christopher D Morozov, Andrew Yu
Published in
PLoS computational biology
Campylobacter jejuni (C. jejuni) causes gastroenteritis following the consumption of contaminated poultry meat, resulting in a large health and economic burden worldwide. Phage therapy is a promising technique for eradicating C. jejuni from poultry flocks and chicken carcasses. However, C. jejuni can resist infections by some phages through stochas...
