Works matching IS 1553734X AND DT 2022 AND VI 18 AND IP 2

Results: 72

Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009876

By:

Bokulich, Nicholas A.;
Łaniewski, Paweł;
Adamov, Anja;
Chase, Dana M.;
Caporaso, J. Gregory;
Herbst-Kralovetz, Melissa M.

Publication type:

Article

In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009918

By:

D'Antonio, Matteo;
Nguyen, Jennifer P.;
Arthur, Timothy D.;
Matsui, Hiroko;
Donovan, Margaret K. R.;
D'Antonio-Chronowska, Agnieszka;
Frazer, Kelly A.

Publication type:

Article

Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009912

By:

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

Publication type:

Article

Meta-control of social learning strategies.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009882

By:

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

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009868

By:

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

Publication type:

Article

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009909

By:

Domingo-Fernández, Daniel;
Gadiya, Yojana;
Patel, Abhishek;
Mubeen, Sarah;
Rivas-Barragan, Daniel;
Diana, Chris W.;
Misra, Biswapriya B.;
Healey, David;
Rokicki, Joe;
Colluru, Viswa

Publication type:

Article

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009907

By:

Heydari, Tiam;
A. Langley, Matthew;
Fisher, Cynthia L.;
Aguilar-Hidalgo, Daniel;
Shukla, Shreya;
Yachie-Kinoshita, Ayako;
Hughes, Michael;
M. McNagny, Kelly;
Zandstra, Peter W.

Publication type:

Article

Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009903

By:

Rosenthal, Sara Brin;
Wang, Hao;
Shi, Da;
Liu, Cin;
Abagyan, Ruben;
McEvoy, Linda K.;
Chen, Chi-Hua

Publication type:

Article

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009888

By:

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

Publication type:

Article

The role of childrens' vaccination for COVID-19—Pareto-optimal allocations of vaccines.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009872

By:

Gavish, Nir;
Katriel, Guy

Publication type:

Article

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009857

By:

Borer, Benedict;
Or, Dani

Publication type:

Article

Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009800

By:

Ferguson, Laura B.;
Roberts, Amanda J.;
Mayfield, R. Dayne;
Messing, Robert O.

Publication type:

Article

Ten simple rules for large-scale data processing.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009757

By:

Fungtammasan, Arkarachai;
Lee, Alexandra;
Taroni, Jaclyn;
Wheeler, Kurt;
Chin, Chen-Shan;
Davis, Sean;
Greene, Casey

Publication type:

Article

Comparative analyses of parasites with a comprehensive database of geno-scale metabolic models.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009870

By:

Carey, Maureen A.;
Medlock, Gregory L.;
Stolarczyk, Michał;
Petri Jr., William A.;
Guler, Jennifer L.;
Papin, Jason A.

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009807

By:

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

Publication type:

Article

Learning as filtering: Implications for spike-based plasticity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009721

By:

Jegminat, Jannes;
Surace, Simone Carlo;
Pfister, Jean-Pascal

Publication type:

Article

RecPD: A Recombination-aware measure of phylogenetic diversity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009899

By:

Bundalovic-Torma, Cedoljub;
Desveaux, Darrell;
Guttman, David S.

Publication type:

Article

Retinal optic flow during natural locomotion.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009575

By:

Matthis, Jonathan Samir;
Muller, Karl S.;
Bonnen, Kathryn L.;
Hayhoe, Mary M.

Publication type:

Article

Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009059

By:

Harrison, Genelle F.;
Leaton, Laura Ann;
Harrison, Erica A.;
Kichula, Katherine M.;
Viken, Marte K.;
Shortt, Jonathan;
Gignoux, Christopher R.;
Lie, Benedicte A.;
Vukcevic, Damjan;
Leslie, Stephen;
Norman, Paul J.

Publication type:

Article

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009871

By:

Moutoussamy, Emmanuel E.;
Waheed, Qaiser;
Binford, Greta J.;
Khan, Hanif M.;
Moran, Shane M.;
Eitel, Anna R.;
Cordes, Matthew H. J.;
Reuter, Nathalie

Publication type:

Article

Phylogenetic inference of changes in amino acid propensities with single-position resolution.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009878

By:

Klink, Galya V.;
Kalinina, Olga V.;
Bazykin, Georgii A.

Publication type:

Article

Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009653

By:

Van Liedekerke, Paul;
Gannoun, Lila;
Loriot, Axelle;
Johann, Tim;
Lemaigre, Frédéric P.;
Drasdo, Dirk

Publication type:

Article

Towards the prediction of non-peptidic epitopes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009151

By:

Zierep, Paul F.;
Vita, Randi;
Blazeska, Nina;
Moumbock, Aurélien F. A.;
Greenbaum, Jason A.;
Peters, Bjoern;
Günther, Stefan

Publication type:

Article

The correlation between cell and nucleus size is explained by an eukaryotic cell growth model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009400

By:

Wu, Yufei;
Pegoraro, Adrian F.;
Weitz, David A.;
Janmey, Paul;
Sun, Sean X.

Publication type:

Article

Computational exploration of treadmilling and protrusion growth observed in fire ant rafts.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009869

By:

Wagner, Robert J.;
Vernerey, Franck J.

Publication type:

Article

High-frequency oscillations and sequence generation in two-population models of hippocampal region CA1.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009891

By:

Braun, Wilhelm;
Memmesheimer, Raoul-Martin

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009861

By:

Ramakrishnan, Nithya;
Pillai, Sibi Raj B.;
Padinhateeri, Ranjith

Publication type:

Article

STENCIL: A web templating engine for visualizing and sharing life science datasets.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009859

By:

Sun, Qi;
Nematbakhsh, Ali;
Kuntala, Prashant K.;
Kellogg, Gretta;
Pugh, B. Franklin;
Lai, William K. M.

Publication type:

Article

Known allosteric proteins have central roles in genetic disease.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009806

By:

Abrusán, György;
Ascher, David B.;
Inouye, Michael

Publication type:

Article

Regulatory network-based imputation of dropouts in single-cell RNA sequencing data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009849

By:

Leote, Ana Carolina;
Wu, Xiaohui;
Beyer, Andreas

Publication type:

Article

Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009726

By:

Foix, Anna;
López, Daniel;
Díez-Fuertes, Francisco;
McConnell, Michael J.;
Martín-Galiano, Antonio J.

Publication type:

Article

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009389

By:

Løchen, Alessandra;
Truscott, James E.;
Croucher, Nicholas J.

Publication type:

Article

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009269

By:

Wang, Ning;
Lysenkov, Vladislav;
Orte, Katri;
Kairisto, Veli;
Aakko, Juhani;
Khan, Sofia;
Elo, Laura L.

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009874

By:

Clark, Nicholas J.;
Proboste, Tatiana;
Weerasinghe, Guyan;
Soares Magalhães, Ricardo J.

Publication type:

Article

Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009760

By:

d'Andrea, Valeria;
Gallotti, Riccardo;
Castaldo, Nicola;
De Domenico, Manlio

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009886

By:

Krishnakumaran, R;
Raees, Mohammed;
Ray, Supratim

Publication type:

Article

Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009862

By:

Diamant, Nathaniel;
Reinertsen, Erik;
Song, Steven;
Aguirre, Aaron D.;
Stultz, Collin M.;
Batra, Puneet

Publication type:

Article

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009835

By:

Irrgang, M. Eric;
Davis, Caroline;
Kasson, Peter M.

Publication type:

Article

Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009833

By:

Longo, Liam M.;
Kolodny, Rachel;
McGlynn, Shawn E.

Publication type:

Article

Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009704

By:

Arboleda-Rivera, Juan Camilo;
Machado-Rodríguez, Gloria;
Rodríguez, Boris A.;
Gutiérrez, Jayson

Publication type:

Article

Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009156

By:

Steijn, Leonie van;
Wortel, Inge M. N.;
Sire, Clément;
Dupré, Loïc;
Theraulaz, Guy;
Merks, Roeland M. H.

Publication type:

Article

A mechanistic modeling framework reveals the key principles underlying tumor metabolism.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009841

By:

Tripathi, Shubham;
Park, Jun Hyoung;
Pudakalakatti, Shivanand;
Bhattacharya, Pratip K.;
Kaipparettu, Benny Abraham;
Levine, Herbert

Publication type:

Article

Bias-free estimation of information content in temporally sparse neuronal activity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009832

By:

Sheintuch, Liron;
Rubin, Alon;
Ziv, Yaniv

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009805

By:

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

Publication type:

Article

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009855

By:

Wang, Siyu;
Reeve, Stephanie M.;
Holt, Graham T.;
Ojewole, Adegoke A.;
Frenkel, Marcel S.;
Gainza, Pablo;
Keshipeddy, Santosh;
Fowler, Vance G.;
Wright, Dennis L.;
Donald, Bruce R.

Publication type:

Article

Machine learning modeling of family wide enzyme-substrate specificity screens.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009853

By:

Goldman, Samuel;
Das, Ria;
Yang, Kevin K.;
Coley, Connor W.

Publication type:

Article

Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009836

By:

Gallinaro, Júlia V.;
Gašparović, Nebojša;
Rotter, Stefan

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009811

By:

Mines, Robert C.;
Lipniacki, Tomasz;
Shen, Xiling

Publication type:

Article

Ten simple rules for improving research data discovery.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009768

By:

Contaxis, Nicole;
Clark, Jason;
Dellureficio, Anthony;
Gonzales, Sara;
Mannheimer, Sara;
Oxley, Peter R.;
Ratajeski, Melissa A.;
Surkis, Alisa;
Yarnell, Amy M.;
Yee, Michelle;
Holmes, Kristi

Publication type:

Article

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

Published in:

2022

By:

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

Publication type:

Literature Review