Works matching IS 1553734X AND DT 2024 AND VI 20 AND IP 2

Results: 69

Ten simple rules to leverage large language models for getting grants.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011863

By:

Seckel, Elizabeth;
Stephens, Brandi Y.;
Rodriguez, Fatima

Publication type:

Article

When do stereotypes undermine indirect reciprocity?

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011862

By:

Kawakatsu, Mari;
Michel-Mata, Sebastián;
Kessinger, Taylor A.;
Tarnita, Corina E.;
Plotkin, Joshua B.

Publication type:

Article

A multiscale computational framework for the development of spines in molluscan shells.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011835

By:

Moulton, Derek E.;
Aubert-Kato, Nathanaël;
Almet, Axel A.;
Sato, Atsuko

Publication type:

Article

Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011833

By:

Peña, Edgar;
Pelot, Nicole A.;
Grill, Warren M.

Publication type:

Article

Twelve quick tips for deploying a Beacon.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011817

By:

Fromont, Lauren A.;
Moldes, Mauricio;
Baudis, Michael;
Brookes, Anthony J.;
Navarro, Arcadi;
Rambla, Jordi

Publication type:

Article

Ten simple rules for pushing boundaries of inclusion at academic events.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011797

By:

Hall, Siobhan Mackenzie;
Kochin, Daniel;
Carne, Carmel;
Herterich, Patricia;
Lewers, Kristen Lenay;
Abdelhack, Mohamed;
Ramasubramanian, Arun;
Michael Alphonse, Juno Felecia;
Ung, Visotheary;
El-Gebali, Sara;
Currin, Christopher Brian;
Plomp, Esther;
Thompson, Rachel;
Sharan, Malvika

Publication type:

Article

Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011247

By:

Valega-Mackenzie, Wencel;
Rodriguez Messan, Marisabel;
Yogurtcu, Osman N.;
Nukala, Ujwani;
Sauna, Zuben E.;
Yang, Hong

Publication type:

Article

HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011928

By:

Voliotis, Margaritis;
Abbara, Ali;
Prague, Julia K.;
Veldhuis, Johannes D.;
Dhillo, Waljit S.;
Tsaneva-Atanasova, Krasimira

Publication type:

Article

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011919

By:

Dougherty, Bonnie V.;
Moore, Connor J.;
Rawls, Kristopher D.;
Jenior, Matthew L.;
Chun, Bryan;
Nagdas, Sarbajeet;
Saucerman, Jeffrey J.;
Kolling, Glynis L.;
Wallqvist, Anders;
Papin, Jason A.

Publication type:

Article

Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011867

By:

Kohsokabe, Takahiro;
Kuratanai, Shigeru;
Kaneko, Kunihiko

Publication type:

Article

TimeTeller: A tool to probe the circadian clock as a multigene dynamical system.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011779

By:

Vlachou, Denise;
Veretennikova, Maria;
Usselmann, Laura;
Vasilyev, Vadim;
Ott, Sascha;
Bjarnason, Georg A.;
Dallmann, Robert;
Levi, Francis;
Rand, David A.

Publication type:

Article

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011586

By:

Schaeffer, R. Dustin;
Zhang, Jing;
Medvedev, Kirill E.;
Kinch, Lisa N.;
Cong, Qian;
Grishin, Nick V.

Publication type:

Article

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011303

By:

Cockx, Bastiaan J. R.;
Foster, Tim;
Clegg, Robert J.;
Alden, Kieran;
Arya, Sankalp;
Stekel, Dov J.;
Smets, Barth F.;
Kreft, Jan-Ulrich

Publication type:

Article

Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011907

By:

Li, Pan;
Kim, Jae Kyoung

Publication type:

Article

DeepD3, an open framework for automated quantification of dendritic spines.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011774

By:

Fernholz, Martin H. P.;
Guggiana Nilo, Drago A.;
Bonhoeffer, Tobias;
Kist, Andreas M.

Publication type:

Article

STGIC: A graph and image convolution-based method for spatial transcriptomic clustering.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011935

By:

Zhang, Chen;
Gao, Junhui;
Chen, Hong-Yu;
Kong, Lingxin;
Cao, Guangshuo;
Guo, Xiangyu;
Liu, Wei;
Ren, Bin;
Wei, Dong-Qing

Publication type:

Article

Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011930

By:

Wang, Rui;
Qu, Zhilin;
Huang, Xiaodong

Publication type:

Article

Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011866

By:

Lim, Hong Seo;
Qiu, Peng

Publication type:

Article

Bidirectional de novo peptide sequencing using a transformer model.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011892

By:

Lee, Sangjeong;
Kim, Hyunwoo

Publication type:

Article

Disentangled deep generative models reveal coding principles of the human face processing network.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011887

By:

Soulos, Paul;
Isik, Leyla

Publication type:

Article

Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011108

By:

Tolley, Nicholas;
Rodrigues, Pedro L. C.;
Gramfort, Alexandre;
Jones, Stephanie R.

Publication type:

Article

Shared input and recurrency in neural networks for metabolically efficient information transmission.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011896

By:

Barta, Tomas;
Kostal, Lubomir

Publication type:

Article

A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011410

By:

Van Wouwe, Tom;
Hicks, Jennifer;
Delp, Scott;
Liu, Karen C.

Publication type:

Article

A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011267

By:

Groden, Moritz;
Moessinger, Hannah M.;
Schaffran, Barbara;
DeFelipe, Javier;
Benavides-Piccione, Ruth;
Cuntz, Hermann;
Jedlicka, Peter

Publication type:

Article

A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011880

By:

Monnier, Lily;
Cournède, Paul-Henry

Publication type:

Article

Diverse mutant selection windows shape spatial heterogeneity in evolving populations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011878

By:

King, Eshan S.;
Tadele, Dagim S.;
Pierce, Beck;
Hinczewski, Michael;
Scott, Jacob G.

Publication type:

Article

Genome scale metabolic network modelling for metabolic profile predictions.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011381

By:

Cooke, Juliette;
Delmas, Maxime;
Wieder, Cecilia;
Rodríguez Mier, Pablo;
Frainay, Clément;
Vinson, Florence;
Ebbels, Timothy;
Poupin, Nathalie;
Jourdan, Fabien

Publication type:

Article

Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011113

By:

Hay, Quintessa;
Grubb, Christopher;
Minucci, Sarah;
Valentine, Michael S.;
Van Mullekom, Jennifer;
Heise, Rebecca L.;
Reynolds, Angela M.

Publication type:

Article

EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011375

By:

Pinotti, Francesco;
Lourenço, José;
Gupta, Sunetra;
Das Gupta, Suman;
Henning, Joerg;
Blake, Damer;
Tomley, Fiona;
Barnett, Tony;
Pfeiffer, Dirk;
Hoque, Md. Ahasanul;
Fournié, Guillaume

Publication type:

Article

Connectivity Matrix Seriation via Relaxation.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011904

By:

Borst, Alexander

Publication type:

Article

Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011890

By:

Eschweiler, Dennis;
Yilmaz, Rüveyda;
Baumann, Matisse;
Laube, Ina;
Roy, Rijo;
Jose, Abin;
Brückner, Daniel;
Stegmaier, Johannes

Publication type:

Article

Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011886

By:

Schieferstein, Natalie;
Schwalger, Tilo;
Lindner, Benjamin;
Kempter, Richard

Publication type:

Article

Fast adaptation to rule switching using neuronal surprise.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011839

By:

Barry, Martin L. L. R.;
Gerstner, Wulfram

Publication type:

Article

Inference of annealed protein fitness landscapes with AnnealDCA.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011812

By:

Sesta, Luca;
Pagnani, Andrea;
Fernandez-de-Cossio-Diaz, Jorge;
Uguzzoni, Guido

Publication type:

Article

The successor representation subserves hierarchical abstraction for goal-directed behavior.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011312

By:

Wientjes, Sven;
Holroyd, Clay B.

Publication type:

Article

Ecological and evolutionary dynamics of cell-virus-virophage systems.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1010925

By:

Nino Barreat, Jose Gabriel;
Katzourakis, Aris

Publication type:

Article

Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1010706

By:

Bird, Alexander D.;
Cuntz, Hermann;
Jedlicka, Peter

Publication type:

Article

Studentsourcing—Aggregating and reusing data from a practical cell biology course.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011836

By:

Goedhart, Joachim

Publication type:

Article

Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011876

By:

Chen, Li-Dunn;
Caprio, Michael A.;
Chen, Devin M.;
Kouba, Andy J.;
Kouba, Carrie K.

Publication type:

Article

magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011875

By:

Guo, Zhenxing;
Duan, Daoyu;
Tang, Wen;
Zhu, Julia;
Bush, William S.;
Zhang, Liangliang;
Zhu, Xiaofeng;
Jin, Fulai;
Feng, Hao

Publication type:

Article

Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011868

By:

Baer, Lachlan;
Barthelson, Karissa;
Postlethwait, John H.;
Adelson, David L.;
Pederson, Stephen M.;
Lardelli, Michael

Publication type:

Article

StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011865

By:

Zhao, Jiao;
Chen, Ke;
Palsson, Bernhard O.;
Yang, Laurence

Publication type:

Article

Accounting for isoform expression increases power to identify genetic regulation of gene expression.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011857

By:

LaPierre, Nathan;
Pimentel, Harold

Publication type:

Article

Learning what matters: Synaptic plasticity with invariance to second-order input correlations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011844

By:

Brito, Carlos Stein Naves de;
Gerstner, Wulfram

Publication type:

Article

Generating synthetic population for simulating the spatiotemporal dynamics of epidemics.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011810

By:

Zhu, Kemin;
Liu, Kang;
Liu, Junli;
Shi, Yepeng;
Li, Xuan;
Zou, Hongyang;
Du, Huibin;
Yin, Ling

Publication type:

Article

An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011873

By:

Liu, Xiang;
Gillis, Nancy;
Jiang, Chang;
McCofie, Anthony;
Shaw, Timothy I.;
Tan, Aik-Choon;
Zhao, Bo;
Wan, Lixin;
Duckett, Derek R.;
Teng, Mingxiang

Publication type:

Article

CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011870

By:

Phillips, Aaron L.;
Ferguson, Scott;
Burton, Rachel A.;
Watson-Haigh, Nathan S.

Publication type:

Article

Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011860

By:

von der Dunk, Samuel H. A.;
Hogeweg, Paulien;
Snel, Berend

Publication type:

Article

Mathematical model of oxygen, nutrient, and drug transport in Tuberculosis Granulomas.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011847

By:

Datta, Meenal;
Kennedy, McCarthy;
Siri, Saeed;
Via, Laura E.;
Baish, James W.;
Xu, Lei;
Dartois, Veronique;
Barry 3rd, Clifton E.;
Jain, Rakesh K.

Publication type:

Article

Robust expansion of phylogeny for fast-growing genome sequence data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011871

By:

Ye, Yongtao;
Shum, Marcus H.;
Tsui, Joseph L.;
Yu, Guangchuang;
Smith, David K.;
Zhu, Huachen;
Wu, Joseph T.;
Guan, Yi;
Lam, Tommy Tsan-Yuk

Publication type:

Article