Works matching IS 1553734X AND DT 2024 AND VI 20 AND IP 8

Results: 55

ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012400

By:

Wang, Tao;
Zhuo, Linlin;
Chen, Yifan;
Fu, Xiangzheng;
Zeng, Xiangxiang;
Zou, Quan

Publication type:

Article

Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011924

By:

Seeler, Daniel;
Grdseloff, Nastasja;
Rödel, Claudia Jasmin;
Kloft, Charlotte;
Abdelilah-Seyfried, Salim;
Huisinga, Wilhelm

Publication type:

Article

Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012408

By:

Ney, Alexander;
Nené, Nuno R.;
Sedlak, Eva;
Acedo, Pilar;
Blyuss, Oleg;
Whitwell, Harry J.;
Costello, Eithne;
Gentry-Maharaj, Aleksandra;
Williams, Norman R.;
Menon, Usha;
Fusai, Giuseppe K.;
Zaikin, Alexey;
Pereira, Stephen P.

Publication type:

Article

CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012344

By:

Tao, Yicheng;
Feng, Fan;
Luo, Xin;
Reihsmann, Conrad V.;
Hopkirk, Alexander L.;
Cartailler, Jean-Philippe;
Brissova, Marcela;
Parker, Stephen C. J.;
Saunders, Diane C.;
Liu, Jie

Publication type:

Article

IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012389

By:

Shi, Peiting;
Han, Junmin;
Zhang, Yinghao;
Li, Guanpu;
Zhou, Xionghui

Publication type:

Article

Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012385

By:

Cohen-Davidi, Efrat;
Veksler-Lublinsky, Isana

Publication type:

Article

Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012356

By:

Ramamurthy, Easwaran;
Agarwal, Snigdha;
Toong, Noelle;
Sestili, Heather;
Kaplow, Irene M.;
Chen, Ziheng;
Phan, BaDoi;
Pfenning, Andreas R.

Publication type:

Article

MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012336

By:

Dey, Anubha;
Mudunuri, Suresh;
Kiran, Manjari

Publication type:

Article

aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012361

By:

Schirmacher, Daniel;
Armagan, Ümmünur;
Zhang, Yang;
Kull, Tobias;
Auler, Markus;
Schroeder, Timm

Publication type:

Article

iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012399

By:

Yuan, Lin;
Zhao, Ling;
Lai, Jinling;
Jiang, Yufeng;
Zhang, Qinhu;
Shen, Zhen;
Zheng, Chun-Hou;
Huang, De-Shuang

Publication type:

Article

Signatures of hierarchical temporal processing in the mouse visual system.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012355

By:

Rudelt, Lucas;
González Marx, Daniel;
Spitzner, F. Paul;
Cramer, Benjamin;
Zierenberg, Johannes;
Priesemann, Viola

Publication type:

Article

A comprehensive data-driven model of cat primary visual cortex.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012342

By:

Antolík, Ján;
Cagnol, Rémy;
Rózsa, Tibor;
Monier, Cyril;
Frégnac, Yves;
Davison, Andrew P.

Publication type:

Article

The rules of multiplayer cooperation in networks of communities.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012388

By:

Pires, Diogo L.;
Broom, Mark

Publication type:

Article

In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011539

By:

Bolaji, Ayooluwa J.;
Duggan, Ana T.

Publication type:

Article

Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011940

By:

Byrne, Catherine M;
Márquez, Ana Citlali;
Cai, Bing;
Coombs, Daniel;
Gantt, Soren

Publication type:

Article

Quantifying the risk of spillover reduction programs for human health.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012358

By:

Nuismer, Scott L.;
Basinski, Andrew J.;
Schreiner, Courtney L.;
Eskew, Evan A.;
Fichet-Calvet, Elisabeth;
Remien, Christopher H.

Publication type:

Article

Ten simple rules for successfully managing EU research grants.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012335

By:

Pina, David G.

Publication type:

Article

Estimating orientation in natural scenes: A spiking neural network model of the insect central complex.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011913

By:

Stentiford, Rachael;
Knight, James C.;
Nowotny, Thomas;
Philippides, Andrew;
Graham, Paul

Publication type:

Article

Influence of surprise on reinforcement learning in younger and older adults.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012331

By:

Koch, Christoph;
Zika, Ondrej;
Bruckner, Rasmus;
Schuck, Nicolas W.

Publication type:

Article

Alternate conformational trajectories in ribosome translocation.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012319

By:

Alejo, Jose L.;
Girodat, Dylan;
Hammerling, Michael J.;
Willi, Jessica A.;
Jewett, Michael C.;
Engelhart, Aaron E.;
Adamala, Katarzyna P.

Publication type:

Article

A proactive/reactive mass screening approach with uncertain symptomatic cases.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012308

By:

Lin, Jiayi;
Aprahamian, Hrayer;
Golovko, George

Publication type:

Article

Impact of oxygen and glucose availability on the viability and connectivity of islet cells: A computational study of reconstructed avascular human islets.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012357

By:

Félix-Martínez, Gerardo J.;
Osorio-Londoño, Diana;
Godínez-Fernández, J. Rafael

Publication type:

Article

The Na<sup>+</sup>/K<sup>+</sup>-ATPase generically enables deterministic bursting in class I neurons by shearing the spike-onset bifurcation structure.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011751

By:

Behbood, Mahraz;
Lemaire, Louisiane;
Schleimer, Jan-Hendrik;
Schreiber, Susanne

Publication type:

Article

OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011723

By:

Dean, William F.;
Nawara, Tomasz J.;
Albert, Rose M.;
Mattheyses, Alexa L.

Publication type:

Article

Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012003

By:

Syga, Simon;
Jain, Harish P.;
Krellner, Marcus;
Hatzikirou, Haralampos;
Deutsch, Andreas

Publication type:

Article

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012339

By:

Qian, Yuqing;
Zou, Quan;
Zhao, Mengyuan;
Liu, Yi;
Guo, Fei;
Ding, Yijie

Publication type:

Article

Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012309

By:

Bouros, Ioana;
Hill, Edward M.;
Keeling, Matt J.;
Moore, Sam;
Thompson, Robin N.

Publication type:

Article

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning.

Published in:: PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012260
Publication type:: Article

Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012376

By:

Mahjoory, Keyvan;
Bahmer, Andreas;
Henry, Molly J.

Publication type:

Article

Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012345

By:

Xiong, Yunfeng;
Wang, Chuntian;
Zhang, Yuan

Publication type:

Article

Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012211

By:

Saad-Roy, Chadi M.;
Morris, Sinead E.;
Boots, Mike;
Baker, Rachel E.;
Lewis, Bryan L.;
Farrar, Jeremy;
Marathe, Madhav V.;
Graham, Andrea L.;
Levin, Simon A.;
Wagner, Caroline E.;
Metcalf, C. Jessica E.;
Grenfell, Bryan T.

Publication type:

Article

Rhythmidia: A modern tool for circadian period analysis of filamentous fungi.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012167

By:

Keeley, Alex T.;
Lotthammer, Jeffrey M.;
Pelham, Jacqueline F.

Publication type:

Article

Bacteria face trade-offs in the decomposition of complex biopolymers.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012320

By:

Guseva, Ksenia;
Mohrlok, Moritz;
Alteio, Lauren;
Schmidt, Hannes;
Pollak, Shaul;
Kaiser, Christina

Publication type:

Article

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011831

By:

Concha-Eloko, Robby;
Stock, Michiel;
De Baets, Bernard;
Briers, Yves;
Sanjuan, Rafael;
Domingo-Calap, Pilar;
Boeckaerts, Dimitri

Publication type:

Article

Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012296

By:

Puebla, Iratxe;
Ascoli, Giorgio A.;
Blume, Jeffrey;
Chodacki, John;
Finnell, Joshua;
Kennedy, David N.;
Mair, Bernard;
Martone, Maryann E.;
Wittenberg, Jamie;
Poline, Jean-Baptiste

Publication type:

Article

Credibility assessment of in silico clinical trials for medical devices.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012289

By:

Pathmanathan, Pras;
Aycock, Kenneth;
Badal, Andreu;
Bighamian, Ramin;
Bodner, Jeff;
Craven, Brent A.;
Niederer, Steven

Publication type:

Article

Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012341

By:

Mykuliak, Vasyl V.;
Rahikainen, Rolle;
Ball, Neil J.;
Bussi, Giovanni;
Goult, Benjamin T.;
Hytönen, Vesa P.

Publication type:

Article

Attentional selection and communication through coherence: Scope and limitations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011431

By:

Greenwood, Priscilla E.;
Ward, Lawrence M.

Publication type:

Article

Bird song comparison using deep learning trained from avian perceptual judgments.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012329

By:

Zandberg, Lies;
Morfi, Veronica;
George, Julia M.;
Clayton, David F.;
Stowell, Dan;
Lachlan, Robert F.

Publication type:

Article

Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012282

By:

Murata, Hiroto;
Toko, Kazuma;
Chikenji, George

Publication type:

Article

rtestim: Time-varying reproduction number estimation with trend filtering.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012324

By:

Liu, Jiaping;
Cai, Zhenglun;
Gustafson, Paul;
McDonald, Daniel J.

Publication type:

Article

Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012343

By:

Commichaux, Seth;
Luan, Tu;
Muralidharan, Harihara Subrahmaniam;
Pop, Mihai

Publication type:

Article

An optimal normalization method for high sparse compositional microbiome data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012338

By:

Sohn, Michael B.;
Monaco, Cynthia;
Gill, Steven R.

Publication type:

Article

Reliable estimation of tree branch lengths using deep neural networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. N.PAG, doi. 10.1371/journal.pcbi.1012337

By:

Suvorov, Anton;
Schrider, Daniel R.

Publication type:

Article

A transfer learning approach to identify Plasmodium in microscopic images.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012327

By:

Ramos, Jonathan da Silva;
Vieira, Ivo Henrique Provensi;
Rocha, Wan Song;
Esquerdo, Rosimar Pires;
Watanabe, Carolina Yukari Veludo;
Zanchi, Fernando Berton

Publication type:

Article

Upper bounds for integrated information.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012323

By:

Zaeemzadeh, Alireza;
Tononi, Giulio

Publication type:

Article

A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012321

By:

Schmidt, Andrew A.;
Grosberg, Alexander Y.;
Grosberg, Anna

Publication type:

Article

Diffusion model predicts the geometry of actin cytoskeleton from cell morphology.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. N.PAG, doi. 10.1371/journal.pcbi.1012312

By:

Li, Honghan;
Liu, Shiyou;
Deguchi, Shinji;
Matsunaga, Daiki

Publication type:

Article

A quantitative description of light-limited cyanobacterial growth using flux balance analysis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012280

By:

Höper, Rune;
Komkova, Daria;
Zavřel, Tomáš;
Steuer, Ralf

Publication type:

Article

COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012275

By:

Rintala, Teemu J.;
Fortino, Vittorio

Publication type:

Article