Works matching IS 1553734X AND DT 2024 AND VI 20 AND IP 9

Results: 75

HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012501

By:

Zeira, Ron;
Anavy, Leon;
Yakhini, Zohar;
Rivlin, Ehud;
Freedman, Daniel

Publication type:

Article

Managing spatio-temporal heterogeneity of susceptibles by embedding it into an homogeneous model: A mechanistic and deep learning study.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012497

By:

Tang, Biao;
Ma, Kexin;
Liu, Yan;
Wang, Xia;
Tang, Sanyi;
Xiao, Yanni;
Cheke, Robert A.

Publication type:

Article

Study of impacts of two types of cellular aging on the yeast bud morphogenesis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012491

By:

Tsai, Kevin;
Zhou, Zhen;
Yang, Jiadong;
Xu, Zhiliang;
Xu, Shixin;
Zandi, Roya;
Hao, Nan;
Chen, Weitao;
Alber, Mark

Publication type:

Article

Exploring the potential of structure-based deep learning approaches for T cell receptor design.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012489

By:

Ribeiro-Filho, Helder V.;
Jara, Gabriel E.;
Guerra, João V. S.;
Cheung, Melyssa;
Felbinger, Nathaniel R.;
Pereira, José G. C.;
Pierce, Brian G.;
Lopes-de-Oliveira, Paulo S.

Publication type:

Article

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012480

By:

Kumagai, Yutaro

Publication type:

Article

A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012462

By:

Molaro, Margherita;
Mohan, Sakshi;
She, Bingling;
Chalkley, Martin;
Colbourn, Tim;
Collins, Joseph H.;
Connolly, Emilia;
Graham, Matthew M.;
Janoušková, Eva;
Li Lin, Ines;
Manthalu, Gerald;
Mnjowe, Emmanuel;
Nkhoma, Dominic;
Twea, Pakwanja D.;
Phillips, Andrew N.;
Revill, Paul;
Tamuri, Asif U.;
Mfutso-Bengo, Joseph;
Mangal, Tara D.;
Hallett, Timothy B.

Publication type:

Article

Integrating dynamic models and neural networks to discover the mechanism of meteorological factors on Aedes population.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012499

By:

Zhang, Mengze;
Wang, Xia;
Tang, Sanyi

Publication type:

Article

Emergent ecological patterns and modelling of gut microbiomes in health and in disease.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012482

By:

Pasqualini, Jacopo;
Facchin, Sonia;
Rinaldo, Andrea;
Maritan, Amos;
Savarino, Edoardo;
Suweis, Samir

Publication type:

Article

The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012471

By:

Velázquez-Vargas, Carlos A.;
Daw, Nathaniel D.;
Taylor, Jordan A.

Publication type:

Article

Effect of aberrant fructose metabolism following SARS-CoV-2 infection on colorectal cancer patients' poor prognosis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012412

By:

Jiang, Jiaxin;
Meng, Xiaona;
Wang, Yibo;
Zhuang, Ziqian;
Du, Ting;
Yan, Jing

Publication type:

Article

HELP: A computational framework for labelling and predicting human common and context-specific essential genes.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012076

By:

Granata, Ilaria;
Maddalena, Lucia;
Manzo, Mario;
Guarracino, Mario Rosario;
Giordano, Maurizio

Publication type:

Article

GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011632

By:

Le Sueur, Cecile;
Rattray, Magnus;
Savitski, Mikhail

Publication type:

Article

A hierarchy of metabolite exchanges in metabolic models of microbial species and communities.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012472

By:

Wedmark, Ylva Katarina;
Vik, Jon Olav;
Øyås, Ove

Publication type:

Article

Celebrating a body of work.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012441

By:

Papin, Jason A.;
Mac Gabhann, Feilim;
Pitzer, Virginia E.

Publication type:

Article

The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012436

By:

Miu, Elena;
Rendell, Luke;
Bowles, Sam;
Boyd, Rob;
Cownden, Daniel;
Enquist, Magnus;
Eriksson, Kimmo;
Feldman, Marcus W.;
Lillicrap, Timothy;
McElreath, Richard;
Murray, Stuart;
Ounsley, James;
Lala, Kevin N.

Publication type:

Article

Impact of occluder device configurations in in-silico left atrial hemodynamics for the analysis of device-related thrombus.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011546

By:

Albors, Carlos;
Mill, Jordi;
Olivares, Andy L.;
Iriart, Xavier;
Cochet, Hubert;
Camara, Oscar

Publication type:

Article

Language models outperform cloze predictability in a cognitive model of reading.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012117

By:

Lopes Rego, Adrielli Tina;
Snell, Joshua;
Meeter, Martijn

Publication type:

Article

GenoTriplo: A SNP genotype calling method for triploids.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012483

By:

Roche, Julien;
Besson, Mathieu;
Allal, François;
Haffray, Pierrick;
Patrice, Pierre;
Vandeputte, Marc;
Phocas, Florence

Publication type:

Article

Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012426

By:

Stock, Michiel;
Van Criekinge, Wim;
Boeckaerts, Dimitri;
Taelman, Steff;
Van Haeverbeke, Maxime;
Dewulf, Pieter;
De Baets, Bernard

Publication type:

Article

Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012457

By:

Malamud, Jolanda;
Guloksuz, Sinan;
van Winkel, Ruud;
Delespaul, Philippe;
De Hert, Marc A. F.;
Derom, Catherine;
Thiery, Evert;
Jacobs, Nele;
Rutten, Bart P. F.;
Huys, Quentin J. M.

Publication type:

Article

A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012452

By:

Keeling, Matt J.;
Dyson, Louise

Publication type:

Article

The neural dynamics associated with computational complexity.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012447

By:

Franco, Juan Pablo;
Bossaerts, Peter;
Murawski, Carsten

Publication type:

Article

Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012428

By:

Atapour, Nafiseh;
Rosa, Marcello G. P.;
Bai, Shi;
Bednarek, Sylwia;
Kulesza, Agata;
Saworska, Gabriela;
Teymornejad, Sadaf;
Worthy, Katrina H.;
Majka, Piotr

Publication type:

Article

Impact of phylogeny on the inference of functional sectors from protein sequence data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012091

By:

Dietler, Nicola;
Abbara, Alia;
Choudhury, Subham;
Bitbol, Anne-Florence

Publication type:

Article

Ten simple rules for successfully carrying out funded research projects.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012431

By:

Forero, Diego A.;
Curioso, Walter H.;
Wang, Wei

Publication type:

Article

Ten quick tips for ensuring machine learning model validity.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012402

By:

Goh, Wilson Wen Bin;
Kabir, Mohammad Neamul;
Yoo, Sehwan;
Wong, Limsoon

Publication type:

Article

Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.

Published in:

2024

By:

Prem, Kiesha;
Zandvoort, Kevin van;
Klepac, Petra;
Eggo, Rosalind M.;
Davies, Nicholas G.

Publication type:

Correction Notice

Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011649

By:

Bastien, G. Eric;
Cable, Rachel N.;
Batterbee, Cecelia;
Wing, A. J.;
Zaman, Luis;
Duhaime, Melissa B.

Publication type:

Article

Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012469

By:

Li, Ke;
Chaguza, Chrispin;
Stamp, Julian;
Chew, Yi Ting;
Chen, Nicholas F. G.;
Ferguson, David;
Pandya, Sameer;
Kerantzas, Nick;
Schulz, Wade;
Hahn, Anne M.;
Ogbunugafor, C. Brandon;
Pitzer, Virginia E.;
Crawford, Lorin;
Weinberger, Daniel M.;
Grubaugh, Nathan D.

Publication type:

Article

Measuring and understanding information storage and transfer in a simulated human gut microbiome.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012359

By:

Zoller, Hannah;
Garcia Perez, Carlos;
Betel Geijo Fernández, Javier;
zu Castell, Wolfgang

Publication type:

Article

The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012459

By:

Amaral, Anibal S.;
Devos, Damien P.

Publication type:

Article

Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012422

By:

Blimkie, Travis M.;
An, Andy;
Hancock, Robert E. W.

Publication type:

Article

Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011718

By:

Tammi, Silja;
Koskela, Satu;
Biobank, Blood Service;
Hyvärinen, Kati;
Partanen, Jukka;
Ritari, Jarmo

Publication type:

Article

Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012411

By:

Luis, Israel;
Afschrift, Maarten;
De Groote, Friedl;
Gutierrez-Farewik, Elena M.

Publication type:

Article

Noise leads to the perceived increase in evolutionary rates over short time scales.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012458

By:

O'Meara, Brian C.;
Beaulieu, Jeremy M.

Publication type:

Article

AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011609

By:

Golumbeanu, Monica;
Briët, Olivier;
Champagne, Clara;
Lemant, Jeanne;
Winkel, Munir;
Zogo, Barnabas;
Gerhards, Maximilian;
Sinka, Marianne;
Chitnis, Nakul;
Penny, Melissa;
Pothin, Emilie;
Smith, Tom

Publication type:

Article

Comparison and benchmark of deep learning methods for non-coding RNA classification.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012446

By:

Creux, Constance;
Zehraoui, Farida;
Radvanyi, François;
Tahi, Fariza

Publication type:

Article

Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012445

By:

Pfennig, Tobias;
Kullmann, Elena;
Zavřel, Tomáš;
Nakielski, Andreas;
Ebenhöh, Oliver;
Červený, Jan;
Bernát, Gábor;
Matuszyńska, Anna Barbara

Publication type:

Article

Calibrating dimension reduction hyperparameters in the presence of noise.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012427

By:

Lin, Justin;
Fukuyama, Julia

Publication type:

Article

An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012417

By:

Steiert, Daniel;
Wittig, Corey;
Banerjee, Priyanka;
Preissner, Robert;
Szulcek, Robert

Publication type:

Article

Ten simple rules for training scientists to make better software.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012410

By:

Gallagher, Kit;
Creswell, Richard;
Lambert, Ben;
Robinson, Martin;
Lok Lei, Chon;
Mirams, Gary R.;
Gavaghan, David J.

Publication type:

Article

Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012384

By:

Plaisier, Seema B.;
Alarid, Danielle O.;
Denning, Joelle A.;
Brownell, Sara E.;
Buetow, Kenneth H.;
Cooper, Katelyn M.;
Wilson, Melissa A.

Publication type:

Article

SEMbap: Bow-free covariance search and data de-correlation.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012448

By:

Grassi, Mario;
Tarantino, Barbara

Publication type:

Article

The primacy model and the structure of olfactory space.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012379

By:

Giaffar, Hamza;
Shuvaev, Sergey;
Rinberg, Dmitry;
Koulakov, Alexei A.

Publication type:

Article

Oscillations in an artificial neural network convert competing inputs into a temporal code.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012429

By:

Duecker, Katharina;
Idiart, Marco;
van Gerven, Marcel;
Jensen, Ole

Publication type:

Article

Construct prognostic models of multiple myeloma with pathway information incorporated.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012444

By:

Wang, Shuo;
Wang, ShanJin;
Pan, Wei;
Yi, YuYang;
Lu, Junyan

Publication type:

Article

Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012435

By:

Sylla, Ahmadou;
Chevillon, Christine;
Djidjiou-Demasse, Ramsès;
Seydi, Ousmane;
Campos, Carlos A. Vargas;
Dogbe, Magdalene;
Fast, Kayla M.;
Pechal, Jennifer L.;
Rakestraw, Alex;
Scott, Matthew E.;
Sandel, Michael W.;
Jordan, Heather;
Benbow, Mark Eric;
Guégan, Jean-François

Publication type:

Article

Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012434

By:

Vemparala, Bharadwaj;
Madelain, Vincent;
Passaes, Caroline;
Millet, Antoine;
Avettand-Fenoel, Véronique;
Djidjou-Demasse, Ramsès;
Dereuddre-Bosquet, Nathalie;
Le Grand, Roger;
Rouzioux, Christine;
Vaslin, Bruno;
Sáez-Cirión, Asier;
Guedj, Jérémie;
Dixit, Narendra M.

Publication type:

Article

Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1012423

By:

Green, Adrian J.;
Truong, Lisa;
Thunga, Preethi;
Leong, Connor;
Hancock, Melody;
Tanguay, Robyn L.;
Reif, David M.

Publication type:

Article

Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011806

By:

Yang, Janice;
Daily, Neil J.;
Pullinger, Taylor K.;
Wakatsuki, Tetsuro;
Sobie, Eric A.

Publication type:

Article