Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 8

Results: 53

Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae506

By:

Weiner, Samson;
Li, Bingjun;
Nabavi, Sheida

Publication type:

Article

ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae507

By:

Li, Douyue;
Min, Zhuochao;
Guo, Jia;
Chen, Yubin;
Zhang, Wenliang

Publication type:

Article

Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae517

By:

Gotoh, Osamu

Publication type:

Article

WatFinder: a ProDy tool for protein–water interactions.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae516

By:

Krieger, James M;
Doljanin, Frane;
Bogetti, Anthony T;
Zhang, Feng;
Manivarma, Thiliban;
Bahar, Ivet;
Mikulska-Ruminska, Karolina

Publication type:

Article

Estimating the mean in the space of ranked phylogenetic trees.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae514

By:

Berling, Lars;
Collienne, Lena;
Gavryushkin, Alex

Publication type:

Article

CatReNet: interactive analysis of (auto-) catalytic reaction networks.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae515

By:

Huson, Daniel H;
Xavier, Joana C;
Steel, Mike A

Publication type:

Article

Disease gene prioritization with quantum walks.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae513

By:

Saarinen, Harto;
Goldsmith, Mark;
Wang, Rui-Sheng;
Loscalzo, Joseph;
Maniscalco, Sabrina

Publication type:

Article

cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae511

By:

Yu, Shilin;
Meng, Guanqun;
Tang, Wen;
Ma, Wenjing;
Wang, Rui;
Zhu, Xiongwei;
Sun, Xiaobo;
Feng, Hao

Publication type:

Article

Publication-ready single nucleotide polymorphism visualization with snipit.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae510

By:

O'Toole, Áine;
Aziz, Ammar;
Maloney, Daniel

Publication type:

Article

pyTWMR: transcriptome-wide Mendelian randomization in python.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae505

By:

Oreshkov, Sergey;
Lepik, Kaido;
Santoni, Federico

Publication type:

Article

TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae502

By:

Wang, Anqi;
Tian, Peixin;
Zhang, Yan Dora

Publication type:

Article

grenedalf: population genetic statistics for the next generation of pool sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae508

By:

Czech, Lucas;
Spence, Jeffrey P;
Expósito-Alonso, Moisés

Publication type:

Article

popDMS infers mutation effects from deep mutational scanning data.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae499

By:

Hong, Zhenchen;
Shimagaki, Kai S;
Barton, John P

Publication type:

Article

Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae504

By:

Li, Fuyi;
Bi, Yue;
Guo, Xudong;
Tan, Xiaolan;
Wang, Cong;
Pan, Shirui

Publication type:

Article

BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae461

By:

Luo, Hanyu;
Tang, Li;
Zeng, Min;
Yin, Rui;
Ding, Pingjian;
Luo, Lingyun;
Li, Min

Publication type:

Article

An Ensemble Spectral Prediction (ESP) model for metabolite annotation.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae490

By:

Li, Xinmeng;
Chen, Yan Zhou;
Kalia, Apurva;
Zhu, Hao;
Liu, Li-ping;
Hassoun, Soha

Publication type:

Article

Interactive visualization of nanopore sequencing signal data with Squigualiser.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae501

By:

Samarakoon, Hiruna;
Liyanage, Kisaru;
Ferguson, James M;
Parameswaran, Sri;
Gamaarachchi, Hasindu;
Deveson, Ira W

Publication type:

Article

ceas: an R package for Seahorse data analysis and visualization.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae503

By:

House, Rachel (Rae) J;
Eapen, James P;
Shen, Hui;
Graveel, Carrie R;
Steensma, Matthew R

Publication type:

Article

RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae478

By:

Firtina, Can;
Soysal, Melina;
Lindegger, Joël;
Mutlu, Onur

Publication type:

Article

Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae498

By:

Lee, Hanbin;
Han, Buhm

Publication type:

Article

PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae497

By:

Hao, Yuelei;
Liu, Xuyang;
Fu, Haohao;
Shao, Xueguang;
Cai, Wensheng

Publication type:

Article

Attention-based approach to predict drug–target interactions across seven target superfamilies.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae496

By:

Schulman, Aron;
Rousu, Juho;
Aittokallio, Tero;
Tanoli, Ziaurrehman

Publication type:

Article

R2Dtool: integration and visualization of isoform-resolved RNA features.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae495

By:

Sethi, Aditya J;
Mateos, Pablo Acera;
Hayashi, Rippei;
Shirokikh, Nikolay E;
Eyras, Eduardo

Publication type:

Article

Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae494

By:

Weine, Eric;
Carbonetto, Peter;
Stephens, Matthew

Publication type:

Article

ModDotPlot—rapid and interactive visualization of tandem repeats.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae493

By:

Sweeten, Alexander P;
Schatz, Michael C;
Phillippy, Adam M

Publication type:

Article

Locuaz: an in silico platform for protein binders optimization.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae492

By:

Barletta, German P;
Tandiana, Rika;
Soler, Miguel;
Fortuna, Sara;
Rocchia, Walter

Publication type:

Article

Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae491

By:

Edmunds, Nicholas S;
Genc, Ahmet G;
McGuffin, Liam J

Publication type:

Article

TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae475

By:

Surana, Pallavi;
Dutta, Pratik;
Davuluri, Ramana V

Publication type:

Article

TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae472

By:

Kim, Ha Young;
Kim, Sungsik;
Park, Woong-Yang;
Kim, Dongsup

Publication type:

Article

FAIRsoft—a practical implementation of FAIR principles for research software.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae464

By:

Pico, Eva Martín del;
Gelpí, Josep Lluís;
Capella-Gutierrez, Salvador

Publication type:

Article

GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae489

By:

Talwar, James V;
Klie, Adam;
Pagadala, Meghana S;
Carter, Hannah

Publication type:

Article

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae488

By:

Grégam, Loïc Le;
Guitton, Yann;
Bellvert, Floriant;
Heux, Stéphanie;
Jourdan, Fabien;
Portais, Jean-Charles;
Millard, Pierre

Publication type:

Article

Epigenomics coverage data extraction and aggregation in R with tidyCoverage.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae487

By:

Serizay, Jacques;
Koszul, Romain

Publication type:

Article

Galaxy Helm chart: a standardized method for deploying production Galaxy servers.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae486

By:

Goonasekera, Nuwan;
Mahmoud, Alexandru;
Suderman, Keith;
Afgan, Enis

Publication type:

Article

Genome-wide detection of somatic mosaicism at short tandem repeats.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae485

By:

Sehgal, Aarushi;
Jam, Helyaneh Ziaei;
Shen, Andrew;
Gymrek, Melissa

Publication type:

Article

Enabling population protein dynamics through Bayesian modeling.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae484

By:

Lehmann, Sylvain;
Vialaret, Jérôme;
Gabelle, Audrey;
Bauchet, Luc;
Villemin, Jean-Philippe;
Hirtz, Christophe;
Colinge, Jacques

Publication type:

Article

Cellular proliferation biases clonal lineage tracing and trajectory inference.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae483

By:

Bonham-Carter, Becca;
Schiebinger, Geoffrey

Publication type:

Article

Generation of a high confidence set of domain–domain interface types to guide protein complex structure predictions by AlphaFold.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae482

By:

Geist, Johanna Lena;
Lee, Chop Yan;
Strom, Joelle Morgan;
Naveja, José de Jesús;
Luck, Katja

Publication type:

Article

DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae481

By:

Elkayam, Shai;
Tziony, Ido;
Orenstein, Yaron

Publication type:

Article

ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae480

By:

Ba, Teer;
Miao, Hao;
Zhang, Lirong;
Gao, Caixia;
Wang, Yong

Publication type:

Article

HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen–Deuterium Exchange Mass-Spectrometry datasets of different protein states.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae479

By:

Janowska, Maria K;
Reiter, Katherine;
Magala, Pearl;
Guttman, Miklos;
Klevit, Rachel E

Publication type:

Article

New GO-based measures in multiple network alignment.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae476

By:

Yazdani, Kimia;
Mousapour, Reza;
Hayes, Wayne B

Publication type:

Article

AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae477

By:

Rashid, Usman;
Wu, Chen;
Shiller, Jason;
Smith, Ken;
Crowhurst, Ross;
Davy, Marcus;
Chen, Ting-Hsuan;
Carvajal, Ignacio;
Bailey, Sarah;
Thomson, Susan;
Deng, Cecilia H

Publication type:

Article

MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae473

By:

Yu, Yunxiang;
Gu, Mengyun;
Guo, Hai;
Deng, Yabo;
Chen, Danna;
Wang, Jianwei;
Wang, Caixia;
Liu, Xia;
Yan, Wenjin;
Huang, Jinqi

Publication type:

Article

BELHD: improving biomedical entity linking with homonym disambiguation.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae474

By:

Garda, Samuele;
Leser, Ulf

Publication type:

Article

Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae463

By:

Gao, Jiahao;
Gerstein, Mark

Publication type:

Article

Best practices to evaluate the impact of biomedical research software—metric collection beyond citations.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae469

By:

Afiaz, Awan;
Ivanov, Andrey A;
Chamberlin, John;
Hanauer, David;
Savonen, Candace L;
Goldman, Mary J;
Morgan, Martin;
Reich, Michael;
Getka, Alexander;
Holmes, Aaron;
Pati, Sarthak;
Knight, Dan;
Boutros, Paul C;
Bakas, Spyridon;
Caporaso, J Gregory;
Fiol, Guilherme Del;
Hochheiser, Harry;
Haas, Brian;
Schloss, Patrick D;
Eddy, James A

Publication type:

Article

PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae467

By:

Wu, Kwan-Ling;
Montalvo, Melisa J;
Menon, Prashant S;
Roysam, Badrinath;
Varadarajan, Navin

Publication type:

Article

Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae465

By:

Silberberg, Mauro;
Hermjakob, Henning;
Malik-Sheriff, Rahuman S;
Grecco, Hernán E

Publication type:

Article

GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae462

By:

Montoto-Louzao, Julián;
Gómez-Carballa, Alberto;
Bello, Xabier;
Pardo-Seco, Jacobo;
Camino-Mera, Alba;
Viz-Lasheras, Sandra;
Martín, María J;
Martinón-Torres, Federico;
Salas, Antonio

Publication type:

Article