Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 9

Results: 60

Correction to: Online bias-aware disease module mining with ROBUST-Web.

Published in:: 2023
Publication type:: Correction Notice

BQsupports: systematic assessment of the support and novelty of new biomedical associations.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad581

By:

Fernández-Torras, Adrià;
Locatelli, Martina;
Bertoni, Martino;
Aloy, Patrick

Publication type:

Article

Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad576

By:

He, Xin;
Huang, Xianhui;
Long, Yuexuan;
Liu, Zhenping;
Chang, Xing;
Zhang, Xianlong;
Wang, Maojun

Publication type:

Article

Correction to: Clustering spatial transcriptomics data.

Published in:: 2023
Publication type:: Correction Notice

AFsample: improving multimer prediction with AlphaFold using massive sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad573

By:

Wallner, Björn

Publication type:

Article

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad570

By:

Callaghan, Jackson;
Xu, Colleen H;
Xin, Jiwen;
Cano, Marco Alvarado;
Riutta, Anders;
Zhou, Eric;
Juneja, Rohan;
Yao, Yao;
Narayan, Madhumita;
Hanspers, Kristina;
Agrawal, Ayushi;
Pico, Alexander R;
Wu, Chunlei;
Su, Andrew I

Publication type:

Article

INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad569

By:

Webster, Jace;
Mai, Hung;
Ly, Amy;
Maher, Christopher

Publication type:

Article

ActivePPI: quantifying protein–protein interaction network activity with Markov random fields.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad567

By:

Wang, Chuanyuan;
Xu, Shiyu;
Sun, Duanchen;
Liu, Zhi-Ping

Publication type:

Article

mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad565

By:

Movassagh, Mercedeh;
Schiff, Steven J;
Paulson, Joseph N

Publication type:

Article

P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad571

By:

Biffignandi, Gherard Batisti;
Bellinzona, Greta;
Petazzoni, Greta;
Sassera, Davide;
Zuccotti, Gian Vincenzo;
Bandi, Claudio;
Baldanti, Fausto;
Comandatore, Francesco;
Gaiarsa, Stefano

Publication type:

Article

chem16S: community-level chemical metrics for exploring genomic adaptation to environments.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad564

By:

Dick, Jeffrey M;
Kang, Xun

Publication type:

Article

A general framework for powerful confounder adjustment in omics association studies.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad563

By:

Roy, Asmita;
Chen, Jun;
Zhang, Xianyang

Publication type:

Article

Correction to: "Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency".

Published in:: 2023
Publication type:: Correction Notice

cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad561

By:

Johnson, Brian;
Shuai, Yubo;
Schweinsberg, Jason;
Curtius, Kit

Publication type:

Article

Correction to: Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization.

Published in:: 2023
Publication type:: Correction Notice

Correction to: Optimal adjustment sets for causal query estimation in partially observed biomolecular networks.

Published in:: 2023
Publication type:: Correction Notice

Correction to: Python interfaces for the Smoldyn simulator.

Published in:: 2023
Publication type:: Correction Notice

aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad556

By:

Klonowski, Jonathan;
Liang, Qianqian;
Coban-Akdemir, Zeynep;
Lo, Cecilia;
Kostka, Dennis

Publication type:

Article

DrForna: visualization of cotranscriptional folding.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad555

By:

Tănasie, Anda Ramona;
Kerpedjiev, Peter;
Hammer, Stefan;
Badelt, Stefan

Publication type:

Article

DataDTA: a multi-feature and dual-interaction aggregation framework for drug–target binding affinity prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad560

By:

Zhu, Yan;
Zhao, Lingling;
Wen, Naifeng;
Wang, Junjie;
Wang, Chunyu

Publication type:

Article

ePlatypus: an ecosystem for computational analysis of immunogenomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad553

By:

Cotet, Tudor-Stefan;
Agrafiotis, Andreas;
Kreiner, Victor;
Kuhn, Raphael;
Shlesinger, Danielle;
Manero-Carranza, Marcos;
Khodaverdi, Keywan;
Kladis, Evgenios;
Perea, Aurora Desideri;
Maassen-Veeters, Dylan;
Glänzer, Wiona;
Massery, Solène;
Guerci, Lorenzo;
Hong, Kai-Lin;
Han, Jiami;
Stiklioraitis, Kostas;
D'Arcy, Vittoria Martinolli;
Dizerens, Raphael;
Kilchenmann, Samuel;
Stalder, Lucas

Publication type:

Article

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad552

By:

Cozzi, Davide;
Rossi, Massimiliano;
Rubinacci, Simone;
Gagie, Travis;
Köppl, Dominik;
Boucher, Christina;
Bonizzoni, Paola

Publication type:

Article

DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad551

By:

Qu, Wei;
You, Ronghui;
Mamitsuka, Hiroshi;
Zhu, Shanfeng

Publication type:

Article

MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad550

By:

Couto, Bárbara Zita Peters;
Robertson, Nicholas;
Patrick, Ellis;
Ghazanfar, Shila

Publication type:

Article

FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad549

By:

Bianca, Federico;
Ispano, Emilio;
Gazzola, Ermanno;
Lavezzo, Enrico;
Fontana, Paolo;
Toppo, Stefano

Publication type:

Article

Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad548

By:

Park, Seong-Joon;
Kim, Sunghwan;
Jeong, Jaeho;
No, Albert;
No, Jong-Seon;
Park, Hosung

Publication type:

Article

PyDESeq2: a python package for bulk RNA-seq differential expression analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad547

By:

Muzellec, Boris;
Teleńczuk, Maria;
Cabeli, Vincent;
Andreux, Mathieu

Publication type:

Article

scAce: an adaptive embedding and clustering method for single-cell gene expression data.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad546

By:

He, Xinwei;
Qian, Kun;
Wang, Ziqian;
Zeng, Shirou;
Li, Hongwei;
Li, Wei Vivian

Publication type:

Article

Genome-wide multimediator analyses using the generalized Berk–Jones statistics with the composite test.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad544

By:

Lai, En-Yu;
Huang, Yen-Tsung

Publication type:

Article

Phylogenetic inference using generative adversarial networks.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad543

By:

Smith, Megan L;
Hahn, Matthew W

Publication type:

Article

Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad542

By:

Hu, Yan;
Keloth, Vipina K;
Raja, Kalpana;
Chen, Yong;
Xu, Hua

Publication type:

Article

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad541

By:

Tan, Wuwei;
Shen, Yang

Publication type:

Article

AliSim-HPC: parallel sequence simulator for phylogenetics.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad540

By:

Ly-Trong, Nhan;
Barca, Giuseppe M J;
Minh, Bui Quang

Publication type:

Article

Advancements in computational modelling of biological systems: seventh annual SysMod meeting.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad539

By:

Puniya, Bhanwar Lal;
Dräger, Andreas

Publication type:

Article

Tracking and curating putative SARS-CoV-2 recombinants with RIVET.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad538

By:

Smith, Kyle;
Ye, Cheng;
Turakhia, Yatish

Publication type:

Article

DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad537

By:

Muntoni, Anna Paola;
Pagnani, Andrea

Publication type:

Article

DecentTree: scalable Neighbour-Joining for the genomic era.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad536

By:

Wang, Weiwen;
Barbetti, James;
Wong, Thomas;
Thornlow, Bryan;
Corbett-Detig, Russ;
Turakhia, Yatish;
Lanfear, Robert;
Minh, Bui Quang

Publication type:

Article

HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad535

By:

Wharrie, Sophie;
Yang, Zhiyu;
Raj, Vishnu;
Monti, Remo;
Gupta, Rahul;
Wang, Ying;
Martin, Alicia;
O'Connor, Luke J;
Kaski, Samuel;
Marttinen, Pekka;
Palamara, Pier Francesco;
Lippert, Christoph;
Ganna, Andrea

Publication type:

Article

Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad534

By:

Park, Jun Young;
Lee, Jang Jae;
Lee, Younghwa;
Lee, Dongsoo;
Gim, Jungsoo;
Farrer, Lindsay;
Lee, Kun Ho;
Won, Sungho

Publication type:

Article

GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad533

By:

Deng, Yuzhong;
Tang, Jianxiong;
Zhang, Jiyang;
Zou, Jianxiao;
Zhu, Que;
Fan, Shicai

Publication type:

Article

A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug–side effects.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad532

By:

Wang, Lin;
Sun, Chenhao;
Xu, Xianyu;
Li, Jia;
Zhang, Wenjuan

Publication type:

Article

Accessibility of covariance information creates vulnerability in Federated Learning frameworks.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad531

By:

Huth, Manuel;
Arruda, Jonas;
Gusinow, Roy;
Contento, Lorenzo;
Tacconelli, Evelina;
Hasenauer, Jan

Publication type:

Article

IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad530

By:

Liu, Yiwei;
Yang, Changhuo;
Li, Hong-Dong;
Wang, Jianxin

Publication type:

Article

Joint embedding of biological networks for cross-species functional alignment.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad529

By:

Li, Lechuan;
Dannenfelser, Ruth;
Zhu, Yu;
Hejduk, Nathaniel;
Segarra, Santiago;
Yao, Vicky

Publication type:

Article

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad527

By:

Chojnowski, Grzegorz;
Zaborowski, Rafał;
Magnus, Marcin;
Mukherjee, Sunandan;
Bujnicki, Janusz M

Publication type:

Article

MULGA, a unified multi-view graph autoencoder-based approach for identifying drug–protein interaction and drug repositioning.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad524

By:

Ma, Jiani;
Li, Chen;
Zhang, Yiwen;
Wang, Zhikang;
Li, Shanshan;
Guo, Yuming;
Zhang, Lin;
Liu, Hui;
Gao, Xin;
Song, Jiangning

Publication type:

Article

metGWAS 1.0: an R workflow for network-driven over-representation analysis between independent metabolomic and meta-genome-wide association studies.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad523

By:

Khan, Saifur R;
Obersterescu, Andreea;
Gunderson, Erica P;
Razani, Babak;
Wheeler, Michael B;
Cox, Brian J

Publication type:

Article

CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad521

By:

Lyu, Pin;
Zhai, Yijie;
Li, Taibo;
Qian, Jiang

Publication type:

Article

Somatic mutation effects diffused over microRNA dysregulation.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad520

By:

Yu, Hui;
Jiang, Limin;
Li, Chung-I;
Ness, Scott;
Piccirillo, Sara G M;
Guo, Yan

Publication type:

Article

diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad517

By:

Huang, Daoyi;
Jiang, Jianping;
Zhao, Tingting;
Wu, Shengnan;
Li, Pin;
Lyu, Yongfen;
Feng, Jincai;
Wei, Mingyue;
Zhu, Zhixing;
Gu, Jianlei;
Ren, Yongyong;
Yu, Guangjun;
Lu, Hui

Publication type:

Article