Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 3

Results: 44

GENLIB: new function to simulate haplotype transmission in large complex genealogies.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad136

By:

Rakesh, Mohan;
Vézina, Hélène;
Laprise, Catherine;
Freeman, Ellen E;
Burkett, Kelly M;
Roy-Gagnon, Marie-Hélène

Publication type:

Article

PATO: genome-wide prediction of lncRNA–DNA triple helices.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad134

By:

Amatria-Barral, Iñaki;
González-Domínguez, Jorge;
Touriño, Juan

Publication type:

Article

Correction to: Improving annotation propagation on molecular networks through random walks: introducing ChemWalker.

Published in:: 2023
Publication type:: Correction Notice

DeepOM: single-molecule optical genome mapping via deep learning.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad137

By:

Nogin, Yevgeni;
Zur, Tahir Detinis;
Margalit, Sapir;
Barzilai, Ilana;
Alalouf, Onit;
Ebenstein, Yuval;
Shechtman, Yoav

Publication type:

Article

sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad131

By:

Zou, Huixi;
Sun, Tianli;
Jin, Bangqun;
Wang, Shengqin

Publication type:

Article

Correction to: SVJedi: genotyping structural variations with long reads.

Published in:: Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad129
Publication type:: Article

vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad128

By:

Munté, Elisabet;
Feliubadaló, Lidia;
Pineda, Marta;
Tornero, Eva;
Gonzalez, Maribel;
Moreno-Cabrera, José Marcos;
Roca, Carla;
Rubio, Joan Bales;
Arnaldo, Laura;
Capellá, Gabriel;
Mosquera, Jose Luis;
Lázaro, Conxi

Publication type:

Article

SLEMM: million-scale genomic predictions with window-based SNP weighting.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad127

By:

Cheng, Jian;
Maltecca, Christian;
VanRaden, Paul M;
O'Connell, Jeffrey R;
Ma, Li;
Jiang, Jicai

Publication type:

Article

Coverage-preserving sparsification of overlap graphs for long-read assembly.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad124

By:

Jain, Chirag

Publication type:

Article

CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad123

By:

Wu, Zhourun;
Guo, Mingyue;
Jin, Xiaopeng;
Chen, Junjie;
Liu, Bin

Publication type:

Article

Accurate and efficient protein sequence design through learning concise local environment of residues.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad122

By:

Huang, Bin;
Fan, Tingwen;
Wang, Kaiyue;
Zhang, Haicang;
Yu, Chungong;
Nie, Shuyu;
Qi, Yangshuo;
Zheng, Wei-Mou;
Han, Jian;
Fan, Zheng;
Sun, Shiwei;
Ye, Sheng;
Yang, Huaiyi;
Bu, Dongbo

Publication type:

Article

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad121

By:

He, Weiming;
Yang, Jian;
Jing, Yi;
Xu, Lian;
Yu, Kang;
Fang, Xiaodong

Publication type:

Article

PhaGAA: an integrated web server platform for phage genome annotation and analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad120

By:

Wu, Jiawei;
Liu, Qingrui;
Li, Min;
Xu, Jiliang;
Wang, Chen;
Zhang, Junyin;
Xiao, Minfeng;
Bin, Yannan;
Xia, Junfeng

Publication type:

Article

genomepy: genes and genomes at your fingertips.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad119

By:

Frölich, Siebren;
van der Sande, Maarten;
Schäfers, Tilman;
Heeringen, Simon J van

Publication type:

Article

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad118

By:

Pillich, Rudolf T;
Chen, Jing;
Churas, Christopher;
Fong, Dylan;
Gyori, Benjamin M;
Ideker, Trey;
Karis, Klas;
Liu, Sophie N;
Ono, Keiichiro;
Pico, Alexander;
Pratt, Dexter

Publication type:

Article

Correction to: SBbadger: biochemical reaction networks with definable degree distributions.

Published in:: 2023
Publication type:: Correction Notice

bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad109

By:

Li, Qizhi;
Zheng, Xubin;
Xie, Jize;
Wang, Ran;
Li, Mengyao;
Wong, Man-Hon;
Leung, Kwong-Sak;
Li, Shuai;
Geng, Qingshan;
Cheng, Lixin

Publication type:

Article

TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad116

By:

Weg, Karel J van der;
Gohlke, Holger

Publication type:

Article

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad114

By:

Wang, Zhikang;
Bi, Yue;
Pan, Tong;
Wang, Xiaoyu;
Bain, Chris;
Bassed, Richard;
Imoto, Seiya;
Yao, Jianhua;
Daly, Roger J;
Song, Jiangning

Publication type:

Article

peaks2utr: a robust Python tool for the annotation of 3′ UTRs.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad112

By:

Haese-Hill, William;
Crouch, Kathryn;
Otto, Thomas D

Publication type:

Article

RSCanner: rapid assessment and visualization of RNA structure content.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad111

By:

Mahadeshwar, Gandhar;
Tavares, Rafael de Cesaris Araujo;
Wan, Han;
Perry, Zion R;
Pyle, Anna Marie

Publication type:

Article

linemodels: clustering effects based on linear relationships.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad115

By:

Pirinen, Matti

Publication type:

Article

ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad108

By:

Li, Zhongshen;
Jin, Junru;
Wang, Yu;
Long, Wentao;
Ding, Yuanhao;
Hu, Haiyan;
Wei, Leyi

Publication type:

Article

Correction to: Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.

Published in:: 2023
Publication type:: Correction Notice

Correction to: On the feasibility of deep learning applications using raw mass spectrometry data.

Published in:: 2023
Publication type:: Correction Notice

MeganServer: facilitating interactive access to metagenomic data on a server.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad105

By:

Gautam, Anupam;
Zeng, Wenhuan;
Huson, Daniel H

Publication type:

Article

Haptools: a toolkit for admixture and haplotype analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad104

By:

Massarat, Arya R;
Lamkin, Michael;
Reeve, Ciara;
Williams, Amy L;
D'Antonio, Matteo;
Gymrek, Melissa

Publication type:

Article

On the effectiveness of compact biomedical transformers.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad103

By:

Rohanian, Omid;
Nouriborji, Mohammadmahdi;
Kouchaki, Samaneh;
Clifton, David A

Publication type:

Article

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad102

By:

Streck, Adam;
Kaufmann, Tom L;
Schwarz, Roland F

Publication type:

Article

MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad101

By:

Srikakulam, Sanjay K;
Keller, Sebastian;
Dabbaghie, Fawaz;
Bals, Robert;
Kalinina, Olga V

Publication type:

Article

StonPy: a tool to parse and query collections of SBGN maps in a graph database.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad100

By:

Rougny, Adrien;
Balaur, Irina;
Luna, Augustin;
Mazein, Alexander

Publication type:

Article

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad099

By:

Yan, Xuhua;
Zheng, Ruiqing;
Wu, Fangxiang;
Li, Min

Publication type:

Article

scGCL: an imputation method for scRNA-seq data based on graph contrastive learning.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad098

By:

Xiong, Zehao;
Luo, Jiawei;
Shi, Wanwan;
Liu, Ying;
Xu, Zhongyuan;
Wang, Bo

Publication type:

Article

AGC: compact representation of assembled genomes with fast queries and updates.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad097

By:

Deorowicz, Sebastian;
Danek, Agnieszka;
Li, Heng

Publication type:

Article

Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad096

By:

Dmitrenko, Andrei;
Reid, Michelle;
Zamboni, Nicola

Publication type:

Article

ecmtool: fast and memory-efficient enumeration of elementary conversion modes.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad095

By:

Buchner, Bianca;
Clement, Tom J;
Groot, Daan H de;
Zanghellini, Jürgen

Publication type:

Article

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad094

By:

Pan, Tong;
Li, Chen;
Bi, Yue;
Wang, Zhikang;
Gasser, Robin B;
Purcell, Anthony W;
Akutsu, Tatsuya;
Webb, Geoffrey I;
Imoto, Seiya;
Song, Jiangning

Publication type:

Article

VirBot: an RNA viral contig detector for metagenomic data.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad093

By:

Chen, Guowei;
Tang, Xubo;
Shi, Mang;
Sun, Yanni

Publication type:

Article

BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad091

By:

Geistlinger, Ludwig;
Vargas, Roger;
Lee, Tyrone;
Pan, Joshua;
Huttlin, Edward L;
Gentleman, Robert

Publication type:

Article

Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad089

By:

Porokhin, Vladimir;
Liu, Li-Ping;
Hassoun, Soha

Publication type:

Article

Generalizations of the genomic rank distance to indels.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad087

By:

Zanetti, João Paulo Pereira;
Oliveira, Lucas Peres;
Chindelevitch, Leonid;
Meidanis, João

Publication type:

Article

GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad069

By:

Khoroshevskyi, Oleksandr;
LeRoy, Nathan;
Reuter, Vincent P;
Sheffield, Nathan C

Publication type:

Article

ARAX: a graph-based modular reasoning tool for translational biomedicine.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad082

By:

Glen, Amy K;
Ma, Chunyu;
Mendoza, Luis;
Womack, Finn;
Wood, E C;
Sinha, Meghamala;
Acevedo, Liliana;
Kvarfordt, Lindsey G;
Peene, Ross C;
Liu, Shaopeng;
Hoffman, Andrew S;
Roach, Jared C;
Deutsch, Eric W;
Ramsey, Stephen A;
Koslicki, David

Publication type:

Article

Improving annotation propagation on molecular networks through random walks: introducing ChemWalker.

Published in:

Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad078

By:

Borelli, Tiago Cabral;
Arini, Gabriel Santos;
Feitosa, Luís G P;
Dorrestein, Pieter C;
Lopes, Norberto Peporine;
Silva, Ricardo R da

Publication type:

Article