Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 1

Results: 56

AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac760

By:

Su, Changqing;
Gao, Yuhan;
Zhou, You;
Sun, Yaoqi;
Yan, Chenggang;
Yin, Haibing;
Xiong, Bo

Publication type:

Article

GSEApy: a comprehensive package for performing gene set enrichment analysis in Python.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac757

By:

Fang, Zhuoqing;
Liu, Xinyuan;
Peltz, Gary

Publication type:

Article

DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac759

By:

Réau, Manon;
Renaud, Nicolas;
Xue, Li C;
Bonvin, Alexandre M J J

Publication type:

Article

Expression of Concern: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking.

Published in:: Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac758
Publication type:: Article

Capturing variation in metagenomic assembly graphs with MetaCortex.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btad020

By:

Martin, Samuel;
Ayling, Martin;
Patrono, Livia;
Caccamo, Mario;
Murcia, Pablo;
Leggett, Richard M.

Publication type:

Article

SIMBSIG: similarity search and clustering for biobank-scale data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac829

By:

Adamer, Michael F.;
Roellin, Eljas;
Bourguignon, Lucie;
Borgwardt, Karsten

Publication type:

Article

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac827

By:

Runzhou Yu;
Dehan Cai;
Yanni Sun

Publication type:

Article

Biophysical informatics reveals distinctive phenotypic signatures and functional diversity of single-cell lineages.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac833

By:

Chan, Trevor J.;
Xingjian Zhang;
Mak, Michael

Publication type:

Article

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac825

By:

Jia-Juan Tu;
Hui-Sheng Li;
Hong Yan;
Xiao-Fei Zhang

Publication type:

Article

ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac842

By:

Shengquan Chen;
Rongxiang Wang;
Wenxin Long;
Rui Jiang

Publication type:

Article

Pharokka: a fast scalable bacteriophage annotation tool.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac776

By:

Bouras, George;
Nepal, Roshan;
Houtak, Ghais;
Psaltis, Alkis James;
Wormald, Peter-John;
Vreugde, Sarah

Publication type:

Article

Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac774

By:

Clausen, Philip T L C

Publication type:

Article

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac772

By:

Kramer, Alexander M;
Sanderson, Theo;
Corbett-Detig, Russell

Publication type:

Article

EDIR: exome database of interspersed repeats.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac771

By:

Ngoc, Laura D T Vo;
Osei, Randy;
Dohr, Katrin;
Olsen, Catharina;
Seneca, Sara;
Gheldof, Alexander

Publication type:

Article

Systematic identification of biochemical networks in cancer cells by functional pathway inference analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac769

By:

Badshah, Irbaz I;
Cutillas, Pedro R

Publication type:

Article

Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac763

By:

Apollonio, Nicola;
Blankenberg, Daniel;
Cumbo, Fabio;
Franciosa, Paolo Giulio;
Santoni, Daniele

Publication type:

Article

Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac761

By:

Didelot, Xavier;
Helekal, David;
Kendall, Michelle;
Ribeca, Paolo

Publication type:

Article

Easy NanoString nCounter data analysis with the NanoTube.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac762

By:

Class, Caleb A;
Lukan, Caiden J;
Bristow, Christopher A;
Do, Kim-Anh

Publication type:

Article

varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac756

By:

Kumar, Ajay Anand;
Loeys, Bart;
Beek, Gerarda Van De;
Peeters, Nils;
Wuyts, Wim;
Laer, Lut Van;
Vandeweyer, Geert;
Alaerts, Maaike

Publication type:

Article

Improving dynamic predictions with ensembles of observable models.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac755

By:

Massonis, Gemma;
Villaverde, Alejandro F;
Banga, Julio R

Publication type:

Article

Integrating heterogeneous knowledge graphs into drug–drug interaction extraction from the literature.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac754

By:

Asada, Masaki;
Miwa, Makoto;
Sasaki, Yutaka

Publication type:

Article

end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac753

By:

Huang, Kaibin;
Huang, Shengyun;
Chen, Guojing;
Li, Xue;
Li, Shawn;
Liang, Ying;
Gao, Yi

Publication type:

Article

AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac752

By:

Binet, Thomas;
Avalle, Bérangère;
Felipe, Miraine Dávila;
Maffucci, Irene

Publication type:

Article

GeoWaVe: geometric median clustering with weighted voting for ensemble clustering of cytometry data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac751

By:

Burton, Ross J;
Cuff, Simone M;
Morgan, Matt P;
Artemiou, Andreas;
Eberl, Matthias

Publication type:

Article

IMMerge: merging imputation data at scale.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac750

By:

Zhu, Wanying;
Chen, Hung-Hsin;
Petty, Alexander S;
Petty, Lauren E;
Polikowsky, Hannah G;
Gamazon, Eric R;
Below, Jennifer E;
Highland, Heather M

Publication type:

Article

AlphaPulldown—a python package for protein–protein interaction screens using AlphaFold-Multimer.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac749

By:

Yu, Dingquan;
Chojnowski, Grzegorz;
Rosenthal, Maria;
Kosinski, Jan

Publication type:

Article

STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac748

By:

Díaz-Seoane, Sandra;
Barreiro, Xabier Rey;
Villaverde, Alejandro F

Publication type:

Article

scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac746

By:

Faure, Louis;
Soldatov, Ruslan;
Kharchenko, Peter V;
Adameyko, Igor

Publication type:

Article

rGREAT: an R/bioconductor package for functional enrichment on genomic regions.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac745

By:

Gu, Zuguang;
Hübschmann, Daniel

Publication type:

Article

Unbiased pangenome graphs.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac743

By:

Garrison, Erik;
Guarracino, Andrea

Publication type:

Article

SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac742

By:

Klonizakis, Antonios;
Nikolaou, Christoforos;
Graf, Thomas

Publication type:

Article

Updated site concordance factors minimize effects of homoplasy and taxon sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac741

By:

Mo, Yu K;
Lanfear, Robert;
Hahn, Matthew W;
Minh, Bui Quang

Publication type:

Article

VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac740

By:

Mo, Qing;
Xu, Zexin;
Yan, Hui;
Chen, Pin;
Lu, Yutong

Publication type:

Article

scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac739

By:

Zeng, Pengcheng;
Ma, Yuanyuan;
Lin, Zhixiang

Publication type:

Article

Achieving improved accuracy for imputation of ancient DNA.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac738

By:

Ausmees, Kristiina;
Nettelblad, Carl

Publication type:

Article

Clustering single-cell multi-omics data with MoClust.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac736

By:

Yuan, Musu;
Chen, Liang;
Deng, Minghua

Publication type:

Article

Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac735

By:

Cousins, Henry;
Hall, Taryn;
Guo, Yinglong;
Tso, Luke;
Tzeng, Kathy T H;
Cong, Le;
Altman, Russ B

Publication type:

Article

Syllable-PBWT for space-efficient haplotype long-match query.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac734

By:

Wang, Victor;
Naseri, Ardalan;
Zhang, Shaojie;
Zhi, Degui

Publication type:

Article

Deep learning of protein sequence design of protein–protein interactions.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac733

By:

Syrlybaeva, Raulia;
Strauch, Eva-Maria

Publication type:

Article

Paragraph—antibody paratope prediction using graph neural networks with minimal feature vectors.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac732

By:

Chinery, Lewis;
Wahome, Newton;
Moal, Iain;
Deane, Charlotte M

Publication type:

Article

SBMLDiagrams: a python package to process and visualize SBML layout and render.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac730

By:

Xu, Jin;
Jiang, Jessie;
Sauro, Herbert M

Publication type:

Article

Robust genetic model-based SNP-set association test using CauchyGM.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac728

By:

Kim, Yeonil;
Chi, Yueh-Yun;
Shen, Judong;
Zou, Fei

Publication type:

Article

PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac727

By:

Ullah, Matee;
Hadi, Fazal;
Song, Jiangning;
Yu, Dong-Jun

Publication type:

Article

CoMutDB: the landscape of somatic mutation co-occurrence in cancers.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac725

By:

Jiang, Limin;
Yu, Hui;
Tang, Jijun;
Guo, Yan

Publication type:

Article

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac724

By:

Petti, Samantha;
Bhattacharya, Nicholas;
Rao, Roshan;
Dauparas, Justas;
Thomas, Neil;
Zhou, Juannan;
Rush, Alexander M;
Koo, Peter;
Ovchinnikov, Sergey

Publication type:

Article

Improving protein structure prediction using templates and sequence embedding.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac723

By:

Wu, Fandi;
Jing, Xiaoyang;
Luo, Xiao;
Xu, Jinbo

Publication type:

Article

framework for group-wise summarization and comparison of chromatin state annotations.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac722

By:

Vu, Ha;
Koch, Zane;
Fiziev, Petko;
Ernst, Jason

Publication type:

Article

ViMRT: a text-mining tool and search engine for automated virus mutation recognition.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac721

By:

Tong, Yuantao;
Tan, Fanglin;
Huang, Honglian;
Zhang, Zeyu;
Zong, Hui;
Xie, Yujia;
Huang, Danqi;
Cheng, Shiyang;
Wei, Ziyi;
Fang, Meng;
Crabbe, M James C;
Wang, Ying;
Zhang, Xiaoyan

Publication type:

Article

Vaeda computationally annotates doublets in single-cell RNA sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac720

By:

Schriever, Hannah;
Kostka, Dennis

Publication type:

Article

Digitally predicting protein localization and manipulating protein activity in fluorescence images using 4D reslicing GAN.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac719

By:

Jiao, Yang;
Gu, Lingkun;
Jiang, Yingtao;
Weng, Mo;
Yang, Mei

Publication type:

Article