Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 7

Results: 50

SBOannotator: a Python tool for the automated assignment of systems biology ontology terms.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad437

By:

Leonidou, Nantia;
Fritze, Elisabeth;
Renz, Alina;
Dräger, Andreas

Publication type:

Article

DREAM: an R package for druggability evaluation of human complex diseases.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad442

By:

Federico, Antonio;
Fratello, Michele;
Pavel, Alisa;
Möbus, Lena;
Giudice, Giusy del;
Serra, Angela;
Greco, Dario

Publication type:

Article

ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0—an improved Bayesian-based method for the annotation of LC–MS/MS untargeted metabolomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad455

By:

Carratore, Francesco Del;
Eagles, William;
Borka, Juraj;
Breitling, Rainer

Publication type:

Article

RDBridge: a knowledge graph of rare diseases based on large-scale text mining.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad440

By:

Xing, Huadong;
Zhang, Dachuan;
Cai, Pengli;
Zhang, Rui;
Hu, Qian-Nan

Publication type:

Article

cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad439

By:

Liao, Yang;
Raghu, Dinesh;
Pal, Bhupinder;
Mielke, Lisa A;
Shi, Wei

Publication type:

Article

PyWGCNA: a Python package for weighted gene co-expression network analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad415

By:

Rezaie, Narges;
Reese, Farilie;
Mortazavi, Ali

Publication type:

Article

AGHmatrix: genetic relationship matrices in R.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad445

By:

Amadeu, Rodrigo R;
Garcia, Antonio Augusto F;
Munoz, Patricio R;
Ferrão, Luís Felipe V

Publication type:

Article

Building protein structure-specific rotamer libraries.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad429

By:

Grybauskas, Algirdas;
Gražulis, Saulius

Publication type:

Article

TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad406

By:

McBride, Ross;
Wandy, Joe;
Weidt, Stefan;
Rogers, Simon;
Davies, Vinny;
Daly, Rónán;
Bryson, Kevin

Publication type:

Article

Chromothripsis detection with multiple myeloma patients based on deep graph learning.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad422

By:

Yu, Jixiang;
Chen, Nanjun;
Zheng, Zetian;
Gao, Ming;
Liang, Ning;
Wong, Ka-Chun

Publication type:

Article

Cytocipher determines significantly different populations of cells in single-cell RNA-seq data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad435

By:

Balderson, Brad;
Piper, Michael;
Thor, Stefan;
Bodén, Mikael

Publication type:

Article

CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad434

By:

Weiner, Samson;
Bansal, Mukul S

Publication type:

Article

Information-incorporated sparse convex clustering for disease subtyping.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad417

By:

Zhang, Xiaoyu;
Liu, Ching-Ti

Publication type:

Article

Testing phylogenetic signal with categorical traits and tree uncertainty.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad433

By:

Ribeiro, Diogo;
Borges, Rui;
Rocha, Ana Paula;
Antunes, Agostinho

Publication type:

Article

MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad432

By:

Ferraro, Luigi;
Scala, Giovanni;
Cerulo, Luigi;
Carosati, Emanuele;
Ceccarelli, Michele

Publication type:

Article

Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad431

By:

Wang, Linhua;
Liu, Chaozhong;
Gao, Yang;
Zhang, Xiang H -F;
Liu, Zhandong

Publication type:

Article

LPF: a framework for exploring the wing color pattern formation of ladybird beetles in Python.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad430

By:

Lee, Daewon

Publication type:

Article

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

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad414

By:

Jiang, Hao;
Zhan, Senwen;
Ching, Wai-Ki;
Chen, Luonan

Publication type:

Article

Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad428

By:

Billows, Nina;
Phelan, Jody E;
Xia, Dong;
Peng, Yonghong;
Clark, Taane G;
Chang, Yu-Mei

Publication type:

Article

MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad427

By:

Oues, Namir;
Dantu, Sarath Chandra;
Patel, Riktaben Jigarkumar;
Pandini, Alessandro

Publication type:

Article

A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad426

By:

Konstantinovsky, Thomas;
Yaari, Gur

Publication type:

Article

Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad425

By:

Seabolt, Matthew H;
Boddapati, Arun K;
Forstedt, Joshua J;
Konstantinidis, Konstantinos T

Publication type:

Article

Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad424

By:

Zhu, Wensi;
Shenoy, Aditi;
Kundrotas, Petras;
Elofsson, Arne

Publication type:

Article

MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad423

By:

Zeng, Yong;
Ye, Wenbin;
Stutheit-Zhao, Eric Y;
Han, Ming;
Bratman, Scott V;
Pugh, Trevor J;
He, Housheng Hansen

Publication type:

Article

LEGO-CSM: a tool for functional characterization of proteins.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad402

By:

Nguyen, Thanh Binh;
Sá, Alex G C de;
Rodrigues, Carlos H M;
Pires, Douglas E V;
Ascher, David B

Publication type:

Article

RNAenrich: a web server for non-coding RNA enrichment.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad421

By:

Zhang, Song;
Amahong, Kuerbannisha;
Zhang, Yintao;
Hu, Xiaoping;
Huang, Shijie;
Lu, Mingkun;
Zeng, Zhenyu;
Li, Zhaorong;
Zhang, Bing;
Qiu, Yunqing;
Dai, Haibin;
Gao, Jianqing;
Zhu, Feng

Publication type:

Article

LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad420

By:

Meng-Papaxanthos, Laetitia;
Zhang, Ran;
Li, Gang;
Cuturi, Marco;
Vert, Jean-Philippe

Publication type:

Article

Counting pseudoalignments to novel splicing events.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad419

By:

Borozan, Luka;
Ringeling, Francisca Rojas;
Kao, Shao-Yen;
Nikonova, Elena;
Monteagudo-Mesas, Pablo;
Matijević, Domagoj;
Spletter, Maria L;
Canzar, Stefan

Publication type:

Article

KG-Hub—building and exchanging biological knowledge graphs.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad418

By:

Caufield, J Harry;
Putman, Tim;
Schaper, Kevin;
Unni, Deepak R;
Hegde, Harshad;
Callahan, Tiffany J;
Cappelletti, Luca;
Moxon, Sierra A T;
Ravanmehr, Vida;
Carbon, Seth;
Chan, Lauren E;
Cortes, Katherina;
Shefchek, Kent A;
Elsarboukh, Glass;
Balhoff, Jim;
Fontana, Tommaso;
Matentzoglu, Nicolas;
Bruskiewich, Richard M;
Thessen, Anne E;
Harris, Nomi L

Publication type:

Article

Accelerating open modification spectral library searching on tensor core in high-dimensional space.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad404

By:

Kang, Jaeyoung;
Xu, Weihong;
Bittremieux, Wout;
Moshiri, Niema;
Rosing, Tajana

Publication type:

Article

CCIBP: a comprehensive cosmetic ingredients bioinformatics platform.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad416

By:

Gong, Linlin;
Zhang, Rui;
Han, Mengying;
Hu, Qian-Nan

Publication type:

Article

ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad403

By:

Bandodkar, Prasad;
Shaikh, Razeen;
Reeves, Gregory T

Publication type:

Article

Inference of microbial covariation networks using copula models with mixture margins.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad413

By:

Deek, Rebecca A;
Li, Hongzhe

Publication type:

Article

MDTips: a multimodal-data-based drug–target interaction prediction system fusing knowledge, gene expression profile, and structural data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad411

By:

Xia, Xiaoqiong;
Zhu, Chaoyu;
Zhong, Fan;
Liu, Lei

Publication type:

Article

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

Published in:: 2023
Publication type:: Correction Notice

Generating interacting protein sequences using domain-to-domain translation.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad401

By:

Meynard-Piganeau, Barthelemy;
Fabbri, Caterina;
Weigt, Martin;
Pagnani, Andrea;
Feinauer, Christoph

Publication type:

Article

Hierarchical graph transformer with contrastive learning for protein function prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad410

By:

Gu, Zhonghui;
Luo, Xiao;
Chen, Jiaxiao;
Deng, Minghua;
Lai, Luhua

Publication type:

Article

Plassembler: an automated bacterial plasmid assembly tool.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad409

By:

Bouras, George;
Sheppard, Anna E;
Mallawaarachchi, Vijini;
Vreugde, Sarah

Publication type:

Article

CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad408

By:

Ndela, Eric Olo;
Enault, François

Publication type:

Article

enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad407

By:

Zhang, Kunyang;
Fenner, Kathrin

Publication type:

Article

Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad400

By:

Moradigaravand, Danesh;
Li, Liguan;
Dechesne, Arnaud;
Nesme, Joseph;
de la Cruz, Roberto;
Ahmad, Huda;
Banzhaf, Manuel;
Sørensen, Søren J;
Smets, Barth F;
Kreft, Jan-Ulrich

Publication type:

Article

S-leaping: an efficient downsampling method for large high-throughput sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad399

By:

Kuwahara, Hiroyuki;
Gao, Xin

Publication type:

Article

JTK: targeted diploid genome assembler.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad398

By:

Masutani, Bansho;
Suzuki, Yoshihiko;
Suzuki, Yuta;
Morishita, Shinichi

Publication type:

Article

COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad397

By:

Li, Jiahang;
Waldherr, Steffen;
Weckwerth, Wolfram

Publication type:

Article

Understanding the complementarity and plasticity of antibody–antigen interfaces.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad392

By:

Myung, Yoochan;
Pires, Douglas E V;
Ascher, David B

Publication type:

Article

Genetic fine-mapping from summary data using a nonlocal prior improves the detection of multiple causal variants.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad396

By:

Karhunen, Ville;
Launonen, Ilkka;
Järvelin, Marjo-Riitta;
Sebert, Sylvain;
Sillanpää, Mikko J

Publication type:

Article

Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad395

By:

Tang, Wenhao;
Jørgensen, Andreas Christ Sølvsten;
Marguerat, Samuel;
Thomas, Philipp;
Shahrezaei, Vahid

Publication type:

Article

Retraction of: Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.

Published in:: Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad394
Publication type:: Article

BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad393

By:

Vigorito, Elena;
Barton, Anne;
Pitzalis, Costantino;
Lewis, Myles J;
Wallace, Chris

Publication type:

Article

MEvA-X: a hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad384

By:

Panagiotopoulos, Konstantinos;
Korfiati, Aigli;
Theofilatos, Konstantinos;
Hurwitz, Peter;
Deriu, Marco Agostino;
Mavroudi, Seferina

Publication type:

Article