Works matching IS 13674803 AND DT 2023 AND VI 39

Results: 754

ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor–ligand interactions that specify cell fate.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad765

By:

Kyaw, Wunna;
Chai, Ryan C;
Khoo, Weng Hua;
Goldstein, Leonard D;
Croucher, Peter I;
Murray, John M;
Phan, Tri Giang

Publication type:

Article

Correction to: KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality.

Published in:: 2023
Publication type:: Correction Notice

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad753

By:

Ma, Steve;
Fan, Longxuan;
Konanki, Sai Anish;
Liu, Eva;
Gennari, John H;
Smith, Lucian P;
Hellerstein, Joseph L;
Sauro, Herbert M

Publication type:

Article

GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad747

By:

Liao, Herui;
Shang, Jiayu;
Sun, Yanni

Publication type:

Article

LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad752

By:

Zeng, Min;
Wu, Yifan;
Li, Yiming;
Yin, Rui;
Lu, Chengqian;
Duan, Junwen;
Li, Min

Publication type:

Article

Correction to: Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads.

Published in:: 2023
Publication type:: Correction Notice

Correction to: Prediction of gene co-expression from chromatin contacts with graph attention network.

Published in:: 2023
Publication type:: Correction Notice

Rarity: discovering rare cell populations from single-cell imaging data.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad750

By:

Märtens, Kaspar;
Bortolomeazzi, Michele;
Montorsi, Lucia;
Spencer, Jo;
Ciccarelli, Francesca;
Yau, Christopher

Publication type:

Article

Correction to: NeoFox: annotating neoantigen candidates with neoantigen features.

Published in:: 2023
Publication type:: Correction Notice

Scaling up single-cell RNA-seq data analysis with CellBridge workflow.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad760

By:

Nouri, Nima;
Kurlovs, Andre H;
Gaglia, Giorgio;
Rinaldis, Emanuele de;
Savova, Virginia

Publication type:

Article

Correction to: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.

Published in:: 2023
Publication type:: Correction Notice

CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad759

By:

Haldar, Anisha;
Oza, Vishal H;
DeVoss, Nathaniel S;
Clark, Amanda D;
Lasseigne, Brittany N

Publication type:

Article

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad756

By:

Díaz-Gay, Marcos;
Vangara, Raviteja;
Barnes, Mark;
Wang, Xi;
Islam, S M Ashiqul;
Vermes, Ian;
Duke, Stephen;
Narasimman, Nithish Bharadhwaj;
Yang, Ting;
Jiang, Zichen;
Moody, Sarah;
Senkin, Sergey;
Brennan, Paul;
Stratton, Michael R;
Alexandrov, Ludmil B

Publication type:

Article

Correction to: PEMT: a patent enrichment tool for drug discovery.

Published in:: 2023
Publication type:: Correction Notice

IntelliGenes: a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad755

By:

DeGroat, William;
Mendhe, Dinesh;
Bhusari, Atharva;
Abdelhalim, Habiba;
Zeeshan, Saman;
Ahmed, Zeeshan

Publication type:

Article

Bibliometric analysis of neuroscience publications quantifies the impact of data sharing.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad746

By:

Emissah, Herve;
Ljungquist, Bengt;
Ascoli, Giorgio A

Publication type:

Article

CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad745

By:

Kaya, Hikmet Emre;
Naidoo, Kevin J

Publication type:

Article

PDBImages: a command-line tool for automated macromolecular structure visualization.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad744

By:

Midlik, Adam;
Nair, Sreenath;
Anyango, Stephen;
Deshpande, Mandar;
Sehnal, David;
Varadi, Mihaly;
Velankar, Sameer

Publication type:

Article

MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad734

By:

Li, Yang;
Guo, Zihou;
Gao, Xin;
Wang, Guohua

Publication type:

Article

EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad743

By:

Korpela, Dani;
Jokinen, Emmi;
Dumitrescu, Alexandru;
Huuhtanen, Jani;
Mustjoki, Satu;
Lähdesmäki, Harri

Publication type:

Article

TADA: taxonomy-aware dataset aggregator.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad742

By:

Hägglund, Emil;
Andersson, Siv G E;
Guy, Lionel

Publication type:

Article

Parsley: a web app for parsing data from plate readers.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad733

By:

Csibra, Eszter;
Stan, Guy-Bart

Publication type:

Article

Protein intrinsically disordered regions have a non-random, modular architecture.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad732

By:

McConnell, Brendan S;
Parker, Matthew W

Publication type:

Article

Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad739

By:

Liu, Zi Hao;
Teixeira, João M C;
Zhang, Oufan;
Tsangaris, Thomas E;
Li, Jie;
Gradinaru, Claudiu C;
Head-Gordon, Teresa;
Forman-Kay, Julie D

Publication type:

Article

FunctanSNP: an R package for functional analysis of dense SNP data (with interactions).

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad741

By:

Ren, Rui;
Fang, Kuangnan;
Zhang, Qingzhao;
Ma, Shuangge

Publication type:

Article

MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad737

By:

Liu, Jian;
Ma, Fubin;
Zhu, Yongdi;
Zhang, Naiqian;
Kong, Lingming;
Mi, Jia;
Cong, Haiyan;
Gao, Rui;
Wang, Mingyi;
Zhang, Yusen

Publication type:

Article

TsImpute: an accurate two-step imputation method for single-cell RNA-seq data.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad731

By:

Zheng, Weihua;
Min, Wenwen;
Wang, Shunfang

Publication type:

Article

Correction to: GIL: a python package for designing custom indexing primers.

Published in:: 2023
Publication type:: Correction Notice

Re-analysis and meta-analysis of summary statistics from gene–environment interaction studies.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad730

By:

Pham, Duy T;
Westerman, Kenneth E;
Pan, Cong;
Chen, Ling;
Srinivasan, Shylaja;
Isganaitis, Elvira;
Vajravelu, Mary Ellen;
Bacha, Fida;
Chernausek, Steve;
Gubitosi-Klug, Rose;
Divers, Jasmin;
Pihoker, Catherine;
Marcovina, Santica M;
Manning, Alisa K;
Chen, Han

Publication type:

Article

Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad729

By:

Morrison, Jacob;
Zhou, Wanding;
Johnson, Benjamin K;
Shen, Hui

Publication type:

Article

Hostile: accurate decontamination of microbial host sequences.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad728

By:

Constantinides, Bede;
Hunt, Martin;
Crook, Derrick W

Publication type:

Article

LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad727

By:

Hoops, Susan L;
Knights, Dan

Publication type:

Article

invMap: a sensitive mapping tool for long noisy reads with inversion structural variants.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad726

By:

Wei, Ze-Gang;
Bu, Peng-Yu;
Zhang, Xiao-Dan;
Liu, Fei;
Qian, Yu;
Wu, Fang-Xiang

Publication type:

Article

ROCCO: a robust method for detection of open chromatin via convex optimization.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad725

By:

Hamilton, Nolan H;
Furey, Terrence S

Publication type:

Article

ProteinMAE: masked autoencoder for protein surface self-supervised learning.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad724

By:

Yuan, Mingzhi;
Shen, Ao;
Fu, Kexue;
Guan, Jiaming;
Ma, Yingfan;
Qiao, Qin;
Wang, Manning

Publication type:

Article

survex: an R package for explaining machine learning survival models.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad723

By:

Spytek, Mikołaj;
Krzyziński, Mateusz;
Langbein, Sophie Hanna;
Baniecki, Hubert;
Wright, Marvin N;
Biecek, Przemysław

Publication type:

Article

Benchmarking and improving the performance of variant-calling pipelines with RecallME.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad722

By:

Vozza, Gianluca;
Bonetti, Emanuele;
Tini, Giulia;
Favalli, Valentina;
Frigè, Gianmaria;
Bucci, Gabriele;
Summa, Simona De;
Zanfardino, Mario;
Zapelloni, Francesco;
Mazzarella, Luca

Publication type:

Article

Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad721

By:

Stribling, Daniel;
Gay, Lauren A;
Renne, Rolf

Publication type:

Article

NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad720

By:

Singh, Jaskaran;
Pan, Yingzhou Edward;
Patten, Shunmoogum A

Publication type:

Article

ReConPlot: an R package for the visualization and interpretation of genomic rearrangements.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad719

By:

Valle-Inclán, Jose Espejo;
Cortés-Ciriano, Isidro

Publication type:

Article

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad718

By:

Fang, Yitian;
Jiang, Yi;
Wei, Leyi;
Ma, Qin;
Ren, Zhixiang;
Yuan, Qianmu;
Wei, Dong-Qing

Publication type:

Article

Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad717

By:

Visonà, Giovanni;
Duroux, Diane;
Miranda, Lucas;
Sükei, Emese;
Li, Yiran;
Borgwardt, Karsten;
Oliver, Carlos

Publication type:

Article

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad716

By:

Groza, Tudor;
Wu, Honghan;
Dinger, Marcel E;
Danis, Daniel;
Hilton, Coleman;
Bagley, Anita;
Davids, Jon R;
Luo, Ling;
Lu, Zhiyong;
Robinson, Peter N

Publication type:

Article

OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad715

By:

Xu, Cuifang;
Huang, Jiating;
Gao, Yongqiang;
Zhao, Weixing;
Shen, Yiqi;
Luo, Feihong;
Yu, Gang;
Zhu, Feng;
Ni, Yan

Publication type:

Article

Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad714

By:

Ghaddar, Bassel;
De, Subhajyoti

Publication type:

Article

deepFPlearn<sup>+</sup>: enhancing toxicity prediction across the chemical universe using graph neural networks.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad713

By:

Soulios, Kyriakos;
Scheibe, Patrick;
Bernt, Matthias;
Hackermüller, Jörg;
Schor, Jana

Publication type:

Article

DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad712

By:

Lee, Jae-Won;
Won, Jong-Hyun;
Jeon, Seonggwang;
Choo, Yujin;
Yeon, Yubin;
Oh, Jin-Seon;
Kim, Minsoo;
Kim, SeonHwa;
Joung, InSuk;
Jang, Cheongjae;
Lee, Sung Jong;
Kim, Tae Hyun;
Jin, Kyong Hwan;
Song, Giltae;
Kim, Eun-Sol;
Yoo, Jejoong;
Paek, Eunok;
Noh, Yung-Kyun;
Joo, Keehyoung

Publication type:

Article

CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad710

By:

Khare, Harshavardhan;
Mendoza, Nathaly Dongo;
Zurzolo, Chiara

Publication type:

Article

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad709

By:

Zhang, Ying;
Wang, Zhikang;
Zhang, Yiwen;
Li, Shanshan;
Guo, Yuming;
Song, Jiangning;
Yu, Dong-Jun

Publication type:

Article

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.

Published in:

Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad708

By:

Wu, Xiaojing;
Han, Mingfei;
Song, Xinyu;
He, Song;
Bo, Xiaochen;
Zhu, Yunping

Publication type:

Article