Works matching IS 14675463 AND DT 2022 AND VI 23 AND IP 3

Results: 102

Correction to: PhosPiR: an automated phosphoproteomic pipeline in R.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac153

By:

Hong, Ye;
Flinkman, Dani;
Suomi, Tomi;
Pietilä, Sami;
James, Peter;
Coffey, Eleanor;
Elo, Laura L

Publication type:

Article

Directed graph attention networks for predicting asymmetric drug–drug interactions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac151

By:

Feng, Yi-Yang;
Yu, Hui;
Feng, Yue-Hua;
Shi, Jian-Yu

Publication type:

Article

scDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA–DNA methylation data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac150

By:

Liu, Yu

Publication type:

Article

GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac148

By:

Du, Zhi-Hua;
Wu, Yang-Han;
Huang, Yu-An;
Chen, Jie;
Pan, Gui-Qing;
Hu, Lun;
You, Zhu-Hong;
Li, Jian-Qiang

Publication type:

Article

D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac147

By:

Yang, Yanqing;
Zhou, Deshan;
Zhang, Xinben;
Shi, Yulong;
Han, Jiaxin;
Zhou, Liping;
Wu, Leyun;
Ma, Minfei;
Li, Jintian;
Peng, Shaoliang;
Xu, Zhijian;
Zhu, Weiliang

Publication type:

Article

Benchmarking of long-read sequencing, assemblers and polishers for yeast genome.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac146

By:

Zhang, Xue;
Liu, Chen-Guang;
Yang, Shi-Hui;
Wang, Xia;
Bai, Feng-Wu;
Wang, Zhuo

Publication type:

Article

systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac145

By:

Huang, Le;
Yang, Yuchen;
Li, Gang;
Jiang, Minzhi;
Wen, Jia;
Abnousi, Armen;
Rosen, Jonathan D;
Hu, Ming;
Li, Yun

Publication type:

Article

On the influence of several factors on pathway enrichment analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac143

By:

Mubeen, Sarah;
Kodamullil, Alpha Tom;
Hofmann-Apitius, Martin;
Domingo-Fernández, Daniel

Publication type:

Article

analysis of protein language model embeddings for fold prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac142

By:

Villegas-Morcillo, Amelia;
Gomez, Angel M;
Sanchez, Victoria

Publication type:

Article

Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac141

By:

Buckley, Paul R;
Lee, Chloe H;
Ma, Ruichong;
Woodhouse, Isaac;
Woo, Jeongmin;
Tsvetkov, Vasily O;
Shcherbinin, Dmitrii S;
Antanaviciute, Agne;
Shughay, Mikhail;
Rei, Margarida;
Simmons, Alison;
Koohy, Hashem

Publication type:

Article

Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac140

By:

Su, Xiaorui;
Hu, Lun;
You, Zhuhong;
Hu, Pengwei;
Zhao, Bowei

Publication type:

Article

Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac139

By:

Wang, Tao;
Liu, Yongzhuang;
Yin, Quanwei;
Geng, Jiaquan;
Chen, Jin;
Yin, Xipeng;
Wang, Yongtian;
Shang, Xuequn;
Tian, Chunwei;
Wang, Yadong;
Peng, Jiajie

Publication type:

Article

Benchmarking differential expression, imputation and quantification methods for proteomics data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac138

By:

Lin, Miao-Hsia;
Wu, Pei-Shan;
Wong, Tzu-Hsuan;
Lin, I-Ying;
Lin, Johnathan;
Cox, Jürgen;
Yu, Sung-Huan

Publication type:

Article

Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac137

By:

Bi, Xia-an;
Zhou, Wenyan;
Luo, Sheng;
Mao, Yuhua;
Hu, Xi;
Zeng, Bin;
Xu, Luyun

Publication type:

Article

quality control portal for sequencing data deposited at the European genome–phenome archive.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac136

By:

Fernández-Orth, Dietmar;
Rueda, Manuel;
Singh, Babita;
Moldes, Mauricio;
Jene, Aina;
Ferri, Marta;
Vasallo, Claudia;
Fromont, Lauren A;
Navarro, Arcadi;
Rambla, Jordi

Publication type:

Article

Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac135

By:

Guo, Xiaoyi;
Jiang, Yizhang;
Zou, Quan

Publication type:

Article

3DGT-DDI: 3D graph and text based neural network for drug–drug interaction prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac134

By:

He, Haohuai;
Chen, Guanxing;
Chen, Calvin Yu-Chian

Publication type:

Article

Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac133

By:

Kowald, Axel;
Barrantes, Israel;
Möller, Steffen;
Palmer, Daniel;
Escobar, Hugo Murua;
Schwerk, Anne;
Fuellen, Georg

Publication type:

Article

MDICC: novel method for multi-omics data integration and cancer subtype identification.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac132

By:

Yang, Ying;
Tian, Sha;
Qiu, Yushan;
Zhao, Pu;
Zou, Quan

Publication type:

Article

Knowledge-based BERT: a method to extract molecular features like computational chemists.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac131

By:

Wu, Zhenxing;
Jiang, Dejun;
Wang, Jike;
Zhang, Xujun;
Du, Hongyan;
Pan, Lurong;
Hsieh, Chang-Yu;
Cao, Dongsheng;
Hou, Tingjun

Publication type:

Article

Expression of Concern to: OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac130

By:

Xu, Gang;
Wang, Qinghua;
Ma, Jianpeng

Publication type:

Article

CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac129

By:

Lin, Anqi;
Qi, Chang;
Wei, Ting;
Li, Mengyao;
Cheng, Quan;
Liu, Zaoqu;
Luo, Peng;
Zhang, Jian

Publication type:

Article

Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac128

By:

Zhang, Ruibo;
Ghosh, Souparno;
Pal, Ranadip

Publication type:

Article

Characterizing the stabilization effects of stabilizers in protein–protein systems with end-point binding free energy calculations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac127

By:

Tang, Rongfan;
Chen, Pengcheng;
Wang, Zhe;
Wang, Lingling;
Hao, Haiping;
Hou, Tingjun;
Sun, Huiyong

Publication type:

Article

Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac126

By:

Xuan, Ping;
Wang, Meng;
Liu, Yong;
Wang, Dong;
Zhang, Tiangang;
Nakaguchi, Toshiya

Publication type:

Article

deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host–pathogen protein–protein interactions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac125

By:

Kaundal, Rakesh;
Loaiza, Cristian D;
Duhan, Naveen;
Flann, Nicholas

Publication type:

Article

Differentially expressed genes prediction by multiple self-attention on epigenetics data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac117

By:

Huang, Zimo;
Wang, Jun;
Yan, Zhongmin;
Guo, Maozu

Publication type:

Article

SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac116

By:

Liu, Yusong;
Wang, Tongxin;
Duggan, Ben;
Sharpnack, Michael;
Huang, Kun;
Zhang, Jie;
Ye, Xiufen;
Johnson, Travis S

Publication type:

Article

Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac121

By:

Yang, Cheng-Hong;
Cheng, Yu-Huei;
Yang, Emirlyn Cheng;
Chuang, Li-Yeh;
Lin, Yu-Da

Publication type:

Article

Correction to: CRAFT a bioinformatics software for custom prediction of circular RNA functions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac119

By:

Molin, Anna Dal;
Gaffo, Enrico;
Difilippo, Valeria;
Buratin, Alessia;
Parenzan, Caterina Tretti;
Bresolin, Silvia;
Bortoluzzi, Stefania

Publication type:

Article

Comprehensive assessment of cellular senescence in the tumor microenvironment.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac118

By:

Wang, Xiaoman;
Ma, Lifei;
Pei, Xiaoya;
Wang, Heping;
Tang, Xiaoqiang;
Pei, Jian-Fei;
Ding, Yang-Nan;
Qu, Siyao;
Wei, Zi-Yu;
Wang, Hui-Yu;
Wang, Xiaoyue;
Wei, Gong-Hong;
Liu, De-Pei;
Chen, Hou-Zao

Publication type:

Article

Heterogeneous multi-scale neighbor topologies enhanced drug–disease association prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac123

By:

Xuan, Ping;
Meng, Xiangfeng;
Gao, Ling;
Zhang, Tiangang;
Nakaguchi, Toshiya

Publication type:

Article

evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac122

By:

Abeysinghe, Rashmie;
Yang, Yuntao;
Bartels, Mason;
Zheng, W Jim;
Cui, Licong

Publication type:

Article

Fast heritability estimation based on MINQUE and batch training.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac115

By:

Tang, Mingsheng;
Hou, Tingting;
Tong, Xiaoran;
Shen, Xiaoxi;
Zhang, Xuefen;
Wang, Tong;
Lu, Qing

Publication type:

Article

Predicting the binding of small molecules to nuclear receptors using machine learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac114

By:

Ramaprasad, Azhagiya Singam Ettayapuram;
Smith, Martyn T;
McCoy, David;
Hubbard, Alan E;
Merrill, Michele A La;
Durkin, Kathleen A

Publication type:

Article

Spectral clustering of single cells using Siamese nerual network combined with improved affinity matrix.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac113

By:

Jiang, Hanjing;
Huang, Yabing;
Li, Qianpeng

Publication type:

Article

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac111

By:

Wu, Fei;
Liu, Yao-Zhong;
Ling, Binhua

Publication type:

Article

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac112

By:

Solayman, Md;
Litfin, Thomas;
Singh, Jaswinder;
Paliwal, Kuldip;
Zhou, Yaoqi;
Zhan, Jian

Publication type:

Article

Privacy preserving validation for multiomic prediction models.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac110

By:

Ahmed, Talal;
Carty, Mark A;
Wenric, Stephane;
Dry, Jonathan R;
Salahudeen, Ameen A;
Khan, Aly A;
Lefkofsky, Eric;
Stumpe, Martin C;
Pelossof, Raphael

Publication type:

Article

DTI-HETA: prediction of drug–target interactions based on GCN and GAT on heterogeneous graph.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac109

By:

Shao, Kanghao;
Zhang, Yunhao;
Wen, Yuqi;
Zhang, Zhongnan;
He, Song;
Bo, Xiaochen

Publication type:

Article

tool for feature extraction from biological sequences.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac108

By:

Amerifar, Sare;
Norouzi, Mahammad;
Ghandi, Mahmoud

Publication type:

Article

RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA–RNA interaction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac107

By:

Kang, Qiang;
Meng, Jun;
Luan, Yushi

Publication type:

Article

Computational methods, databases and tools for synthetic lethality prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac106

By:

Wang, Jing;
Zhang, Qinglong;
Han, Junshan;
Zhao, Yanpeng;
Zhao, Caiyun;
Yan, Bowei;
Dai, Chong;
Wu, Lianlian;
Wen, Yuqi;
Zhang, Yixin;
Leng, Dongjin;
Wang, Zhongming;
Yang, Xiaoxi;
He, Song;
Bo, Xiaochen

Publication type:

Article

JSNMF enables effective and accurate integrative analysis of single-cell multiomics data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac105

By:

Ma, Yuanyuan;
Sun, Zexuan;
Zeng, Pengcheng;
Zhang, Wenyu;
Lin, Zhixiang

Publication type:

Article

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac104

By:

Liu, Wei;
Lin, Hui;
Huang, Li;
Peng, Li;
Tang, Ting;
Zhao, Qi;
Yang, Li

Publication type:

Article

Protein design via deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac102

By:

Ding, Wenze;
Nakai, Kenta;
Gong, Haipeng

Publication type:

Article

Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac101

By:

Bonomo, Mariella;
Giancarlo, Raffaele;
Greco, Daniele;
Rombo, Simona E

Publication type:

Article

DeepTTA: a transformer-based model for predicting cancer drug response.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac100

By:

Jiang, Likun;
Jiang, Changzhi;
Yu, Xinyu;
Fu, Rao;
Jin, Shuting;
Liu, Xiangrong

Publication type:

Article

efficient curriculum learning-based strategy for molecular graph learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac099

By:

Gu, Yaowen;
Zheng, Si;
Xu, Zidu;
Yin, Qijin;
Li, Liang;
Li, Jiao

Publication type:

Article

S2Snet: deep learning for low molecular weight RNA identification with nanopore.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac098

By:

Guan, Xiaoyu;
Wang, Yuqin;
Shao, Wei;
Li, Zhongnian;
Huang, Shuo;
Zhang, Daoqiang

Publication type:

Article