Works matching IS 14675463 AND DT 2022 AND VI 23 AND IP 1

Results: 195

Erratum to: Machine learning meets omics applications and perspectives.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab560

By:

Li, Rufeng;
Li, Lixin;
Xu, Yungang;
Yang, Juan

Publication type:

Article

SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab547

By:

Luo, Qinhuan;
Yu, Yongzhen;
Lan, Xun

Publication type:

Article

AMDE: a novel attention-mechanism-based multidimensional feature encoder for drug–drug interaction prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab545

By:

Pang, Shanchen;
Zhang, Ying;
Song, Tao;
Zhang, Xudong;
Wang, Xun;
Rodriguez-Patón, Alfonso

Publication type:

Article

Comprehensive assessment of deep generative architectures for de novo drug design.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab544

By:

Wang, Mingyang;
Sun, Huiyong;
Wang, Jike;
Pang, Jinping;
Chai, Xin;
Xu, Lei;
Li, Honglin;
Cao, Dongsheng;
Hou, Tingjun

Publication type:

Article

TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab542

By:

Li, Peng;
Zhang, Haoran;
Zhang, Wuxia;
Zhang, Yuanyuan;
Zhan, Lingmin;
Wang, Ning;
Chen, Caiping;
Fu, Bangze;
Zhao, Jinzhong;
Zhou, Xuezhong;
Guo, Shuzhen;
Chen, Jianxin

Publication type:

Article

Predicting miRNA-disease associations using an ensemble learning framework with resampling method.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab543

By:

Dai, Qiguo;
Wang, Zhaowei;
Liu, Ziqiang;
Duan, Xiaodong;
Song, Jinmiao;
Guo, Maozu

Publication type:

Article

Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab541

By:

Goossens, Sander N;
Heupink, Tim H;
Vos, Elise De;
Dippenaar, Anzaan;
Vos, Margaretha De;
Warren, Rob;
Rie, Annelies Van

Publication type:

Article

Protein–RNA interaction prediction with deep learning: structure matters.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab540

By:

Wei, Junkang;
Chen, Siyuan;
Zong, Licheng;
Gao, Xin;
Li, Yu

Publication type:

Article

Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab531

By:

Flores, Mario;
Liu, Zhentao;
Zhang, Tinghe;
Hasib, Md Musaddaqui;
Chiu, Yu-Chiao;
Ye, Zhenqing;
Paniagua, Karla;
Jo, Sumin;
Zhang, Jianqiu;
Gao, Shou-Jiang;
Jin, Yu-Fang;
Chen, Yidong;
Huang, Yufei

Publication type:

Article

MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab538

By:

Song, Meng-Huan;
Yan, Chaochao;
Li, Jia-Tang

Publication type:

Article

BML: a versatile web server for bipartite motif discovery.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab536

By:

Vahed, Mohammad;
Vahed, Majid;
Garmire, Lana X

Publication type:

Article

Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab533

By:

Li, Hongfei;
Gong, Yue;
Liu, Yifeng;
Lin, Hao;
Wang, Guohua

Publication type:

Article

Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression-based clustering.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab532

By:

Zhang, Bo;
He, Jianghua;
Hu, Jinxiang;
Koestler, Devin C;
Chalise, Prabhakar

Publication type:

Article

Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab530

By:

Ge, Fang;
Zhang, Ying;
Xu, Jian;
Muhammad, Arif;
Song, Jiangning;
Yu, Dong-Jun

Publication type:

Article

ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab537

By:

Suryatenggara, Jeremiah;
Yong, Kol Jia;
Tenen, Danielle E;
Tenen, Daniel G;
Bassal, Mahmoud A

Publication type:

Article

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. 1, p. 1, doi. 10.1093/bib/bbab529

By:

Xu, Gang;
Wang, Qinghua;
Ma, Jianpeng

Publication type:

Article

AMDBNorm: an approach based on distribution adjustment to eliminate batch effects of gene expression data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab528

By:

Zhang, Xu;
Ye, Zhiqiang;
Chen, Jing;
Qiao, Feng

Publication type:

Article

Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab527

By:

Jiang, Peiran;
Chi, Ying;
Li, Xiao-Shuang;
Liu, Xiang;
Hua, Xian-Sheng;
Xia, Kelin

Publication type:

Article

deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab526

By:

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

Publication type:

Article

novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab525

By:

Zhang, Yongqing;
Wang, Zixuan;
Zeng, Yuanqi;
Liu, Yuhang;
Xiong, Shuwen;
Wang, Maocheng;
Zhou, Jiliu;
Zou, Quan

Publication type:

Article

Artificial intelligence in clinical research of cancers.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab523

By:

Shao, Dan;
Dai, Yinfei;
Li, Nianfeng;
Cao, Xuqing;
Zhao, Wei;
Cheng, Li;
Rong, Zhuqing;
Huang, Lan;
Wang, Yan;
Zhao, Jing

Publication type:

Article

integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab522

By:

Lin, Cui-Xiang;
Li, Hong-Dong;
Deng, Chao;
Liu, Weisheng;
Erhardt, Shannon;
Wu, Fang-Xiang;
Zhao, Xing-Ming;
Guan, Yuanfang;
Wang, Jun;
Wang, Daifeng;
Hu, Bin;
Wang, Jianxin

Publication type:

Article

DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab521

By:

Zhang, Fuhao;
Zhao, Bi;
Shi, Wenbo;
Li, Min;
Kurgan, Lukasz

Publication type:

Article

novel fast multiple nucleotide sequence alignment method based on FM-index.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab519

By:

Liu, Huan;
Zou, Quan;
Xu, Yun

Publication type:

Article

Heavy chain sequence-based classifier for the specificity of human antibodies.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab516

By:

Wang, Yaqi;
Mai, Guoqin;
Zou, Min;
Long, Haoyu;
Chen, Yao-Qing;
Sun, Litao;
Tian, Dechao;
Zhao, Yang;
Jiang, Guozhi;
Cao, Zicheng;
Du, Xiangjun

Publication type:

Article

HINGRL: predicting drug–disease associations with graph representation learning on heterogeneous information networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab515

By:

Zhao, Bo-Wei;
Hu, Lun;
You, Zhu-Hong;
Wang, Lei;
Su, Xiao-Rui

Publication type:

Article

META-DDIE: predicting drug–drug interaction events with few-shot learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab514

By:

Deng, Yifan;
Qiu, Yang;
Xu, Xinran;
Liu, Shichao;
Zhang, Zhongfei;
Zhu, Shanfeng;
Zhang, Wen

Publication type:

Article

LR-GNN: a graph neural network based on link representation for predicting molecular associations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab513

By:

Kang, Chuanze;
Zhang, Han;
Liu, Zhuo;
Huang, Shenwei;
Yin, Yanbin

Publication type:

Article

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab512

By:

Nguyen, Thanh Binh;
Pires, Douglas E V;
Ascher, David B

Publication type:

Article

Predicting drug–drug interactions by graph convolutional network with multi-kernel.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab511

By:

Wang, Fei;
Lei, Xiujuan;
Liao, Bo;
Wu, Fang-Xiang

Publication type:

Article

PhosPiR: an automated phosphoproteomic pipeline in R.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab510

By:

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

Publication type:

Article

HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab509

By:

Wang, Jiankang;
Nakato, Ryuichiro

Publication type:

Article

scIAE: an integrative autoencoder-based ensemble classification framework for single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab508

By:

Yin, Qingyang;
Wang, Yang;
Guan, Jinting;
Ji, Guoli

Publication type:

Article

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab507

By:

Serra, Angela;
Fratello, Michele;
Federico, Antonio;
Ojha, Ravi;
Provenzani, Riccardo;
Tasnadi, Ervin;
Cattelani, Luca;
Giudice, Giusy del;
Kinaret, Pia A S;
Saarimäki, Laura A;
Pavel, Alisa;
Kuivanen, Suvi;
Cerullo, Vincenzo;
Vapalahti, Olli;
Horvath, Peter;
Lieto, Antonio Di;
Yli-Kauhaluoma, Jari;
Balistreri, Giuseppe;
Greco, Dario

Publication type:

Article

FusionDTA: attention-based feature polymerizer and knowledge distillation for drug-target binding affinity prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab506

By:

Yuan, Weining;
Chen, Guanxing;
Chen, Calvin Yu-Chian

Publication type:

Article

iCRISEE: an integrative analysis of CRISPR screen by reducing false positive hits.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab505

By:

Zhang, Tengbo;
Li, Yaxu;
Yang, Yanrong;
Weng, Linjun;
Wu, Zhiqiang;
Zhu, Jiali;
Qin, Jieling;
Liu, Qi;
Wang, Ping

Publication type:

Article

Tumor immune microenvironment lncRNAs.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab504

By:

Park, Eun-Gyeong;
Pyo, Sung-Jin;
Cui, Youxi;
Yoon, Sang-Ho;
Nam, Jin-Wu

Publication type:

Article

ResNet18DNN: prediction approach of drug-induced liver injury by deep neural network with ResNet18.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab503

By:

Chen, Zhao;
Jiang, Yin;
Zhang, Xiaoyu;
Zheng, Rui;
Qiu, Ruijin;
Sun, Yang;
Zhao, Chen;
Shang, Hongcai

Publication type:

Article

Accurate protein function prediction via graph attention networks with predicted structure information.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab502

By:

Lai, Boqiao;
Xu, Jinbo

Publication type:

Article

deep learning model to identify gene expression level using cobinding transcription factor signals.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab501

By:

Zhang, Lirong;
Yang, Yanchao;
Chai, Lu;
Li, Qianzhong;
Liu, Junjie;
Lin, Hao;
Liu, Li

Publication type:

Article

Dual-Network Collaborative Matrix Factorization for predicting small molecule-miRNA associations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab500

By:

Wang, Shu-Hao;
Wang, Chun-Chun;
Huang, Li;
Miao, Lian-Ying;
Chen, Xing

Publication type:

Article

Accelerating bioactive peptide discovery via mutual information-based meta-learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab499

By:

He, Wenjia;
Jiang, Yi;
Jin, Junru;
Li, Zhongshen;
Zhao, Jiaojiao;
Manavalan, Balachandran;
Su, Ran;
Gao, Xin;
Wei, Leyi

Publication type:

Article

FedSPL: federated self-paced learning for privacy-preserving disease diagnosis.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab498

By:

Wang, Qingyong;
Zhou, Yun

Publication type:

Article

eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab497

By:

Yang, Yingxi;
Sun, Quan;
Huang, Le;
Broome, Jai G;
Correa, Adolfo;
Reiner, Alexander;
Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed);
Raffield, Laura M;
Yang, Yuchen;
Li, Yun

Publication type:

Article

Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab496

By:

Shukla, Priyank;
Pandey, Preeti;
Prasad, Bodhayan;
Robinson, Tony;
Purohit, Rituraj;
D'Cruz, Leon G;
Tambuwala, Murtaza M;
Mutreja, Ankur;
Harkin, Jim;
Rai, Taranjit Singh;
Murray, Elaine K;
Gibson, David S;
Bjourson, Anthony J

Publication type:

Article

Addressing noise in co-expression network construction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab495

By:

Burns, Joshua J R;
Shealy, Benjamin T;
Greer, Mitchell S;
Hadish, John A;
McGowan, Matthew T;
Biggs, Tyler;
Smith, Melissa C;
Feltus, F Alex;
Ficklin, Stephen P

Publication type:

Article

KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab494

By:

Lan, Wei;
Dong, Yi;
Chen, Qingfeng;
Zheng, Ruiqing;
Liu, Jin;
Pan, Yi;
Chen, Yi-Ping Phoebe

Publication type:

Article

tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab493

By:

Tran, Ngoc Hieu;
Xu, Jinbo;
Li, Ming

Publication type:

Article

DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab492

By:

Khanal, Jhabindra;
Tayara, Hilal;
Zou, Quan;
Chong, Kil To

Publication type:

Article

BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab491

By:

Yang, Xi;
Wang, Wei;
Ma, Jing-Lun;
Qiu, Yan-Long;
Lu, Kai;
Cao, Dong-Sheng;
Wu, Cheng-Kun

Publication type:

Article