Works matching IS 14675463 AND DT 2023 AND VI 24 AND IP 4

Results: 78

Editorial.

Published in:

2023

By:

Ma, Shuangge

Publication type:

Editorial

ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad257

By:

Yan, Junyu;
Li, Shuai;
Zhang, Ying;
Hao, Aimin;
Zhao, Qinping

Publication type:

Article

iBT-Net: an incremental broad transformer network for cancer drug response prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad256

By:

Zhan, Yongkang;
Guo, Jifeng;
Chen, C L Philip;
Meng, Xian-Bing

Publication type:

Article

iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad251

By:

Yan, Ke;
Feng, Jiawei;
Huang, Jing;
Wu, Hao

Publication type:

Article

GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad247

By:

Wei, Jinhang;
Zhuo, Linlin;
Zhou, Zhecheng;
Lian, Xinze;
Fu, Xiangzheng;
Yao, Xiaojun

Publication type:

Article

Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad238

By:

Duan, Meiyu;
Wang, Yueying;
Zhao, Dong;
Liu, Hongmei;
Zhang, Gongyou;
Li, Kewei;
Zhang, Haotian;
Huang, Lan;
Zhang, Ruochi;
Zhou, Fengfeng

Publication type:

Article

Large-scale predicting protein functions through heterogeneous feature fusion.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad243

By:

Zheng, Rongtao;
Huang, Zhijian;
Deng, Lei

Publication type:

Article

An interpretable block-attention network for identifying regulatory feature interactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad250

By:

Prakash, Anil;
Banerjee, Moinak

Publication type:

Article

Predicting potential microbe–disease associations based on multi-source features and deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad255

By:

Wang, Liugen;
Wang, Yan;
Xuan, Chenxu;
Zhang, Bai;
Wu, Hanwen;
Gao, Jie

Publication type:

Article

Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad254

By:

Toseef, Muhammad;
Petinrin, Olutomilayo Olayemi;
Wang, Fuzhou;
Rahaman, Saifur;
Liu, Zhe;
Li, Xiangtao;
Wong, Ka-Chun

Publication type:

Article

An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad252

By:

Elimelech-Zohar, Karin;
Orenstein, Yaron

Publication type:

Article

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad242

By:

Conev, Anja;
Rigo, Mauricio Menegatti;
Devaurs, Didier;
Fonseca, André Faustino;
Kalavadwala, Hussain;
Freitas, Martiela Vaz de;
Clementi, Cecilia;
Zanatta, Geancarlo;
Antunes, Dinler Amaral;
Kavraki, Lydia E

Publication type:

Article

From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad248

By:

Ruiz, José Luis;
Reimering, Susanne;
Escobar-Prieto, Juan David;
Brancucci, Nicolas M B;
Echeverry, Diego F;
Abdi, Abdirahman I;
Marti, Matthias;
Gómez-Díaz, Elena;
Otto, Thomas D

Publication type:

Article

E-value: a superior alternative to P-value and its adjustments in DNA methylation studies.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad241

By:

Yang, Yifan;
Liu, Haoyuan;
Liu, Yi;
Zhou, Liyuan;
Zheng, Xiaoqi;
Yue, Rongxian;
Mattson, David L;
Kidambi, Srividya;
Liang, Mingyu;
Liu, Pengyuan;
Pan, Xiaoqing

Publication type:

Article

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad240

By:

Xu, Jing;
Li, Fuyi;
Li, Chen;
Guo, Xudong;
Landersdorfer, Cornelia;
Shen, Hsin-Hui;
Peleg, Anton Y;
Li, Jian;
Imoto, Seiya;
Yao, Jianhua;
Akutsu, Tatsuya;
Song, Jiangning

Publication type:

Article

DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad246

By:

He, Chun;
Ye, Xinhai;
Yang, Yi;
Hu, Liya;
Si, Yuxuan;
Zhao, Xianxin;
Chen, Longfei;
Fang, Qi;
Wei, Ying;
Wu, Fei;
Ye, Gongyin

Publication type:

Article

iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad245

By:

Li, Kai;
Zhang, Ping;
Wang, Zilin;
Shen, Wei;
Sun, Weicheng;
Xu, Jinsheng;
Wen, Zi;
Li, Li

Publication type:

Article

An integrated deep learning framework for the interpretation of untargeted metabolomics data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad244

By:

Tian, Leqi;
Yu, Tianwei

Publication type:

Article

PharmBERT: a domain-specific BERT model for drug labels.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad226

By:

ValizadehAslani, Taha;
Shi, Yiwen;
Ren, Ping;
Wang, Jing;
Zhang, Yi;
Hu, Meng;
Zhao, Liang;
Liang, Hualou

Publication type:

Article

C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad225

By:

Ibéné, Mandy;
Legendre, Audrey;
Postic, Guillaume;
Angel, Eric;
Tahi, Fariza

Publication type:

Article

TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad214

By:

Gao, Siqi;
Zhu, Hanwen;
Cai, Kangwen;
Liu, Leiqin;
Zhang, Zhiqiang;
Ding, Yi;
Xu, Yaochen;
Zheng, Xiaoqi;
Shi, Jiantao

Publication type:

Article

Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad217

By:

Meng, Qiaozhen;
Guo, Fei;
Tang, Jijun

Publication type:

Article

Network integration and protein structural binding analysis of neurodegeneration-related interactome.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad237

By:

Chen, Hongjun;
Zhou, Yekai;
Liu, Yongjing;
Zhang, Peijing;
Chen, Ming

Publication type:

Article

Comprehensive evaluation of deep and graph learning on drug–drug interactions prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad235

By:

Lin, Xuan;
Dai, Lichang;
Zhou, Yafang;
Yu, Zu-Guo;
Zhang, Wen;
Shi, Jian-Yu;
Cao, Dong-Sheng;
Zeng, Li;
Chen, Haowen;
Song, Bosheng;
Yu, Philip S;
Zeng, Xiangxiang

Publication type:

Article

Predicting potential small molecule–miRNA associations utilizing truncated schatten p-norm.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad234

By:

Wang, Shudong;
Liu, Tiyao;
Ren, Chuanru;
Wu, Wenhao;
Zhao, Zhiyuan;
Pang, Shanchen;
Zhang, Yuanyuan

Publication type:

Article

ProJect: a powerful mixed-model missing value imputation method.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad233

By:

Kong, Weijia;
Wong, Bertrand Jern Han;
Hui, Harvard Wai Hann;
Lim, Kai Peng;
Wang, Yulan;
Wong, Limsoon;
Goh, Wilson Wen Bin

Publication type:

Article

Leveraging trans-ethnic genetic risk scores to improve association power for complex traits in underrepresented populations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad232

By:

Lu, Haojie;
Zhang, Shuo;
Jiang, Zhou;
Zeng, Ping

Publication type:

Article

DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad231

By:

Ding, Pengju;
Wang, Yifei;
Zhang, Xinyu;
Gao, Xin;
Liu, Guozhu;
Yu, Bin

Publication type:

Article

A novel statistical method for decontaminating T-cell receptor sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad230

By:

Li, Ruoxing;
Altan, Mehmet;
Reuben, Alexandre;
Lin, Ruitao;
Heymach, John V;
Tran, Hai;
Chen, Runzhe;
Little, Latasha;
Hubert, Shawna;
Zhang, Jianjun;
Li, Ziyi

Publication type:

Article

A feature extraction free approach for protein interactome inference from co-elution data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad229

By:

Chen, Yu-Hsin;
Chao, Kuan-Hao;
Wong, Jin Yung;
Liu, Chien-Fu;
Leu, Jun-Yi;
Tsai, Huai-Kuang

Publication type:

Article

DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad228

By:

Feng, Ze-Ying;
Wu, Xue-Hong;
Ma, Jun-Long;
Li, Min;
He, Ge-Fei;
Cao, Dong-Sheng;
Yang, Guo-Ping

Publication type:

Article

Correction: Comparison and benchmark of structural variants detected from long read and long-read assembly.

Published in:: 2023
Publication type:: Correction Notice

MPCLCDA: predicting circRNA–disease associations by using automatically selected meta-path and contrastive learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad227

By:

Liu, Wei;
Tang, Ting;
Lu, Xu;
Fu, Xiangzheng;
Yang, Yu;
Peng, Li

Publication type:

Article

Machine learning modeling of RNA structures: methods, challenges and future perspectives.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad210

By:

Wu, Kevin E;
Zou, James Y;
Chang, Howard

Publication type:

Article

TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad209

By:

Zhu, Yan;
Li, Fuyi;
Guo, Xudong;
Wang, Xiaoyu;
Coin, Lachlan J M;
Webb, Geoffrey I;
Song, Jiangning;
Jia, Cangzhi

Publication type:

Article

scDFC: A deep fusion clustering method for single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad216

By:

Hu, Dayu;
Liang, Ke;
Zhou, Sihang;
Tu, Wenxuan;
Liu, Meng;
Liu, Xinwang

Publication type:

Article

scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad223

By:

Zhu, Hao;
Liu, Tong;
Wang, Zheng

Publication type:

Article

Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad222

By:

Gan, Yanglan;
Chen, Yuhan;
Xu, Guangwei;
Guo, Wenjing;
Zou, Guobing

Publication type:

Article

Improved the heterodimer protein complex prediction with protein language models.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad221

By:

Chen, Bo;
Xie, Ziwei;
Qiu, Jiezhong;
Ye, Zhaofeng;
Xu, Jinbo;
Tang, Jie

Publication type:

Article

Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad220

By:

Peng, Kerui;
Nowicki, Theodore S;
Campbell, Katie;
Vahed, Mohammad;
Peng, Dandan;
Meng, Yiting;
Nagareddy, Anish;
Huang, Yu-Ning;
Karlsberg, Aaron;
Miller, Zachary;
Brito, Jaqueline;
Nadel, Brian;
Pak, Victoria M;
Abedalthagafi, Malak S;
Burkhardt, Amanda M;
Alachkar, Houda;
Ribas, Antoni;
Mangul, Serghei

Publication type:

Article

GraphGPSM: a global scoring model for protein structure using graph neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad219

By:

He, Guangxing;
Liu, Jun;
Liu, Dong;
Zhang, Guijun

Publication type:

Article

Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad218

By:

Yang, Maohua;
Bo, Zonghua;
Xu, Tao;
Xu, Bo;
Wang, Dongdong;
Zheng, Hang

Publication type:

Article

MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad201

By:

Wang, Zhongyu;
Deng, Zhaohong;
Zhang, Wei;
Lou, Qiongdan;
Choi, Kup-Sze;
Wei, Zhisheng;
Wang, Lei;
Wu, Jing

Publication type:

Article

DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA–disease associations and graph convolutional networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad212

By:

Bai, Tao;
Yan, Ke;
Liu, Bin

Publication type:

Article

MCFF-MTDDI: multi-channel feature fusion for multi-typed drug–drug interaction prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad215

By:

Han, Chen-Di;
Wang, Chun-Chun;
Huang, Li;
Chen, Xing

Publication type:

Article

MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad202

By:

Darmawan, Jeremie Theddy;
Leu, Jenq-Shiou;
Avian, Cries;
Ratnasari, Nanda Rizqia Pradana

Publication type:

Article

Evaluation of sequence-based predictors for phase-separating protein.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad213

By:

Liao, Shaofeng;
Zhang, Yujun;
Qi, Yifei;
Zhang, Zhuqing

Publication type:

Article

Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences.

Published in:: 2023
Publication type:: Correction Notice

MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad207

By:

Cai, Guoxin;
Zhao, Wenyi;
Zhou, Zhan;
Gu, Xun

Publication type:

Article

A Bayesian approach to estimate MHC-peptide binding threshold.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad208

By:

Liu, Ran;
Hu, Ye-Fan;
Huang, Jian-Dong;
Fan, Xiaodan

Publication type:

Article