Works matching IS 14675463 AND DT 2023 AND VI 24 AND IP 1

Results: 146

Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.

Published in:: 2023
Publication type:: Correction Notice

scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac625

By:

Wang, Jing;
Xia, Junfeng;
Wang, Haiyun;
Su, Yansen;
Zheng, Chun-Hou

Publication type:

Article

GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac620

By:

Wang, Kai

Publication type:

Article

Modeling and analyzing single-cell multimodal data with deep parametric inference.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbad005

By:

Hu, Huan;
Feng, Zhen;
Lin, Hai;
Zhao, Junjie;
Zhang, Yaru;
Xu, Fei;
Chen, Lingling;
Chen, Feng;
Ma, Yunlong;
Su, Jianzhong;
Zhao, Qi;
Shuai, Jianwei

Publication type:

Article

Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac619

By:

Yeung, Wayland;
Zhou, Zhongliang;
Mathew, Liju;
Gravel, Nathan;
Taujale, Rahil;
O'Boyle, Brady;
Salcedo, Mariah;
Venkat, Aarya;
Lanzilotta, William;
Li, Sheng;
Kannan, Natarajan

Publication type:

Article

Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers.

Published in:: 2023
Publication type:: Correction Notice

Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac630

By:

Yuan, Qitong;
Chen, Keyi;
Yu, Yimin;
Le, Nguyen Quoc Khanh;
Chua, Matthew Chin Heng

Publication type:

Article

Integrated mRNA sequence optimization using deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbad001

By:

Gong, Haoran;
Wen, Jianguo;
Luo, Ruihan;
Feng, Yuzhou;
Guo, JingJing;
Fu, Hongguang;
Zhou, Xiaobo

Publication type:

Article

Comparative epigenome analysis using Infinium DNA methylation BeadChips.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac617

By:

Ding, Wubin;
Kaur, Diljeet;
Horvath, Steve;
Zhou, Wanding

Publication type:

Article

Tracing human life trajectory using gut microbial communities by context-aware deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac629

By:

Zhang, Haohong;
Chong, Hui;
Yu, Qingyang;
Zha, Yuguo;
Cheng, Mingyue;
Ning, Kang

Publication type:

Article

Reducing false positive rate of docking-based virtual screening by active learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac626

By:

Wang, Lei;
Shi, Shao-Hua;
Li, Hui;
Zeng, Xiang-Xiang;
Liu, Su-You;
Liu, Zhao-Qian;
Deng, Ya-Feng;
Lu, Ai-Ping;
Hou, Ting-Jun;
Cao, Dong-Sheng

Publication type:

Article

A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac616

By:

Deng, Wenxuan;
Li, Bolun;
Wang, Jiawei;
Jiang, Wei;
Yan, Xiting;
Li, Ningshan;
Vukmirovic, Milica;
Kaminski, Naftali;
Wang, Jing;
Zhao, Hongyu

Publication type:

Article

A novel strategy for designing the magic shotguns for distantly related target pairs.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac621

By:

Luo, Yongchao;
Wang, Panpan;
Mou, Minjie;
Zheng, Hanqi;
Hong, Jiajun;
Tao, Lin;
Zhu, Feng

Publication type:

Article

Computational model for disease research.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac615

By:

Chen, Xing;
Huang, Li

Publication type:

Article

Benchmarking of computational methods for predicting circRNA-disease associations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac613

By:

Lan, Wei;
Dong, Yi;
Zhang, Hongyu;
Li, Chunling;
Chen, Qingfeng;
Liu, Jin;
Wang, Jianxin;
Chen, Yi-Ping Phoebe

Publication type:

Article

Systematic benchmarking of statistical methods to assess differential expression of circular RNAs.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac612

By:

Buratin, Alessia;
Bortoluzzi, Stefania;
Gaffo, Enrico

Publication type:

Article

A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac611

By:

Lee, Sanghun;
Hahn, Georg;
Hecker, Julian;
Lutz, Sharon M;
Mullin, Kristina;
(ADNI), Alzheimer's Disease Neuroimaging Initiative;
Hide, Winston;
Bertram, Lars;
DeMeo, Dawn L;
Tanzi, Rudolph E;
Lange, Christoph;
Prokopenko, Dmitry

Publication type:

Article

slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac610

By:

Song, Bo;
Li, Hao;
Jiang, Mengyun;
Gao, Zhongtian;
Wang, Suikang;
Gao, Lei;
Chen, Yunsheng;
Li, Wujiao

Publication type:

Article

Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac609

By:

Zhu, Xi-Liang;
Bao, Lin-Xia;
Xue, Min-Qi;
Xu, Ying-Ying

Publication type:

Article

Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac608

By:

Xu, Xinyi;
Li, Xiangjie

Publication type:

Article

Benchmarking differential abundance analysis methods for correlated microbiome sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac607

By:

Yang, Lu;
Chen, Jun

Publication type:

Article

AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac606

By:

Fang, Yitian;
Xu, Fan;
Wei, Lesong;
Jiang, Yi;
Chen, Jie;
Wei, Leyi;
Wei, Dong-Qing

Publication type:

Article

A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac605

By:

Shen, Bihan;
Feng, Fangyoumin;
Li, Kunshi;
Lin, Ping;
Ma, Liangxiao;
Li, Hong

Publication type:

Article

Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human–virus protein–protein interactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac604

By:

Ma, Yingjun;
Zhong, Junjiang

Publication type:

Article

Leveraging scaffold information to predict protein–ligand binding affinity with an empirical graph neural network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac603

By:

Xia, Chunqiu;
Feng, Shi-Hao;
Xia, Ying;
Pan, Xiaoyong;
Shen, Hong-Bin

Publication type:

Article

A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac602

By:

Feng, Yue-Hua;
Zhang, Shao-Wu;
Feng, Yi-Yang;
Zhang, Qing-Qing;
Shi, Ming-Hui;
Shi, Jian-Yu

Publication type:

Article

From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac600

By:

Defo, Joel;
Awany, Denis;
Ramesar, Raj

Publication type:

Article

Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac599

By:

Yeung, Wayland;
Zhou, Zhongliang;
Li, Sheng;
Kannan, Natarajan

Publication type:

Article

Deleterious synonymous mutation identification based on selective ensemble strategy.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac598

By:

Wang, Lihua;
Zhang, Tao;
Yu, Lihong;
Zheng, Chun-Hou;
Yin, Wenguang;
Xia, Junfeng;
Zhang, Tiejun

Publication type:

Article

DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac597

By:

Li, Zimeng;
Zhu, Shichao;
Shao, Bin;
Zeng, Xiangxiang;
Wang, Tong;
Liu, Tie-Yan

Publication type:

Article

Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac596

By:

Yang, Bo;
Chen, Hailin

Publication type:

Article

Predicting lncRNA–disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac595

By:

Xie, Guo-Bo;
Chen, Rui-Bin;
Lin, Zhi-Yi;
Gu, Guo-Sheng;
Yu, Jun-Rui;
Liu, Zhen-guo;
Cui, Ji;
Lin, Lie-qing;
Chen, Lang-cheng

Publication type:

Article

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac594

By:

Zhou, Jiayin;
Song, Wen;
Tu, Qichao

Publication type:

Article

An evolution-based machine learning to identify cancer type-specific driver mutations.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac593

By:

Kim, Donghyo;
Ha, Doyeon;
Lee, Kwanghwan;
Lee, Heetak;
Kim, Inhae;
Kim, Sanguk

Publication type:

Article

Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac592

By:

Wang, Dong;
Wu, Zhenxing;
Shen, Chao;
Bao, Lingjie;
Luo, Hao;
Wang, Zhe;
Yao, Hucheng;
Kong, De-Xin;
Luo, Cheng;
Hou, Tingjun

Publication type:

Article

bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac591

By:

Moutsopoulos, Ilias;
Williams, Eleanor C;
Mohorianu, Irina I

Publication type:

Article

SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac590

By:

Sun, Lei;
Wang, Gongming;
Zhang, Zhihua

Publication type:

Article

Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac589

By:

Molin, Anna Dal;
Parenzan, Caterina Tretti;
Gaffo, Enrico;
Borin, Cristina;
Boldrin, Elena;
Meyer, Lueder H;
Kronnie, Geertruij te;
Bresolin, Silvia;
Bortoluzzi, Stefania

Publication type:

Article

CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac588

By:

Hosseini, Sayed-Rzgar;
Zhou, Xiaobo

Publication type:

Article

Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac587

By:

Tang, Zhenshuang;
Yin, Lilin;
Yin, Dong;
Zhang, Haohao;
Fu, Yuhua;
Zhou, Guangliang;
Zhao, Yunxiang;
Wang, Zhiquan;
Liu, Xiaolei;
Li, Xinyun;
Zhao, Shuhong

Publication type:

Article

Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac586

By:

Lin, Zerun;
Ou-Yang, Le

Publication type:

Article

scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac585

By:

Wang, Hai-Yun;
Zhao, Jian-Ping;
Zheng, Chun-Hou;
Su, Yan-Sen

Publication type:

Article

SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac584

By:

Fan, Xiao;
Pan, Hongbing;
Tian, Alan;
Chung, Wendy K;
Shen, Yufeng

Publication type:

Article

EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac583

By:

Zhou, Bailing;
Ding, Maolin;
Feng, Jing;
Ji, Baohua;
Huang, Pingping;
Zhang, Junye;
Yu, Xue;
Cao, Zanxia;
Yang, Yuedong;
Zhou, Yaoqi;
Wang, Jihua

Publication type:

Article

CODA: a combo-Seq data analysis workflow.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac582

By:

Nazzari, Marta;
Hauser, Duncan;
Herwijnen, Marcel van;
Romitti, Mírian;
Carvalho, Daniel J;
Kip, Anna M;
Caiment, Florian

Publication type:

Article

RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac581

By:

He, Shujun;
Gao, Baizhen;
Sabnis, Rushant;
Sun, Qing

Publication type:

Article

Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac580

By:

Chen, Siqi;
Yan, Xuhua;
Zheng, Ruiqing;
Li, Min

Publication type:

Article

LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac579

By:

Liu, Tianyuan;
Zou, Bohao;
He, Manman;
Hu, Yongfei;
Dou, Yiying;
Cui, Tianyu;
Tan, Puwen;
Li, Shaobin;
Rao, Shuan;
Huang, Yan;
Liu, Sixi;
Cai, Kaican;
Wang, Dong

Publication type:

Article

Metapath-aggregated heterogeneous graph neural network for drug–target interaction prediction.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac578

By:

Li, Mei;
Cai, Xiangrui;
Xu, Sihan;
Ji, Hua

Publication type:

Article

Identification of vital chemical information via visualization of graph neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac577

By:

Wang, Yimeng;
Huang, Mengting;
Deng, Hua;
Li, Weihua;
Wu, Zengrui;
Tang, Yun;
Liu, Guixia

Publication type:

Article