• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4603440)   Today's Articles (4206)   Subscriber (49369)
For: Zhang Y, Wang Z, Zeng Y, Zhou J, Zou Q. High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method. Brief Bioinform 2021;22:6322761. [PMID: 34272562 DOI: 10.1093/bib/bbab273] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Yan W, Tan L, Mengshan L, Weihong Z, Sheng S, Jun W, Fu-An W. Time series-based hybrid ensemble learning model with multivariate multidimensional feature coding for DNA methylation prediction. BMC Genomics 2023;24:758. [PMID: 38082253 PMCID: PMC10712061 DOI: 10.1186/s12864-023-09866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023]  Open
2
Yang M, Chen S, Huang Z, Gao S, Yu T, Du T, Zhang H, Li X, Liu CM, Chen S, Li H. Deep learning-enabled discovery and characterization of HKT genes in Spartina alterniflora. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;116:690-705. [PMID: 37494542 DOI: 10.1111/tpj.16397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
3
Liu Y, Wang Z, Yuan H, Zhu G, Zhang Y. HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction. Brief Bioinform 2023;24:bbad286. [PMID: 37539835 DOI: 10.1093/bib/bbad286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]  Open
4
Zhang Q, Xu Y, Wang S, Wu Y, Ye Y, Yuan CA, Gribova V, Filaretov VF, Huang DS. Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2690-2699. [PMID: 36374878 DOI: 10.1109/tcbb.2022.3219831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
5
Choi SR, Lee M. Transformer Architecture and Attention Mechanisms in Genome Data Analysis: A Comprehensive Review. BIOLOGY 2023;12:1033. [PMID: 37508462 PMCID: PMC10376273 DOI: 10.3390/biology12071033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
6
Jing Y, Zhang S, Wang H. DapNet-HLA: Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites. Anal Biochem 2023;666:115075. [PMID: 36740003 DOI: 10.1016/j.ab.2023.115075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
7
Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Brief Bioinform 2023;24:7005164. [PMID: 36702751 DOI: 10.1093/bib/bbad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/02/2023] [Accepted: 01/08/2023] [Indexed: 01/28/2023]  Open
8
Wang Z, Zhang Y, Yu Y, Zhang J, Liu Y, Zou Q. A Unified Deep Learning Framework for Single-Cell ATAC-Seq Analysis Based on ProdDep Transformer Encoder. Int J Mol Sci 2023;24:ijms24054784. [PMID: 36902216 PMCID: PMC10003007 DOI: 10.3390/ijms24054784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/02/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023]  Open
9
Zhang Y, Wang M, Wang Z, Liu Y, Xiong S, Zou Q. MetaSEM: Gene Regulatory Network Inference from Single-Cell RNA Data by Meta-Learning. Int J Mol Sci 2023;24:ijms24032595. [PMID: 36768917 PMCID: PMC9916710 DOI: 10.3390/ijms24032595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]  Open
10
Tang X, Zheng P, Liu Y, Yao Y, Huang G. LangMoDHS: A deep learning language model for predicting DNase I hypersensitive sites in mouse genome. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:1037-1057. [PMID: 36650801 DOI: 10.3934/mbe.2023048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
11
Yan W, Li Z, Pian C, Wu Y. PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites. Brief Bioinform 2022;23:6713513. [PMID: 36155619 DOI: 10.1093/bib/bbac425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 12/14/2022]  Open
12
Towards a better understanding of TF-DNA binding prediction from genomic features. Comput Biol Med 2022;149:105993. [DOI: 10.1016/j.compbiomed.2022.105993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
13
Zhang Y, Bao W, Cao Y, Cong H, Chen B, Chen Y. A survey on protein–DNA-binding sites in computational biology. Brief Funct Genomics 2022;21:357-375. [DOI: 10.1093/bfgp/elac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023]  Open
14
Base-resolution prediction of transcription factor binding signals by a deep learning framework. PLoS Comput Biol 2022;18:e1009941. [PMID: 35263332 PMCID: PMC8982852 DOI: 10.1371/journal.pcbi.1009941] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/05/2022] [Accepted: 02/19/2022] [Indexed: 01/13/2023]  Open
15
Zhang L, Yang Y, Chai L, Li Q, Liu J, Lin H, Liu L. A deep learning model to identify gene expression level using cobinding transcription factor signals. Brief Bioinform 2021;23:6447678. [PMID: 34864886 DOI: 10.1093/bib/bbab501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 01/02/2023]  Open
16
Jiang Z, Xiao SR, Liu R. Dissecting and predicting different types of binding sites in nucleic acids based on structural information. Brief Bioinform 2021;23:6384399. [PMID: 34624074 PMCID: PMC8769709 DOI: 10.1093/bib/bbab411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA