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For: Kumar S, Bucher P. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinformatics 2016;17 Suppl 1:4. [PMID: 26818008 PMCID: PMC4895346 DOI: 10.1186/s12859-015-0846-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023;13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]  Open
2
Sghaier N, Essemine J, Ayed RB, Gorai M, Ben Marzoug R, Rebai A, Qu M. An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa. PLANTS (BASEL, SWITZERLAND) 2022;12:71. [PMID: 36616201 PMCID: PMC9824623 DOI: 10.3390/plants12010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
3
Rivière Q, Corso M, Ciortan M, Noël G, Verbruggen N, Defrance M. Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants. PLANT & CELL PHYSIOLOGY 2022;63:1457-1473. [PMID: 35799371 DOI: 10.1093/pcp/pcac095] [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: 06/12/2021] [Revised: 06/07/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
4
SemanticCAP: Chromatin Accessibility Prediction Enhanced by Features Learning from a Language Model. Genes (Basel) 2022;13:genes13040568. [PMID: 35456374 PMCID: PMC9028922 DOI: 10.3390/genes13040568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]  Open
5
D’Arienzo V, Ferguson J, Giraud G, Chapus F, Harris JM, Wing PAC, Claydon A, Begum S, Zhuang X, Balfe P, Testoni B, McKeating JA, Parish JL. The CCCTC-binding factor CTCF represses hepatitis B virus enhancer I and regulates viral transcription. Cell Microbiol 2021;23:e13274. [PMID: 33006186 PMCID: PMC7116737 DOI: 10.1111/cmi.13274] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022]
6
Zhou M, Li H, Wang X, Guan Y. Evidence of widespread, independent sequence signature for transcription factor cobinding. Genome Res 2021;31:265-278. [PMID: 33303494 PMCID: PMC7849410 DOI: 10.1101/gr.267310.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/03/2020] [Indexed: 01/03/2023]
7
Srivastava D, Aydin B, Mazzoni EO, Mahony S. An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding. Genome Biol 2021;22:20. [PMID: 33413545 PMCID: PMC7788824 DOI: 10.1186/s13059-020-02218-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/03/2020] [Indexed: 02/06/2023]  Open
8
Wang H, Liu Y, Guan H, Fan GL. The Regulation of Target Genes by Co-occupancy of Transcription Factors, c-Myc and Mxi1 with Max in the Mouse Cell Line. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191106103633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
9
Chen L, Capra JA. Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput Biol 2020;16:e1008334. [PMID: 33137083 PMCID: PMC7660921 DOI: 10.1371/journal.pcbi.1008334] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 11/12/2020] [Accepted: 09/12/2020] [Indexed: 12/12/2022]  Open
10
Zhou J, Lu Q, Xu R, Gui L, Wang H. Prediction of TF-Binding Site by Inclusion of Higher Order Position Dependencies. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1383-1393. [PMID: 30629513 DOI: 10.1109/tcbb.2019.2892124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
11
Zhou J, Lu Q, Gui L, Xu R, Long Y, Wang H. MTTFsite: cross-cell type TF binding site prediction by using multi-task learning. Bioinformatics 2020;35:5067-5077. [PMID: 31161194 PMCID: PMC6954652 DOI: 10.1093/bioinformatics/btz451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022]  Open
12
Using Machine-Learning Algorithms for Eutrophication Modeling: Case Study of Mar Menor Lagoon (Spain). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020;17:ijerph17041189. [PMID: 32069834 PMCID: PMC7068380 DOI: 10.3390/ijerph17041189] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 11/16/2022]
13
Homotypic cooperativity and collective binding are determinants of bHLH specificity and function. Proc Natl Acad Sci U S A 2019;116:16143-16152. [PMID: 31341088 DOI: 10.1073/pnas.1818015116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
14
Lan G, Zhou J, Xu R, Lu Q, Wang H. Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network. Int J Mol Sci 2019;20:ijms20143425. [PMID: 31336830 PMCID: PMC6679139 DOI: 10.3390/ijms20143425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 01/18/2023]  Open
15
Keilwagen J, Posch S, Grau J. Accurate prediction of cell type-specific transcription factor binding. Genome Biol 2019;20:9. [PMID: 30630522 PMCID: PMC6327544 DOI: 10.1186/s13059-018-1614-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/18/2018] [Indexed: 01/11/2023]  Open
16
Girgis HZ, Velasco A, Reyes ZE. HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures. BMC Bioinformatics 2018;19:310. [PMID: 30176808 PMCID: PMC6122555 DOI: 10.1186/s12859-018-2312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 08/14/2018] [Indexed: 12/11/2022]  Open
17
Chen A, Chen D, Chen Y. Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals. Gene 2018;667:83-94. [DOI: 10.1016/j.gene.2018.05.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/04/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
18
Aziz HA, Abdel-Salam ASG, Al-Obaide MAI, Alobydi HW, Al-Humaish S. Kynurenine 3-Monooxygenase Gene Associated With Nicotine Initiation and Addiction: Analysis of Novel Regulatory Features at 5' and 3'-Regions. Front Genet 2018;9:198. [PMID: 29951083 PMCID: PMC6008986 DOI: 10.3389/fgene.2018.00198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/17/2018] [Indexed: 11/13/2022]  Open
19
Behera V, Evans P, Face CJ, Hamagami N, Sankaranarayanan L, Keller CA, Giardine B, Tan K, Hardison RC, Shi J, Blobel GA. Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. Nat Commun 2018;9:782. [PMID: 29472540 PMCID: PMC5823854 DOI: 10.1038/s41467-018-03082-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 01/18/2018] [Indexed: 12/13/2022]  Open
20
Liu S, Zibetti C, Wan J, Wang G, Blackshaw S, Qian J. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. BMC Bioinformatics 2017;18:355. [PMID: 28750606 PMCID: PMC5530957 DOI: 10.1186/s12859-017-1769-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 12/04/2022]  Open
21
Weber B, Zicola J, Oka R, Stam M. Plant Enhancers: A Call for Discovery. TRENDS IN PLANT SCIENCE 2016;21:974-987. [PMID: 27593567 DOI: 10.1016/j.tplants.2016.07.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/18/2016] [Accepted: 07/28/2016] [Indexed: 05/12/2023]
22
Sharmin M, Bravo HC, Hannenhalli S. Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Res 2016;26:1110-23. [PMID: 27311443 PMCID: PMC4971765 DOI: 10.1101/gr.199166.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 06/16/2016] [Indexed: 12/24/2022]
23
Volkova OA, Kondrakhin YV, Yevshin IS, Valeev TF, Sharipov RN. Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data. J Bioinform Comput Biol 2016;14:1641006. [PMID: 27122318 DOI: 10.1142/s0219720016410067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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