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For: Zhao J, Li D, Seo J, Allen AS, Gordân R. Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Res Comput Mol Biol 2017;10229:336-352. [PMID: 28691125 DOI: 10.1007/978-3-319-56970-3_21] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Number Cited by Other Article(s)
1
Baumgarten N, Rumpf L, Kessler T, Schulz MH. A statistical approach for identifying single nucleotide variants that affect transcription factor binding. iScience 2024;27:109765. [PMID: 38736546 PMCID: PMC11088338 DOI: 10.1016/j.isci.2024.109765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 01/30/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]  Open
2
Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. BMC Bioinformatics 2024;25:179. [PMID: 38714913 PMCID: PMC11075237 DOI: 10.1186/s12859-024-05794-7] [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: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]  Open
3
Marin-Bejar O, Romero-Moya D, Rodriguez-Ubreva J, Distefano M, Lessi F, Aretini P, Liquori A, Castaño J, Kozyra E, Kotmayer L, Bueno C, Cervera J, Rodriguez-Gallego JC, Nomdedeu JF, Murillo-Sanjuán L, De Heredia CD, Pérez-Martinez A, López-Cadenas F, Martínez-Laperche C, Dorado-Herrero N, Marco FM, Prósper F, Menendez P, Valcárcel D, Ballestar E, Bödör C, Bigas A, Catalá A, Wlodarski MW, Giorgetti A. Epigenome profiling reveals aberrant DNA methylation signature in GATA2 deficiency. Haematologica 2023;108:2551-2557. [PMID: 36815365 PMCID: PMC10483368 DOI: 10.3324/haematol.2022.282305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023]  Open
4
Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023;28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
5
De Vas MG, Boulet F, Joshi SS, Garstang MG, Khan TN, Atla G, Parry D, Moore D, Cebola I, Zhang S, Cui W, Lampe AK, Lam WW, Ferrer J, Pradeepa MM, Atanur SS. Regulatory de novo mutations underlying intellectual disability. Life Sci Alliance 2023;6:e202201843. [PMID: 36854624 PMCID: PMC9978454 DOI: 10.26508/lsa.202201843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023]  Open
6
PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. J Cheminform 2023;15:31. [PMID: 36864534 PMCID: PMC9983232 DOI: 10.1186/s13321-023-00701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023]  Open
7
Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2022;13278:36-51. [PMID: 36507923 PMCID: PMC9740185 DOI: 10.1007/978-3-031-04749-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
8
Dietlein F, Wang AB, Fagre C, Tang A, Besselink NJM, Cuppen E, Li C, Sunyaev SR, Neal JT, Van Allen EM. Genome-wide analysis of somatic noncoding mutation patterns in cancer. Science 2022;376:eabg5601. [PMID: 35389777 PMCID: PMC9092060 DOI: 10.1126/science.abg5601] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
9
Padhi EM, Hayeck TJ, Cheng Z, Chatterjee S, Mannion BJ, Byrska-Bishop M, Willems M, Pinson L, Redon S, Benech C, Uguen K, Audebert-Bellanger S, Le Marechal C, Férec C, Efthymiou S, Rahman F, Maqbool S, Maroofian R, Houlden H, Musunuri R, Narzisi G, Abhyankar A, Hunter RD, Akiyama J, Fries LE, Ng JK, Mehinovic E, Stong N, Allen AS, Dickel DE, Bernier RA, Gorkin DU, Pennacchio LA, Zody MC, Turner TN. Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. Hum Genomics 2021;15:44. [PMID: 34256850 PMCID: PMC8278787 DOI: 10.1186/s40246-021-00342-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023]  Open
10
Zhang Y, Ho TD, Buchler NE, Gordân R. Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Res 2021;31:1216-1229. [PMID: 33975875 PMCID: PMC8256859 DOI: 10.1101/gr.275145.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/06/2021] [Indexed: 11/24/2022]
11
Rovirosa L, Ramos-Morales A, Javierre BM. The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer. Front Immunol 2020;11:592087. [PMID: 33117405 PMCID: PMC7575776 DOI: 10.3389/fimmu.2020.592087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022]  Open
12
Zhu C, Miller M, Zeng Z, Wang Y, Mahlich Y, Aptekmann A, Bromberg Y. Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-030320-041014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
13
Martin V, Zhao J, Afek A, Mielko Z, Gordân R. QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic Acids Res 2020;47:W127-W135. [PMID: 31114870 PMCID: PMC6602471 DOI: 10.1093/nar/gkz363] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/13/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022]  Open
14
Campbell MC, Ashong B, Teng S, Harvey J, Cross CN. Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6. BMC Evol Biol 2019;19:218. [PMID: 31791241 PMCID: PMC6889576 DOI: 10.1186/s12862-019-1516-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022]  Open
15
Haas J, Mester S, Lai A, Frese KS, Sedaghat-Hamedani F, Kayvanpour E, Rausch T, Nietsch R, Boeckel JN, Carstensen A, Völkers M, Dietrich C, Pils D, Amr A, Holzer DB, Martins Bordalo D, Oehler D, Weis T, Mereles D, Buss S, Riechert E, Wirsz E, Wuerstle M, Korbel JO, Keller A, Katus HA, Posch AE, Meder B. Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy. EMBO Mol Med 2019;10:107-120. [PMID: 29138229 PMCID: PMC5760848 DOI: 10.15252/emmm.201707838] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
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