Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

Autor: Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin, Ekta Khurana

Publikováno v: Genome Biology, Vol 18, Iss 1, Pp 1-23 (2017)

Abstract We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensit

Externí odkaz: https://doaj.org/article/7d6a18d3f0444aceadbe8d4b57bb15bb

Discovery of novel therapeutic targets in cancer using patient-specific gene regulatory networks

Autor: Andre Neil Forbes, Duo Xu, Sandra Cohen, Priya Pancholi, Ekta Khurana

Most cancer types lack effective targeted therapeutic options and in cancers where first-line targeted therapies are available, treatment resistance is a huge challenge. Recent technological advances enable the use of ATAC-seq and RNA-seq on patient

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8ac0b3ea4df7ac92f102fbf7cb5afaf7
https://doi.org/10.1101/2022.01.31.478503

Abstract 2034: Patient-specific enhancer-gene networks for hundreds of primary cancer samples

Autor: Ann Palladino, Duo Xu, Tatiana Karadimitriou, Andre Neil Forbes, Ekta Khurana, Sandra Cohen

Publikováno v: Cancer Research. 81:2034-2034

Epigenomic alterations at regulatory elements have been implicated in cancer tumorigenesis. As a hallmark for epigenetic changes, chromatin accessibility profiles are generated for cancer patients. However, not all accessible regions are active regul

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1f5598d59fb01f53ea7c732e8838cbb7
https://doi.org/10.1158/1538-7445.am2021-2034

MYBL1rearrangements andMYBamplification in breast adenoid cystic carcinomas lacking theMYB-NFIBfusion gene

Autor: Raymond S. Lim, Fresia Pareja, Pier Selenica, Anne Vincent-Salomon, Britta Weigelt, Rajesh Kumar, Larry Norton, Felipe C. Geyer, Odette Mariani, Sunil V. Badve, Rodrigo Gularte-Mérida, Charlotte K.Y. Ng, Andre Neil Forbes, Jisun Kim, Marcia Edelweiss, Ekta Khurana, Nicola Fusco, Luciano G. Martelotto, Jorge S. Reis-Filho, Anqi Li

Publikováno v: The Journal of Pathology. 244:143-150

Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer, has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangeme

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::abad616c4c6cb32a9f0c89827c8eed50
https://doi.org/10.1002/path.5006

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

Autor: Alexander Martinez-Fundichely, Adeline Berger, Priyanka Dhingra, Pablo Tamayo, Andrea Sboner, David S. Rickman, Mark A. Rubin, Andre Neil Forbes, Deli Liu, Ekta Khurana, Eric Minwei Liu, Franklin W. Huang

Publikováno v: Genome Biology
Genome biology, vol 18, iss 1
Dhingra, Priyanka; Martinez-Fundichely, Alexander; Berger, Adeline; Huang, Franklin W; Forbes, Andre Neil; Liu, Eric Minwei; Liu, Deli; Sboner, Andrea; Tamayo, Pablo; Rickman, David S; Rubin, Mark Andrew; Khurana, Ekta (2017). Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome biology, 18(1), p. 141. BioMed Central Ltd. 10.1186/s13059-017-1266-3
Genome Biology, Vol 18, Iss 1, Pp 1-23 (2017)

We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity bas

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ec0f40bd4fd4724c5f5d978d188aa696
https://pubmed.ncbi.nlm.nih.gov/28750683