Selected Publications:
1: Tham CY, Tirado-Magallanes R, Goh Y, Fullwood MJ, Koh BTH, Wang W, Ng CH, Chng WJ, Thiery A, Tenen DG, Benoukraf T. NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing. Genome Biol. 2020 Mar 3;21(1):56.
2: Lin QXX, Sian S, Jha S, Benoukraf T. TFregulomeR reveals transcription factors’ context-specific features and functions. Nucleic Acids Res. 2019 Nov, DOI: 10.1093/nar/gkz1088.
3: Adusumalli S, Ngian ZK, Lin WQ, Benoukraf T*, Ong CT*. Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer's disease. Aging Cell. 2019 Jun;18(3):e12928. doi: 10.1111/acel.12928.
4: Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res. 2019 Jan 47 (D1) D145–D154,.
5: Abdul Hadi LH, Xuan Lin QX, Minh TT, Loh M, Ng HK, Salim A, Soong R*, Benoukraf T*. miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set. BMC Bioinformatics. 2018 Aug 10;19(1):299.
6: Rajagopalan D, Tirado-Magallanes R, Bhatia SS, Teo WS, Sian S, Hora S, Lee KK, Zhang Y, Jadhav SP, Wu Y, Gan YH, Karnani N, Benoukraf T, Jha S. TIP60 represses activation of endogenous retroviral elements. Nucleic Acids Res. 2018 Oct 12;46(18):9456-9470.
7: Tirado-Magallanes R, Rebbani K, Lim R, Pradhan S, Benoukraf T. Whole genome DNA methylation: beyond genes silencing. Oncotarget. 2017 Jan 17;8(3):5629-5637.
8: Adusumalli S, Mohd Omar MF, Soong R, Benoukraf T. Methodological aspects of whole-genome bisulfite sequencing analysis. Brief Bioinform. 2015 May;16(3):369-79.
9: Bard-Chapeau EA, Nguyen AT, Rust AG, Sayadi A, Lee P, Chua BQ, New LS, de Jong J, Ward JM, Chin CK, Chew V, Toh HC, Abastado JP, Benoukraf T, Soong R, Bard FA, Dupuy AJ, Johnson RL, Radda GK, Chan EC, Wessels LF, Adams DJ, Jenkins NA, Copeland NG. Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model. Nat Genet. 2014 Jan;46(1):24-32.
10: Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL and Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21;503(7476):371-6.
*: co-last authors
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