Touati BENOUKRAF

Dr Touati Benoukraf’s research focus is the role of non-coding segments of the genome in order to identify novel regulatory elements such as enhancers or silencers with the aim of understanding their function in human physiology and pathology. More specifically, he uses epigenetic marks and transcription factor binding site datasets derived from high-throughput sequencing technologies to annotate and predict the function of these uncharacterized loci.

benoukraf@nus.edu.sg

Biosketch

Dr Touati Benoukraf’s research focus is the role of non-coding segments of the genome in order to identify novel regulatory elements such as enhancers or silencers with the aim of understanding their function in human physiology and pathology. More specifically, he uses epigenetic marks and transcription factor binding site datasets derived from high-throughput sequencing technologies to annotate and predict the function of these uncharacterized loci. This information allows the investigation of genomic and epigenomic aberrations in cancers beyond genes and the delineation of novel disease-related signaling pathways. Dr Benoukraf has developed several open source software applications to manage large epigenetic datasets and one of his contributions in this field was to describe the association between histone post-translational modifications and enhancer activities which enables the prediction of enhancer states from in vivo epigenetic data.

Principal Associate, Cancer Science Institute of Singapore, National University of Singapore
Canada Research Chair in Bioinformatics for Personalised Medicine & Assistant Professor, Faculty of Medicine, Discipline of Genetics, Memorial University of Newfoundland

Year(s) Degree (if applicable) Institute
2010 Ph.D. Immunology Center of Marseille-Luminy (CIML), National Center for Scientific Research (CNRS), University of Aix-Marseille II, France
2006 Master Department of Biology, University of Aix-Marseille II, France
2004 BSc Department of Computer Science, University of Aix-Marseille II, France
2019 – Present Principal Associate, Cancer Science Institute of Singapore, National University of Singapore
2018 – Present Canada Research Chair in Bioinformatics for Personalised Medicine & Assistant Professor, Faculty of Medicine, Discipline of Genetics, Memorial University of Newfoundland
2014 – Present Head, Computational Core, Cancer Science Institute of Singapore, National University of Singapore
2018 Principal Investigator, Cancer Science Institute of Singapore, National University of Singapore
2012 – 2018 Research Assistant Professor, Cancer Science Institute of Singapore, National University of Singapore
2010 – 2012 Research Fellow, Cancer Science Institute of Singapore, National University of Singapore
2008 – 2010 Lecturer, Department of Mathematics, University of Aix-Marseille II, France
2002 – 2009 Co-founder & co-chairman, startup company Comline, Marseille, France

Research

Deep sequencing is enabling new insights into mechanisms of gene regulation including the involvement of intergenic elements. 97% of human DNA is non-coding, and significant portions of this comprise cis-regulatory elements such as enhancers, silencers or insulators which are involved in the spacial-temporal gene regulation. Recent whole genome sequencing as well genome-wide association studies have shown that alterations of these non-coding elements can modify specific signaling pathways and consequently lead to disease. However, in contrast to coding genes, there is no comprehensive record of such regions, making the investigation of regulatory elements alterations challenging. We are developing informatics solutions for integrating in-house and published high-throughput sequencing data (genome and epigenome) in order to decipher and annotate these unexplored segments of DNA. This will allow us to build a framework for the investigation of cancers genomic aberrations moving forward from coding genes, and identify non-coding alterations involved in tumorigenesis.

Lab Members

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 Biology. 2020 March;21(56)

2. Lin QXX, Thieffry D, Jha S, Benoukraf T. TFregulomeR reveals transcription factors’ context-specific features and functions. Nucleic Acids Res. 2019 Nov. doi: 10.1093/nar/gkz1088.

3. 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 8;47(D1):D145-D154.

4. Abdul Hadi LH, Lin QXX, Minh Tran T, 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.

5. Ponnaluri VKC, Zhang G, Estève PO, Spracklin G, Sian S, Xu SY, Benoukraf T, Pradhan S. NicE-seq: high-resolution open chromatin profiling. Genome Biol. 2017 Jun 28;18(1):122.

6. 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.

7. 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.

8. 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. Nature Genetics. 2014 Jan;4(1):24-32.

9. 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’Alo F,Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21;503(7476):371-6.

10. Benoukraf T*, Wongphayak S, Hadi LH, Wu M, Soong R*. GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. Nucleic Acids Res. 2013 Feb 1;41(4):e55.

*: Corresponding authors