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Touati Benoukraf

Genetics
PhD (Aix-Marseille II)

Canada Research Chair in Bioinformatics for Personalized Medicine
Assistant Professor, Discipline of Genetics

Laboratory website: http://benoukraf-lab.com

Craig L. Dobbin Genetics Research Centre, Room: M5M317
Faculty of Medicine, Memorial University of Newfoundland
St. John’s, NL, Canada A1B 3V6
 
t: (709) 864-6671
f: (709) 864-6537
lab:

tbenoukraf@mun.ca


Research Interests:

Dr. Benoukraf focuses his research on pan-omics analytics with a particular interest in integrating genomics, epigeneomics and microbiomics information to decipher novel pathophysiological mechanisms.

Education:

2010: PhD (Bioinformatics, Structural Biology, and Genomics), University of Aix-Marseille II, Marseille, France.
2006: MSc (Bioinformatics, Structural Biology, and Genomics), University of Aix-Marseille II, Marseille, France.
2004: BSc (Computer Sciences), University of Aix-Marseille II, Marseille, France.
2003: Associate Degree (Mathematics), University of Aix-Marseille II, Marseille, France

Honours & Awards:

2018: Canada Research Chair (Tier II)
2012-2018: Special Fellow, Cancer Science Institute of Singapore
2015: Unique Presentation Award, 7th HOPE Meeting with Nobel Laureates, JSPS, Tokyo, Japan
2009: Doctoral scholarship, French Foundation for Medical Research (FRM)

Professional Experience: 

11/2018 – present: Assistant Professor and Canada Research Chair in Bioinformatics for Personalized Medicine, Discipline of Genetics, Faculty of Medicine, Memorial University

2018 – present: Visiting Assistant Professor, 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 and Special Fellow, Cancer Science Institute of Singapore, National University of Singapore 

2010 – 2012: Research Fellow (Postdoctoral Fellow), Cancer Science Institute of Singapore, National University of Singapore


Research: Fighting diseases with genome analytics

High-throughput sequencing has revolutionized the way in which scientists study physiopathology. In this context, bioinformatics is used, thanks to “Big Data”, to harness and even produce the knowledge indispensable to the discovery of new treatments tailored to the patient.
Very recently, sequencing technologies have been used successfully in clinics, but it is only offered to diagnose or select treatment strategies for a limited number of conditions. Dr. Benoukraf’s laboratory combines multidisciplinary expertise ranging from mathematics and computer sciences to molecular biology, allowing the integration of epigenetics and microbiomics dimensions to patients’ genomic information, hence the discovery of novel mechanisms involved in pathogenesis or therapeutic resistance.


Current Financial Support:
  •   Canada Research Chair program
  •   Canada Foundation for Innovation
  •   Canadian Institutes of Health Research
  •   Faculty of Medicine

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

Full Publication list