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Benoukraf Lab

> Fighting Disease with Genome Analytics

Research Areas

Our multi-disciplinary laboratory focuses on omics interplay mechanisms in physiopathology.

 

Our hybrid (wet & dry) laboratory develops computational methods and an integrative database for sequencing analyses and omics interplay mining. Overall, our research on pan-omics analytics is divided into three axes:

  • Understand the chromatin dynamics governed by the transcription factors and DNA methylation,
  • Understand the micro-environment molecular changes governed by the microbiome
  • Genome-wide mapping of structural variants and transposable elements and interplay with DNA methylation aberrations

Tools & Database

NanoVar

Structural variant caller for low-depth Nanopore Sequencing in Patients’ samples

 

MethMotif

A transcription factor binding motifs database coupled with DNA methylation profiles

TFRegulomeR

Characterization of transcription factors’ context-specific features and functions

Selected Publications

Teaching

Impact de la méthylation de l’ADN sur la régulation transcriptionnelle

Biologie computationnelle des systèmes

9 Novembre 2022 à 14h

Université Saint Joseph de Beyrouth

DNA sequencing technologies

Module MED 6591

November 29th 2022, 2.00pm – 5.00pm 

Memorial University of Newfoundland

Future of Genetics

Class of 2025 / Phase 3 Schedule

Future of Genetics

January 20th, 2023 11.30am (1M101)

Memorial University of Newfoundland

 

DNA sequencing technologies

Module CDM5104

January 27th 2023 4.00pm – 6.00pm.

National University of Singapore

ACC Workshop On RNAseq 2022 Atlantic Cancer Consortium (ACC) Workshop – Terry Fox Research Institute – May 16-19, 2022

Team Members

Touati Benoukraf, PhD

Group Leader

Canada Research Chair in Bioinformatics for Personalised Medicine & Assistant Professor | Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland

Visiting Assistant Professor & co-Head: Genomics and Data Analytics Core (GeDaC) at the Cancer Science Institute of Singapore, National University of Singapore

Dr. Akinola A. Alafiatayo

MoH-TFRI / MITACS Post Doctoral Fellow

Omics in Colorectal Cancer

Zia Hasan

PhD Student (Neuro – Qi lab)

Alzheimer’s single cell omics interplays

Matthew Dyer

PhD Student (Genetics)

DNA methylation dynamics

MethMotif maintenance

Asmaa Mahmoud

PhD student (Genetics)

Characterization of structural variants and repetitive elements

Tian Qin

PhD Student (Neuro – Qi lab)

Dynamics of single-cell brain epigenomics during fear communication

Sofiia Shapoval

Master’s Students (Genetics)

Transcription factors and DNA methylation insterplays

Chen Xiang

Master’s Student (Comp. Sci.)

Z-stack images processing

Zahra Vafadoost

Master’s Student (Genetics)

Microbiome analysis

Pipeline development

Gastongay Siu

Master’s Student (Genetics)

Computational epigenomics methods

Jason Huan

Professional Associate (Invited)

Full-stack software developer

Lab News

Seminar on structural variations in Leukemia. Invited speakers: Touati Benoukraf.

TAGC, Aix-Marseille University, France | December 16, 2022

Conference on Microbiome. Poster presentation: Akinola A. Alafiatayo.

Cold Spring Harbor, NY, USA | October 25 – 29, 2022

Invited speaker (TB) at the Toronto Bioinformatics Users Group seminar.
Toronto, ON, Canada | Feb. 24th, 2021.

Epigenetics in Cancer Symposium 2021. Our team is invited to talk (TB) and Matthew is presenting a poster on MethMotif.org.
NUS – Singapore | Feb. 15-17, 2021