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Benoukraf Lab

> Fighting Disease with Genome Analytics

Research Areas

Integrative Omics Approaches to Studying Epigenomic Drift in Disease

Our hybrid laboratory (combining wet and dry methods) focuses on developing computational tools and producing sequencing datasets for analyzing multi-omics interactions in the context of epigenomics drift.

 

Our research is divided into three main axes:

  • Investigating the chromatin dynamics regulated by transcription factors in the context of epigenomic drift.

  • Investigating the contribution of the microbiome in the epigenomic drift.

  • Investigating the contribution of the epigenomic drift in genome instability.

Overall, using integrative approaches, our laboratory’s goal is to deepen our understanding of epigenomic drift and its underlying mechanisms. By analyzing these different omics layers, we aim to better describe and understand the role of epigenomic drift in pathophysiology.

Tools & Database

NanoVar

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

 

MethMotif 2024
New release!

A transcription factor binding motifs database coupled with DNA methylation profiles

forkedTF

ForkedTF is an R-library that introduces Forked-PMW and Forked-Sequence Logos  to provide a more comprehensive depiction of the sequence affinity of a TF of interest

TFRegulomeR

Characterization of transcription factors’ context-specific features and functions

Selected Publications

Teaching

Human Genetics & Genomics/Cancer & Development Seminar Series

Modules:
MED 6400, 6401, 6402, 6403: Msc students
MED 6410, 6411, 6412, 6413: PhD students

Every Monday at 12:00pm (check D2L for schedule).
Memorial University of Newfoundland

Bioinformatics

Module MED 6393

October 18th 2023,
4.00pm – 5.00pm

October 25th 2023,
2.00pm – 3.45pm 

Memorial University of Newfoundland

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

Biologie computationnelle des systèmes

6 Décembre 2023 Université Saint Joseph de Beyrouth

DNA sequencing technologies

Module CDM5104

January 26th 2024 4.00pm – 6.00pm.

National University of Singapore

Future of Genetics

Class of 2025 / Phase 3 Schedule

Future of Genetics

January 19th, 2024 11.30am (1M101)

Memorial University of Newfoundland

 

Team Members

Dr. Akinola A. Alafiatayo

MoH-TFRI / MITACS Post Doctoral Fellow

Omics in Colorectal Cancer

Dr. Hayley Alloway-Pike

Post Doctoral Fellow

Chromatin Structure

Dr. Modeline Longjohn

MoH-TFRI / MITACS Post Doctoral Fellow

Cancer Bioinformatics

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 interplays

Chen Xiang

Master’s Student (Comp. Sci.)

Z-stack images processing

Gastongay Siu

Master’s Student (Genetics)

Computational epigenomics methods

Jason Huan

Professional Associate (Invited)

Full-stack software developer

External Collaborators 

Lab News

November 12 – 14,  2023 | The Canadian Cancer Research Conference (CCRC) @ Halifax, NS. T. Benoukraf: invited Chair of the Multi-Omics and Epigenomics Session & speaker: “Characterizing the Interplay of Multi-Omics Mechanisms in Cancers”

October 26,  2023 – 🎓👏 A new Master in the place! Congrats to Zahra Vafadoost on earning her Master’s degree! 🌟 We’re incredibly proud of your achievement. 🙌👩‍🎓

July 25, 2023 @ 10X Genomics user group meeting | Very proud to see our former students’ success in the industry! Nice job, Quy & Cheng Yong!

July 5-7, 2023 | Congratulations to Asmaa, Matthew, and Gaston for receiving awards during the BioMedicine 2023 symposium!

May 26, 2023 | Very delighted to have shared science with high school students during Discovery Day @ Memorial University. We hope we were able to instill a passion for genomics in these future bright scientists.

April 2023 | Very delighted to meet Fred Fox, Terry Fox‘s brother, who was a Canadian athlete, humanitarian, and cancer research activist. The Terry Fox Research Institute, which was named in honor of Terry Fox, is a key player in cancer research in Canada, and one of our sponsors.

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

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