Genomic Annotation in R

CellbaseR backage in Bioconductor

The Sudanese Genetic Variation portal

The SGVA Poster

In Singapore

From the Cancer research conference

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Mohammed O.E Abdallah

Post-Doctoral Fellow, Department of Human Genetics

University of Cape Town

OpenCB

Biography

Mohammed O.E. Abdallah is a post-doctoral fellow in the department of human genetics at professor Raj Ramesar group. His research interests includes Genomics, Cancer Genomics, Pharmacogenomics, and Bioinformatics.

I am a physician who turned into a bioinformatician, and R and Python developer with the ultimate goal of utilizing cutting edge technologies for understanding common medical and research problems, especially for understudied populations

Interests

  • Genomics
  • Genomics Data Science
  • Data Visualization, and Web technologies

Education

  • PhD in Molecular Biology, 2019

    University of Khartoum

  • Msc Molecular Medicine, 2012

    University of Khartoum

  • MBBS Bachelor of Medicine and Surgery, 2005

    Faculty of Medicine University of Khartoum

Skills

Genomics

Statistics

Linux

R

Python

Docker

Apache Spark

Shiny

HPC

Experience

 
 
 
 
 

Post-Doctoral Fellow

University of Cape Town

Feb 2019 – Present South Africa
Responsibilities include:

  • Analysis Of Exome Sequencing Data
  • Curation and modeling of genomics and clinical data

 
 
 
 
 

Head of NGS Analysis Team

Institute of Endemic Diseases, University of Khartoum

Jan 2014 – May 2018 Sudan
 
 
 
 
 

Lecturer

Faculty of Medicine, International University of Africa

Dec 2012 – Jan 2019 Sudan

Recent Publications

Quickly discover relevant content by filtering publications.
January 2020 Medicine (United States)

Age, absolute CD4 count, and CD4 percentage in relation to HPV infection and the stage of cervical disease in HIV-1-positive women

DOI
January 2018 BMC genomics

Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data

January 2018 Frontiers in oncology

EBV associated Breast Cancer whole methylome analysis reveals viral and developmental enriched pathways

January 2018 bioRxiv

Recurrent AIPL1 c. 487C> T truncating variant in Leber Congenital Amaurosis: Support of pathogenicity and regional implications

January 2017 Khartoum Medical Journal

Five decades lead in biomedical research: University of Khartoum tops Sudanese universities in PubMed articles

See all publications

Recent Posts

Simplifying Genomic Annotations in R

In this blog post I will be introducing cellbaseR R package, which makes use of the exhaustive RESTful Web service API that has been …
Last updated on Ocotober 10, 2109 7 min read Genomics, variant annotation, cellbaseR, Bioconductor

Projects

African Genome Variation Database

The aim of the project is to create an African Genome Variation Database (AGVD) that will provide searching and visualisation …

The Sudanese Genetics Variation Portal

The Sudanese Genetic Variation Archive is the first comprehensive resource for medical and population genetics in Sudan. It catalogs …

Accomplish­ments

Supervised Learning in R: Classification Course

DataCamp Jun 2018
Supervised Learning in R

Statistics and R for the Life Sciences

edX Jun 2016
Statistics and R for the Life Sciences

Case study: DNA methylation data analysis

edX Jun 2016
Case study: DNA methylation data analysis

Case Study: Variant Discovery and Genotyping

edX Sep 2015
Case Study: Variant Discovery and Genotyping

Introduction to Bioconductor

edX Sep 2015
Introduction to Bioconductor.

Data Analysis for Genomics

edX Jun 2014
Data Analysis for Genomics.

Popular Topics

Africa age and cervical cancer Bioinformatics CD4 count and CD4 percentage disconnect cellbaseR cervical tumor biopsies Genetic Variation Genomics HIV-1/HPV co-infection HPV genotypes OpenCGA Sudan variant Annotation

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