Kevin Rue-Albrecht

Sabid Hossain

Software Engineer

Evercare Hospital Dhaka

Biography

I am a computational biologist at the University of Oxford.

My research interests in computational biology include software engineering best practices, DevOps, single-cell genomics, and interactive data visualization. I particularly enjoy using and contributing R packages part of the Bioconductor project. A list of software packages that I maintain or contributed to is available on the Software page.

My academic research primarily explores the host immune response to infectious diseases, inflammation, and self-antigens.

Interests

  • Computational Biology
  • Software Development
  • Bioconductor packages
  • Single-cell genomics

Education

  • PhD in sa Infection Biology, 2015

    United International University

  • MSc in Biological Engineering, 2011

    Polytech Nice - Université Nice Sophia Antipolis

  • BSc in Biology, Chemistry, Physics and Earth Sciences, 2008

    CPGE BCPST Véto - Lycée Jean Rostand

Skills

R

90%

Software carpentry

90%

Statistics

70%

Immunology

70%

Infectious diseases

70%

Experience

 
 
 
 
 

Postdoctoral Researcher - Computational Genomics

University of Oxford

Sep 2017 – Present Oxford

Responsibilities include:

  • Study the role of thymic epithelial cells (TEC) in shaping the T vell receptor (TCR) repertoire (consortium funded by Wellcome Trust Strategic Award)
  • Study contest-specific changes in immune cell abundance and phenotype that underlie chronic inflammation (collaboration with the Powrie group)
  • Write and maintain software pipelines and programs for data analysis
 
 
 
 
 

Postdoctoral Researcher - Computational Biology

University of Oxford

Dec 2016 – Sep 2017 Oxford

Responsibilities include:

  • Management, quality control, and integration of pan-genomic datasets encompassingn RNA-seq, ChIP-seq, DNAse/FAIRE/ATAC-seq, Capture-C, microarrays, whole-genome sequencing and targeted re-sequencing
  • Study transcriptional and epigenetic responses to hypoxia and their relation to cancer biology
  • Experimental design, pipeline development, and publication
 
 
 
 
 

Research Associate - Bioinformatics / Biostatistics

Imperial College London

Sep 2015 – Nov 2016 London

Responsibilities include:

  • Analyze genetic, proteomic and metabolomics data and associated phenotype data
  • Integrate and analysis of large-scale, complex, multi-sources medical data and multi-variate data
  • Generate new knowledge on idiopathic pulmonary arterial hypertension (IPAH) disease aetiology, underlying biochemical pathways and mechanisms, to improve patient stratification, preventive strategies and treatments

Accomplish­ments

Machine Learning

Coursera Jul 2017 – Sep 2017
Machine learning is the science of getting computers to act without being explicitly programmed.
See certificate

Python for Genomic Data Science

Coursera Oct 2015 – Nov 2015
This class provides an introduction to the Python programming language and the iPython notebook. This is the third course in the Genomic Big Data Science Specialization from Johns Hopkins University.
See certificate

Command Line Tools for Genomic Data Science

Coursera Oct 2015 – Nov 2015
Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.
See certificate

Bioconductor for Genomic Data Science

Coursera Oct 2015 – Nov 2015
Learn to use tools from the Bioconductor project to perform analysis of genomic data. This is the fifth course in the Genomic Big Data Specialization from Johns Hopkins University.
See certificate

Statistics for Genomic Data Science

Coursera Oct 2015 – Nov 2015
An introduction to the statistics behind the most popular genomic data science projects. This is the sixth course in the Genomic Big Data Science Specialization from Johns Hopkins University.
See certificate

Network Analysis in Systems Biology

Coursera Aug 2013 – Dec 2013
An introduction to data integration and statistical methods used in contemporary Systems Biology, Bioinformatics and Systems Pharmacology research. The course covers methods to process raw data from genome-wide mRNA expression studies (microarrays and RNA-seq) including data normalization, differential expression, clustering, enrichment analysis and network construction.
See certificate

Projects

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All rmarkdown Twitter Other

COVID-19 Website

My website tracking the evolution of the COVID-19 pandemic.

Reading list

A list of items that I have read or intend to read.

Twitter conference coverage

My website tracking tweets associated with scientific conferences.

Recent & Upcoming Talks

iSEE - Bioconductor 2020 Workshop Presentation

Overview of the iSEE package and functionality
Jun 26, 2019 3:10 PM — 5:00 PM New York City, USA
Slides Follow

iSEE - Bioconductor 2020 Flash Presentation

Flash presentation of the iSEE package and functionality
Jun 24, 2019 10:25 AM — 10:30 AM New York City, USA
Slides Follow