Summary
Overview
Work History
Education
Skills
Accomplishments
Publications
References
Training
Timeline
Generic
Muhammad Imran Khan

Muhammad Imran Khan

Rostock

Summary

With two decades of R&D prowess, I am an accomplished Human Geneticist and Bioinformatician, ready to propel your team's success to new heights. My robust expertise in Genomics is complemented by a keen proficiency in programming, comprehensive analysis of extensive datasets, and the development of cutting-edge NGS pipelines. My academic journey culminated in a PhD in Medical Sciences, obtained in 2013, which underpins my dedication to innovation and critical thinking. I pride myself on my exceptional communication skills, ensuring that complex scientific concepts are conveyed with clarity and impact. Allow me to bring my wealth of knowledge and technical acumen to your organization, where I am poised to make a significant contribution.

Overview

19
19
years of professional experience
6
6
years of post-secondary education
4
4
Languages

Work History

Bioinformatician R&D

Cologne Center for Genomics
02.2023 - 05.2023
  • Development, validation and implementation of NGS pipeline for Enzymatic Methyl-sequencing, data analysis using workflow language Nextflow
  • Programing in Pyhton and bash shell within Linux enviroment (HPC cluster)
  • Tested and reviewed two newly developed bioinformatics tools that determine biological sex from NGS data.

Scientist Medical Bioinformatics

Centogene
07.2020 - 07.2022
  • NGS data analysis, establishing genetics diagnosis for various rare diseases
  • Whole Genome & Exome sequencing (WGS & WES) data (analyzed > 3500 samples)
  • Filtering the list of variants for the best candidates
  • Genotype-phenotype correlation & classification of variants.

Postdoctoral Research Fellow

Department of Human Genetics, Radboud University Medical Center
04.2013 - 08.2018
  • Target enrichment & library preparation for high-throughput sequencing
  • Developed and optimized cost-effective screening method, making use of molecular inversion probes (MIPs)
  • Screened > 6,000 cases from Asia, Canada, and Europe for mutations in 108 retinal disease-associated genes simultaneously for 65€ per sample
  • Bioinformatic analysis of data (Perl, Java, python and R based scripts), filtering and prioritizing disease causing genetic variants
  • Project management: European retinal disease consortium (ERDC), 15 members (12 in Europe, and 1 each from Canada, US and Israel)
  • WGS &WES data analysis
  • Supervising research students (Master & PhD).

Researcher

Department of Human Genetics, Radboud University Medical Center
06.2009 - 03.2013
  • Molecular genetic elucidation of inherited retinal diseases
  • Identity-by-Descent (IBD) Mapping using genome-wide SNP microarrays & Candidate gene sequencing, targeted exome & WES.

Research Associate

Environmental analytical laboratory, Pakistan council of scientific and industrial research (PCSIR)
03.2004 - 08.2005
  • Biochemical and Microbiological analysis of drinking water quality in teaching institute of federal and provincial capital of Pakistan.

Education

PhD. Medical Sciences - Human Genetics

Radboud University Medical Center
Nijmegen, the Netherlands
06.2009 - 05.2013

M.s. Bio Sciences -

COMSATS University Islamabad
Islamabad, Pakistan
08.2005 - 05.2007

Skills

Programming

Accomplishments

  • May 1-5, 2016, & May 2-6, 2010 - Arvo travel grant, to attend ARVO’s annual meeting, Seattle, USA
  • Feb 4-5, 2016 - Best oral presentation by young investigator award, in the first joint meeting of Netherlands and Belgian society for Human genetics, Leuven, Belgium
  • 2014, 2013 & 2012 - Research productivity award, COMSATS University Islamabad, Pakistan
  • 2005 - 2009 - Merit scholarship, for MS & PhD studies by, COMSATS University Islamabad, Pakistan

Publications

  • Late-onset autosomal dominant macular degeneration caused by deletion of the CRX gene. Yahya S, Smith CE, Poulter JA, McKibbin M, Arno G, Ellingford J, Kämpjärvi K, Khan MI, Cremers FP, Hardcastle AJ, Castle B, Steel DHW, The UK Inherited Retinal Disease Consortium, Genomics England Research Consortium, Webster AR, Black GC, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Ophthalmology 2023 Jan;130(1):68-76.
  • Targeted gene sequencing of FYCO1 identified a novel mutation in a Pakistani family for autosomal recessive congenital cataract. Saleem RS, Siddiqui SN, Irshad S, Ashraf NM, Hamid A, Khan MAU, Khan MI, Micheal S. Mol Genet Genomic Med. 2022 Aug;10(8):e1985.
  • Cost-effective molecular inversion probe-based ABCA4 sequencing reveals deep-intronic variants in Stargardt disease. Khan M, Cornelis SS, Khan MI, Elmelik D, Manders E, Bakker S, Derks R, Neveling K, van de Vorst M, Gilissen C, Meunier I, Defoort S, Puech B, Devos A, Schulz HL, Stöhr H, Grassmann F, Weber BHF, Dhaenens CM, Cremers FPM. Hum Mutat. 2019;40:1749-1759.
  • Homozygosity mapping identifies genetic defects in four consanguineous families with retinal dystrophy from Pakistan. Khan MI, Ajmal M, Micheal S, Azam M, Hussain H, Shehzad A, de Wijs IJ, Hoefsloot LH, Gill M, Waheed NK, Collin RWJ, den Hollander AI, Qamar R, Cremers FPM. Clin. Genet. 2013; 84:290-3.
  • CLRN1 mutations cause nonsyndromic retinitis pigmentosa. Khan MI, Kersten FFJ, Azam M, Collin RWJ, Hussain A, Shah STA, Keunen JEE, Kremer H, Cremers FPM, Qamar R, den Hollander AI. Ophthalmology 2011; 118:1444-8

References

  • Prof. Dr. Frans P.M. Cremers, Professor in Ophthalmogenetics, Department of Human Genetics, Radboud University Medical center, Nijmegen, The Netherlands, Frans.Cremers@radboudumc.nl
  • Dr. Rob W.J. Collin, Professor - Faculty of Medical Science, Department of Human Genetics, Radboud University Medical center, Nijmegen, The Netherlands, rob.collin@radboudumc.nl

Training

  • Advance training in Applied Bioinformatics & Biostatistics, CQ Beratung+Bildung, Berlin, Germany, 09/01/22, 04/01/23, Applied Bioinformatics BASH under LINUX, Python Bioinformatics & database management (SQL) Applied Biostatistics (R/R studio)
  • German language course, inligua, Rostock, Germany, 05/01/23, 04/01/24, DTZ (B1) Certificate
  • Professional German language course, inligua, Rostock, Germany, 03/01/24, Language level B2

Timeline

Bioinformatician R&D

Cologne Center for Genomics
02.2023 - 05.2023

Scientist Medical Bioinformatics

Centogene
07.2020 - 07.2022

Postdoctoral Research Fellow

Department of Human Genetics, Radboud University Medical Center
04.2013 - 08.2018

PhD. Medical Sciences - Human Genetics

Radboud University Medical Center
06.2009 - 05.2013

Researcher

Department of Human Genetics, Radboud University Medical Center
06.2009 - 03.2013

M.s. Bio Sciences -

COMSATS University Islamabad
08.2005 - 05.2007

Research Associate

Environmental analytical laboratory, Pakistan council of scientific and industrial research (PCSIR)
03.2004 - 08.2005
Muhammad Imran Khan