Kumar Veerapen, PhD

Experience

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  Sime Darby Technology Centre Sdn. Bhd.

  Nov 2006 - Dec 2006

  Intern

  I was working with Julia Ibrahim in the Bioprocess Technology lab where most work involved fungal manipulation and enzyme characterization.

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  Malaysian Rubber Board

  Aug 2008 - Nov 2008

  Intern

  I was in the Bioinformatics and Genomics lab under Dr Chow Keng See where we looked at characterizing interesting hits on an EST database that is already established for Hevea brasiliensis. All of this is in effort to understand the rubber transcriptome.

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  UCSI Education Group

  Jan 2009 - Jul 2011

  Tutor, Faculty of Applied Sciences

  • Led 3 courses and co-led 2 during my tenure.• Supervisor for honors dissertations of 11 undergraduate and 1 graduate (MSc) students.• Dissertation committee member for 15 undergraduate students (biotechnology majors). • Co-led the genotyping of candidate genes in myopia and obesity in a cohort of Malaysian adolescents. Funded by the Fundamental Research Grant Scheme (Malaysia).• Co-led the purification of recombinant Ara h 2.02 allergen and Bromelain • Co-led the identification and characterization of lipase producing bacteria, and bioactive compounds obtained from home garden plants.• Research and Development award for outstanding scientific progress (2011). Show less

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  University of Miami

  Aug 2011 - Apr 2016

  PHD Candidate

  • Dissertation title: The Genetics of Preterm Birth• Completed the final 16 months of the dissertation work at Boston Children’s Hospital, Boston, MA.• Developed a method to extract, quantify, and perform whole exome sequencing on membrane and umbilical cord tissue from 23 maternal-fetal pairs.• Analyzed RNA-seq and methylation data in longitudinal maternal samples from Emory University Birth Biobank. • Analyzed on whole exome sequencing data for trio and quad analyses in proband patients with rare diseases.• Investigated metagenome sequencing from mice (fecal samples) that were exposed to PCP.• Annual Biomedical Graduate Student Government Research Symposium, University of Miami Miller School of Medicine (Poster Presentation) (2014)• Course and Travel Award: Summer Institute in Statistical Genetics 2014 [University of Washington, Seattle] (2014)• Mentored by Olaf A. Bodamer, M.D., Ph.D. and Evadnie Rampersaud, Ph.D Show less

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  Boston Children's Hospital

  Jan 2015 - Jun 2016

  Graduate Student

  I completed my PhD in the genetics of preterm birth at the Olaf Bodamer Research Lab which moved from the University of Miami to Boston Children's Hospital in 2015. We used a multi-omics approach in determining risk factors in the etiology of preterm birth.

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  Massachusetts General Hospital

  Jul 2016 - Sept 2021

  Postdoctoral Research Fellow

  My primary affiliation for my postdoctoral research fellow position was at MGH.

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  Broad Institute of MIT and Harvard

  Jul 2016 - Mar 2022

  • Software support and community engagement provided by assisting users in troubleshooting and optimizing Hail analytical pipelines for genomic analysis using Hail forum (discuss.hail.is) and Hail Zulip chat (hail.zulipchat.com).• In-person software support and community engagement provided by assisting users in debugging Hail scripts using Hail office hours that we organize every Thursday at 1 pm (virtually with zoom.us, during the COVID-19 pandemic)• Ongoing curation and development of documentation on https://hail.is/docs/0.2/index.html• Maintenance, curation, and development of content on the Hail website (hail.is) and blog site (blog.hail.is).• Team lead for website development and content curation for hail.is • Education outreach on the use of Hail as a tool for scalable genomic analysis by means of workshops, webinars, how-to guides, and YouTube videos.• Manages Hail Twitter account (@hailgenetics) on team updates and Hail release notifications.• Manages Hail support forum on Zulip and discuss.hail.com • Organization and coordination of social outreach events such as Stanley Center socials co-chaired with Hail and meet and discuss sessions with target user groups at the Broad Institute. • Management and coordination of design, purchase, and distribution of Hail merchandise e.g. outerwear, stickers, and pins.• Led the curation of best practices for whole exome and whole genome sequencing methods for COVID-19 Global Host Genetics Initiative (https://github.com/covid19-hg/covid19_sequencing).• Led scientific communication efforts for COVID-19 Global Host Genetics Initiative (https://www.covid19hg.org/) Show less • Facilitate community and analytical support for FinnGen i.e., leading monthly user workshops on use of Sandbox (a cloud interactive virtual machine system), documentation updating, and content curation for the FinnGen Analyst Handbook.• Lead analyst for understanding drug response variability of selective serotonin reuptake inhibitor (SSRI) for the FinnGen Depression Task Force.• Co-supervised 1 undergraduate honours dissertation student.• Supervised by Mark Daly, Ph.D. and Benjamin Neale, Ph.D. Show less • Performed interaction analysis on drug and intervention using a multiple phenotype approach on FinnGen. • Developed a framework to combine linkage analysis with whole genome sequencing analysis to identify previously unidentified rare and damaging variants in the Finnish migraine family collection (N(ind)=14,064). • Characterized polygenic risk in complex migraine traits in multiplex families and population controls using logistic mixed model regression analysis (N = 23,797).• Explained over transmission of polygenic risk in complex migraine traits in multiplex families using polygenic risk score transmission disequilibrium test (N = 8,964).• Collaborated on the analysis of candidate gene studies in a clinical cohort (Malaysia) of rheumatoid arthritis towards the efficacy of methotrexate as a treatment plan. Funded by the Sunway Medical Center Sdn. Bhd.• Designed framework for the analysis of RNA sequencing in the “Use of Bikram yoga as an intervention method in clinical depression” (N(cases)=40; N(controls)=42). In collaboration with Maren Nyer, Ph.D. and Simmie Foster, M.D. in the Department of Psychiatry, MGH.• Collaborated on elucidating transcriptomic changes in muscular dystrophy related to mutations in SPEG using speg knockout mice. The PI for this project is Pankaj Agrawal, M.D. at Boston Children’s Hospital.• Led one course in the GINGER, Harvard School of Public Health. • Gordon Research Seminar for Human Genetics and Genomics (Co-chair). Funds raised: $8,000 (7/10-11/2022) • Supervised honours dissertations: 2 undergraduate and 1 graduate (MSc) students (2019-2021)• ATGU Community Building Award, ATGU Annual Retreat [Massachusetts General Hospital, Boston, MA] (2020)• Mentored by Mark Daly, Ph.D. [from 10/2019], Benjamin Neale, Ph.D. [from 8/2019], and Aarno Palotie, M.D., Ph.D. [until 12/2019]. Show less

  • Community Support and Outreach Manager

    Jan 2020 - Mar 2022

  • Computational Scientist I

    Sept 2021 - Feb 2022

  • Postdoctoral Research Fellow

    Jul 2016 - Sept 2021
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  Harvard Medical School

  Jul 2016 - Sept 2021

  Postdoctoral Research Fellow

  My tertiary affiliation for my postdoctoral research fellow position was at MGH.

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  UCSI

  Nov 2020 - Jun 2022

  Adjunct Lecturer

  • Invitations to teach classes at UCSI University as and when needed such as in Current Topics of Biotechnology and Molecular Cell Biology and Genetics (Graduate course). • Supervise one undergraduate research project per year.

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  Novartis Institutes for BioMedical Research (NIBR)

  Mar 2022 - now

  Senior Expert I Data Science

  Using genomic datasets to increase precision in drug targeting.