Ashish Kumar

About me
Public outreach and news

About me

I am working in the domain of complex disease medical research, with
specialization in bioinformatics, biostatistics, computational genetics and
high-performance computing (HPC).
I am technology enthusiast, with expertise around convergence of different
scientific disciplines spanning medical science, computer science, data
science, high-performance computing, biostatistics, biophysics and scientific
application around business process automation and re-engineering.
I am additionally focussing on developing new Indo-European collaborative
research projects in complex diseases as well as technology convergence in
the genomics domain. At Karolinska Institutet [1] (since 2012), I'm providing
consultancy to Prof. Erik Melén's [2] group and affiliated to Department of
Clinical Science and Education [3] at the Södersjukhuset (KI SÖS) [4] - one
of the largest hospitals in Stockholm.
[1] http://www.google.com/url?q=http%3A%2F%2Fki.se%2Fen&
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[2] http://www.google.com/url?q=http%3A%2F%2Fki.se%2Fen%2Fpeople%2Ferimel&
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[3] https://www.google.com/url?q=https%3A%2F%2Fki.se%2Fen%2Fkisos%2Fdepartment-of-clinical-science-and-education-sodersjukhuset&
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[4] https://www.google.com/url?q=https%3A%2F%2Fki.se%2Fen%2Fkisos%2Fresearch-ki-sos&
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Research

Previously, I was working with Diabetes Research group [1], led by Prof. Mark
McCarthy [2] at the Wellcome Centre for Human Genetics [3], University of
Oxford [4] (from 2006-2014) and Genetic Epidemiology group [5], led by Prof.
Nicole Probst-Hensch [6] at the Swiss Tropical and Public Health Institute
[7], University of Basel [8] in Switzerland (from 2010-2018).
*Research Summary:*
* OMICs data integration involving GWAS and imputed datasets, sequencing
(genomic and exomes), methylation/epigenomics data, transcriptomics,
expression arrays, proteomics and biological pathways.
* Application of methodologies in artificial intelligence/machine learning
into genomics.
* Complex diseases like asthma, type-2 diabetes, pulmonary function traits
like lung function, COPD, eczema, rhinitis, obesity, BMI and related
phenotypes.
* GWAS analysis in consortium projects like DIAGRAM [9], ENGAGE [10], EGG,
EAGLE, SpiroMeta, MAGIC, GoDMC [11], etc.
* EWAS analysis in consortium projects with PACE [12] and MeDALL [13]
* Discovery, genotyping and association evaluation of variants in projects
like GoT2D [14], GABRIEL and SUMMIT project (developing SOPs and pipelines
for discovery/analysis on HPC servers and super-computing clusters).
* Evaluations of methylation chip data using various normalisation methods
* Annotation challenges with genetics and epigenetics datasets.
*Expertise:*
* Covering diverse range of platforms including low-coverage sequencing,
exome-sequencing, dense-array genotyping on various chips from Illumina &
Affy, methylation arrays from Illumina, custom i-Select chips like
Metabochip, HumanCoreExome, etc.
* Multivariate statistics like logistic regression, principal components
analysis, etc. to analyse various cohort datasets.
* Gene and environment interactions, rare variants and fine mapping
analysis.
* Building and incorporating large QC and bioinformatics-pipelines for
various types of -omics datasets like genotyped/imputed SNPs, methylation
CpGs, RNA-seq, proteomics, expression, etc.
* Managing Data centre
high-performance computing resources.
* Large scale data storage, handling, formatting and visualisation.
* Bioinformatics education &
training.
*For detailed publications list, please follow this link:*
http://scholar.google.co.uk/citations?user=j-eQjGEAAAAJ&
hl=en
[1] https://www.google.com/url?q=https%3A%2F%2Fwww.well.ox.ac.uk%2Fresearch%2Fresearch-groups%2Fmccarthy-group&
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[2] https://www.google.com/url?q=https%3A%2F%2Fwww.well.ox.ac.uk%2Fpeople%2Fmark-mccarthy&
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[3] http://www.google.com/url?q=http%3A%2F%2Fwww.well.ox.ac.uk%2F&
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[4] http://www.google.com/url?q=http%3A%2F%2Fwww.ox.ac.uk%2F&
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[5] https://www.google.com/url?q=https%3A%2F%2Fwww.swisstph.ch%2Fen%2Fabout%2Feph%2Fchronic-disease-epidemiology%2Fgenetic-epidemiology-of-non-communicable-diseases%2F&
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[6] https://www.google.com/url?q=https%3A%2F%2Fwww.swisstph.ch%2Fen%2Fstaff%2Fnicole-probst-hensch%2F&
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[7] https://www.google.com/url?q=https%3A%2F%2Fwww.swisstph.ch%2Fen%2F&
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[8] http://www.google.com/url?q=http%3A%2F%2Fwww.unibas.ch%2Findex.cfm%3Fo_lang_id%3D2&
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[9] https://www.google.com/url?q=https%3A%2F%2Fwww.diagram-consortium.org%2F&
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[10] http://www.google.com/url?q=http%3A%2F%2Fwww.euengage.org%2F&
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[11] http://www.google.com/url?q=http%3A%2F%2Fwww.godmc.org.uk%2F&
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[12] https://www.google.com/url?q=https%3A%2F%2Fwww.niehs.nih.gov%2Fresearch%2Fatniehs%2Flabs%2Fepi%2Fpi%2Fgenetics%2Fpace%2Findex.cfm&
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[13] https://www.google.com/url?q=https%3A%2F%2Fwww.isglobal.org%2Fen%2Fproject%2F-%2Fasset_publisher%2Fqf6QOKuKkIC3%2Fcontent%2Fmedall&
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[14] http://www.google.com/url?q=http%3A%2F%2Fwww.type2diabetesgenetics.org%2Fprojects%2Fgot2d&
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About me

Research

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