Ashish Kumar
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- (since 2012), I'm providing consultancy to Prof. Erik Melén's group and affiliated to Department of Clinical Science and Education at the Södersjukhuset (KI SÖS) - one of the largest hospitals in Stockholm.
Previously, I was working with Diabetes Research group, led by Prof. Mark McCarthy at the Wellcome Centre for Human Genetics, - University of Oxford (from 2006-2014) and Genetic Epidemiology group, led by Prof. Nicole Probst-Hensch at the Swiss Tropical and Public Health Institute, University of Basel in Switzerland (from 2010-2018).
Research
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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 , ENGAGE , EGG, EAGLE, SpiroMeta, MAGIC, GoDMC, etc.
* EWAS analysis in consortium projects with PACE and MeDALL
* 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.
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For detailed publications list, please follow this link:
hl=en">http://scholar.google.co.uk/citations?user=j-eQjGEAAAAJ& - hl=en