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 a 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.
At Karolinska (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 in 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). I am also into developing new Indo-European collaborative research projects in complex diseases as well as technology convergence in the genomics domain.
Research
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, 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:
- Statistical genetics and multivariate analytics.
- AI/ML applications in genomics.
- Diverse range of OMICs 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.
- 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 and big-data analytics pipeline development.
- Large scale data storage, handling, formatting and visualisation.
- Bioinformatics education and training.
For detailed publications list, please follow this link:
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- hl=en
Articles
- Article: G3: GENES, GENOMES, GENETICS. 2024;14(8):jkae116
- Article: NATURE COMMUNICATIONS. 2023;14(1):6172
- Article: CLINICAL EPIGENETICS. 2023;15(1):148
- Article: ALLERGY. EUROPEAN JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2023;78(3):836-850
- Article: NATURE GENETICS. 2021;53(9):1311-1321
- Article: GENOME MEDICINE. 2020;12(1):25
- Journal article: GENOME MEDICINE. 2020;12:1-17Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
- Journal article: MEDRXIV. 2020;:2020-09Genomic and phenomic insights from an atlas of genetic effects on DNA methylation
- Article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2019;144(3):857-860.e7
- Article: EUROPEAN JOURNAL OF EPIDEMIOLOGY (EJE). 2019;34(3):279-300
- Journal article: NATURE. 2019;570:71-76Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls
- Article: NATURE GENETICS. 2018;50(8):1072-1080
- Journal article: WELLCOME OPEN RESEARCH. 2018;3:4
- Article: THE LANCET RESPIRATORY MEDICINE. 2018;6(5):379-388
- Article: EUROPEAN RESPIRATORY JOURNAL. 2018;51(3):1701377
- Article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2018;141(3):1105-1114
- Journal article: WELLCOME OPEN RESEARCH. 2018;3:4
- Journal article: WELLCOME OPEN RESEARCH. 2018;3:4
- Journal article: SCIENTIFIC DATA. 2018;5:1-2Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- Journal article: F1000RESEARCH. 2018;7:253Meta-analysis of exome array data identifies six novel genetic loci for lung function
- Journal article: SCIENTIFIC DATA. 2018;5Sequence data and association statistics from 12,940 type 2 diabetes cases and controls (vol 4, 170179, 2017)
- Article: NATURE GENETICS. 2018;50(1):42-53
- Journal article: INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH. 2017;14(12):E1492-1492
- Article: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2017;195(10):1373-1383
- Journal article: SCIENTIFIC REPORTS. 2017;7:45040
- Journal article: JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY. 2017;28(3):981-994
- Journal article: 2017A Low-Frequency Inactivating Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.
- Journal article: DIABETES. 2017;66:2019-2032A low-frequency inactivating AKT2 variant enriched in the Finnish population is associated with fasting insulin levels and type 2 diabetes risk
- Journal article: PLOS ONE. 2017;12:e0172716Adult onset asthma and interaction between genes and active tobacco smoking: The GABRIEL consortium
- Journal article: SCIENTIFIC DATA. 2017;4:1-22Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- Article: ENVIRONMENTAL HEALTH PERSPECTIVES. 2017;125(1):104-110
- Journal article: ENVIRONMENT INTERNATIONAL. 2016;94:263-271
- Journal article: AGE. 2016;38(3):52
- Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2016;98(4):680-696
- Journal article: ENVIRONMENTAL HEALTH: A GLOBAL ACCESS SCIENCE SOURCE. 2016;15:39
- Journal article: 2016The genetic architecture of type 2 diabetes.
- Journal article: AMERICAN JOURNAL OF HUMAN GENETICS. 2016;98:680-696Bonnie R. Joubert, Janine F. Felix, 2, 3, 4, 58 Paul Yousefi, 5, 58 Kelly M. Bakulski, 6, 58 Allan C. Just, 7, 58 Carrie Breton, 8, 58 Sarah E. Reese, Christina A. Markunas, Rebecca C. Richmond, 10, 58
- Journal article: AGE. 2016;38:1-13Common SIRT1 variants modify the effect of abdominal adipose tissue on aging-related lung function decline
- Journal article: AMERICAN JOURNAL OF HUMAN GENETICS. 2016;98:680-696DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis
- Journal article: NATURE. 2016;536:41-47The genetic architecture of type 2 diabetes
- Journal article: NATURE. 2016;536The genetic architecture of type 2 diabetes
- Journal article: ENVIRONMENTAL HEALTH: A GLOBAL ACCESS SCIENCE SOURCE. 2016;15:1-11A common functional variant on the pro-inflammatory Interleukin-6 gene may modify the association between long-term PM 10 exposure and diabetes
- Article: NATURE COMMUNICATIONS. 2015;6:8658
- Journal article: NATURE COMMUNICATIONS. 2015;6
- Article: NATURE GENETICS. 2015;47(12):1449-1456
- Journal article: PLOS GENETICS. 2015;11(4):e1005165
- Journal article: ENVIRONMENTAL HEALTH PERSPECTIVES. 2015;123(1):72–79
- Journal article: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2015;191:1B59 ASTHMA-LIKE PHENOTYPE: EMERGENCE OF (EPI) GENETICS AND TARGETED TRANSGENESIS:(epi) genetic Regulation Of Expression Of Il1rl1 Mrna And Il1rl1-A Protein Levels In Asthma
- Journal article: PLOS GENETICS. 2015;11:e1004876Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus
- Journal article: ENVIRONMENTAL HEALTH PERSPECTIVES. 2015;123:72-79Modification of the association between PM10 and lung function decline by cadherin 13 polymorphisms in the SAPALDIA cohort: a genome-wide interaction analysis
- Journal article: NATURE COMMUNICATIONS. 2015;6Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation
- Journal article: PLOS GENETICS. 2015;11:e1005165The power of gene-based rare variant methods to detect disease-associated variation and test hypotheses about complex disease
- Journal article: TROPICAL MEDICINE AND INTERNATIONAL HEALTH. 2015;20:127-128Modification of ambient air pollution and diabetes association by type 2 diabetes genetic risk score of 48 variants
- Journal article: PLOS ONE. 2014;9:e100776
- Journal article: AMERICAN JOURNAL OF HUMAN GENETICS. 2014;94(5):710–720
- Journal article: PLOS GENETICS. 2014;10(4):e1004235
- Article: NATURE GENETICS. 2014;46(3):234-244
- Journal article: PLOS GENETICS. 2014;10:e1004235A Central Role for GRB10 in Regulation of Islet Function in Man
- Journal article: NATURE GENETICS. 2014;46:234-244Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility
- Journal article: PLOS ONE. 2014;9(7):e100776
- Journal article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2014;133:885-888Novel childhood asthma genes interact with in utero and early-life tobacco smoke exposure
- Journal article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2014;111:13127-13132Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes
- Journal article: AMERICAN JOURNAL OF HUMAN GENETICS. 2014;94:710-720Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland
- Journal article: NATURE GENETICS. 2013;45(12):1418–1427
- Article: CLINICAL AND EXPERIMENTAL ALLERGY. 2013;43(4):463-474
- Journal article: PLOS GENETICS. 2013;9(8):e1003585
- Journal article: PLOS GENETICS. 2013;9:e1003585Causal and synthetic associations of variants in the serpina gene cluster with alpha1-antitrypsin serum levels
- Journal article: NATURE GENETICS. 2013;45:1418Evaluating empirical bounds on complex disease genetic architecture
- Journal article: CLINICAL AND EXPERIMENTAL ALLERGY. 2013;43:463-474Genome-wide association study of body mass index in 23 000 individuals with and without asthma
- Article: NATURE GENETICS. 2012;44(9):981-990
- Journal article: PLOS ONE. 2012;7:e40175
- Journal article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2012;129(5):1218–1228
- Journal article: 2012Different Genes Interact with Particulate Matter and Tobacco Smoke Exposure in
- Journal article: PLOS ONE. 2012;7(7):e40175
- Journal article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2012;129:1218-1228Genome-wide association study of lung function decline in adults with and without asthma
- Journal article: NATURE GENETICS. 2012;44:981Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
- Journal article: BMC PROCEEDINGS. 2011;5(Suppl 9):s107
- Journal article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2011;128(5):996–1005
- Journal article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2011;128:996-1005A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order
- Journal article: PLOS ONE. 2010;5(11):e13894
- Journal article: JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY. 2010;21(10):1791–1797
- Article: NEW ENGLAND JOURNAL OF MEDICINE. 2010;363(13):1211-1221
- Journal article: NEW ENGLAND JOURNAL OF MEDICINE. 2010;363:1211-1221A large-scale, consortium-based genomewide association study of asthma
- Journal article: J. AM. SOC. NEPHROL. 2010;2010010076Genome-Wide Analysis Identifies Strong Association Between HLA and IgA Nephropathy
- Journal article: JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY. 2010;21:1791-1797HLA has strongest association with IgA nephropathy in genome-wide analysis
- Journal article: DIABETOLOGIA. 2010;53:S28Identification of additional type 2 diabetes susceptibility loci through large-scale replication using" Metabochip": early result
- Journal article: PLOS ONE. 2010;5:e13894Unifying candidate gene and GWAS approaches in asthma
- Journal article: BIOINFORMATICS. 2007;23(12):1545–1549
- Journal article: BIOINFORMATICS. 2007;23:1545-1549Management, presentation and interpretation of genome scans using GSCANDB
- Journal article:A Central Role for GRB10 in Regulation of Islet Function
- Journal article:Online Repository Genome wide association study of lung function decline in adults with and without asthma.
- Journal article:genetic loci for lung function [version 3; referees: 2 approved]
- Journal article:loci for lung function [version 1; referees: 1 approved
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All other publications
- Review: THE LANCET. 2024;403(10435):1494-1503
- Conference publication: 2024;:123
- Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2023;62:PA3674
- Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2022;60:1771
- Conference publication: ALLERGY. EUROPEAN JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2021;76:406-407
- Preprint: MEDRXIV. 2020
- Corrigendum: NATURE GENETICS. 2018;50(9):1343
- Preprint: BIORXIV. 2017
- Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2016;48:pa1209
- Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2016;48:oa5004
- Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2015;46:oa1455
- Conference publication: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2015;191
- Letter: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2014;133(3):885-888
- Conference publication: DIABETES. 2014;63:A413Identification of Gene Loss of Function Deletions from Dense Exome Array Data and Their Role in Type 2 Diabetes
- Conference publication: DIABETES. 2014;63:A37Whole-Exome Sequencing in Type 1 Diabetic Nephropathy
- Conference publication: ISEE CONFERENCE ABSTRACTS 25. 2013;2013:4247Genome-wide interaction study identifies Cadherin 13 as effect modifier of cumulative PM10 exposure on lung function decline.
- Conference publication: GENETIC EPIDEMIOLOGY. 2012;36:143Interaction of oxidative stress pathway genes with particulate matter and tobacco smoke on the course of airflow obstruction during 11 years
- Conference publication: BMC PROCEEDINGS. 2011;5:1-6Assessing the impact of missing genotype data in rare variant association analysis
- Conference publication: ISEE CONFERENCE ABSTRACTS 23. 2011;2011GENOME-WIDE INTERACTION STUDY OF CUMULATIVE PARTICULATE MATTER EXPOSURE ON AGE-RELATED LUNG FUNCTION DECLINE IN ADULTS, THE SAPALDIA COHORT.
- Book chapter: D101. ASTHMA GENETICS. 2011;p. A6184Genome Wide Association Study Identifies Locus Determining Genetic Heterogeneity Of Lung Function Decline In Asthmatic And Non-Asthmatic Adults
- Book chapter: A51. GENETIC STUDIES OF LUNG DISEASE. 2011;p. A1755Genomewide Association With Alpha1-Antitrypsin Blood Levels In A Subset Of The SAPALDIA Cohort Study
- Conference publication: ISEE CONFERENCE ABSTRACTS 23. 2011;2011Oxidative stress pathway genes, particulate matter, and lung function decline
- Conference publication: GENETIC EPIDEMIOLOGY. 2010;34:972Genomewide Association with Alpha1-Antitrypsin Blood Levels in a Subset of the SAPALDIA Cohort Study
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