Ewen Kirkness, PhD

Professor

Ewen Kirkness is a professor in the Human Genomics Group where his primary interests are the assembly and analysis of human genome sequences.

Dr. Kirkness rejoined JCVI in 2019 after five years at Human Longevity, Inc. (HLI), where he led their genomics research efforts. Over the course of almost 30 years at The Institute for Genomic Research (TIGR), JCVI, and HLI, Dr. Kirkness has acquired substantial experience in the production and analysis of DNA sequence data. Starting with high-throughput production of human ESTs, he has managed a variety of large-scale genomics projects, including de novo assembly of complex eukaryotic genomes, and analyses of genomes and transcriptomes from thousands of human samples. Dr. Kirkness is coauthor of more than 120 scientific publications, and coinventor for more than 30 patents.

Dr. Kirkness earned his BSc. In Biochemistry from Heriot-Watt University, Edinburgh, and his PhD in Biochemistry from the University of Leeds. While at TIGR, he was also an Associate Professor in the Department of Pharmacology, The George Washington University, Washington, D.C. (2000-2012).

Patents

Li, Yi; Kirkness, Ewen F. US Patent No. US5654172.

Gabaa receptor epsilon subunit. Retrieved from https://patents.google.com/patent/US5654172A/en.

Kirkness, Ewen F. US Patent No. US6462188B1.

Human 5-HT3 receptor. Retrieved from https://patents.google.com/patent/US6462188B1/en.

Research Priorities

Improving the quality of human genome assemblies
  • Application of new sequencing and assembly technologies
  • Focus on phasing of variants, especially structural variants
Interpretation of human genomic variation
  • Effects of genomic structural variation on gene expression patterns
  • Combining genomics with other omics data to identify patterns of biomarkers that are hallmarks of traits and disease susceptibilities
Genomic basis of neurological functions
  • Polygenic scores
  • Somatic mutations

Publications

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.
Genome medicine. 2020-01-10; 12.1: 7.
PMID: 31924279
Profound Perturbation of the Metabolome in Obesity Is Associated with Health Risk.
Cell metabolism. 2019-02-05; 29.2: 488-500.e2.
PMID: 30318341
Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders.
European journal of human genetics : EJHG. 2019-01-01; 27.1: 150-159.
PMID: 30254217
Comparison of phasing strategies for whole human genomes.
PLoS genetics. 2018-04-05; 14.4: e1007308.
PMID: 29621242
The human noncoding genome defined by genetic diversity.
Nature genetics. 2018-03-01; 50.3: 333-337.
PMID: 29483654
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
Proceedings of the National Academy of Sciences of the United States of America. 2017-07-25; 114.30: 8059-8064.
PMID: 28674023
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.
Nature genetics. 2017-04-01; 49.4: 568-578.
PMID: 28263315
The blood DNA virome in 8,000 humans.
PLoS pathogens. 2017-03-22; 13.3: e1006292.
PMID: 28328962
Deep sequencing of 10,000 human genomes.
Proceedings of the National Academy of Sciences of the United States of America. 2016-10-18; 113.42: 11901-11906.
PMID: 27702888
Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.
BMC genomics. 2015-08-22; 16.631.
PMID: 26296559
Sequencing of isolated sperm cells for direct haplotyping of a human genome.
Genome research. 2013-05-01; 23.5: 826-32.
PMID: 23282328
Ancient noncoding elements conserved in the human genome.
Science (New York, N.Y.). 2006-12-22; 314.5807: 1892.
PMID: 17185593
Short interspersed elements (SINEs) are a major source of canine genomic diversity.
Genome research. 2005-12-01; 15.12: 1798-808.
PMID: 16339378
The dog genome: survey sequencing and comparative analysis.
Science (New York, N.Y.). 2003-09-26; 301.5641: 1898-903.
PMID: 14512627
The 5-HT3B subunit is a major determinant of serotonin-receptor function.
Nature. 1999-01-28; 397.6717: 359-63.
PMID: 9950429
Insensitivity to anaesthetic agents conferred by a class of GABA(A) receptor subunit.
Nature. 1997-02-27; 385.6619: 820-3.
PMID: 9039914
Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
Nature. 1995-09-28; 377.6547 Suppl: 3-174.
PMID: 7566098
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Science (New York, N.Y.). 1995-07-28; 269.5223: 496-512.
PMID: 7542800

Research Priorities

Improving the quality of human genome assemblies
  • Application of new sequencing and assembly technologies
  • Focus on phasing of variants, especially structural variants
Interpretation of human genomic variation
  • Effects of genomic structural variation on gene expression patterns
  • Combining genomics with other omics data to identify patterns of biomarkers that are hallmarks of traits and disease susceptibilities
Genomic basis of neurological functions
  • Polygenic scores
  • Somatic mutations

Individual Human Diploid Genome

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