David Dooling, Ph.D.
Research Accomplishments & Interests
Dr. David Dooling joined The Genome Institute at Washington University in 2001 as part of the Mapping Informatics group. He became the Information Systems group leader in 2002 and in 2006 was named Assistant Director of Informatics. He currently oversees the Laboratory Information Management Systems (LIMS), Analysis Developers and the Information Systems groups at The Genome Institute. Dr. Dooling has played a critical role in the implementation of massively-parallel, next-generation sequencing technologies including Roche/454, Illumina/Solexa, and AB/SOLiD. As part of a multidisciplinary team at The Genome Institute, he oversaw the informatics and analysis automation for the sequencing of the first human cancer genome. Throughout his tenure at The Genome Institute, Dr. Dooling has contributed to building one of the most advanced and powerful data tracking systems in the world.
Dr. Dooling is focused on bringing a wide range of scientific and computational disciplines to bear on problems in genomics and medicine. In addition to tracking data as it flows through the laboratory and processing pipelines, Dr. Dooling is investigating methods to more efficiently store, compare and operate on sequence data to reduce computational and storage requirements. It is only with continued improvements in data tracking, processing and analysis that projects like The Cancer Genome Atlas, 1000 Genomes and the Human Microbiome Project will be successful.
Other Biographical Information
Dr. Dooling received a B.Ch.E. degree from the University of Dayton (Chemical Engineering, 1995) and a Ph.D. from Northwestern University (Chemical Engineering, 2000) where he was the recipient of a Walter P. Murphy Fellowship and Dissertation Year Graham Fellowship. During graduate school he had an internship at UOP developing reaction engineering software. In 2000, he joined ExxonMobil Research and Engineering and developed detailed kinetic models of refinery processes.
Selected Publications
Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan…
Clonal Architecture of Secondary Acute Myeloid Leukemia.
N Engl J Med. 2012 Mar 14. [Epub ahead of print] PubMed | View Abstract
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young…
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] PubMed | View Abstract
Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen…
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
Nature. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725. PubMed | View Abstract
Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu…
A novel retinoblastoma therapy from genomic and epigenetic analyses.
Nature. 2012 Jan 11. doi: 10.1038/nature10733. [Epub ahead of print] PubMed | View Abstract
Graubert T, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, Krysiak K, Harris…
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Nature Genetics. 2011 Dec 11. [Advanced online publication] PubMed | View Abstract
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis…
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data.
Bioinformatics. 2011 Dec 6. [Epub ahead of print] PubMed | View Abstract
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst…
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. PubMed | View Abstract
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge…
The functional spectrum of low-frequency coding variation.
Genome Biol. 2011 Sep 14;12(9):R84. [Epub ahead of print] PubMed | View Abstract
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter…
The variant call format and VCFtools.
Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7. PubMed | View Abstract
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs…
Demographic history and rare allele sharing among human populations.
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-11988. Epub 2011 Jul 5. PubMed | View Abstract
The Cancer Genome Atlas Research Network
Integrated genomic analyses of ovarian carcinoma
Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. PubMed | View Abstract
The 1000 Genomes Project, Conrad DF, Keebler JE, Depristo MA, Lindsay SJ, Zhang Y, Casals…
Variation in genome-wide mutation rates within and between human families.
Nat Genet. 2011 Jun 12;43(7):712-714. doi: 10.1038/ng.862. PubMed | View Abstract
Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich…
Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML
JAMA. 2011 Apr 20;305(15):1568-1576. PubMed | View Abstract
Ye L, Hillier LW, Minx P, Thane N, Locke D, Martin JC, Chen L, Mitreva…
A vertebrate case study of the quality of assemblies derived from next-generation sequences.
Genome Biol. 2011 Mar 31;12(3):R31. [Epub ahead of print] PubMed | View Abstract
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon…
Mapping copy number variation by population-scale genome sequencing.
Nature. 2011 Feb 3;470(7332):59-65. PubMed | View Abstract
