Bio-informatics: Dan Koboldt
Dan Koboldt joined the SNP Research Facility under Dr. Raymond D. Miller in 2003.
Data management for the
International HapMap Project
was his initial responsibility. The laboratory, in collaboration with Pui Kwok's
group at the University of California, San Francisco, served as a major genotyping center for the first phase of the project.
Using primarily open-source technologies, Dan constructed an efficient, user-friendly laboratory information management system (LIMS) that was featured in
BioInform magazine.
Assay design
for FP-TDI genotyping and targeted resequencing is one of Dan's primary areas of research. He developed software to design assays based on a standardized,
laboratory-validated set of protocols. In a contract project for PerkinElmer, he designed FP-TDI assays for more than 6 million SNPs in the human genome.
He has also provided high-throughput resequencing assays for several researchers at Washington University.
Research Publications
|
A second generation human haplotype map of over 3.1 million SNPs
|
A higher-density haplotype map of the human genome constructed in Phase II of the HapMap Project.
International HapMap Consortium. Nature. 2007 Oct; 449:851-861.
|
|
Genome-wide detection and characterization of positive selection in human populations
|
An analysis of recent positive selection in the human genome using Phase II HapMap data.
P.C. Sabeti and the International HapMap Consortium. Nature. 2007 Oct; 449:913-918.
|
|
C. briggsae chromosomal organization
|
The first publication describing our genetic map of C. briggsae and comparative genomics with C. elegans.
LaDeana W. Hillier et al. .
PLoS Biology. 2007 Jul;5(7):e167
|
|
Immunogenetics of smallpox vaccination
|
A report of association between innate immunity gene variants and acute vaccinia syndrome (AVS).
Samuel L. Stanley Jr. et al. J. Infect. Dis.. 2007 Jul;196(2):212-219.
|
|
Distribution of human SNPs and its effect on high-throughput genotyping
|
The distribution of human SNPs and the SNP-in-primer effect on HapMap genotyping.
Daniel C. Koboldt, Pui-Yan Kwok, and Raymond D. Miller. Human Mutation. 2006 Mar;27(3):249-54.
|
|
A haplotype map of the human genome
|
A high-density haplotype map of the human genome constructed in Phase I of the HapMap Project.
International HapMap Consortium. Nature. 2005 Oct;437(7063):1299-320.
|
|
High-density single-nucleotide polymorphism maps of the human genome
|
A SNP map of the human genome constructed from the characterization of over 50,000 SNPs in multiple populations.
Raymond D. Miller et al. Genomics. 2005 Aug;86(2):117-26.
|
Talks, Reviews, and Posters
|
Identification of functional SNPs in noncoding regions of the human genome
|
Describing the identification of putative functional SNPs and assessing evidence of
purifying selection against genome annotations with the HapMap data set.
Daniel C. Koboldt and Raymond D. Miller, HGM2007.
[Talk]
Abstract
PDF
|
|
The identification of functional noncoding human SNPs
|
Describing the identification and evaluation of putative
functional SNPs using genome annotation data and HapMap minor allele frequencies.
Daniel C. Koboldt and Raymond D. Miller, CSHL Biology of Genomes 2007.
[Poster]
|
|
High-throughput identification of structural variations from sequence trace data
|
A presentation given by D. Koboldt at the MC-GARD conference in Amsterdam describing a method to find putative deletions, insertions,
and copy number variants from individual sequencing reads.
[Talk]
Abstract
PDF
|
|
Phythopthora Genome Sequences
|
A journal club presentation discussing the first two Phythopthora genome sequences
published in Science by B.M. Tyler et al. Daniel C. Koboldt. December 2006.
[Talk]
|
|
Genetics of Cystic Fibrosis
|
A journal club presentation discussing cystic fibrosis genotype-phenotype correlations based on a review article
in Lancet by E.F. McKone et al. Daniel C. Koboldt. November 2006.
[Talk]
|
|
Book Review: Eugenics in the Deep South
|
A review of Edward J. Larson's 1995 book,
Sex, Race, and Science: Eugenics in the Deep South. Johns Hopkins University Press. Daniel C. Koboldt. November 2006.
[Review]
|
|
Integrating genetic and genomic resources for C. briggsae
|
A presentation about the genetic map and other resources for C. briggsae.
Daniel C. Koboldt et al. Caenorhabditis Evolution Workshop. May 2006.
[Talk]
|
|
Genomics of Complex Traits
|
A journal club presentation discussing the article,
"Genome-wide associations of gene expression variation in humans"
published in PLoS Genetics by B. Stranger et al. Daniel C. Koboldt. April 2006.
[Talk]
|
|
A SNP-marked assembly of the human genome for optimal assay design
|
Describing a version of the human genome sequence in which SNP positions are marked with ambiguity codes.
Daniel C. Koboldt and Raymond D. Miller. AAAS. February 2006.
[Poster]
|
|
Building a Laboratory Information Management System for FP-TDI Genotyping Research
|
A presentation of the high-throughput data pipeline that we built for SNP genotyping.
Daniel C. Koboldt, Pui-Yan Kwok, and Raymond D. Miller. RECOMB. March 2004.
[Poster]
|
Technical Skills
| Programming: |
Perl/CGI, PHP, Javascript, HTML/CSS, ASP |
| Databases: |
MySQL, MS Access, c-tree Plus |
| Environments: |
Solaris 8, Debian Linux, Windows 95/98/NT/2000/XP |
| Software: |
RepeatMasker, Primer3, WU-BLAST, DreamWeaver, PhotoShop |
Employment History
| 2003-present |
|
Washington University School of Medicine |
|
Saint Louis, MO |
|
Bio-informatics Specialist
|
|
LIMS design and development for high-throughput genotyping
Shell scripting and Perl programming in a UNIX environment
Web based interface development using Perl/CGI and MySQL
|
| |
| 2001-2003 |
|
Erudite Systems |
|
Columbia, MO |
|
Web Developer / Programmer
|
|
Web programming, design, modification and maintenance
Web application programming with PHP, Perl, Java, and others.
Systems analysis and design services.
|
| |
| 2001-2002 |
|
FairCom Corporation |
|
Columbia, MO |
|
Product Team - Technical Lead
|
|
Product development of raw database technologies.
Documentation, quality assurance and support.
Product planning, software development.
|
Education
|
University of Missouri- Columbia (1998-2001)
Bachelor's degree in Computer Science
Bachelor's degree in French
|
|
Washington University - Master's in Biology Program (2003-present)
Modern Genetics
Molecular Cell Biology
Virology
Immunology
Genomics in the Post-Genome Era
Preparing Biomedical Manuscripts
Human Heredity (present)
Molecular and Biochemical Basis of Bio-Warfare (present)
Course completion: May 2007
|
Poker Mate player tracking software for party poker
|
