1. The relative contributions of mutation, drift and Natural Selection in shaping molecular variation of natural populations and divergence between species
2. Using computational methods and diverse biological data to generate novel hypothesis
3. Quantifying the genetic component to human disease
4. Metazoan phylogenetics
5. IndoPacific phylogeography of marine invertebrates and fish

I am a Bioinformaticist working on the Genome Wide Association of HIV as part of the The Women's Interagency HIV Study with Bradley Aouzerat in the School of Nursing Genetics/Genomic Research Lab at UCSF. In 2006, we developed a novel software tool called GATUP (Genome Association Tool Using Pools) which implements methodologies for gene association studies using pooled DNA samples and the Affymetrix GeneChip Human Mapping Array Sets.

With the Human Genetics group at Navigenics, Inc., I developed tools to integrate the product pipeline from curation through assay, testing and release and analysis tools to validate TaqMan and Affymetrix array data. The first consulting engagements began as a result of a fruitful internship in summer 2008 end continued through the end of 2009. A second engagement was during the summer of 2011.

I was a Biological Data Engineer in the Cancer Genomics Group in the UCSC Center for Biomolecular Science and Engineering , where I worked on the UCSC Cancer Genome Browser from 2010-11. My primary roles were to wrangle data and develop analysis pipelines for experiments generated as part of the NHGRI/National Cancer Institute Cancer Genome Atlas and I-SPY trials, Stand Up 2 Cancer, and UCSF Helen Diller Family Comprehensive Cancer Center's projects.

In collaboration with the UCSC Genome Bioinformatics Group, I have brought the Baylor College of Medicine HGSC v2.1 Spur_2.1 assembly of the California Sea Urchin (Stronglycentrotus purpuatus) genome assembly to the UCSC Genome Browser as the strPur2 browser. It was released on Oct. 10, 2007. I performed the track annotations and predictions directly on this release, rather then on a previous one, including gene predictions and genomewide comparisons to H. sapien and C. intestinalis. As appropriate to my work, I continue to develop the strPur2 browser with new tracks. Additionally, I have created the beginnings of a Nematostella vectensis browser based on the JGI Jun 2007 assembly as nemVec1 and a new S. purpuratus browser based on the Baylor College of Medicine HGSC v2.5 assembly strPur3.

As a Reseach Associate at UCSF with Dr. Aouizerat during 2006, I genotyped a cohort of individuals (N>200) at six candidate loci in the molecular lab using RFLP for a case-control genetic association study of Non-Alcoholic Steatohepatitis (NASH) /Non-Alcoholic Fatty Liver Disease (NAFLD).

From the Summer of 2005 through the Summer of 2006, I was fortunate enough to be an intern with Scott A. Nichols in Nicole King's Lab at UC Berkeley. Our phylogenetic study of sponges and other early branching metazoans identifies the monophyly and unique position of the sponge Family Poesclosclerida within a paraphyletic Family Hadromerida using rRNA (LSU and SSU) sequences. The Poecilosclerids are both the most prolific and diverse family of sponges and show uniquely viviparous reproduction. Our findings (1) suggest that major extant sponge clades radiated early and may extend far into early animal ancestry and (2) support the hypothesis of sponge paraphyly, with a Homoscleromorph and Calcarea clade and Hexactinellid and Demosponge clade.

Up until early 2005, I was the Director of the eCommerce Operations and Infrastructure Architecture group at Prosodie Interactive, successfully facilitating commerce between those selling and those purchasing beauty products, luxury items, and branded products. Prior to that, I served for four years as a Senior and Lead UNIX System Administrator for the same group. The three years before that I did systems administration and IT service for UC Berkeley. Although now I only do UNIX system administration recreationally and on a smaller scale for our research labs, I still enjoy it and treat it as an art.

I developed an online Hexactinellid Sponge Key while working identifying specimens from the UC Museum of Paleontology for Allen G. Collins in 1999. It is likely now to be inaccurate. If you use it, please let me know!

D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney, B. Rhead, K. R. Rosenbloom, K. E. Smith, M. Stanke, A. Thakkapallayil, H. Trumbower, T. Wang, A. S. Zweig, D. Haussler and W. J. Kent. 2007 The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research. 1-7. doi:10.1093/nar/gkm966 PDF

K. M. Kober and S. A. Nichols. 2007. On the phylogenetic relationships of hadromerid and poecilosclerid sponges. Journal of the Marine Biological Association of the United Kingdom. 87, 1585-1598. Spec. issue on Sponge biodiversity. doi:10.1017/S0025315407058237 PDF

Synonymous codon usage in Strongylocentrotus purpuratus. K. M. Kober. UCSC EEB Departmental Symposia. March 11, 2010. Santa Cruz, CA.

Sanborn, J. Z., S. C. Benz, B. Craft, C. Szeto, K. M. Kober, L. Meyer, C. J. Vaske, M. Goldman, W. J. Kent, E. Collisson, C. Benz, J. M. Stuart, D. Haussler, and J. Zhu. TCGA Data in the UCSC Cancer Genomics Browser. The Cancer Genome Atlas (TCGA) annual meeting, November 17-19, 2010. Long Beach, CA.

Silver, E. S., E. Halperin, K. M. Kober, B. Padhukasahasram, N. Patil, M. Sommargren, D. A. Stephan, D. J. Thomas, H. Trumbower, and M. Cargill. 2009. Curating Genetic Association Literature For Common Diseases. Third International Biocuration Conference , April 16-19, 2009. Berlin, Germany. Available from Nature Precedings doi:10.1038/npre.2009.3174.1 PDF

Cartwright, P., and A. Collins. 2007. Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages. Integr. Comp. Biol. doi:10.1093/icb/icm071

Nichols, S. A., W. Dirks, J. S. Pearse, and N. King. 2006. Early evolution of animal cell signaling and adhesion genes. Proceedings of the National Academy of Sciences of the United States of America 103:12451-12456. 10.1073/pnas.0604065103 (King Lab member)

I'm a Cub Scout Den Leader for Pack 83 of the Pacific Skyline Council in Belmont, CA.

Private Pilot, Airplane Single Engine Land (Tailwheel endorsed). I enjoy flying the Cessna 172 and the Citabra 7ECA out of San Carlos Airport (KSQL). I have been a mentor for new pilots in the AOPA Project Pilot program.

Visit my personal page.

UCSC Dept. of Ecology and Evolutionary Biology
Bernardi Lab
Center for Ocean Health (LML)
100 Schaffer Rd.
Santa Cruz, CA 95060
Fax: 831-459-3383
Mail stop Code: LML-EEB

or

UCSC Dept. of Ecology and Evolutionary Biology
Pogson Lab
A316 Earth & Marine Sciences Bldg.
Santa Cruz, CA 95064
Fax: 831-459-5353
Mail stop Code: EMS-EEB

E-mail: kober AT biology.ucsc.edu
Dept. Phone: (831) 459-5358