Michael Patrick McLeod

office: (713) 677-7723
fax: (815) 572-8714
voice mail: (815) 572-8714

Summary

Senior bioinformatics scientist with over ten years of experience. Resourceful and creative IT leader with the unique skill set necessary to make the organization more successful by integrating science, business and technology. Developed algorithms and processes for protein and nucleic acid sequence analysis. Co-authored peer-reviewed articles in high ranking journals. Took a leading role in representing the organization to the local and international scientific community.

Education

Ph.D. Computational Biology and Bioinformatics	Dec 2003
University of Texas Health Science Center at Houston; Houston, Texas
Thesis: The sequence comparison index: a novel method for comparing proteins and proteomes
M.S. Biochemistry	May 1998
University of Texas Health Science Center at Houston; Houston, Texas
Thesis: Identification and characterization of the phospholipids of Enterococcus faecalis and E. faecium
B.S. Biology	May 1992
Abilene Christian University; Abilene, Texas

Fellowships

Keck Center for Structural and Computational Biology Pre-Doctoral Fellowship	2000-2003
Robert A. Welch Foundation Graduate Student Fellowship	1996-1998

Experience

Senior Scientist

Sep 2006-present

The Texas Institute for Genomic Medicine; Houston, Texas

Planned and led international meeting on analysis of genomic sequence tags
Represented TIGM at several international meetings
Provided support to TIGM marketing
Provided oversight for all information technologies at TIGM
Hosted MGI training seminars in the Texas Medical Center
Coordinated move of technologies from Lexicon to TIGM
Trained TIGM staff in use of software
Rewrote code to allow searching TIGM's collection by the public
Redesigning and rewriting complete software to be more useful to TIGM
Installed and maintained all Linux systems and software including:
- Oracle, MySQL,Redhat, Fedora, Apache, JBoss, Tomcat
Maintain and redesign of the TIGM website
Managed of other IT staff
Develop bioinformatics code for analysis of TIGM data

Postdoctoral Fellow

Feb 2004-Sep 2006

University of British Columbia, Microbiology and Immunology; Vancouver, BC Canada

Developing the Generic Utility for Research Unification, a publicly available tool for integrating in silico, in vivo, and in vitro data (e.g. genomic, transcriptomic, proteomic, knock-out, etc.) to allow complex queries across disparate and non-discreet datasets.
Head annotator for the Rhodococcus sp. RHA1 genome project.
Supervised and trained four undergraduate co-op students.
Supervised two full-time staff members.
Trained members of the group in the use of bioinformatic tools for genome annotation.

Predoctoral Student	2000-Dec 2003
University of Texas Health Science Center at Houston; Houston, Texas (Located at Baylor College of Medicine Human Genome Sequencing Center)

Designed and implemented the Sequence Comparison Index, an algorithm which describes relationships between proteins and between proteomes.
Single-handedly assembled and annotated the complete mitochondrial genome of Rattus norvegicus strain Brown Norway (GenBank AY172581).
Directed the annotation of the Rickettsia typhi genome project (GenBank AE017197).
Assisted in the analysis and/ or annotation of eukaryotic and prokaryotic genome projects including: human, rat, E. coli DH10B, Fusobacterium nucleatum, Enterococcus faecium, Mannheimia haemolytica, and Treponema denticola.

Computational Biologist	1998-2000
Baylor College of Medicine Human Genome Sequencing Center; Houston, Texas

Baylor College of Medicine Search Launcher.
- Continued development and expansion of the Search Launcher
- Rewrote code to reduce human maintenance from a FTE to a few hours a month.
Human Transcript Database
- Assisted in development of database design and core code
- Developed website interface and search code
Designed and maintained initial BCM HGSC website and ftp site.
Demonstrated cost-effectiveness of Linux/ x86 vs. Solaris/ SPARC
Implemented and maintained initial 32 CPU Linux cluster at HGSC.
Designed and wrote software for analysis of genomes sequenced at the HGSC.

Masters Student	1995-1998
University of Texas Health Science Center at Houston; Houston, Texas

Using thin layer chromatography, radiolabeling, mass spectrometry and MS/ MS characterized the phospholipids, including aminoacylated-phosphatidylglycerol, in Enterococcus faecalis and Enterococcus faecium under a number of growth conditions.
Taught bioinformatics portion of Molecular Basis of Gene Action as a teaching assistant.
In collaboration with Los Alamos National Laboratory:
- Personally annotated the complete genome of Treponema pallidum.
- Analyzed portions of the M. genitalium genome.
- Edited database entries for the M. genitalium and C. trachomatis genome.

Publications

McLeod M.P., et al. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci. accepted.

Gioia J., et. al. 2006. The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence and Pasteurellaceae phylogeny. J Bacteriol. accepted.

McLeod M.P., et al. 2004. The complete genome of Rickettsia typhi and comparison with sequences of other Rickettsiae. J Bacteriol. 186(17):5842-55.

Seshadri R., et al. 2004. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes Proc Natl Acad Sci. 101(15):5646-51.

Rat Genome Sequencing Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428(6982):493-521.

International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409(6822):860-921.

Bouck J, McLeod MP, Worley K, Gibbs RA. 2000. The human transcript database: a catalogue of full length cDNA inserts. Bioinformatics. 16(2):176-7.

Adams, M.D., et al. 2000. The genome sequence of Drosophila melanogaster Science. 287(5461):2185-95.

Weinstock G.M., J.M. Hardham, M.P. McLeod, E.J. Sodergren, S.J. Norris. 1998. The genome of Treponema pallidum: new light on the agent of syphilis". FEMS Microbiol Rev. 22(4):323-32

Fraser C.M., et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete Science. 281(5375):375-88.

Recent Presentations

"The Generic Utility for Research Unification: Application to Functional Genomics Projects"
Genome Informatics, Cold Spring Harbor, New York (October 26-Nov 1, 2005)
"Annotation of Rhodococcus sp. RHA1 Using the GURU Genome Package"
International Conference on Microbial Genomes, Halifax, Nova Scotia (April 13-16, 2005)
"GURU: a Tool for Integrating Genomic, Proteomic, and Transcriptomic Information for the Rhodococcus sp. RHA1 Genome Project"
National Genomics and Proteomics Symposium, Vancouver, BC (November 24-25, 2004)
"GURU: a Tool for Integrating Functional and Electronic Information for the Rhodococcus sp. RHA1 Genome Project"
7th Annual Conference on Computational Genomics, Reston, VA (October 21-24, 2004)
"The complete genome of Rickettsia typhi and comparison to R. prowazekii and R. conorii"
University of Texas Medical Branch, Galveston, TX (December 9, 2003)
"The complete genome of Rickettsia typhi and comparison to R. prowazekii and R. conorii"
Texas ASM Annual Meeting, College Station, TX (November 6-8,2003)
"The Similarity Constant: A Heuristic to Estimate the Evolutionary Distance Between Organisms"
7th Structural Biology Symposium, Galveston, TX; (May 17-19, 2002)
"Microbial Genome Sequencing at the BCM HGSC"
ASM TIGR Conference on Microbial Genomes, Las Vegas, NV (Feb 2002)
"A Graphical Overlap Map Viewer"
Keck 2000 Symposium; Houston, TX (October 16-17, 2000)
"Sequence Analysis Tools at the Baylor Human Genome Sequencing Center"
Genome Sequencing and Analysis; Cold Spring Harbor, New York (May 10-14, 2000)

Awards

ASM Student Travel Awards:

ASM & TIGR Conference on Microbial Genomes, Las Vegas, NV (Feb 2002)
Genomes 2000 Conference, Paris, France (May 2000)
Small Genomes Conference, Snowbird, Utah (Oct 1997)

Professional Memberships

American Society for Microbiology	since 1997
American Association for the Advancement of Science	since 1998
Institute of Electrical and Electronics Engineers	since 2000
Association for Computing Machinery	since 2001
New York Academy of Sciences	since 2002

Other Work and Interests

Contributed code which allows the use of NIS for the open source software package.