CURRICULUM VITAE

W. Richard McCombie, Ph.D

# [EDUCATION]{.underline}

Wabash College, Crawfordsville, Indiana Biology B.A. 1977

The University of Michigan, Ann Arbor, MI Cellular and Molecular Biology
Ph.D. 1982

# [APPOINTMENTS]{.underline}

11/01-present Professor, Cold Spring Harbor Laboratory, Cold Spring
Harbor, NY

9/99-11/01 Associate Professor, Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY

7/96-9/99 Associate Investigator, Cold Spring Harbor Laboratory, Cold
Spring Harbor,NY

9/92-6/96 Senior Staff Investigator, Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY

8/91-9/92 Principle Investigator, \"Structure and Function of
Neurological Genes in

*Caenorhabditis elegans\".* NINDS Division of Intramural Research
Project.

10/89-9/92 Chief, Unit on Neurological Disease Gene Structure and
Function Section of

> Receptor Biochemistry and Molecular Biology, LMCN, NINDS National
>
> Institutes of Health, Bethesda, Maryland.

8/88-7/92 Senior Staff Fellow, Section of Receptor Biochemistry and
Molecular Biology,

LMCN, NINDS, National Institutes of Health, Bethesda, Maryland.

12/86-6/88 Staff Research Chemist, Phillips Petroleum Company,
Biotechnology Division.

5/86-12/86 Postgraduate Biochemist, Phillips Petroleum Company,
Biotechnology Division.

3/84-5/86 National Cancer Institute Postdoctoral Fellow, The University
of Texas at Austin.

6/82-2/84 Postdoctoral Research Associate, Department of Microbiology,
The University of

> Texas at Austin.

9/80-5/82 Graduate Student Research Assistant, Department of
Microbiology and

> Immunology, The University of Michigan Medical School.

9/77-8/80 National Institutes of Health Predoctoral Fellow. Program in
Cellular and Molecular Biology,

> The University of Michigan.

# [PUBLICATIONS]{.underline}

Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos,
M.H., Xiao, H., Merril, C.R., Wu, A.,

Olde, B., Moreno, R.F., Kerlavage, A.R., **McCombie, W.R.** and Venter,
J.C. (1991). Complementary DNA

sequencing: Expressed sequence tags and human genome project. *Science*
**252**:1651-1656.

Dedhia, N.N., **McCombie, W.R**. (1998). Kaleidaseq: A Web-based tool to
monitor data flow in a high throughput sequencing facility. *Genome
Res*. **8**:313-318.

Rabinowicz, P., Schutz, K., Dedhia, N., Yordan, C., Parnell, L., Stein,
L., **McCombie, W.R.** and Martienssen, R.

(1999). Differential methylation of genes and retrotransposons
facilitates shotgun sequencing of the maize

genome. *Nature Genetics* **23**:305-308.

The Arabidopsis Genome Initiative. (2000). The analysis of the genome
sequence of the flowering plant *Arabidopsis*

> *thaliana*. *Nature* **408**:796-815.

The International Human Sequencing Consortium. (2001). The human genome:
Sequencing and initial analysis. *Nature* **409**:860-921.

Palmer, L.E., Rabinowicz, P.D., O'Shaughnessy, A.L., Balija, V.S.,
Nascimento, L.U., Dike, S., de la Bastide, M.,

Martienssen, R.A., **McCombie, W.R**. (2003). Maize genome sequencing by
methylation filtration. *Science*

> Dec19; **302**(5653):2115-7.

Rabinowicz, P.D., Palmer, L.E., May, B.P., Hemann, M.T., Lowe, S.W.,
**McCombie, W.R**., Martienssen, R.A. (2003). Genes and transposons are
differentially methylated in plants, but not in mammals. *Genome
Res*.**12**:2658-64.

International Rice Genome Sequencing Project.^.^ (2005). The map-based
sequence of the rice genome.

*Nature***436**:793-800.

Katari, M., Balija, V., Wilson, R.K., Martienssen, R.A., **McCombie
W.R**. (2005).

Comparing low coverage random shotgun sequence data from Brassica
oleracea

and Oryza sativa genome sequence for their ability to add to the
annotation of

Arabidopsis thaliana. *Genome Research* **15**: 496-504.

Rabinowicz, P.D., Citek, R., Budiman, M.A., Nunberg, A., Bedell, J.A.,
Lakey, N., O'Shaughnessy, A.L., Nascimento, L.U., **McCombie, W.R.**,
Martienssen, R.A. (2005). Differential methylation of genes and repeats
in land plants. *Genome Research* **15**:1431-1440.

# [SYNERGISTIC ACTIVITIES]{.underline}

1\) Organized module on "genomics and proteomics" for "scientific
reasoning and logic course"

at Watson School of Biological Sciences.

2\) Organized and lead instructor with L. Joshua-Tor and M. Myers in the
specialized discipline course "Molecules

to Networks", Watson School of Biological Sciences (2004).

3\) Instructor in the specialized discipline course "The Genome" with R.
Martienssen and L. Stein. Watson School

of Biological Sciences (2000-2002).

4\) Organizer of the Scientific Reasoning and Logic core course at the
Watson School of Biological Sciences (1999).

5\) Developed and am the lead instructor in the Cold Spring Harbor
Course, "Advance Genome Sequence Analysis".

6\) Participated in training of high school teachers at the Cold Spring
Harbor DNA Learning Center.

7\) Carried out DNA sequencing in support of teaching at the DNA
Learning Center

8\) Developed web pages to disseminate Arabidopsis mapping and
sequencing data to the community.

# 

# 

# [COLLABORATORS AND OTHER AFFILIATES]{.underline}

Mike Bevan (John Innes Centre, UK), Michael Black (Purdue University),
Paola Capodieci ((Mem. Sloan Kettering

Can. Ctr.), Asif Chinwalla (Wash. Univ. Gen. Seq. Ctr.), Michele Cleary
(Rosetta Impharmatics), Douglas Cook,

(Texas A&M University), Stephen Elledge (Baylor College of Medicine),
Leland Ellis (Texas A&M University),

Gregory Hannon (Cold Spring Harbor Lab.), Hong Ma (Penn State
University), Elaine Mardis (Wash. Univ. Gen.

Seq. Ctr.), Marco Marra (Wash. Univ. Gen. Seq. Ctr.), ((Robert
Martienssen (Cold Spring Harbor Lab.), John

McPherson (Baylor College of Medicine), Joachim Messing (Rutgers
University), Trilochan Mohapatra (Indian

Agricultural Res. Inst.), Elaine Ostrander (Fred Hutchinson Cancer
Inst.), Ajit Pal (Indian Agricultural Res. Inst.),

Scott Powers (Cold Spring Harbor Lab.), Daphne Preuss (HHMI-Univ.
Chicago), Saurabh Raguvanshi (Univ.

Delhi So. Campus), Takuji Sasaki (Nat'l Inst. Argrobiological Sciences),
Tilak Sharma (Indian AgriculturalRes. Inst.),

Archana Singh (Indian Agricultural Res. Inst.), Subodh Srivastava
(Indian Agricultural Res. Inst.), Lincoln Stein

(Cold Spring Harbor Lab.), Akhilesh Tyagi (Univ. Delhi So. Campus),
Robert Waterson (Wash. Univ. Gen. Seq. Ctr.), Michael Wigler (Cold
Spring Harbor Lab.), Richard Wilson (Wash. Univ. Gen. Seq. Ctr.), Rod
Wing (University of

Arizona). Mahavir Yadav (Indian Agricultural Res. Inst.).

**[Graduate Students (Total of 3)]{.underline}**

Manpreet Katari New York University

Min Yu SUNY Stonybrook

James Gergel SUNY Stonybrook

**[Postdoctoral Scholars (Total of 9)]{.underline}**

Harshawardhan Bal MIT

Vivekanand Balija Cold Spring Harbor Lab.

Neilay Dedhia India

Arthur Johnston NC State University

Mauhammad Lodhi Sequana California

Alexander Melnikov \-\--

Lance Palmer Cold Spring Harbor Lab.

Lawrence Parnell Tufts

CanZhu Yang University California San Diego

**[Postdoctoral Advisors]{.underline}**

David T. Gibson University of Iowa

John C. Venter The Institute of Genomic Research

**[Thesis Advisor]{.underline}**

Ronald H. Olsen Retired