Dennis Wall

Dennis Paul Wall
Department of Integrative Biology
University of California, Berkeley. Berkeley, CA 94720
email: dpwall@socrates.berkeley.edu
Fax: (510) 643-5390

 

EDUCATION

Bachelor of Science (Ecology, Evolution, and Organismal Biology), Tulane University, New Orleans, Louisiana (May 1996).

Doctor of Philosophy in Integrative Biology, University of California, Berkeley, California (pending, summer 2001). 

 

RESEARCH INTERESTS

Bioinformatics especially as it pertains to mining protein and gene databases to understand molecular relationships and predict protein function.

Reconstructing the evolution of genes and proteins, including codon usage patterns and biases to understand the causal/selectional link between gene and protein organization.

Using phylogenies to test evolutionary and population demographic hypotheses and to predict evolutionary trends in organisms and organismal characteristics.


 

LABORATORY AND COMPUTER SKILLS

Genetic Techniques: DNA isolation, primer design, PCR, cloning, and sequencing using automated ABI machines (377, 310) Sequence analysis: Sequence Analysis, Sequence Navigator, Sequencher. Analysis of full and partial gene sequences and single nucleotide polymorphisms (SNP’s). Intimate knowledge of BLAST and other NCBI resources.

Statistical Software: PAUP (phylogenetic analysis using parsimony), PHYLIP, Hy-Phy (for testing hypotheses using maximum likelihood), SAS, JMP and STATA statistical packages.

Programming: C/C++ programming.

 

ACADEMIC ACHIEVEMENTS, HONORS AND FELLOWSHIPS 

Grants and Awards Biological Informatics Post Doctoral Fellowship from the National Science Foundation (October 1, 2001 through October 1, 2003)

Co-author of successful National Science Foundation PEET grant awarded September, 1997 (P.I., Dr. Brent D. Mishler NSF DEB-9712347; Period Covered: 9/1/1997 to 8/30/2002) 

Vice Chancellor's Award for Research from University of California, Berkeley (2000)

Research Fellowship in Integrative Biology (2000)

Sigma Xi "Grants-in-Aid" award (1997)

University of California, Berkeley Gump Research Station Fellowship (1997) 

Full scholarship to the Summer Institute in Statistical Genetics, Raleigh, NC (2000)

Travel/expenses award from the Green Plant Phylogeny Research Coordination Group to attend and present at the conference on "The Computational Challenges of building the Green Plant Phylogeny" University of Maryland, College Park, MD (2000)

Academic honors Phi Beta Kappa, Tulane University Chapter (inducted May, 1996)             Tulane University Dean’s List (1992-1996)  Tulane University Randall Lee Gibson Honor Society Member (1992-1996) Fred R. Cagle Award for Outstanding Achievement in Ecology, Evolution and Organismal Biology (1996)

"Who’s Who" in Colleges and Universities (inducted 1996)

Teaching awards

Outstanding Student Teacher Award (1997&1998) 

Teaching Effectiveness Award, May (1998)

 

MANUSCRIPTS (published, submitted, and in preparation)

published

Wall, D. P. and S. P. Darwin. 1999. Vegetation and elevational gradients within a bottomland hardwood forest of southeastern Louisiana. American Midland Naturalist 142: 17-30.  C. La Farge, B. D. Mishler, J. Wheeler, D. P. Wall, and K. Johannes. 2000. Phylogenetic relationships within the haplolepideous mosses. The Bryologist 103 (2): 257-276.

in press/submitted

Wall, D. P. and J. T. Herbeck. (submitted). Evolutionary patterns of codon usage in the chloroplast gene, rbcL. Molecular Biology and Evolution.

John A. Wheeler, Dennis P. Wall, Kirtsen Johannes, and Brent D. Mishler. (in press). Congruence and convergence in the moss family Calymperaceae: phylogenetic analysis of two chloroplast genes (rbcL and rps4) and morphology. Systematic Biology.

in preparation

Wall, D. P. (in prep.). Population structure and patterns of island radiation in the paleotropic endemic moss, Mitthyridium: insights from a rapidly evolving nuclear gene glyceraldehyde 3-phosphate dehydrogenase (gpd). Proceedings of the National Academy of Sciences

Wall, D. P. and Bunje, P. (in prep). The criteria of adaptive radiations. Trends in Ecology and Evolution.


PRESENTED PAPERS AND ABSTRACTS AT PROFESSIONAL MEETINGS 

Wall, D. P. and Herbeck, J. T. A comparative analysis of codon usage bias in green plants. Meetings of The Society for the Study of Evolution &The Society of Systematic Biologists 1999, Madison WI  Wall, D. P. and Herbeck, J. T. A comparative analysis of codon usage bias in green plants. XVI International Botanical Congress, St. Louis, MO 1999.

Wall, D. P. 2000. Population structure and patterns of island radiation in the paleotropic endemic moss, Mitthyridium: insights from a rapidly evolving nuclear gene, gpd. Botany 2000 meetings, Portland, OR.

Wall, D. P. and Herbeck. 2000. Evolutionary patterns of codon usage in the chloroplast gene, rbcL. Conference on the computational challenges of the Green Plant Phylogeny, College Park, MD.

Wall, D. P. and Herbeck, J. T. 2000. A new program for analyzing codon usage bias using maximum likelihood. Evolution meetings, Bloomington, IN.

LANGUAGES French (solid speaking and reading; working knowledge of writing) and Latin

 

TEACHING AND LEADERSHIP EXPERIENCE 

Classroom

"Biology 1B." 1996. Introductory course in Ecology, Evolution and Organismal Biology 

"California Plant Life." 1997. Upper-division undergraduate course, both lab and field oriented.

"Principles of Plant Morphology." 1998. Upper division undergrad/graduate student course. 

"IB200B: Principles of Phylogenetics II--Ecology and Evolution." 1999, Graduate-level course. Primary duties: Develop and teach laboratory; create and maintain website (http://ucjeps.berkeley.edu/bryolab/ib200/); Develop syllabus and reading list.

"Darwinian Revolution." Guest lecturer, freshman seminar (1999&2000).

MCAT-Medical College Admissions Prep Course Instructor at The Princeton Review, 1999-2000. 

Laboratory

Molecular Laboratory Supervisor and Instructor of new graduate students and advanced undergrads in DNA techniques. Techniques include: general protocols for DNA extraction, amplification, troubleshooting, primer design, automated DNA sequencing, sequence analysis and database assembly. Lab supervisor for development of the PEET Calymperaceae website by web designers Rosalyn Sayman and Canyon Fisher.

Other

Author of the "Evolution and Ecology" section of the educational web-site, Mentor.com

Sailing Instructor, Racing division@ Encinal and San Francisco Yacht Clubs, CA (1996-present).