Associate Professor, 2005-present
Department of Biological Sciences
Cedar Crest College
100 College Drive
Allentown, PA 18104-6196
(610) 606-4666 ext 3501
rmkliman@cedarcrest.edu
www.cedarcrest.edu/rmkliman
Education
- A.B., Colby College (Biology & Music), 1984
- Ph.D., Wesleyan University (Biology), 1990
Previous Professional Experience
- High School Teacher, Sprinfield, VT, 1984-1985
- Postdoctoral Fellow, Rutgers University, 1990-1993
- Postdoctoral Fellow, Harvard University, 1993-1994
- Assistant Professor, Radford University, 1994-1998
- Research Associate, Rutgers University, 1998-1999
- Assistant Professor, Kean University, 1999-2002
- Assistant Professor, Cedar Crest College, 2002-2005
Professional Workshops
- Short Course in Experimental Medical and Mammalian Genetics, The Jackson Laboratory, 1988
- Workshop in Molecular Evolution, Marine Biological Laboratory, 1992
- Summer Institute in Statistical Genetics, North Carolina State University, 2003
Courses taught
CCC, Cedar Crest College; KU, Kean University; RU, Radford University
- Advanced Bioinformatics (lecture/applications), CCC
- Advanced Mendelian and Population Genetics (lecture, new for Spring 2010), CCC
- Advanced Recombinant DNA Techniques (lecture), CCC
- Ecology (lecture/lab), CCC
- Ecology, Evolution & Genetics (lecture/lab), CCC
- Evolution (lecture), RU
- Genetics (lecture/lab), RU, KU, CCC
- Independent Research, RU, KU, CCC
- Introduction to Bioinformatics (lecture/applications), CCC
- Junior Colloquium (lecture/seminar), CCC
- Law & Science (Political Science course; lecture), CCC
- Medical Genetics and Genomics (lecture), CCC
- Molecular Biology (lecture/lab), RU
- Neurobiology (lecture), RU
- Nucleic Acid Sequencing/Sequence Analysis (graduate; lecture/lab), KU
- Principles of Biology (for majors; lecture/lab), CCC
- Principles of Biology (for non-majors; lecture/lab), CCC, RU
- Principles of Biology (mixed majors, non-majors; lecture/lab), KU
- Pseudoscience, Junk Science & Skepticism (Honors course; lecture), CCC
- Science, Ethics and Society (seminar), CCC
Research Support
I. Extramural Support - Grants
- Virginia Academy of Sciences, "Estimation of components of genetic variance in Drosophila sechellia." 1995-1996
- Jeffress Memorial Trust, "Genealogical analysis of species formation in the Drosophila simulans species complex." 1995-1998
- NIH (R15), "Analysis of eukaryotic compositional and codon biases." 2001-2004
- NIH (R15), "Assessment of codon usage at the gene and genome levels." 2004-2007
- Conservation International Foundation (Dr. John Cigliano, Cedar Crest College, co-PI), "Assessment of DNA sequence variation and population structure in queen conch of Belize." 2006-2009
- NIH (R15) (Dr. Amy Reese, Cedar Crest College, co-PI), "Empirical analysis of natural selection on codon usage in eukaryotes." 2007-2010
- NIH (R01) (Multiple-PI with Dr. Mohamed Noor, Duke), "Fine-scale recombination, variation, divergence, and codon bias in Drosophila." 2009-2013
- NIH (R01, ARRA supplemental) (Multiple-PI with Dr. Mohamed Noor, Duke), "Fine-scale recombination, variation, divergence, and codon bias in Drosophila." 2009-2011
- Earthwatch Institute (with Dr. John Cigliano), 2008, 2010
- Oceanic Society (with Dr. John Cigliano), 2008
- Busch Postdoctoral Fellowship (Rutgers University), 1990-1993
- Radford University (Seed Grant), 1994-1995
- Kean University Untenured Faculty Research Initiative, 2000-2001
- Cedar Crest College Faculty Development Grants, 2002-2004, 2005-2010
Current Professional Society Memberships
- American Association for the Advancement of Science
- Genetics Society of America
- Society for the Study of Evolution
- Society for Molecular Biology and Evolution
Current Service and Activities
- Associate Editor, Journal of Molecular Evolution, 2004-present
- Athletic Advisory Board, 2006-present
- Tri-Beta, Faculty Advisor, 2005-present
- Co-organizer of NSF-sponsored program to increase undergraduate diversity at the annual Evolution meeting, 2003-present
- Reviewer: Behavior Genetics; BMC Journals; Evolution; Genetica; Genome Biology; Genetics; International Journal of Plant Sciences; Journal of Molecular Evolution; Journal of Theoretical Biology; Molecular Biology and Evolution; Molecular Ecology; Molecular Phylogenetics and Evolution; PLoS Genetics; PLoS ONE; Proceedings of the National Academy of Science; Proceedings of the Royal Society; Proteins: Structure, Function and Genetics; Science. Guest Associate Editor for Evolution.
- NSF grant review panelist and ad hoc reviewer.
Past Service and Activities (selected list)
- Associate Editor, Genetica, 2001-7
- Lead Editor, Population, Quantitative and Evolutionary Genetics, Nature Education (a.k.a., Scitable), 2007-9
- Cedar Crest College: Director, Bioinformatics Program, 2002-8
- Cedar Crest College: Curriculum and Academic Policy Committee (College-level), 2007-10
- Cedar Crest College (College-level): Institutional Review Board, 2005-8
- Cedar Crest College (College-level): Graduate Programs Committee, 2006
- Cedar Crest College (College-level): Grievance Committee, 2005-6
- Kean University (University-level): Information Technology Strategic Plan Task Force, Technology Institute for Professionals (Instructor, technical and pedagogical aspects of course web site design)
- Kean University (College-level): ad hoc Major Equipment Committee, M.S. Biotechnology Steering Committee
- Kean University, (Department-level): Curriculum Committee, Grievance Committee, Tri-Beta (faculty advisor)
- Radford University (University-level): Academic Policies and Procedures Committee
- Radford University (College-level): Curriculum Committee, Liaison to the Honors Program
- Radford University (Department-level): Curriculum Committee (chair), Graduate School Assessment Committee (chair), Biology Club (faculty advisor)
Software Developed
- EvolGenius Population Genetics Simulation. Two-locus population genetics simulation for instruction and research.
- LU1, LU2 and CODON10. Used to construct "lookup tables" of protein-coding genes in NCBI genome files, and to then analyze codon usage and base composition (see Kliman et al., JME 2003)
- MONTECOD. Used to test for natural selection on codon usage (see Llopart et al., JME 2008)
- ISOLATION. Used to estimate species isolation times and other parameters from multilocus DNA sequence data (see McDermott and Kliman, PLoS One 2008)
- MicroScan_rk2. Perl program to find microsatellites in Fasta libraries (modification of MicroScan by Mohamed Noor)
Patent
- Barany, F., M. Zirvi, N.P. Gerry, R. Favis & R. Kliman. "Method of designing an addressable array suitable for detection of nucleic acid sequence differences using the ligase detection reaction and addressable arrays."
Publications and Presentations
I. Research Articles
- McDermott, S.R. & R.M. Kliman (2008) Estimation of isolation times of the island species in the D. simulans complex from multilocus DNA sequence data. PLoS One 3:e2442. Abstract | Full-text
- Llopart, A., A. Mabille, J.R. Peters-Hall, J.M. Comeron & R.M. Kliman (2008) A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana. Journal of Molecular Evolution 66:224-231. Abstract
- Cirulli, E.T., R.M. Kliman & M.A.F. Noor (2007) Fine-scale crossover rate heterogeneity in Drosophila pseudoobscura. Journal of Molecular Evolution 64:129-135. Abstract
- Kliman, R.M. & C.A. Bernal (2005) Unusual usage of AGG and TTG codons in humans and their viruses. Gene 352:92-99. Abstract
- Kliman, R.M. & A.N. Henry (2005) Inference of codon preferences in Arabidopsis thaliana. International Journal of Plant Sciences 166:3-11. Abstract
- Kliman, R.M., N. Irving & M Santiago (2003) Selection conflicts, gene expression and codon usage trends in yeast. Journal of Molecular Evolution 57:98-109. Abstract
- Kliman, R.M. & J. Hey (2003) Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud & Duret. Genetical Research 81:89-90. Abstract
- Noor, M.A.F. & R.M. Kliman (2003) Variability on the dot chromosome in the Drosophila simulans clade. Genetica 118:51-58. Abstract
- Machado, C.A., R.M. Kliman, J. Markert & J. Hey (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19:472-488. Abstract | Full-text
- Hey, J. & R.M. Kliman (2002) Interactions between natural selection, recombination, and gene density in the genes of Drosophila. Genetics 160:595-608. Abstract | Full-text
- Noor, M.A.F., R.M. Kliman & C. Machado (2001) Evolutionary history of microsatellites in the obscura group of Drosophila. Molecular Biology and Evolution 18:551-556. Abstract | Full-text
- Kliman, R.M., P. Andolfatto, J.A. Coyne, F. Depaulis, M. Kreitman, A.J. Berry, J. McCarter, J. Wakeley & J. Hey (2000) The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931. Abstract | Full-text
- Kliman, R.M. (1999) Recent selection on synonymous codon usage in Drosophila. Journal of Molecular Evolution 49:343-351. Abstract
- Kliman, R.M. & A. Eyre-Walker (1998) Patterns of base composition within the genes of Drosophila melanogaster. Journal of Molecular Evolution 46:534-541. Abstract
- Kliman, R.M. & J. Hey (1994) The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137:1049-1056. Abstract | Full-text
- Hilton, H., R.M. Kliman & J. Hey (1994) Using hitchhiking genes to study adaptation and divergence during speciation within the Drosophila melanogaster species complex. Evolution 48:1900-1913. Abstract
- Kliman, R.M. & J. Hey (1993) Reduced natural selection associated with low recombination in Drosophila melanogaster. Molecular Biology and Evolution 10:1239-1258. Abstract | Full-text
- Hey, J. & R.M. Kliman (1993) Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology and Evolution 10:804-822. Abstract | Full-text
- Kliman, R.M. & J. Hey (1993) DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex. Genetics 133:375-387. Abstract | Full-text
- Kliman, R.M. & G.R. Lynch (1992) Evidence for genetic variation in the occurrence of the photoresponse of the Djungarian hamster, Phodopus sungorus. Journal of Biological Rhythms 7:161-173. Abstract
- Kliman, R.M. & G.R. Lynch (1991) Evidence for independence of circadian characters and the extent of photoresponsiveness in the Djungarian hamster, Phodopus sungorus. Journal of Biological Rhythms 6:159-166. Abstract
- Lynch, G.R., C.B. Lynch & R.M. Kliman (1989) Genetic analyses of photoresponsiveness in the Djungarian hamster, Phodopus sungorus. Journal of Comparative Physiology A 164:475-481. Abstract
- Puchalski, W.R., R. Kliman & G.R. Lynch (1988) Differential effects of short day pretreatment on melatonin-induced adjustments in Djungarian hamsters. Life Science 43:1005-1012. Abstract
- Kliman, R.M. (2008) Book Review: Theories of Population Variation in Genes and Genomes, by F.B. Christiansen. Quarterly Review of Biology 83:407.
- Comeron, J.M., A. Williford & R.M. Kliman (2008) The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100:19-31. Abstract
- Kliman, R.M., F. Barany, N. Cohen & R. Favis (2007) Association studies: practical and theoretical considerations for drug discovery, evaluation, and beyond. In Biochips as Pathways to Drug Discovery (eds. A. Carmen & G. Hardimann), pp. 169-192. CRC Press, New York.
- Kliman, R.M. & N.A. Johnson (2005) What every undergraduate should know about evolution (and why). BioScience 55:926-927. Full-text
- Kirk, B.W., M. Feinsod, R. Favis, R.M. Kliman & F. Barany (2002) Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Research 30:3295-3311. Abstract | Full-text
- Johnson, N.A. & R.M. Kliman (2002) Hidden evolution: progress and limitations in detecting multifarious natural selection. Genetica 114:281-291. Abstract
- Kliman, R.M., B.T. Rogers & M.A.F. Noor (2001) Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation. Journal of Theoretical Biology 209:131-141. Abstract | Full-text PDF
- Akashi, H., R.M. Kliman & A. Eyre-Walker (1998) Mutation pressure, natural selection, and the evolution of base composition in Drosophila. Genetica 102/103:49-60. Abstract
- Hey, J. & R.M. Kliman (1994) Genealogical portraits of speciation in the Drosophila melanogaster species complex. In Non-neutral evolution: Theories and Molecular Data (ed. G.B. Golding), pp. 208-216. Chapman and Hall, New York and London.
- Kliman, R.M. (2008) The EvolGenius population genetics computer simulation: how it works. Nature Education 1(3). | Full-text
- Kliman, R., B. Sheehy & J. Schultz (2008) Genetic drift and effective population size. Nature Education 1(3). | Full-text
- Kliman, R.M. (2001) A project-based approach to teaching complex population genetics to undergraduates. Bioscene: The Journal of College Biology Teaching 27:13-20. Full-text
- Kliman, R., J. Cigliano & R. Vereneck (2010) Science to Action Symposium (Marine Management Area Science Project), Belize City, Belize. Genetic variation within and among queen conch populations.
- Kliman, R.M. (2008) Forensic Science Training Institute, Cedar Crest College. Workshop on Bayesian approaches in forensic science.
- Kliman, R.M. (2005) VIII Simposio de Genetica, Sao Jose do Rio Preto, Brazil. Inferring natural history of closely related species from multilocus DNA sequence data. Also taught a 3-day postgraduate course in Molecular Population Genetics.
- Kliman, R.M. (2005) Entomology Seminar, University of Massachusetts - Amherst. Reconstructing the history of divergence of closely related Drosophila species.
- Kliman, R.M. (2004) Biology Department Seminar, Louisiana State University. Codon usage as a model for the study of selection conflicts.
- Kliman, R.M. (2003) Johnson & Johnson Pharmaceutical Research and Development, Dept. of Pharmacogenomics. Caveats in association studies: a population genetics perspective.
- Kliman, R.M. (2009) Lehigh Valley Ecology and Evolution Society, Allentown, PA. Absence of mitochondrial population structure in queen conch.
- Kliman, R.M. & S.M. McDermott (2008) Society for the Study of Evolution, Minneapolis, MN. Genetic evidence for contemporaneous origin of Drosophila sechellia and D. mauritiana.
- M.J. Smith & R.M. Kliman (2008) Society for the Study of Evolution, Minneapolis, MN. Evidence for changing base composition in human papillomaviruses.
- R.M. Vereneck, J.A. Cigliano & R.M. Kliman (2008) Society for the Study of Evolution, Minneapolis, MN. DNA sequence variation at the COI locus of Strombus gigas and S. costatus.
- Vereneck, R., M. Sandridge, P. Miller, J. Cigliano & R. Kliman (2007) 3rd International Conservation Genetics Symposium, American Museum of Natural History, New York, NY. DNA sequence variation within and among populations of queen conch in Belize.
- Kliman, R. & K. Miede (2007) Lehigh Valley Evolution and Ecology Symposium, Center Valley, PA. Coevolution of bacteriophage and host codon and amino acid usage.
- Kliman, R.M. & S.M. McDermott (2007) Drosophila Research Conference, Philadelphia, PA. The divergence population genetics of the D. simulans species complex.
- Kliman, R.M. & J.A. Cigliano (2006) Society for the Study of Evolution, Stony Brook, NY. The Cow Diversity Project: molecular population genetics for undergraduates.
- Burgett, K., A. Mabille, J. Shaffer & R. Kliman (2006) Society for the Study of Evolution, Stony Brook, NY. Testing for ongoing selection on codon usage in Drosophila.
- McDermott, S., P. Miller & R. Kliman (2006) Society for the Study of Evolution, Stony Brook, NY. Testing the strict isolation model in the Drosophila simulans species complex.
- Kliman, R.M. (2005) Society for the Study of Evolution, Fairbanks, AK. DNA sequence variation at the wds and cdc37 loci within and among species of the Drosophila simulans complex.
- Kliman, R.M. (2004) Society for the Study of Evolution, Fort Collins, CO. Preferred codon usage as it relates to gene density.
- Bernal, C.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Codon usage trends of humans and their viruses.
- Botens, C.M. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Synonymous codon variation in human papillomaviruses.
- Hild, R.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Preferred codon usage trends within eukaryote genes.
- Miede, K.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Bacteriophage codon usage reflects host codon usage.
- Kliman, R.M. (2004) Lehigh Valley Ecology and Evolution Society, Allentown, PA. Selection conflicts from linkage and pleiotropy.
- Kliman, R.M. & M.A.F. Noor (2003) Society for Molecular Biology and Evolution, Newport Beach, CA. Is a strict isolation model appopriate for the Drosophila simulans species complex?
- Kliman, R.M., N. Irving & M. Santiago. (2002). Gordon Research Conference on Genomics and Structural/Evolutionary Bioinformatics, South Hadley, MA. Codon usage in Saccharomyces cerevisiae reflects gene expression, gene spacing and compositional biases.
- Santiago, M., N. Irving & R.M. Kliman (2002). Society for the Study of Evolution, Urbana, IL. Patterns of codon usage in the yeast genome.
- Kliman, R.M. & J. Hey (2001). New England Molecular Evolutionary Biologists, Northampton, MA. Hill-Robertson interference and regulatory conflicts in Drosophila.
- Kliman, R.M. & J. Hey (2001). Society for the Study of Evolution, Bloomington, IN. Inference of Hill-Robertson interference on codon usage in Drosophila.
- Kliman, R.M. et al. (2000). Society for the Study of Evolution, Knoxville, TN. The population genetics of the origin and divergence of the Drosophila simulans complex species.