Michael Cummings

Professor
3107 Biomolecular Sciences Building
(301) 405-9903
Education: 
Ph.D., Harvard University, (Organismic and Evolutionary Biology)
Biography: 

Michael Cummings is a professor of biology.

He was the first faculty member hired into the Center for Bioinformatics and Computational Biology, where he leads the Laboratory of Molecular Evolution.

He has published extensively in molecular evolution, phylogenetics, computational biology and bioinformatics (including genotype-phenotype relationships using machine learning), computer science (particularly in the area of grid computing), and bioinformatics education. He has lectured extensively throughout the U.S. and internationally, including Australia, Brazil, Canada, Czech Republic, England, Germany, Korea, México, Portugal, Spain, Sweden, Switzerland and Wales. Because of his varied expertise, he has served the scientific community through participation in numerous national and international committees, panels, symposia, workshops and advisory boards.

From 2000 through 2011, he directed or co-directed the Workshop on Molecular Evolution, with 17 instances held in Atlanta (at the Centers for Disease Control and Prevention), Fort Collins, Washington, D.C. (at the National Museum of Natural History, Smithsonian Institution), Woods Hole, and Český Krumlov in the Czech Republic. From 2009 through 2011, he co-directed the Workshop on Comparative Genomics with three instances held in Fort Collins, Washington, D.C., and Český Krumlov. These advanced workshops have trained more than 1200 faculty/principal investigators, postdoctoral scholars and graduate students from more than 70 countries.

He received his doctorate in organismic and evolutionary biology from Harvard University in 1992, and completed postdoctoral research at the University of California, Berkeley, as an Alfred P. Sloan Foundation Postdoctoral Fellow in Molecular Studies of Evolution, and at the University of California, Riverside. He was a scientist at the Marine Biological Laboratory and has held a guest professorship at the University of Konstanz.

Publications

2012


Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst Biol. 61(1):170-173.

2011


Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S et al..  2011.  Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? Systematic BiologySyst Biol. 60(6):782-796.

Bazinet AL, Cummings MP.  2011.  Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids. Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on.
:1896-1902.

Kawahara AY, Ohshima I, Kawakita A, Regier JC, Mitter C, Cummings MP, Davis DR, Wagner DL, De Prinis J, Lopez-Vaamonde C.  2011.  Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evol Biol. 11:182

2010


Roe A, Weller S, Baixeras J, Brown JW, Cummings MP, Davis DR, Horak M, Kawahara AY, Mitter C, Parr CS et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
:1-24.

2009


Regier JC, Zwick A, Cummings MP, Kawahara AY, Cho S, Weller S, Roe A, Baixeras J, Brown JW, Parr C et al..  2009.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol. 9:280-280.

Takala SL, Coulibaly D, Thera MA, Batchelor AH, Cummings MP, Escalante AA, Ouattara A, Traoré K, Niangaly A, Djimdé AA et al..  2009.  Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development. Sci Transl Med. 1(2):2ra5-2ra5.

2008


Myers DS, Bazinet AL, Cummings MP.  2008.  Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology.
:71-85.

Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, Ball B, Zwick A, Stajich JE, Cummings MP, Martin JW et al..  2008.  Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol. 57(6):920-938.

Kohlsdorf T, Cummings MP, Lynch VJ, Stopper GF, Takahashi K, Wagner GP.  2008.  A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13. J Mol Evol. 67(6):581-593.

Bazinet AL, Cummings MP.  2008.  The Lattice Project: a Grid research and production environment combining multiple Grid computing models. Distributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed & Grid Computing — Science Made Transparent for Everyone. Principles, Applications and Supporting Communities.
:2-13.

2007


Grand J, Cummings MP, Rebelo TG, Ricketts TH, Neel MC.  2007.  Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters. 10(5):364-374.

Lee S, Wang TD, Hashmi N, Cummings MP.  2007.  Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Comp Syst. 23(3):497-509.

2005


Cummings MP, Huskamp JC.  2005.  Grid computing. EDUCAUSE Review. 40:116-117.

Parr CS, Cummings MP.  2005.  Data sharing in ecology and evolution. Trends in Ecology & Evolution. 20(7):362-363.

2004


Cummings MP.  2004.  A book like its cover. Heredity. 93(2):234-235.

Welch D MB, Cummings MP, Hillis DM, Meselson M.  2004.  Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families. Proceedings of the National Academy of Sciences of the United States of AmericaPNAS. 101(6):1622-1625.

2003


Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, Winka K.  2003.  Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol. 52(4):477-487.

2002


García-Varela M, Cummings MP, Pérez-Ponce de León G, Gardner SL, Laclette JP.  2002.  Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol Phylogenet Evol. 23(2):288-292.

2001

2000


García-Varela M, Pérez-Ponce de León G, de la Torre P, Cummings MP, Sarma SS, Laclette JP.  2000.  Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol Evol. 50(6):532-540.

Pollock DD, Eisen JA, Doggett NA, Cummings MP.  2000.  A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity. Molecular Biology and EvolutionMol Biol Evol. 17(12):1776-1788.

1999


Cummings MP, Otto SP, Wakeley J.  1999.  Genes and other samples of DNA sequence data for phylogenetic inference. The Biological Bulletin. 196(3):345-350.

1998


Tilghman S, Astin HS, Brinkley W, Chilton MD, Cummings MP, Ehrenberg RG, Fox MF, Glenn K, Green PJ, Hans S et al..  1998.  Trends in the Early Careers of Life Scientists.

Campos A, Cummings MP, Reyes JL, Laclette JP.  1998.  Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences. Mol Phylogenet Evol. 10(1):1-10.

Tilghman S, Astin HS, Brinkley W, Chilton MD, Cummings MP, Ehrenberg RG, Fox MF, Glenn K, Green PJ, Hans S et al..  1998.  Trends in the early careers of life scientists - Preface and executive summary. Mol Biol Cell. 9(11):3007-3015.

Cummings MP, Welschmeyer NA.  1998.  Pigment composition of putatively achlorophyllous angiosperms. Plant Syst Evol. 210(1-2):105-111.

1997


Clegg MT, Cummings MP, Durbin ML.  1997.  The evolution of plant nuclear genes. Proc Natl Acad Sci USA. 94(15):7791-7798.

1996


Otto SP, Cummings MP, Wakeley J.  1996.  Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
:103-115.

1995

1994

1992


Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR.  1992.  copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA. 89(15):7124-7128.

1991


Konieczny A, Voytas DF, Cummings MP, Ausubel FM.  1991.  A superfamily of ıt Arabidopsis thaliana retrotransposons. Genetics. 127(4):801-809.

1990