Michael Cummings

Professor
3240 Iribe Center
(301) 405-9903
Academic Web Page
Research Group(s): 
Center for Bioinformatics and Computational Biology
Education: 
Ph.D., Harvard University, (Organismic and Evolutionary Biology)
Biography: 

Michael Cummings is a professor of biology with an appointment in the University of Maryland Institute for Advanced Computer Studies. He is director of the Center for Bioinformatics and Computational Biology (CBCB).

Cummings’s research involves bioinformatics, computational biology and molecular evolutionary genetics, and includes examination of patterns and processes of sequence evolution to understand molecular evolutionary mechanisms that bring about biological change. In addition to answering specific biological questions, a substantial portion of his research has focused on experimental design and data analysis methods, and software development.

Go here to view Cummings‘s academic publications on Google Scholar.

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

Zwick A, Regier JC, Mitter C, Cummings MP.  2011.  Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera). Systematic Entomology. 36(1):31-43.

2010


Reyna-Fabian ME, Laclette JP, Cummings MP, García-Varela M.  2010.  Validating the systematic position of ıt Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase. Hydrobiologia. 644(1):361-370.

Cummings MP, Temple GG.  2010.  Broader incorporation of bioinformatics in education: opportunities and challenges. Brief Bioinform. 11(537-543)

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


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.

Cummings MP, Neel MC, Shaw KL.  2008.  A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. Evolution. 62(9):2411-2422.

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.

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.

2007


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.

Bazinet AL, Myers DS, Fuetsch J, Cummings MP.  2007.  Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services. Future Generation Comp Syst. 23(3):517-522.

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.

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.

Cummings MP, Meyer A.  2005.  Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena). 108(4):329-336.

2004


Cummings MP, Segal MR.  2004.  Few amino acid positions in ıt rpoB are associated with most of the rifampin resistance in ıt Mycobacterium tuberculosis. BMC Bioinformatics. 5:137-137.

Neel MC, Cummings MP.  2004.  Section-level relationships of North American ıt Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions. BMC Evol Biol. 4:15-15.

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

Cummings MP, Myers DS.  2004.  Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics. 5:132-132.

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.

Hashmi N, Lee S, Cummings MP.  2004.  Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences.

Cummings MP, Myers DS, Mangelson M.  2004.  Applying permutation tests to tree-based statistical models: extending the R package rpart. 2004-24

2003


Neel MC, Cummings MP.  2003.  Genetic consequences of ecological reserve design guidelines: An empirical investigation. Conserv Genet. 4(4):427-439.

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.

Myers DS, Cummings MP.  2003.  Necessity is the mother of invention: a simple grid computing system using commodity tools. J Parallel Distr Com. 63(5):578-589.

Neel MC, Cummings MP.  2003.  Effectiveness of conservation targets in capturing genetic diversity. Conserv Biol. 17(1):219-229.

Cummings MP, Nugent JM, Olmstead RG, Palmer JD.  2003.  Phylogenetic analysis reveals five independent transfers of the chloroplast gene ıt rbcL to the mitochondrial genome in angiosperms. Curr Genet. 43(2):131-138.

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


Segal MR, Cummings MP, Hubbard AE.  2001.  Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics. 57(2):632-642.

2000


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.

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.

Förster H, Cummings MP, Coffey MD.  2000.  Phylogenetic relationships of ıt Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycol Res. 104:1055-1061.

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


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

Cummings MP, Clegg MT.  1998.  Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (ıt Hordeum vulgare ssp. ıt spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci USA. 95(10):5637-5642.

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.

1997


King LM, Cummings MP.  1997.  Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus ıt Nicrophorus (Coleoptera: Silphidae). Mol Biol Evol. 14(11):1088-1095.

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.

Marks JC, Cummings MP.  1996.  DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater ıt Cladophora species (Chlorophyta). J Phycol. 32(6):1035-1042.

Blair D, Campos A, Cummings MP, Laclette JP.  1996.  Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics. Parasitol Today. 12(2):66-71.

1995


Cummings MP, Otto SP, Wakeley J.  1995.  Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 12(5):814-822.

1994


Cummings MP, King LM, Kellogg EA.  1994.  Slipped-strand mispairing in a plastid gene: ıt rpoC2 in grasses (Poaceae). Mol Biol Evol. 11(1):1-8.

Cummings MP.  1994.  Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer. Trends Ecol Evol. 9(4):141-145.

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.

Cummings MP.  1992.  Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics Newsletter. 8(4):38-41.

1991


Cummings MP.  1991.  Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur. Cladistics. 7:310-312.

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

1990


Furnier GR, Cummings MP, Clegg MT.  1990.  Evolution of avocados as revealed by DNA restriction fragment variation. J Hered. 81(3):183-188.

Voytas DF, Konieczny A, Cummings MP, Ausubel FM.  1990.  The structure, distribution and evolution of the ıt Ta1 retrotransposable element family of ıt Arabidopsis thaliana. Genetics. 126(3):713-721.