Michael Cummings
Professor
3240 Iribe Center
(301) 405-9903
Research Group(s):
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
2012. BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst Biol. 61(1):170-173.
2011
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.
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.
2011. Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera). Systematic Entomology. 36(1):31-43.
2010
2010. Broader incorporation of bioinformatics in education: opportunities and challenges. Brief Bioinform. 11(537-543)
2010. Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera. :1-24.
2009
2009. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol. 9:280-280.
2009. Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development. Sci Transl Med. 1(2):2ra5-2ra5.
2008
2008. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol. 57(6):920-938.
2008. A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. Evolution. 62(9):2411-2422.
2008. A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13. J Mol Evol. 67(6):581-593.
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.
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
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.
2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters. 10(5):364-374.
2007. Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Comp Syst. 23(3):497-509.
2005
2005. Grid computing. EDUCAUSE Review. 40:116-117.
2005. Data sharing in ecology and evolution. Trends in Ecology & Evolution. 20(7):362-363.
2005. Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena). 108(4):329-336.
2004
2004. A book like its cover. Heredity. 93(2):234-235.
2004. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics. 5:132-132.
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.
2004. Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences.
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.
2003
2003. Genetic consequences of ecological reserve design guidelines: An empirical investigation. Conserv Genet. 4(4):427-439.
2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol. 52(4):477-487.
2003. Necessity is the mother of invention: a simple grid computing system using commodity tools. J Parallel Distr Com. 63(5):578-589.
2003. Effectiveness of conservation targets in capturing genetic diversity. Conserv Biol. 17(1):219-229.
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
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
2001. Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics. 57(2):632-642.
2000
2000. A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity. Molecular Biology and EvolutionMol Biol Evol. 17(12):1776-1788.
2000. Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol Evol. 50(6):532-540.
1999
1999. Genes and other samples of DNA sequence data for phylogenetic inference. The Biological Bulletin. 196(3):345-350.
1998
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.
1998. Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences. Mol Phylogenet Evol. 10(1):1-10.
1998. Trends in the early careers of life scientists - Preface and executive summary. Mol Biol Cell. 9(11):3007-3015.
1998. Pigment composition of putatively achlorophyllous angiosperms. Plant Syst Evol. 210(1-2):105-111.
1997
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.
1997. The evolution of plant nuclear genes. Proc Natl Acad Sci USA. 94(15):7791-7798.
1996
1996. Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies. :103-115.
1996. DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater ıt Cladophora species (Chlorophyta). J Phycol. 32(6):1035-1042.
1996. Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics. Parasitol Today. 12(2):66-71.
1995
1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 12(5):814-822.
1994
1994. Slipped-strand mispairing in a plastid gene: ıt rpoC2 in grasses (Poaceae). Mol Biol Evol. 11(1):1-8.
1994. Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer. Trends Ecol Evol. 9(4):141-145.
1992
1992. copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA. 89(15):7124-7128.
1992. Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics Newsletter. 8(4):38-41.
1991
1991. Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur. Cladistics. 7:310-312.
1991. A superfamily of ıt Arabidopsis thaliana retrotransposons. Genetics. 127(4):801-809.
1990
1990. Evolution of avocados as revealed by DNA restriction fragment variation. J Hered. 81(3):183-188.
1990. The structure, distribution and evolution of the ıt Ta1 retrotransposable element family of ıt Arabidopsis thaliana. Genetics. 126(3):713-721.