Michael Cummings
Michael Cummings is the director of the Center for Bioinformatics and Computational Biology (CBCB) and a professor in the Department of Biology. He also holds an appointment in the University of Maryland Institute for Advanced Computer Studies.
His was the first faculty member hired into CBCB, where he leads the Laboratory of Molecular Evolution. He received his Ph.D. from Harvard University, and did 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.
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 USA 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, held in Atlanta (at the Centers for Disease Control and Prevention), Fort Collins, Washington (at the National Museum of Natural History, Smithsonian Institution), and Woods Hole in the USA, and Český Krumlov in the Czech Republic. From 2009 through 2011 he has co-directed the Workshop on Comparative Genomics held in Fort Collins and Washington (at the National Museum of Natural History, Smithsonian Institution) in the USA, and Český Krumlov in the Czech Republic. These advanced workshops have trained more than 1200 faculty/principal investigators, postdoctoral scholars, and graduate students from more than 70 countries.
Publications
2015
2015. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.
2015. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype. Infection, Genetics and Evolution. 30:318-322.
2014
2013
2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 110
2012
2012. A comparative evaluation of sequence classification programs. BMC BioinformaticsBMC Bioinformatics. 13
2012. BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61
2012. A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification. Systematic Entomology. 37(4):635-656.
2011
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.
2011. Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evol BiolBMC Evol Biol. 11:182
2011. Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera). Systematic EntomologySystematic Entomology. 36
2011. Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? Systematic BiologySyst BiolSystematic BiologySyst Biol. 60
2010
2010. Broader incorporation of bioinformatics in education: opportunities and challenges. Brief BioinformBrief Bioinform. 11
2010. Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
2009
2009. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol BiolBMC Evol Biol. 9
2009. Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development. Sci Transl MedSci Transl Med. 1
2008
2008. A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. EvolutionEvolution. 62
2008. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst BiolSyst Biol. 57
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.
2008. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology.
2008. A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13. J Mol EvolJ Mol Evol. 67
2007
2007. Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services. Future Generation Comp SystFuture Generation Comp Syst. 23
2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology LettersEcology Letters. 10
2007. Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Comp SystFuture Generation Comp Syst. 23
2005
2005. Data sharing in ecology and evolution. Trends in Ecology & EvolutionTrends in Ecology & Evolution. 20
2005. Grid computing. EDUCAUSE ReviewEDUCAUSE Review. 40
2005. Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena)Zoology (Jena). 108
2004
2004. Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences.
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 AmericaPNASProceedings of the National Academy of Sciences of the United States of AmericaPNAS. 101
2004. A book like its cover. HeredityHeredity. 93
2004. Section-level relationships of North American ıt Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions. BMC Evol BiolBMC Evol Biol. 4
2004. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC BioinformaticsBMC Bioinformatics. 5
2004. BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView. Dictionary of Bioinformatics. :39-40,123-124,146,288-289,305,318,337,352,388,392,398-399,455,457,502,522,568.
2004. Few amino acid positions in ıt rpoB are associated with most of the rifampin resistance in ıt Mycobacterium tuberculosis. BMC BioinformaticsBMC Bioinformatics. 5
2003
2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst BiolSyst Biol. 52
2003. Genetic consequences of ecological reserve design guidelines: An empirical investigation. Conserv GenetConserv Genet. 4
2003. Effectiveness of conservation targets in capturing genetic diversity. Conserv BiolConserv Biol. 17
2003. Necessity is the mother of invention: a simple grid computing system using commodity tools. J Parallel Distr ComJ Parallel Distr Com. 63
2002
2002. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol Phylogenet EvolMol Phylogenet Evol. 23
2001
2001. Relating amino acid sequence to phenotype: analysis of peptide-binding data. BiometricsBiometrics. 57
2000
2000. Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J Mol EvolJ Mol Evol. 50
2000. A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity. Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol. 17
1999
1999. Genes and other samples of DNA sequence data for phylogenetic inference. The Biological BulletinThe Biological Bulletin. 196
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 USAProc Natl Acad Sci USA. 95
1998. Trends in the early careers of life scientists - Preface and executive summary. Mol Biol CellMol Biol Cell. 9
1998. Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences. Mol Phylogenet EvolMol Phylogenet Evol. 10
1998. Pigment composition of putatively achlorophyllous angiosperms. Plant Syst EvolPlant Syst Evol. 210
1997
1997. The evolution of plant nuclear genes. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 94
1997. Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus ıt Nicrophorus (Coleoptera: Silphidae). Mol Biol EvolMol Biol Evol. 14
1996
1996. Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
1996. Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics. Parasitol TodayParasitol Today. 12
1995
1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol EvolMol Biol Evol. 12
1994
1994. Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer. Trends Ecol EvolTrends Ecol Evol. 9
1994. Slipped-strand mispairing in a plastid gene: ıt rpoC2 in grasses (Poaceae). Mol Biol EvolMol Biol Evol. 11
1992
1992. copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 89
1992. Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics NewsletterThe Plant Genetics Newsletter. 8