Publications

49. Cummings, M. P., M. C. Neel and K. L. Shaw. A genealogical approach to quantifying lineage divergence. Evolution Accepted.
48. Regier, J. C., J. W. Shultz, A. Ganley, A. Hussesy, D. Shi, B. Ball, J. Stajich, M. P. Cummings, J. W. Martin and C. W. Cunningham. Deep-level arthropod phylogeny resolved: a multigenic investigation into the effects of data partitioning and exclusion. Systematic Biology Accepted.
47. Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters 10:364-374.
46. Bazinet, A. L., D. S. Myers, J. Fuetsch and M. P. Cummings. 2007. Grid Services Base Library: a high-level, procedural application program interface for writing Globus-based Grid services. Future Generation Computer Systems 23:517-522.
45. Lee, S., T. D. Wang, N. Hashmi and M. P. Cummings. 2007. Bio-STEER: a Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Computer Systems 23:497-509.
44. Cummings, M. P., and A. Meyer. 2005. Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology 108:329-336.
43. Parr, C. S., and M. P. Cummings. 2005. Data sharing in ecology and evolution. Trends in Ecology and Evolution 20:362-363.
42. Cummings, M. P., and M. R. Segal. 2004. Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. BMC Bioinformatics 5:137.
41. Cummings, M. P., and D. S. Myers. 2004. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics 5:132.
40. Neel, M. C., and M. P. Cummings. 2004. Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions. BMC Evolutionary Biology 4:15.
39. Mark Welch, D. B., M. P. Cummings, D. M. Hillis and M. Meselson. 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, USA 101:1622-1625.
38. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology 52:477-487.
37. Neel, M. C., and M. P. Cummings. 2003. Genetic consequences of ecological reserve design guidelines: an empirical investigation. Conservation Genetics 4:427-439.
36. Myers, D. S., and M. P. Cummings. 2003. Necessity is the mother of invention: a simple Grid computing system using commodity tools. Journal of Parallel and Distributed Computing 63:578-589.
35. Cummings, M. P., J. M. Nugent, R. G. Olmstead and J. D. Palmer. 2003. Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Current Genetics 43:131-138.
34. Neel, M. C., and M. P. Cummings. 2003. Effectiveness of conservation targets in capturing genetic diversity. Conservation Biology 17:219-229.
33. García-Varela, M., M. P. Cummings, G. Pérez-Ponce de León, S. L. Gardner and J. P. Laclette. 2002. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Molecular Phylogenetics and Evolution 23:288-292.
32. Segal, M. R., M. P. Cummings and A. E. Hubbard. 2001. Relating amino acid sequence to phenotype: analysis of peptide binding data. Biometrics 57:632-643.
31. Pollock, D. D., J. A. Eisen, N. A. Doggett and M. P. Cummings. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular Biology and Evolution 17:1776-1788.
30. Förster, H., M. P. Cummings and M. D. Coffey. 2000. Phylogenetic relationships of Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI. Mycological Research 104:1055-1061.
29. García-Varela, M., G. Pérez-Ponce de León, P. de la Torre, M. P. Cummings, S. S. S. Sarma and J. P. Laclette. 2000. Phylogenetic analysis of Acanthocephala based on 18S ribosomal gene sequences. Journal of Molecular Evolution 50:532-540.
28. Cummings, M. P., S. P. Otto and J. Wakeley. 1999. Genes and other samples of DNA sequence data for phylogenetic inference. Biological Bulletin 196:345-350.
27. Campos, A., M. P. Cummings, J. L. Reyes and J. P. Laclette. 1998. Phylogenetic relationships of Platyhelminthes based on 18S ribosomal gene sequences. Molecular Phylogenetics and Evolution 10:1-10.
26. Cummings, M. P., and M. T. Clegg. 1998. Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proceedings of the National Academy of Sciences, USA 95:5637-5642.
25. Cummings, M. P., and N. Welschmeyer. 1998. Pigment composition of putatively achlorophyllous angiosperms. Plant Systematics and Evolution 210:105-111.
24. King, L. M., and M. P. Cummings. 1997. Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae). Molecular Biology and Evolution 14:1088-1095.
23. Clegg, M. T., M. P. Cummings and M. L. Durbin. 1997. The evolution of plant nuclear genes. Proceedings of the National Academy of Sciences, USA 94:7791-7798.
22. Marks, J. C., and M. P. Cummings. 1996. DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater Cladophora (Chlorophyta). Journal of Phycology 32:1035-1042.
21. Blair, D., A. Campos, M. P. Cummings, and J. P. Laclette. 1996. Evolutionary biology of platyhelminths comes of age: the role of molecular phylogenetics. Parasitology Today 12:66-71.
20. Cummings, M. P., S. P. Otto and J. Wakeley. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution 12:814-822.
19. Cummings, M. P. 1994. Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer. Trends in Ecology and Evolution 9:141-148.
18. Cummings, M. P., L. M. King and E. A. Kellogg. 1994. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Molecular Biology and Evolution 11:1-8.
17. Voytas, D. F., M. P. Cummings, A. Konieczny, F. M. Ausubel and S. R. Rodermel. 1992. copia-like retrotransposons are ubiquitous among plants. Proceedings of the National Academy of Sciences, USA 89:7124-7128.
16. Konieczny, A., D. F. Voytas, M. P. Cummings and F. M. Ausubel. 1991. A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127:801-809.
15. Voytas, D. F., A. Konieczny, M. P. Cummings and F. M. Ausubel. 1990. The structure, distribution and evolution of the Ta1 retrotransposable element family of Arabidopsis thaliana. Genetics 126:713-721.
14. Furnier, G. R., M. P. Cummings and M. T. Clegg. 1990. Evolution of the avocados as revealed by DNA restriction site variation. Journal of Heredity 81:183-188.

Invited Papers

13. Cummings, M. P., J. C. Huskamp. 2005. Grid computing. EDUCAUSE Review 40:116-117.
12. Tilghman, S., H. S. Astin, W. Brinkley, M. D. Chilton, M. P. Cummings, R. G. Ehrenberg, M. F. Fox, K. Glenn, P. J. Green, S. Hans, A. Kelman, J. LaPidus, B. Levin, J. R. McIntosh, H. Riecken and P. E. Stephans. 1998. Trends in the early careers of life scientists - Preface and executive summary. Molecular Biology of the Cell 9:3007-3015.
11. Cummings, M. P. 1992. Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics Newsletter 8:38-41.

Conference Papers

10. Hashmi, N., S. Lee and M. P. Cummings. 2004. Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services. W3C Workshop on Semantic Web for Life Sciences, Cambridge, Massachusetts USA.

Books

9. Tilghman, S., H. S. Astin, W. Brinkley, M. D. Chilton, M. P. Cummings, R. G. Ehrenberg, M. F. Fox, K. Glenn, P. J. Green, S. Hans, A. Kelman, J. LaPidus, B. Levin, J. R. McIntosh, H. Riecken and P. E. Stephans. 1998. Trends in the early careers of life scientists. National Academy Press, Washington, DC. 178 Pages.

Book Chapters

8. Roe, A. D., S. J. Weller, J. Baixeras-Almela, J. Brown, M. P. Cummings, D. Davis, M. Horak, A. Kawahara, C. Mitter, C. Parr, J. C. Regier, D. Rubinoff, T. J. Simonsen, N. Wahlberg and A. Zwick. Evolutionary framework for Lepidoptera model systems. In Goldsmith, M., and F. Marec (Eds.) Genetics and Molecular Biology of Lepidoptera. Taylor and Francis. Accepted.
7. Bazinet, A. L., and M. P. Cummings. The Lattice Project: a Grid research and production environment combining multiple Grid computing models. In Weber, M. H. W. (Ed.) Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities. Tectum Publishing House, Marburg. In press.
6. Myers, D. S., A. L. Bazinet and M. P. Cummings. 2008. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Pages 71-85. In Talbi, E.-G. and A. Zomaya (Eds.) Grids for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing. John Wiley & Sons, New York.
5. Cummings, M. P. 2004. Sixteen entries on molecular evolution software packages: BAMBE pgs. 39-40, DnaSP pgs. 123-124, ENCprime/SeqCount pg. 146, LAMARC pgs. 288-289, MacClade pg. 305, MEGA pg. 318, Modeltest pg. 337, MrBayes pg. 352, PAML pg. 388, PAUP* pg. 392, PHYLIP pgs. 398-399, r8s pg. 455, readseq pg. 457, Seq-Gen pg. 502, Sites pg. 522, TreeView pg. 568. In Hancock, J. M. and M. J. Zvelebil (Eds.) Dictionary of Bioinformatics. John Wiley & Sons, New York.
4. Otto, S. P., M. P. Cummings and J. Wakeley. 1996. Inferring phylogenies from DNA sequence data: The effects of sampling. Pages 103-115. In Harvey, P. H., A. J. Leigh Brown, J. Maynard Smith and S. Nee (Eds.) New Uses for New Phylogenies. Oxford University Press.

Book Reviews

3. Cummings, M. P. 2004. A book like its cover - The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny, Edited by M. Salemi and A.-M. Vandamme. Heredity 93:234-235.
2. Cummings, M. P. 1991. Review of Fundamentals of Molecular Evolution, by Li, W.-H. and D. Graur. Cladistics 7:310-312.

Technical Reports

1. Cummings, M. P. , D. S. Myers, and M. Mangelson. 2004. Applying Permutation Tests to Tree-Based Statistical Models: Extending the R Package rpart. Technical Report CS-TR-4581, UMIACS-TR-2004-24, Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland.