Publications | The Cummings Lab

DL Ayres, MP Cummings, G Baele, AE Darling, PO Lewis, DL Swofford, JP Huelsenbeck, P Lemey, A Rambaut, MA Suchard (2019). BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. Syst Biol, 68, 1052–1061.

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JA Goodheart, S Bleidißel, D Schillo, EE Strong, DL Ayres, A Preisfeld, AG Collins, MP Cummings, H Wägele (2018). Comparative morphology and evolution of the cnidosac in Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia). Front Zool, 15, 43.

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DL Ayres, MP Cummings (2018). Rerooting Trees Increases Opportunities for Concurrent Computation and Results in Markedly Improved Performance for Phylogenetic Inference. 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (pp. 247–256). IEEE.

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JA Goodheart, AL Bazinet, Á Valdés, AG Collins, MP Cummings (2017). Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia). BMC Evol Biol, 17, 221.

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JC Regier, C Mitter, K Mitter, MP Cummings, AL Bazinet, W Hallwachs, DH Janzen, A Zwick (2017). Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample. Syst Entomol, 42, 82–93.

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DL Ayres, MP Cummings (2017). Heterogeneous hardware support in BEAGLE, a high-performance computing library for statistical phylogenetics. 2017 46th International Conference on Parallel Processing Workshops (ICPPW) (pp. 23–32). IEEE.

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DL Ayres, MP Cummings (2017). Configuring concurrent computation of phylogenetic partial likelihoods: accelerating analyses using the BEAGLE library. In S Ibrahim, KK Choo, Z Yan, and W Pedrycz (Eds.), Algorithms and Architectures for Parallel Processing. ICA3PP 2017. Lecture Notes in Computer Science (pp. 533–547). Springer, Cham.

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AL Bazinet, KT Mitter, DR Davis, EJ Van Nieukerken, MP Cummings, C Mitter (2017). Phylotranscriptomics resolves ancient divergences in the Lepidoptera. Syst Entomol, 42, 305–316.

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C Mitter, DR Davis, MP Cummings (2017). Phylogeny and Evolution of Lepidoptera. Annu Rev Entomol, 62, 265–283.

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DH Huson, R Tappu, AL Bazinet, C Xie, MP Cummings, K Nieselt, R Williams (2017). Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. Microbiome, 5, 11.

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AL Bazinet, MP Cummings (2016). Subdividing long-running, variable-length analyses into short, fixed-length BOINC workunits. J Grid Comput, 14, 429–441.

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J-C Sohn, C Regier, C Mitter, D Adamski, J-F Landry, M Heikkilä, K-T Park, T Harrison, K Mitter, A Zwick, A Kawahara, S Cho, MP Cummings, P Schmitz (2016). Phylogeny and feeding trait evolution of the mega-diverse Gelechioidea (Lepidoptera: Obtectomera): new insight from 19 nuclear genes. Syst Entomol, 41, 112–132.

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JC Regier, C Mitter, DR Davis, TL Harrison, J-C Sohn, MP Cummings, A Zwick, KT Mitter (2015). A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Syst Entomol, 40, 409–432.

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JA Goodheart, AL Bazinet, AG Collins, MP Cummings (2015). Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. R Soc Open Sci, 2, 150196.

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JA Goodheart, AL Bazinet, AG Collins, MP Cummings (2015). Phylogeny of Cladobranchia (Gastropoda: Nudibranchia): a total evidence analysis using DNA sequence data from public databases. Digital Repository at the University of Maryland.

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JC Regier, C Mitter, NP Kristensen, DR Davis, EJ Van Nieukerken, J Rota, TJ Simonsen, KT Mitter, AY Kawahara, S-H Yen, MP Cummings, A Zwick (2015). A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Syst Entomol, 40, 671–704.

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S Takala-Harrison, CG Jacob, C Arze, MP Cummings, JC Silva, AM Dondorp, MM Fukuda, TT Hien, M Mayxay, H Noedl, F Nosten, MP Kyaw, NTT Nhien, M Imwong, D Bethell, Y Se, C Lon, SD Tyner, DL Saunders, F Ariey, O Mercereau-Puijalon, D Menard, PN Newton, M Khanthavong, B Hongvanthong, P Starzengruber, H-P Fuehrer, P Swoboda, WA Khan, AP Phyo, MM Nyunt, MH Nyunt, TS Brown, M Adams, CS Pepin, J Bailey, JC Tan, MT Ferdig, TG Clark, O Miotto, B MacInnis, DP Kwiatkowski, NJ White, P Ringwald, CV Plowe (2015). Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. J Infect Dis, 211, 670–679.

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TS Brown, CG Jacob, JC Silva, S Takala-Harrison, A Djimdé, AM Dondorp, M Fukuda, H Noedl, MM Nyunt, MP Kyaw, M Mayxay, TT Hien, CV Plowe, MP Cummings (2015). Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype. Infect Genet Evol, 30, 318–322.

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AL Bazinet, DJ Zwickl, MP Cummings (2014). A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0. Syst Biol, 63, 812–818.

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MP Cummings (2014). AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite, MIGRATE-N, Modeltest, Mr- Bayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, Structure, Structurama, Tracer, TreeStat, TreeView X. Concise Encyclopaedia of Bioinformatics and Computational Biology (pp. 33–34, 40, 45–46, 54, 135, 145, 156, 184–185, 219, 238, 271–272, 325, 330–331, 352–353, 372–373, 395, 407, 409, 428, 440, 460–461, 510–511, 516–517, 524–525, 607, 611, 672–663, 684, 701–702, 727, 741, 757). Wiley-Liss, 2nd edition.

AL Bazinet, MP Cummings, KT Mitter, CW Mitter (2013). Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS One, 8, e82615.

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JC Regier, C Mitter, A Zwick, AL Bazinet, MP Cummings, AY Kawahara, J-C Sohn, DJ Zwickl, S Cho, DR Davis, J Baixeras, J Brown, C Parr, S Weller, DC Lees, KT Mitter (2013). A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS One, 8, e58568.

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S Takala-Harrison, TG Clark, CG Jacob, MP Cummings, O Miotto, AM Dondorp, MM Fukuda, F Nosten, H Noedl, M Imwong, D Bethell, Y Se, C Lon, SD Tyner, DL Saunders, D Socheat, F Ariey, AP Phyo, P Starzengruber, H-P Fuehrer, P Swoboda, K Stepniewska, J Flegg, C Arze, GC Cerqueira, JC Silva, SM Ricklefs, SF Porcella, RM Stephens, M Adams, LJ Kenefic, S Campino, S Auburn, B MacInnis, DP Kwiatkowski, X-z Su, NJ White, P Ringwald, CV Plowe (2013). Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proc Natl Acad Sci USA, 110, 240–245.

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J-C Sohn, JC Regier, C Mitter, D Davis, J-F Landry, A Zwick, MP Cummings (2013). A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and the evolution of host plant use. PLoS One, 8, e55066.

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JC Regier, C Mitter, MA Solis, JE Hayden, B Landry, M Nuss, TJ Simonsen, S-H Yen, A Zwick, MP Cummings (2012). A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification. Syst Entomol, 37, 635–656.

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AL Bazinet, MP Cummings (2012). A comparative evaluation of sequence classification programs. BMC Bioinformatics, 13, 92.

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JC Regier, JW Brown, C Mitter, J Baixeras, S Cho, MP Cummings, A Zwick (2012). A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution. PLoS One, 7, e35574.

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DL Ayres, A Darling, DJ Zwickl, P Beerli, MT Holder, PO Lewis, JP Huelsenbeck, F Ronquist, DL Swofford, MP Cummings, A Rambaut, MA Suchard (2012). BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol, 61, 170–173.

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S Cho, A Zwick, JC Regier, C Mitter, MP Cummings, J Yao, Z Du, H Zhao, AY Kawahara, S Weller, DR Davis, J Baixeras, JW Brown, C Parr (2011). Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?. Syst Biol, 60, 782–796.

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A Zwick, JC Regier, C Mitter, MP Cummings (2011). Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera). Syst Entomol, 36, 31–43.

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

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

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

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AD Roe, SJ Weller, J Baixeras, J Brown, MP Cummings, DR Davis, AY Kawahara, CS Parr, JC Regier, D Rubinoff, TJ Simonsen, N Wahlberg, A Zwick (2010). Evolutionary framework for Lepidoptera model systems. In M Goldsmith and F Marec (Eds.), Genetics and Molecular Biology of Lepidoptera (pp. 1–24). CRC Press, Boca Raton.

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ME Reyna-Fabián, JP Laclette, MP Cummings, M García-Varela (2010). Validating the systematic position of 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, 361–370.

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JC Regier, A Zwick, MP Cummings, AY Kawahara, S Cho, S Weller, A Roe, J Baixeras, JW Brown, C Parr, DR Davis, M Epstein, W Hallwachs, A Hausmann, DH Janzen, IJ Kitching, MA Solis, S-H Yen, AL Bazinet, C Mitter (2009). Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol, 9, 280.

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

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

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

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MP Cummings, MC Neel, KL Shaw (2008). A genealogical approach to quantifying lineage divergence. Evolution, 62, 2411–2422.

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AL Bazinet, MP Cummings (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 Communities.

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

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DS Myers, AL Bazinet, MP Cummings (2007). Expanding the reach of Grid computing: combining Globus-and BOINC-based systems. In E-G Talbi and AY Zomaya (Eds.), Grid Computing for Bioinformatics and Computational Biology (chapter 4). Wiley-Interscience, Hoboken.

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

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

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Michael P Cummings, Axel Meyer (2005). Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena), 108, 329–336.

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MP Cummings, JC Huskamp (2005). Grid computing. EDUCAUSE review, 40, 116–117.

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CS Parr, MP Cummings (2005). Data sharing in ecology and evolution. Trends Ecol Evol, 20, 362-363.

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

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

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

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MP Cummings (2004). BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView. In JM Hancock and MJ Zvelebil (Eds.), Dictionary of Bioinformatics and Computational Biology (pp. 39–40, 123–124, 146, 288–289, 305, 318, 337, 352, 388, 392, 398–399, 455, 457, 502, 522, 568). Wiley-Liss, Hoboken.

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MP Cummings (2004). A book like its cover. Heredity, 93, 234–235.

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

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DB Mark Welch, MP Cummings, DM Hillis, M Meselson (2004). Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc Natl Acad Sci USA, 101, 1622–1625.

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MP Cummings, DS Myers, 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, University of Maryland.

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

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

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

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

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

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

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MR Segal, MP Cummings, AE Hubbard (2001). Relating Amino Acid Sequence to Phenotype: analysis of Peptide-Binding Data. Biometrics, 57, 632–643.

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DD Pollock, JA Eisen, NA Doggett, MP Cummings (2000). A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol, 17, 1776–1788.

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

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

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MP Cummings, SP Otto, J Wakeley (1999). Genes and other samples of DNA sequence data for phylogenetic inference. Biol Bull, 196, 345–350.

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Committee on Dimensions, Causes, Implications of Recent Trends in the Careers of Life Scientists (1998). Trends in early research careers of life scientists. Physiologist, 41, 385–393.

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Committee on Dimensions, Causes, Implications of Recent Trends in the Careers of Life Scientists (1998). Trends in the early careers of life scientists. Preface and Executive Summary. Mol Biol Cell, 9, 3007–3015.

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

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MP Cummings, MT 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. Proc Natl Acad Sci USA, 95, 5637–5642.

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

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Committee on Dimensions, Causes, Implications of Recent Trends in the Careers of Life Scientists (1998). Trends in the Early Careers of Life Scientists. National Academies Press, Washington, DC.

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

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

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

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

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SP Otto, MP Cummings, J Wakeley (1996). Inferring phylogenies from DNA sequence data: the effects of sampling. In. PH Harvey, AJ Leigh Brown, JM Smith and S Nee (Eds.), New Uses for New Phylogenies (pp. 103–115). Oxford University Press.

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

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

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

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

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MP Cummings (1992). Patterns and processes of sequence evolution: Plant organelle genomes and copia-like retrotransposons. PhD thesis, Harvard University, Cambridge, Massachusetts USA.

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

MP Cummings (1991). Fundamentals of Molecular Evolution—Wen-Hsiung Li and Dan Graur. Cladistics, 7, 310–312.

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

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

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

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