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Items: 1 to 50 of 51

1.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Apr 23. pii: syz020. doi: 10.1093/sysbio/syz020. [Epub ahead of print]

PMID:
31034053
2.

Comparative morphology and evolution of the cnidosac in Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).

Goodheart JA, Bleidißel S, Schillo D, Strong EE, Ayres DL, Preisfeld A, Collins AG, Cummings MP, Wägele H.

Front Zool. 2018 Nov 13;15:43. doi: 10.1186/s12983-018-0289-2. eCollection 2018.

3.

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).

Goodheart JA, Bazinet AL, Valdés Á, Collins AG, Cummings MP.

BMC Evol Biol. 2017 Oct 26;17(1):221. doi: 10.1186/s12862-017-1066-0.

4.

Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity.

Agrawal S, Moser KA, Morton L, Cummings MP, Parihar A, Dwivedi A, Shetty AC, Drabek EF, Jacob CG, Henrich PP, Parobek CM, Jongsakul K, Huy R, Spring MD, Lanteri CA, Chaorattanakawee S, Lon C, Fukuda MM, Saunders DL, Fidock DA, Lin JT, Juliano JJ, Plowe CV, Silva JC, Takala-Harrison S.

J Infect Dis. 2017 Aug 15;216(4):468-476. doi: 10.1093/infdis/jix334.

5.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R.

Microbiome. 2017 Jan 25;5(1):11. doi: 10.1186/s40168-017-0233-2.

6.

Phylogeny and Evolution of Lepidoptera.

Mitter C, Davis DR, Cummings MP.

Annu Rev Entomol. 2017 Jan 31;62:265-283. doi: 10.1146/annurev-ento-031616-035125. Epub 2016 Nov 16. Review.

PMID:
27860521
7.

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.

Goodheart JA, Bazinet AL, Collins AG, Cummings MP.

R Soc Open Sci. 2015 Sep 23;2(9):150196. doi: 10.1098/rsos.150196. eCollection 2015 Sep.

8.

Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.

Brown TS, Jacob CG, Silva JC, Takala-Harrison S, Djimdé A, Dondorp AM, Fukuda M, Noedl H, Nyunt MM, Kyaw MP, Mayxay M, Hien TT, Plowe CV, Cummings MP.

Infect Genet Evol. 2015 Mar;30:318-322. doi: 10.1016/j.meegid.2014.12.010. Epub 2014 Dec 13.

9.

Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.

Takala-Harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H, Nosten F, Kyaw MP, Nhien NT, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Ariey F, Mercereau-Puijalon O, Menard D, Newton PN, Khanthavong M, Hongvanthong B, Starzengruber P, Fuehrer HP, Swoboda P, Khan WA, Phyo AP, Nyunt MM, Nyunt MH, Brown TS, Adams M, Pepin CS, Bailey J, Tan JC, Ferdig MT, Clark TG, Miotto O, MacInnis B, Kwiatkowski DP, White NJ, Ringwald P, Plowe CV.

J Infect Dis. 2015 Mar 1;211(5):670-9. doi: 10.1093/infdis/jiu491. Epub 2014 Sep 1.

10.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

Bazinet AL, Zwickl DJ, Cummings MP.

Syst Biol. 2014 Sep;63(5):812-8. doi: 10.1093/sysbio/syu031. Epub 2014 Apr 30.

11.

Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study.

Bazinet AL, Cummings MP, Mitter KT, Mitter CW.

PLoS One. 2013 Dec 4;8(12):e82615. doi: 10.1371/journal.pone.0082615. eCollection 2013.

12.

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).

Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn JC, Zwickl DJ, Cho S, Davis DR, Baixeras J, Brown J, Parr C, Weller S, Lees DC, Mitter KT.

PLoS One. 2013;8(3):e58568. doi: 10.1371/journal.pone.0058568. Epub 2013 Mar 12.

13.

A molecular phylogeny for yponomeutoidea (insecta, Lepidoptera, ditrysia) and its implications for classification, biogeography and the evolution of host plant use.

Sohn JC, Regier JC, Mitter C, Davis D, Landry JF, Zwick A, Cummings MP.

PLoS One. 2013;8(1):e55066. doi: 10.1371/journal.pone.0055066. Epub 2013 Jan 31.

14.

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia.

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Socheat D, Ariey F, Phyo AP, Starzengruber P, Fuehrer HP, Swoboda P, Stepniewska K, Flegg J, Arze C, Cerqueira GC, Silva JC, Ricklefs SM, Porcella SF, Stephens RM, Adams M, Kenefic LJ, Campino S, Auburn S, MacInnis B, Kwiatkowski DP, Su XZ, White NJ, Ringwald P, Plowe CV.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):240-5. doi: 10.1073/pnas.1211205110. Epub 2012 Dec 17.

15.

A comparative evaluation of sequence classification programs.

Bazinet AL, Cummings MP.

BMC Bioinformatics. 2012 May 10;13:92. doi: 10.1186/1471-2105-13-92.

16.

A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution.

Regier JC, Brown JW, Mitter C, Baixeras J, Cho S, Cummings MP, Zwick A.

PLoS One. 2012;7(4):e35574. doi: 10.1371/journal.pone.0035574. Epub 2012 Apr 19.

17.

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.

18.

Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?

Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S, Davis DR, Baixeras J, Brown JW, Parr C.

Syst Biol. 2011 Dec;60(6):782-96. doi: 10.1093/sysbio/syr079. Epub 2011 Aug 16.

19.

Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae).

Kawahara AY, Ohshima I, Kawakita A, Regier JC, Mitter C, Cummings MP, Davis DR, Wagner DL, De Prins J, Lopez-Vaamonde C.

BMC Evol Biol. 2011 Jun 24;11:182. doi: 10.1186/1471-2148-11-182.

20.

Broader incorporation of bioinformatics in education: opportunities and challenges.

Cummings MP, Temple GG.

Brief Bioinform. 2010 Nov;11(6):537-43. doi: 10.1093/bib/bbq058. Epub 2010 Aug 26.

PMID:
20798182
21.

Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development.

Takala SL, Coulibaly D, Thera MA, Batchelor AH, Cummings MP, Escalante AA, Ouattara A, Traoré K, Niangaly A, Djimdé AA, Doumbo OK, Plowe CV.

Sci Transl Med. 2009 Oct 14;1(2):2ra5. doi: 10.1126/scitranslmed.3000257.

22.

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study.

Regier JC, Zwick A, Cummings MP, Kawahara AY, Cho S, Weller S, Roe A, Baixeras J, Brown JW, Parr C, Davis DR, Epstein M, Hallwachs W, Hausmann A, Janzen DH, Kitching IJ, Solis MA, Yen SH, Bazinet AL, Mitter C.

BMC Evol Biol. 2009 Dec 2;9:280. doi: 10.1186/1471-2148-9-280.

23.

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.

Regier JC, Shultz JW, Ganley AR, Hussey A, Shi D, Ball B, Zwick A, Stajich JE, Cummings MP, Martin JW, Cunningham CW.

Syst Biol. 2008 Dec;57(6):920-38. doi: 10.1080/10635150802570791.

PMID:
19085333
24.

A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13.

Kohlsdorf T, Cummings MP, Lynch VJ, Stopper GF, Takahashi K, Wagner GP.

J Mol Evol. 2008 Dec;67(6):581-93. doi: 10.1007/s00239-008-9156-7.

PMID:
18855040
25.

A genealogical approach to quantifying lineage divergence.

Cummings MP, Neel MC, Shaw KL.

Evolution. 2008 Sep;62(9):2411-22. doi: 10.1111/j.1558-5646.2008.00442.x. Epub 2008 Jun 28.

PMID:
18564377
26.

Biased data reduce efficiency and effectiveness of conservation reserve networks.

Grand J, Cummings MP, Rebelo TG, Ricketts TH, Neel MC.

Ecol Lett. 2007 May;10(5):364-74.

PMID:
17498135
27.

Data sharing in ecology and evolution.

Parr CS, Cummings MP.

Trends Ecol Evol. 2005 Jul;20(7):362-3. No abstract available.

PMID:
16701396
28.

Magic bullets and golden rules: data sampling in molecular phylogenetics.

Cummings MP, Meyer A.

Zoology (Jena). 2005;108(4):329-36. Epub 2005 Oct 25.

PMID:
16351981
29.
30.

Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA.

Cummings MP, Myers DS.

BMC Bioinformatics. 2004 Sep 16;5:132.

32.

Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families.

Mark Welch DB, Cummings MP, Hillis DM, Meselson M.

Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1622-5. Epub 2004 Jan 27.

33.

Comparing bootstrap and posterior probability values in the four-taxon case.

Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, Winka K.

Syst Biol. 2003 Aug;52(4):477-87.

PMID:
12857639
34.

Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms.

Cummings MP, Nugent JM, Olmstead RG, Palmer JD.

Curr Genet. 2003 May;43(2):131-8. Epub 2003 Mar 14.

PMID:
12695853
35.

Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class polyacanthocephala (acanthocephala).

García-Varela M, Cummings MP, Pérez-Ponce de León G, Gardner SL, Laclette JP.

Mol Phylogenet Evol. 2002 May;23(2):288-92.

PMID:
12069558
36.

Relating amino acid sequence to phenotype: analysis of peptide-binding data.

Segal MR, Cummings MP, Hubbard AE.

Biometrics. 2001 Jun;57(2):632-42.

PMID:
11414594
37.

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Pollock DD, Eisen JA, Doggett NA, Cummings MP.

Mol Biol Evol. 2000 Dec;17(12):1776-88. Review.

PMID:
11110893
38.

Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences.

García-Varela M, Pérez-Ponce de León G, de la Torre P, Cummings MP, Sarma SS, Laclette JP.

J Mol Evol. 2000 Jun;50(6):532-40.

PMID:
10835483
39.

Genes and other samples of DNA sequence data for phylogenetic inference.

Cummings MP, Otto SP, Wakeley J.

Biol Bull. 1999 Jun;196(3):345-50. No abstract available.

PMID:
10447352
40.

Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences.

Campos A, Cummings MP, Reyes JL, Laclette JP.

Mol Phylogenet Evol. 1998 Aug;10(1):1-10.

PMID:
9751913
43.

The evolution of plant nuclear genes.

Clegg MT, Cummings MP, Durbin ML.

Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7791-8.

44.

Linear IgA disease with clinical and immunopathological features of epidermolysis bullosa acquisita.

Mutasim DF, Cummings MP.

Pediatr Dermatol. 1997 Jul-Aug;14(4):303-6.

PMID:
9263315
45.

Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics.

Blair D, Campos A, Cummings MP, Laclette JP.

Parasitol Today. 1996 Feb;12(2):66-71.

PMID:
15275257
46.

Sampling properties of DNA sequence data in phylogenetic analysis.

Cummings MP, Otto SP, Wakeley J.

Mol Biol Evol. 1995 Sep;12(5):814-22.

PMID:
7476127
47.

Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer.

Cummings MP.

Trends Ecol Evol. 1994 Apr;9(4):141-5. doi: 10.1016/0169-5347(94)90179-1.

PMID:
21236798
48.

Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae).

Cummings MP, King LM, Kellogg EA.

Mol Biol Evol. 1994 Jan;11(1):1-8.

PMID:
8121278
49.

copia-like retrotransposons are ubiquitous among plants.

Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR.

Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7124-8.

50.

A superfamily of Arabidopsis thaliana retrotransposons.

Konieczny A, Voytas DF, Cummings MP, Ausubel FM.

Genetics. 1991 Apr;127(4):801-9.

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