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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;30:318-22. doi: 10.1016/j.meegid.2014.12.010. Epub 2014 Dec 13.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Data sharing in ecology and evolution.

Parr CS, Cummings MP.

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

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