Publications

Hybrid selection for sequencing pathogen genomes from clinical samples.

Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D, Sene PD, Wirth DF, Nusbaum C, Volkman SK, Birren BW, Gnirke A, Neafsey DE.

Genome Biol. 2011 Aug 11;12(8):R73. [Epub ahead of print]

PMID: 21835008

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs.

Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, Rinn JL.

Genome Biol. 2011 Jun 20;12(6):R56. [Epub ahead of print]

PMID: 21689454

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.

Van Tyne D, Park DJ, Schaffner SF, Neafsey DE, Angelino E, Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA Jr, Johnson CA, Shlyakhter I, Grossman SR, Becker JS, Yamins D, Karlsson EK, Ndiaye D, Sarr O, Mboup S, Happi C, Furlotte NA, Eskin E, Kang HM, Hartl DL, Birren BW, Wiegand RC, Lander ES, Wirth DF, Volkman SK, Sabeti PC.

PLoS Genet. 2011 Apr;7(4):e1001383. Epub 2011 Apr 21.

PMID: 21533027

A high-throughput screen targeting malaria transmission stages opens new avenues for drug development.

Buchholz K, Burke TA, Williamson KC, Wiegand RC, Wirth DF, Marti M.

J Infect Dis. 2011 May 15;203(10):1445-53.

PMID: 21502082

Aminoindoles, a novel scaffold with potent activity against Plasmodium falciparum.

Barker RH Jr, Urgaonkar S, Mazitschek R, Celatka C, Skerlj R, Cortese JF, Tyndall E, Liu H, Cromwell M, Sidhu AB, Guerrero-Bravo JE, Crespo-Llado KN, Serrano AE, Lin JW, Janse CJ, Khan SM, Duraisingh M, Coleman BI, Angulo-Barturen I, Jiménez-Díaz MB, Magán N, Gomez V, Ferrer S, Martínez MS, Wittlin S, Papastogiannidis P, O'Shea T, Klinger JD, Bree M, Lee E, Levine M, Wiegand RC, Munoz B, Wirth DF, Clardy J, Bathurst I, Sybertz E.

Antimicrob Agents Chemother. 2011 Jun;55(6):2612-22. Epub 2011 Mar 21.

PMID: 21422215

A research agenda for malaria eradication: vaccines.

malERA Consultative Group on Vaccines.

PLoS Med. 2011 Jan 25;8(1):e1000398. Review.

PMID: 21311586

A research agenda for malaria eradication: basic science and enabling technologies.

malERA Consultative Group on Basic Science and Enabling Technologies.

PLoS Med. 2011 Jan 25;8(1):e1000399. Review. Erratum in: PLoS Med. 2011 May;8(5).doi: 10.1371/annotation/e6a85761-7a23-435a-97df-f13c1ba4e8da. Gilberger, Tim [added].

PMID: 21311584

A research agenda for malaria eradication: drugs.

malERA Consultative Group on Drugs.

PLoS Med. 2011 Jan 25;8(1):e1000402. Review.

PMID: 21311580

A concise silylamine approach to 2-amino-3-hydroxy-indoles with potent in vivo antimalaria activity.

Urgaonkar S, Cortese JF, Barker RH, Cromwell M, Serrano AE, Wirth DF, Clardy J, Mazitschek R.

Org Lett. 2010 Sep 17;12(18):3998-4001.

PMID: 20718474

Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model.

Booker ML, Bastos CM, Kramer ML, Barker RH Jr, Skerlj R, Sidhu AB, Deng X, Celatka C, Cortese JF, Guerrero Bravo JE, Crespo Llado KN, Serrano AE, Angulo-Barturen I, Jiménez-Díaz MB, Viera S, Garuti H, Wittlin S, Papastogiannidis P, Lin JW, Janse CJ, Khan SM, Duraisingh M, Coleman B, Goldsmith EJ, Phillips MA, Munoz B, Wirth DF, Klinger JD, Wiegand R, Sybertz E.

J Biol Chem. 2010 Oct 22;285(43):33054-64. Epub 2010 Aug 11.

PMID: 20702404

Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies.

Orjuela-Sánchez P, Karunaweera ND, da Silva-Nunes M, da Silva NS, Scopel KK, Gonçalves RM, Amaratunga C, Sá JM, Socheat D, Fairhust RM, Gunawardena S, Thavakodirasah T, Galapaththy GL, Abeysinghe R, Kawamoto F, Wirth DF, Ferreira MU.

BMC Genet. 2010 Jul 13;11:65.

PMID: 20626846

Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome.

Zilversmit MM, Volkman SK, DePristo MA, Wirth DF, Awadalla P, Hartl DL.

Mol Biol Evol. 2010 Sep;27(9):2198-209. Epub 2010 Apr 28.

PMID: 20427419

Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia.

Gunawardena S, Karunaweera ND, Ferreira MU, Phone-Kyaw M, Pollack RJ, Alifrangis M, Rajakaruna RS, Konradsen F, Amerasinghe PH, Schousboe ML, Galappaththy GN, Abeyasinghe RR, Hartl DL, Wirth DF.

Am J Trop Med Hyg. 2010 Feb;82(2):235-42.

PMID: 20133999

A non-radioactive DAPI-based high-throughput in vitro assay to assess Plasmodium falciparum responsiveness to antimalarials--increased sensitivity of P. falciparum to chloroquine in Senegal.

Ndiaye D, Patel V, Demas A, LeRoux M, Ndir O, Mboup S, Clardy J, Lakshmanan V, Daily JP, Wirth DF.

Am J Trop Med Hyg. 2010 Feb;82(2):228-30.

PMID: 20133997

In vivo profiles in malaria are consistent with a novel physiological state.

Wirth D, Daily J, Winzeler E, Mesirov JP, Regev A.

Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):E70; author reply E71-2. Epub 2009 Jul 1. No abstract available.

PMID: 19570993

Identification and characterization of small molecule inhibitors of a class I histone deacetylase from Plasmodium falciparum.

Patel V, Mazitschek R, Coleman B, Nguyen C, Urgaonkar S, Cortese J, Barker RH, Greenberg E, Tang W, Bradner JE, Schreiber SL, Duraisingh MT, Wirth DF, Clardy J.

J Med Chem. 2009 Apr 23;52(8):2185-7.

PMID:19317450

Colorimetric high-throughput screen for detection of heme crystallization inhibitors.

Rush MA, Baniecki ML, Mazitschek R, Cortese JF, Wiegand R, Clardy J, Wirth DF.

Antimicrob Agents Chemother. 2009 Jun;53(6):2564-8. Epub 2009 Mar 23.

PMID:19307367

Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum.

Dharia NV, Sidhu AB, Cassera MB, Westenberger SJ, Bopp SE, Eastman RT, Plouffe D, Batalov S, Park DJ, Volkman SK, Wirth DF, Zhou Y, Fidock DA, Winzeler EA.

Genome Biol. 2009 Feb 13;10(2):R21.

PMID:19216790

Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle.

Sims JS, Militello KT, Sims PA, Patel VP, Kasper JM, Wirth DF.

Eukaryot Cell. 2009 Mar;8(3):327-38. Epub 2009 Jan 16.

PMID:19151330

Type II NADH dehydrogenase of the respiratory chain of Plasmodium falciparum and its inhibitors.

Dong CK, Patel V, Yang JC, Dvorin JD, Duraisingh MT, Clardy J, Wirth DF.

Bioorg Med Chem Lett. 2009 Feb 1;19(3):972-5. Epub 2008 Nov 24.

PMID: 19097788