Department of Biology

Jane Carlton

Lab Homepage: 

http://carltonlab.bio.nyu.edu

Research:

In the Carlton lab, we use the tools of comparative genomics – whole genome sequencing and genomics, bioinformatics, molecular biology and population genetics – to study the biology and evolution of closely related strains or species of parasite. In medicine and global public health, the term parasite is used to describe a group of eukaryotic microbes and helminths that cause some of the world’s most devastating diseases. The parasites that we study include:

(1) Species of the malaria parasite Plasmodium: more than half the world’s population is at risk from malaria, and the disease causes ~216 million cases and ~655,000 deaths per year. The most deadly form of the parasite, Plasmodium falciparum, is found mostly in sub-Saharan Africa where it causes the deaths of children < 5 years old. Plasmodium vivax is the most common species outside Africa in South America and Southeast Asia, and is closely related to a group of species that infect Asian Old World monkeys from Taiwan to Sri Lanka, called the monkey malaria clade.

Map of malaria distribution. Picture Credit: World Malaria Report 2005

(2) The sexually transmitted parasite Trichomonas vaginalis and related trichomonads: T. vaginalis is the most common non-viral STI, and causes ~249 million cases per year world-wide. It is associated with increased risk of HIV-1 infection, and serious complications during pregnancy. Other trichomonads include Trichomonas tenax found in the mouth, Pentatrichomonas hominis a zoonotic gut parasite, and Tritrichomonas foetus a serious venereal pathogen that causes abortion in cattle.

T. vaginalis parasites adhering to pink vaginal tissue.Image courtesy of Antonio Pereira-Neves and Marlene Benchimol, Santa Ursula University, Rio de Janeiro, Brazil

(3) Other fascinating parasites such as species of the enteric pathogen Cryptosporidium, the bovine parasite Theileria, and Babesia.

Our research often begins with generation of a resource such as sequencing, assembly and annotation of a parasite’s genome. For example, we have been involved in the sequencing of P. falciparum [1], species of rodent malaria (Plasmodium yoelii yoelii [2], Plasmodium chabaudi chabaudi and Plasmodium berghei [3]), several strains of P. vivax [4, 5], several strains of the monkey malaria Plasmodium cynomolgi [6], and the first T. vaginalis genome [7].

Sequencing the genome of a parasite enables the complete gene and protein repertoire to be identified and provides a wealth of data about the basic biology of that organism, leading to hypothesis-driven studies. Generating sequences of multiple strains or species enables studies of whole genome evolution, genetic diversity and population genetics/genomics. Some of the research areas that members of the Carlton lab undertake in these areas include:

• Developing polymorphic genetic markers from sequenced genomes to determine the genetic diversity and population structure of extant parasites, or for association mapping of parasite traits, for example:
• genetic diversity and population structure of T. vaginalis in New York City STD clinics
• identifying genetic determinants of metronidazole resistance in T. vaginalis
• developing a global genetic diversity map of P. vivax
• population genetics of P. cynomolgi in Southeast Asia
• genetic epidemiology of P. falciparum and P. vivax in India
• Using molecular and cell biology to investigate the presence, function and mechanism of groups of genes identified in a parasite’s genome sequence, for example:
• determining the function of meiosis-specific genes in nominally asexual T. vaginalis
• function and evolution of transposable element families in species of trichomonad
• prevalence, diversity and function of the TVV virus in T. vaginalis

Since many of the parasites we work on are important global public health problems in lower and middle income countries as well as poor regions of the United States, we collaborate with researchers and clinicians who work in public health clinics in order to move our research from the bench to the field. Some examples of our collaborations include:

• Center for the Study of Complex Malaria in India, with the National Institute of Malaria Research of the Indian Council of Medical Research, New Delhi
• Population genetics of T. vaginalis in India, with Professor Nancy Malla, PGMRI, India
• T. vaginalis repeat infections among HIV negative women, with Dr Patty Kissinger, Tulane University of Louisiana
• Development of new T. vaginalis diagnostic tests with BioHelix, Atlas Genetics and PATH

Footnotes:

1. Gardner, M.J., et al., Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 2002. 419(6906): p. 498-511.
2. Carlton, J.M., et al., Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature, 2002. 419(6906): p. 512-9.
3. Hall, N., et al., A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science, 2005. 307(5706): p. 82-6.
4. Carlton, J.M., et al., Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature, 2008. 455(7214): p. 757-63.
5. Neafsey, D.E., et al., The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet, 2012. 44(9): p. 1046-50.
6. Tachibana, S., et al., Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade. Nat Genet, 2012. 44(9): p. 1051-5.
7. Carlton, J.M., et al., Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. Science, 2007. 315(5809): p. 207-212.

Genomics, population genetics and evolutionary history of Plasmodium vivax. Adv Parasitol   (2013) Carlton JM, Das A, Escalante AA

Getting trichy: tools and approaches to interrogating Trichomonas vaginalis in a post-genome world. Trends Parasitol   (2013 Jan) Conrad MD, Bradic M, Warring SD, Gorman AW, Carlton JM

Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Sex Transm Dis   (2012 Oct) Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J

Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade. Nat Genet   (2012 Sep) Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, Goto N, Arisue N, Palacpac NM, Honma H, Yagi M, Tougan T, Katakai Y, Kaneko O, Mita T, Kita K, Yasutomi Y, Sutton PL, Shakhbatyan R, Horii T, Yasunaga T, Barnwell JW, Escalante AA, Carlton JM, Tanabe K

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet   (2012 Sep) Neafsey DE, Galinsky K, Jiang RH, Young L, Sykes SM, Saif S, Gujja S, Goldberg JM, Young S, Zeng Q, Chapman SB, Dash AP, Anvikar AR, Sutton PL, Birren BW, Escalante AA, Barnwell JW, Carlton JM

Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis. PLoS Negl Trop Dis   (2012) Conrad MD, Gorman AW, Schillinger JA, Fiori PL, Arroyo R, Malla N, Dubey ML, Gonzalez J, Blank S, Secor WE, Carlton JM

The complexities of malaria disease manifestations with a focus on asymptomatic malaria. Malar J   (2012) Laishram DD, Sutton PL, Nanda N, Sharma VL, Sobti RC, Carlton JM, Joshi H

Malaria in India: the center for the study of complex malaria in India. Acta Trop   (2012 Mar) Das A, Anvikar AR, Cator LJ, Dhiman RC, Eapen A, Mishra N, Nagpal BN, Nanda N, Raghavendra K, Read AF, Sharma SK, Singh OP, Singh V, Sinnis P, Srivastava HC, Sullivan SA, Sutton PL, Thomas MB, Carlton JM, Valecha N

The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms. Ann N Y Acad Sci   (2011 Aug) Reed DL, Currier RW, Walton SF, Conrad M, Sullivan SA, Carlton JM, Read TD, Severini A, Tyler S, Eberle R, Johnson WE, Silvestri G, Clarke IN, Lagergard T, Lukehart SA, Unemo M, Shafer WM, Beasley RP, Bergstrom T, Norberg P, Davison AJ, Sharp PM, Hahn BH, Blomberg J

Why is Plasmodium vivax a neglected tropical disease? PLoS Negl Trop Dis   (2011 Jun) Carlton JM, Sina BJ, Adams JH

Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene. PLoS One   (2011) Malik SB, Brochu CD, Bilic I, Yuan J, Hess M, Logsdon JM Jr, Carlton JM

Linkage maps from multiple genetic crosses and loci linked to growth-related virulent phenotype in Plasmodium yoelii. Proc Natl Acad Sci U S A   (2011 Aug 2) Li J, Pattaradilokrat S, Zhu F, Jiang H, Liu S, Hong L, Fu Y, Koo L, Xu W, Pan W, Carlton JM, Kaneko O, Carter R, Wootton JC, Su XZ

Genome sequences reveal divergence times of malaria parasite lineages. Parasitology   (2011 Nov) Silva JC, Egan A, Friedman R, Munro JB, Carlton JM, Hughes AL

Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite. Mol Biochem Parasitol   (2011 Jan) Conrad M, Zubacova Z, Dunn LA, Upcroft J, Sullivan SA, Tachezy J, Carlton JM

Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. Artif Intell Med   (2010 Jul) Mitrofanova A, Kleinberg S, Carlton J, Kasif S, Mishra B

A systems-based analysis of Plasmodium vivax lifecycle transcription from human to mosquito. PLoS Negl Trop Dis   (2010) Westenberger SJ, McClean CM, Chattopadhyay R, Dharia NV, Carlton JM, Barnwell JW, Collins WE, Hoffman SL, Zhou Y, Vinetz JM, Winzeler EA

Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria parasite. Lancet Infect Dis   (2009 Sep) Mueller I, Galinski MR, Baird JK, Carlton JM, Kochar DK, Alonso PL, del Portillo HA

Hundreds of microsatellites for genotyping Plasmodium yoelii parasites. Mol Biochem Parasitol   (2009 Aug) Li J, Zhang Y, Liu S, Hong L, Sullivan M, McCutchan TF, Carlton JM, Su XZ

Carotenoid biosynthesis in intraerythrocytic stages of Plasmodium falciparum. J Biol Chem   (2009 Apr 10) Tonhosolo R, D'Alexandri FL, de Rosso VV, Gazarini ML, Matsumura MY, Peres VJ, Merino EF, Carlton JM, Wunderlich G, Mercadante AZ, Kimura EA, Katzin AM

IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics   (2008) Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC

Comparative evolutionary genomics of human malaria parasites. Trends Parasitol   (2008 Dec) Carlton JM, Escalante AA, Neafsey D, Volkman SK

The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites. Proc Natl Acad Sci U S A   (2008 Oct 21) Bozdech Z, Mok S, Hu G, Imwong M, Jaidee A, Russell B, Ginsburg H, Nosten F, Day NP, White NJ, Carlton JM, Preiser PR

Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature   (2008 Oct 9) Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res   (2009 Jan) Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H

Plasmodium vivax in India. Trends Parasitol   (2008 May) Joshi H, Prajapati SK, Verma A, Kang'a S, Carlton JM

Local adaptation and vector-mediated population structure in Plasmodium vivax malaria. Mol Biol Evol   (2008 Jun) Joy DA, Gonzalez-Ceron L, Carlton JM, Gueye A, Fay M, McCutchan TF, Su XZ

Evidence-based annotation of the malaria parasite's genome using comparative expression profiling. PLoS One   (2008) Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA

Contrasting genetic structure in Plasmodium vivax populations from Asia and South America. Int J Parasitol   (2007 Jul) Imwong M, Nair S, Pukrittayakamee S, Sudimack D, Williams JT, Mayxay M, Newton PN, Kim JR, Nandy A, Osorio L, Carlton JM, White NJ, Day NP, Anderson TJ

Relapses of Plasmodium vivax infection usually result from activation of heterologous hypnozoites. J Infect Dis   (2007 Apr 1) Imwong M, Snounou G, Pukrittayakamee S, Tanomsing N, Kim JR, Nandy A, Guthmann JP, Nosten F, Carlton J, Looareesuwan S, Nair S, Sudimack D, Day NP, Anderson TJ, White NJ

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science   (2007 Jan 12) Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ

Toward a malaria haplotype map. Nat Genet   (2007 Jan) Carlton JM

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol   (2006 Sep) Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol   (2006) Sargeant TJ, Marti M, Caler E, Carlton JM, Simpson K, Speed TP, Cowman AF

A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes. PLoS Pathog   (2005 Dec) Kooij TW, Carlton JM, Bidwell SL, Hall N, Ramesar J, Janse CJ, Waters AP

Comparative genomics of malaria parasites. Curr Opin Genet Dev   (2005 Dec) Hall N, Carlton J

Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis. Mol Biochem Parasitol   (2005 Oct) Lal K, Field MC, Carlton JM, Warwicker J, Hirt RP

Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Mol Biochem Parasitol   (2005 Nov) Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JM

Comparative genomics of trypanosomatid parasitic protozoa. Science   (2005 Jul 15) El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science   (2005 Jul 1) Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V

Immune responses to Plasmodium vivax pre-erythrocytic stage antigens in naturally exposed Duffy-negative humans: a potential model for identification of liver-stage antigens. Eur J Immunol   (2005 Jun) Wang R, Arevalo-Herrera M, Gardner MJ, Bonelo A, Carlton JM, Gomez A, Vera O, Soto L, Vergara J, Bidwell SL, Domingo A, Fraser CM, Herrera S

Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol Biol Evol   (2005 Aug) Mu J, Joy DA, Duan J, Huang Y, Carlton J, Walker J, Barnwell J, Beerli P, Charleston MA, Pybus OG, Su XZ

Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. Proc Natl Acad Sci U S A   (2005 Mar 22) Vanacova S, Yan W, Carlton JM, Johnson PJ

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science   (2005 Jan 7) Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature   (2004 Dec 16) Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N

The genome of model malaria parasites, and comparative genomics. Curr Issues Mol Biol   (2005 Jan) Carlton J, Silva J, Hall N

Gene synteny and chloroquine resistance in Plasmodium chabaudi. Mol Biochem Parasitol   (2004 Aug) Hunt P, Martinelli A, Fawcett R, Carlton J, Carter R, Walliker D

A potentially functional mariner transposable element in the protist Trichomonas vaginalis. Mol Biol Evol   (2005 Jan) Silva JC, Bastida F, Bidwell SL, Johnson PJ, Carlton JM

Mind the gap: bridging the divide between clinical and molecular studies of the trichomonads. Trends Parasitol   (2004 May) Lyons EJ, Carlton JM

Novel antigen identification method for discovery of protective malaria antigens by rapid testing of DNA vaccines encoding exons from the parasite genome. Infect Immun   (2004 Mar) Haddad D, Bilcikova E, Witney AA, Carlton JM, White CE, Blair PL, Chattopadhyay R, Russell J, Abot E, Charoenvit Y, Aguiar JC, Carucci DJ, Weiss WR

Chloroquine resistance in Plasmodium chabaudi: are chloroquine-resistance transporter (crt) and multi-drug resistance (mdr1) orthologues involved? Mol Biochem Parasitol   (2004 Jan) Hunt P, Cravo PV, Donleavy P, Carlton JM, Walliker D

Genome sequencing and comparative genomics of tropical disease pathogens. Cell Microbiol   (2003 Dec) Carlton JM

Identification of a polymorphic Plasmodium vivax microsatellite marker. Am J Trop Med Hyg   (2003 Oct) Gomez JC, McNamara DT, Bockarie MJ, Baird JK, Carlton JM, Zimmerman PA

Plasmepsin 4, the food vacuole aspartic proteinase found in all Plasmodium spp. infecting man. Mol Biochem Parasitol   (2003 Aug 11) Dame JB, Yowell CA, Omara-Opyene L, Carlton JM, Cooper RA, Li T

Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proc Natl Acad Sci U S A   (2003 Jul 8) Feng X, Carlton JM, Joy DA, Mu J, Furuya T, Suh BB, Wang Y, Barnwell JW, Su XZ

The Plasmodium vivax genome sequencing project. Trends Parasitol   (2003 May) Carlton J

Genetics of mefloquine resistance in the rodent malaria parasite Plasmodium chabaudi. Antimicrob Agents Chemother   (2003 Feb) Cravo PV, Carlton JM, Hunt P, Bisoni L, Padua RA, Walliker D

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature   (2002 Oct 3) Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, Granger D, Fujii C, Hansen C, Pederson J, Feldblyum T, Peterson J, Suh B, Angiuoli S, Pertea M, Allen J, Selengut J, White O, Cummings LM, Smith HO, Adams MD, Venter JC, Carucci DJ, Hoffman SL, Fraser CM

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature   (2002 Oct 3) Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature   (2002 Oct 3) Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B

Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res   (2002 Jun 1) Delcher AL, Phillippy A, Carlton J, Salzberg SL

The shikimate pathway and its branches in apicomplexan parasites. J Infect Dis   (2002 Feb 15) Roberts CW, Roberts F, Lyons RE, Kirisits MJ, Mui EJ, Finnerty J, Johnson JJ, Ferguson DJ, Coggins JR, Krell T, Coombs GH, Milhous WK, Kyle DE, Tzipori S, Barnwell J, Dame JB, Carlton J, McLeod R

Rodent models of malaria in the genomics era. Trends Parasitol   (2002 Mar) Carlton JM, Carucci DJ