Jane Carlton

Professor of Biology; Director, Center for Genomics and Systems Biology


Areas of Research/Interest

Comparative genomics of eukaryotic microbes (protists); genomics and global public health


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



  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.


External Affiliations

Research Associate, American Museum of Natural History

Adjunct Professor, Dept of Microbiology, NYU School of Medicine



    • PubMed Search Criteria: Carlton, Jane
    • Search Date: June 11 2017

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads.
Microb Ecol (2017 May 24) PMID: 28540488
Maritz JM, Rogers KH, Rock TM, Liu N, Joseph S, Land KM, Carlton JM

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City.
PLoS One (2017) PMC5383295 free full-text archive
Maritz JM, Sullivan SA, Prill RJ, Aksoy E, Scheid P, Carlton JM

A Feast of Malaria Parasite Genomes.
Cell Host Microbe (2017 Mar 08) PMID: 28279339
Carlton JM, Sullivan SA

Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays.
PLoS Negl Trop Dis (2017 Jan) PMC5291533 free full-text archive
Uplekar S, Rao PN, Ramanathapuram L, Awasthi V, Verma K, Sutton P, Ali SZ, Patel A, G SL, Ravishankaran S, Desai N, Tandel N, Choubey S, Barla P, Kanagaraj D, Eapen A, Pradhan K, Singh R, Jain A, Felgner PL, Davies DH, Carlton JM, Das J

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City.
mSphere (2016 Nov-Dec) PMC5112336 free full-text archive
Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM

The use of mosquito repellents at three sites in India with declining malaria transmission: surveys in the community and clinic.
Parasit Vectors (2016 Jul 27) PMC4963934 free full-text archive
van Eijk AM, Ramanathapuram L, Sutton PL, Peddy N, Choubey S, Mohanty S, Asokan A, Ravishankaran S, Priya GS, Johnson JA, Velayutham S, Kanagaraj D, Patel A, Desai N, Tandel N, Sullivan SA, Wassmer SC, Singh R, Pradhan K, Carlton JM, Srivasatava HC, Eapen A, Sharma SK

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax.
Nat Genet (2016 Aug) PMC5347536 free full-text archive
Hupalo DN, Luo Z, Melnikov A, Sutton PL, Rogov P, Escalante A, Vallejo AF, Herrera S, Arevalo-Herrera M, Fan Q, Wang Y, Cui L, Lucas CM, Durand S, Sanchez JF, Baldeviano GC, Lescano AG, Laman M, Barnadas C, Barry A, Mueller I, Kazura JW, Eapen A, Kanagaraj D, Valecha N, Ferreira MU, Roobsoong W, Nguitragool W, Sattabonkot J, Gamboa D, Kosek M, Vinetz JM, Gonzalez-Ceron L, Birren BW, Neafsey DE, Carlton JM

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
Cell Syst (2015 Jul 29) PMID: 27135689
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Henaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE

Modern Methods for Delineating Metagenomic Complexity.
Cell Syst (2015 Jul 29) PMID: 27135684
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Henaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE

A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India.
J Clin Microbiol (2016 Jun) PMC4879288 free full-text archive
Rao PN, Uplekar S, Kayal S, Mallick PK, Bandyopadhyay N, Kale S, Singh OP, Mohanty A, Mohanty S, Wassmer SC, Carlton JM

Comparative assessment on the prevalence of mutations in the Plasmodium falciparum drug-resistant genes in two different ecotypes of Odisha state, India.
Infect Genet Evol (2016 Jul) PMC4868809 free full-text archive
Kar NP, Chauhan K, Nanda N, Kumar A, Carlton JM, Das A

Characterizing the genetic diversity of the monkey malaria parasite Plasmodium cynomolgi.
Infect Genet Evol (2016 Jun) PMC4844884 free full-text archive
Sutton PL, Luo Z, Divis PC, Friedrich VK, Conway DJ, Singh B, Barnwell JW, Carlton JM, Sullivan SA

What is the value of reactive case detection in malaria control? A case-study in India and a systematic review.
Malar J (2016 Feb 06) PMC4744450 free full-text archive
van Eijk AM, Ramanathapuram L, Sutton PL, Kanagaraj D, Sri Lakshmi Priya G, Ravishankaran S, Asokan A, Tandel N, Patel A, Desai N, Singh R, Sullivan SA, Carlton JM, Srivastava HC, Eapen A

Glycophorins, Blood Groups, and Protection from Severe Malaria.
Trends Parasitol (2016 Jan) PMC4713327 free full-text archive
Wassmer SC, Carlton JM

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
Cell Syst (2015 Jul 29) PMC4651444 free full-text archive
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Henaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE

Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network.
Am J Trop Med Hyg (2015 Sep) PMC4574277 free full-text archive
Escalante AA, Ferreira MU, Vinetz JM, Volkman SK, Cui L, Gamboa D, Krogstad DJ, Barry AE, Carlton JM, van Eijk AM, Pradhan K, Mueller I, Greenhouse B, Pacheco MA, Vallejo AF, Herrera S, Felger I

Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research.
Am J Trop Med Hyg (2015 Sep) PMC4574278 free full-text archive
Carlton JM, Volkman SK, Uplekar S, Hupalo DN, Pereira Alves JM, Cui L, Donnelly M, Roos DS, Harb OS, Acosta M, Read A, Ribolla PE, Singh OP, Valecha N, Wassmer SC, Ferreira M, Escalante AA

The biology of Plasmodium vivax explored through genomics.
Ann N Y Acad Sci (2015 Apr) PMC4405435 free full-text archive
Luo Z, Sullivan SA, Carlton JM

The impact of genomics on population genetics of parasitic diseases.
Curr Opin Microbiol (2015 Feb) PMC4323873 free full-text archive
Hupalo DN, Bradic M, Carlton JM

What is the importance of zoonotic trichomonads for human health?
Trends Parasitol (2014 Jul) PMID: 24951156
Maritz JM, Land KM, Carlton JM, Hirt RP

A review of malaria transmission dynamics in forest ecosystems.
Parasit Vectors (2014 Jun 09) PMC4057614 free full-text archive
Kar NP, Kumar A, Singh OP, Carlton JM, Nanda N

The origin and diversification of the merozoite surface protein 3 (msp3) multi-gene family in Plasmodium vivax and related parasites.
Mol Phylogenet Evol (2014 Sep) PMC4406276 free full-text archive
Rice BL, Acosta MM, Pacheco MA, Carlton JM, Barnwell JW, Escalante AA

The Tc1/mariner transposable element family shapes genetic variation and gene expression in the protist Trichomonas vaginalis.
Mob DNA (2014) PMC4021607 free full-text archive
Bradic M, Warring SD, Low V, Carlton JM

Chloroquine efficacy studies confirm drug susceptibility of Plasmodium vivax in Chennai, India.
Malar J (2014 Mar 31) PMC4021252 free full-text archive
Shalini S, Chaudhuri S, Sutton PL, Mishra N, Srivastava N, David JK, Ravindran KJ, Carlton JM, Eapen A

Vaccines against sexually transmitted infections: the way forward.
Vaccine (2014 Mar 20) PMID: 24480024
Broutet N, Fruth U, Deal C, Gottlieb SL, Rees H

Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.
PLoS Negl Trop Dis (2013) PMC3777877 free full-text archive
Prajapati SK, Joshi H, Carlton JM, Rizvi MA

Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum.
Infect Genet Evol (2013 Oct) PMC3799960 free full-text archive
Mallick PK, Sutton PL, Singh R, Singh OP, Dash AP, Singh AK, Carlton JM, Bhasin VK

Ahead of the curve: next generation estimators of drug resistance in malaria infections.
Trends Parasitol (2013 Jul) PMC3694767 free full-text archive
Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF

Genetic diversity in Trichomonas vaginalis.
Sex Transm Infect (2013 Sep) PMID: 23702460
Meade JC, Carlton JM

Genetic diversity of Trichomonas vaginalis reinfection in HIV-positive women.
Sex Transm Infect (2013 Sep) PMC3755760 free full-text archive
Conrad MD, Kissinger P, Schmidt N, Martin DH, Carlton JM

Genomics, population genetics and evolutionary history of Plasmodium vivax.
Adv Parasitol (2013) PMID: 23384624
Carlton JM, Das A, Escalante AA

Getting trichy: tools and approaches to interrogating Trichomonas vaginalis in a post-genome world.
Trends Parasitol (2013 Jan) PMC3534864 free full-text archive
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) PMC3458234 free full-text archive
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) PMC3759362 free full-text archive
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) PMC3432710 free full-text archive
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) PMC3313929 free full-text archive
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 Jan 31) PMC3342920 free full-text archive
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) PMC3294179 free full-text archive
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) PMC3694397 free full-text archive
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) PMC3125139 free full-text archive
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) PMC3111441 free full-text archive
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 02) PMC3150948 free full-text archive
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) PMC3081533 free full-text archive
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) PMC2974001 free full-text archive
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) PMID: 20580212
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 Apr 06) PMC2850316 free full-text archive
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) PMID: 19695492
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) PMC2787103 free full-text archive
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) PMC2665121 free full-text archive
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 Dec 08) PMC2655098 free full-text archive
Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC

Comparative evolutionary genomics of human malaria parasites.
Trends Parasitol (2008 Dec) PMID: 18938107
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) PMC2571024 free full-text archive
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 09) PMC2651158 free full-text archive
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) PMC2686445 free full-text archive
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) PMID: 18403267
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) PMC2386084 free full-text archive
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 Feb 13) PMC2215772 free full-text archive
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) PMID: 17442318
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 01) PMID: 17330781
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) PMC2080659 free full-text archive
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) PMID: 17192778
Carlton JM

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
PLoS Biol (2006 Sep) PMC1557398 free full-text archive
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) PMC1431722 free full-text archive
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) PMC1317653 free full-text archive
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) PMID: 16182520
Hall N, Carlton J

Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis.
Mol Biochem Parasitol (2005 Oct) PMID: 16099517
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) PMID: 16085323
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) PMID: 16020724
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 01) PMID: 15994558
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) PMID: 15864779
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) PMID: 15858201
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) PMC554003 free full-text archive
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 07) PMID: 15637271
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) PMID: 15602564
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) PMID: 15580778
Carlton J, Silva J, Hall N

Gene synteny and chloroquine resistance in Plasmodium chabaudi.
Mol Biochem Parasitol (2004 Aug) PMID: 15478795
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) PMC1406841 free full-text archive
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) PMID: 15105016
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) PMC356014 free full-text archive
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) PMID: 14668009
Hunt P, Cravo PV, Donleavy P, Carlton JM, Walliker D

Genome sequencing and comparative genomics of tropical disease pathogens.
Cell Microbiol (2003 Dec) PMID: 14641172
Carlton JM

Identification of a polymorphic Plasmodium vivax microsatellite marker.
Am J Trop Med Hyg (2003 Oct) PMC3728893 free full-text archive
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) PMID: 14550891
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 08) PMC166258 free full-text archive
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) PMID: 12763429
Carlton J

Genetics of mefloquine resistance in the rodent malaria parasite Plasmodium chabaudi.
Antimicrob Agents Chemother (2003 Feb) PMC151772 free full-text archive
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 03) PMID: 12368868
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 03) PMID: 12368865
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 03) PMC3836256 free full-text archive
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 01) PMC117189 free full-text archive
Delcher AL, Phillippy A, Carlton J, Salzberg SL

The shikimate pathway and its branches in apicomplexan parasites.
J Infect Dis (2002 Feb 15) PMID: 11865437
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) PMID: 11854077
Carlton JM, Carucci DJ