Carlton Lab
Center for Genomics & Systems Biology



We use the tools of comparative genomics – whole genome sequencing and ‘omics technologies, bioinformatics, molecular biology and population genetics – to study the biology and evolution of several different species of parasite.

Parasites include eukaryotic microbes that cause some of the world’s most devastating diseases. We study species of the malaria parasite Plasmodium, and Trichomonas vaginalis that causes the most common, non-viral, human sexually transmitted infection.

We led the projects to sequence the first reference genomes of Plasmodium falciparum (Gardner et al, Nature, 2002), Plasmodium vivax (Carlton et al, Nature 2008), Plasmodium yoelii (Carlton et al, Nature 2002), Plasmodium cynomolgi  (Tachibana, Nature Genetics, 2012), and the first T. vaginalis genome (Carlton et al, Science, 2007).

We have also characterized the genomes of parasites from hundreds of clinical isolates collected around the globe (Neafsey et al., Nature Genetics, 2012; Hupalo et al., Nature Genetics, 2016; Bradic et al., Genome Biology & Evolution, 2017), as well as urban samples from ATMs, sewage, and the pets and pests of New Yorkers (Bik et al., mSphere, 2016; Maritz et al., PLoS One, 2017; Maritz et al., Microbial Ecology, 2017).

photograph of a baby under a malaria net in a stroller


3.2 billion people live in areas at risk of malaria transmission in 106 countries and territories.


Our research focuses on the genomic epidemiology and evolution of malaria parasites in humans and mosquitoes in India.


A fascinating group of parasites that infect humans, birds, livestock e.g. cattle and pigs, and pets e.g. cats and dogs.


We study the genetic diversity, populatiuon structure and mechanisms of genome plasticity in trichomonads.


The City of New York is home to 8.6 million people on a land mass of 302 sq miles.

NYC Microbiome

Collaborating with New York City officials, we use genomics to characterize urban microbes.


The Carlton Lab loves to sequence microbes! We utilize the latest genomics technology developed by biotech companies Illumina, Oxford Nanopore Technology, Phase Genomics etc., and tweak the protocols and fine-tune the methodology to use out in the real world in New York City and India.


DNA Double helix montage

Current Topics in Biology IV: SARS-COV-2

(BIOL-GA 2008)

The coronavirus SARS-CoV-2 causes COVID-19, a respiratory illness that spread globally during 2020. This course aims to provide students with the skills to read critically and evaluate primary literature articles concerning SARS-CoV-2 evolution, clinical manifestation, epidemiology, and the development of diagnostics, treatments and vaccines, as well as the public health consequences of the pandemic.

Genomics and Global Public Health

(BIOL-GA 2015/GPH-GU 2015)

This course describes the developing relationship between genomics and genomic technologies with the health of populations in a global context.


Current Topics in Biology II: Malaria

(BIOL-GA 2006)

This course describes key concepts in the biology of malaria parasites and their infection of human and mosquito hosts.


Jane Carlton

Julius Silver, Roslyn S. Silver, and Enid Silver Winslow Professor at NYU Department of Biology, Faculty Director of Genomics at the Center for Genomics & Systems Biology, affiliated appointments at NYU College of Global Public Health, NYU School of Medicine, and the American Museum of Natural History.

After graduating with a Ph.D. in Genetics from Edinburgh University in 1995, Professor Carlton took up research positions at the University of Florida, then NCBI at NIH, and then TIGR (The Institute for Genomic Research, founded by J. Craig Venter and Claire Fraser).

Since 2006, her group has been at New York University undertaking research into the biology and evolution of important human parasites. She is Program Director of the Center for the Study of Complex Malaria in India, an NIH-funded International Center of Excellence for Malaria Research. In 2010 she was awarded the Stoll-Stunkard Award from the American Society for Parasitologists; in 2012 she was elected a Fellow of AAAS; and in 2018 she was honored with a Julius Silver, Roslyn S. Silver, and Enid Silver Winslow endowed chair from NYU.

Steve Sullivan

Steven Sullivan

Senior Research Scientist

I'm interested in the peculiarities and evolution of genomes, particularly those of parasites. My research involves identifying families of genes and transposable elements across related parasite species, to investigate how they evolved.
Annie Kessler

Annie Kessler

Associate Research Scientist

As the Program Manager of the CSCMi, I manage all aspects of the Center including personnel coordination, administration, and project development and implementation at NYU and our Indian field sites. My research interests include combining field-based epidemiology and population studies with powerful high-throughput molecular and immunology-based tools to better understand individual and population level disease patterns and pathologies.
Tyler Clabby

Tyler Clabby

Lab Manager

As the Carlton lab manager, I culture malaria and trichomonas parasites, maintain lab supplies, make genomic libraries for sequencing, and extract nucleic acids for PCR and Sanger sequencing. Currently, I am a master's student at NYU focusing on bioinformatics and genomics. The lab's combination of molecular, genomic and evolutionary investigation and use of bioinformatic techniques on natural populations of parasites in real-world settings is a big attraction for me.
Frances Blow

Frances Blow

Postdoctoral Associate

I'm interested in the evolution of host-microbe interactions. I use a combination of molecular, computational and experimental approaches to investigate the evolution of symbiotic and antagonistic traits in host-microbe associations. The current focus of my research is the regulation of transposable elements in Trichomonas vaginalis, and their influence on phenotypic traits.
Francisco Callejas Hernández

Francisco Callejas Hernández

Postdoctoral Associate

My principal interests as a researcher involve functional genomics and transcriptomics of parasites. Using bioinformatics tools, I focus on understanding how these complex organisms are capable of evolving in order to survive adverse environments, infect their hosts, and cause diseases of important human health consequences.
Maansi Jayade

Maansi Jayade

Lab Technician

I am interested in infectious diseases, specifically COVID-19 and its effects on other communicable diseases such as malaria. I also work in the lab as a technician, completing a project to identify and characterize T. stableri and T. vaginalis-like parasites in columbids (pigeons and doves).
Jessica Jimenez

Jessica Jimenez

Lab Technician

My role in the lab is to propagate parasite cultures including P. falciparum and T. vaginalis, while also extracting DNA, making solutions, and generally maintaining the lab. As an NYU Biology Masters student, my research interests lie in developing a diagnostic PCR assay to identify Trichomonas stableri isolated from the throats of band tailed pigeons and other columbids from various wildlife sanctuaries in California.
Maria Nikulkova

Maria Nikulkova

PhD Student

Since undergraduate study, I have been fascinated by 'omics' research and its vast applications to the world of microbiology and beyond. I am interested in using this technology to enhance understanding of different malaria parasites, which are a major health burden. Greater understanding of the functional and genomic differences of these parasites has important applications to public health.
Jordan Orosco

Jordan Orosco

PhD Student

I am interested in understanding the evolutionary forces that have shaped trichomonad parasite diversity as well as their adaptation to new host species. To accomplish this, I am applying population genetic models and statistics to observed patterns of trichomonad genetic variation.
Mari Shiratori

Mari Shiratori

PhD Student

My research interests broadly are in infectious disease, immunology, and public health. I am interested in combining experimental and bioinformatic approaches to better understand host-pathogen dynamics. Currently, I am working on characterizing the pseudocyst form of Trichomonas vaginalis.
Sophie Spector

Sophie Spector

Lab Technician

As a technician in the Carlton Lab, I support wet lab operations such as propagating Trichomonad parasite cultures, performing DNA extractions, and running PCR assays. My interests as an undergraduate student at NYU lie in infectious disease research and global health equity.
Sophie Spector

Harsh Srivastava

PhD Student

I am interested in bringing advancements made in de novo protein design and machine learning to anti-Plasmodium therapeutics. By creating new computational tools, I want to optimize and develop novel protein-based therapies that target an array of Plasmodium antigens. Furthermore, I am interested in investigating the diversity of Plasmodium proteins at various stages in the parasite life cycle to inform better therapeutic design.

Research Scientists

  • Anna Maria van Eijk, 2013-2018
  • Lalitha Ramanathapuram, 2010-2016
  • Sam C. Wassmer, 2012
  • Joana C. Silva, 2003-2006

Postdoctoral Fellows

  • Martina Bradic, 2011-2017
  • Holly Bik, 2015-2016
  • Swapna Uplekar, 2013-2017
  • Susan Joseph, 2013-2015
  • Daniel Hupalo, 2014-2017
  • Pavitra Rao, 2014-2017
  • Patrick Sutton, 2010-2014
  • Ryan Kim, 2011
  • Martine Zilversmit, 2008
  • Shree-Banoo Malik, 2007-2009
  • Simon Kang’a, 2006-2009
  • Fernando Merino, 2006-2009
  • Hangbang Zhang, 2006

PhD Students

  • Julia Maritz, graduated 2018
  • Zunping Luo, graduated 2018
  • Sally Warring, graduated 2017
  • Andrew Gorman, graduated 2015
  • Melissa Conrad, graduated 2013
  • Narayani Kar, graduated 2017
  • Sneh Shalini, graduated 2016
  • Prashant Mallik, graduated 2016
  • Dolie Devi, graduated 2016

Masters Students

  • Morgan Horner, 2019
  • Jessica Jimenez, 2018-2019
  • Theresa Ten Eyck, 2016
  • Jonathan Bermeo, 2016
  • Vivien Low, 2013

MPH Students

  • Hassan Funchess, 2020
  • Shahzeb Khan, 2020
  • Natsumi Nemoto, 2019
  • Sarah Barns, 2019
  • Asad Mannan, 2017/2018
  • Emily Lam, 2017
  • Ingrid Zambrano, 2016/17

Undergraduate Students

Krystal Sotolongo 2008 (SURP awardee), Alice Ford 2009 (SURP awardee), Mark Jelcic 2009, Kevin Dell’Aquila 2011 (DURF awardee), Kharisa Rachmasari 2012 (NYUAD), Grace Tooley 2013-2015 (2 times GURF awardee), Elisha Wang 2013 (DURF awardee, Roger and Beth Carlton Research Scholar for 2014, recipient of the Chair's Biology Award at the CAS Dean's Awards Ceremony), Sarah Batbold 2014/15 (summer research fellow and Capstone project, NYUAD), Dhriti Tandon 2015, Stephen Coyle 2015, Aaron Dank 2016/17, Aditya Bhagirath 2016 (SURP fellow), Giovanni Cervine 2017/18, Justin Huang 2017/18, Kaitlyn Julian 2019


Sven Rosandic, 2016; Volney French, 2013; Emre Aksoy, 2011

Lab Managers

Shipra Mittal, Priyanka Ganesh, Amanda Heim, Rebecca Susko, Shelby Bidwell


The list below represents a selection of key publications from the lab over the past decade.
You can also find our publications in NCBI PubMed and Google Scholar.
Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax
Hupalo DN, et al., Nat Genet. 2016 Aug;48(8):953-8.
Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade
Tachibana S, et al Nat Genet. 2012 Sep;44(9):1051-5
Comparative Genomics of the Neglected Human Malaria Parasite Plasmodium vivax
Carlton JM, et al., Nature. 2008 Oct 9;455(7214):757-63.

Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis
Carlton J. et al., Science. 2007 Jan 12;315(5809):207-12.
Genome Sequence and Comparative Analysis of the Model Rodent Malaria parasite Plasmodium yeolii yeolii
Carlton JM, et al., Nature. 2002 Oct 3;419(6906):512-9
Getting trichy: tools and approaches to interrogating Trichomonas vaginalis in a post-genome world.
Conrad MD, et al., Trends Parasitol. 2013 Jan 29; (1):17-25


Selected articles, reports, events and other media coverage about Carlton Lab.
"What Our Sewage Can Teach Us"
New York Times
Dogs Do Their Duty for Science
Pet City, Andy Newman, New York Times
Researchers Uncover Global Evolving and Historic Make up of Malaria Species


Determining the Origins of Repeat Trichomonas vaginalis Infections Using Clinical Versus Genotype-Informed Criteria.

Cover of Cornucopia paper.

PUBLISHED Commentary by Jane on the Fourth Rodent Malaria Parasite – With Special Acknowledgment to Malaria Technicians

A cornucopia of research resources for the fourth rodent malaria parasite species.

Sally Warring

By PhD student Sally Warring

Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis.


The burden of asymptomatic and submicroscopic malaria in India.


Patterns of protist diversity associated with raw sewage in New York City.


Carlton Lab
Center for Genomics & Systems Biology

New York University, Department of Biology, 12 Waverly Place