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Carlton Lab
Center for Genomics & Systems Biology

USING GENOMICS TO STUDY THE BIOLOGY AND EVOLUTION OF PARASITES
IN ORDER TO DEVELOP BETTER METHODS FOR THEIR SURVEILLANCE AND CONTROL

Research

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

MALARIA WORDLWIDE

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

Malaria

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

TRICHOMONADS

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

TRICHOMONADS

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

NYC MICROBIOME

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.

Technology

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.

Teaching

DNA Double helix montage

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.


People

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.
Julia Maritz

Julia Maritz

Postdoctoral Associate

I am passionate about metagenomics and the power this technology has to yield practical insights for the sustainability of urban areas, the health of human populations, and our impact on natural ecosystems. My research involves sequencing microbial communities, with an emphasis on microbial eukaryotes, in the five boroughs of New York City including on circulating paper currency, ATM buttons, raw sewage, and human pets (cat, dog) and pests (rat, pigeon, cockroach).
Tobi Schraink

Tobi Schraink

PhD Student

I am interested in how mutations are acquired in malaria parasites and how they can influence resistance of the parasite to antimalarial drugs as well as its interaction with the human host. To this end I leverage publically-available whole genome sequence data as well as genetic data from patient samples collected at field sites of the CSCMi and from other International Centers of Excellence in Malaria Research.
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.
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.

Research Scientists

  • 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

  • Theresa Ten Eyck, 2016
  • Jonathan Bermeo, 2016
  • Vivien Low, 2013

MPH Students

  • 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

Volunteers/interns

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

Lab Managers

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

PUBLICATIONS

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

MEDIA and EVENTS

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

NYC MICROBIOME 1-DAY SYMPOSIUM
HOSTED BY CARLTON LAB AND NYC DEPT. HEALTH
FRIDAY OCTOBER 12, 2018

It's a Brave New World: The Applications, Promise, and Public Implications of Metagenomics in Urban Settings

NEW CARLTON LAB MALARIA PUBLICATION
FEATURED ARTICLE ON THE MALARIA JOURNAL WEBSITE
NOVEMBER 2018

Malaria in Meghalaya: a systematic literature review and analysis of data from the National Vector-Borne Disease Control Programme.

NEW CARLTON LAB TRICHOMONAS PUBLICATION
WITH COLLABORATORS DRS. PATTY KISSINGER AND DAVID MARTIN LANCET INFECTIOUS DISEASES
OCTOBER 2018

Single-dose versus 7-day-dose metronidazole for the treatment of trichomoniasis in women: an open-label, randomised controlled trial.

Au Revoir Dr. Julia Maritz!!

Julia, who worked for 6 months as a postdoc after graduating with her PhD from the Carlton Lab, left November 2018 to join Merck Research Labs in Boston. Good luck Julia!

PhD Student Tobi Schraink Gave Oral Presentation at Genomic Epidemiology of Malaria Conference, Wellcome Trust Sanger Institute, England, June 2018

Tobi presented former Carlton Lab PhD student Zunping Luo's work using ONTs' MinION sequencer at one of our field sites in India.


Contact

Carlton Lab
Center for Genomics & Systems Biology

Address
New York University, Department of Biology, 12 Waverly Place
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