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research areas

Students interested in research mentioned below or on the Publications page, please contact us for research opportunities. We are involved in field work, laboratory analyses, and computation. Evolution is the driving force behind everything in our research. We are not limited by one single organism, but study members of all domains of life from retroviruses to bacteria, vertebrates to seed plants.

Bacterial phylogenomics


High-throughput sequencing technologies are opening the door to large-scale collection of prokaryotic genome sequence data. We are investigating genome-wide patterns of phylogenetic agreement and incongruence to understand and quantify the evolutionary heterogeneity of different genome segments and gene families in various bacterial phyla. We are applying this framework in conjunction with phylodynamics and selection pressure scans to understand the molecular epidemiology and adaption in infectious pathogens, e.g. Mycobacterium tuberculosis, Staphylococcus aureus. In collaboration with Paul Planet (CHOP), Barun Mathema (Columbia U), Barry Kreiswirth (Rutgers U), and Apurva Narechania (AMNH). 


In a parallel line of research we are examining the dynamics of expansion and contraction of bacterial gene families in the light of newly established phylogenetic backgrounds based on finished genomes and novel algorithmic implementations – in collaboration with Julio Rozas (U Barcelona), funded by the Spanish ex Ministry of Science & Innovation.


Disease vector molecular ecology


Prevalence of tick-borne pathogens varies across and within regions. We are using as a model system the blacklegged tick (Ixodes scapularis), the pathogens it transmits, and the major Lyme disease reservoir – the white-footed mouse (Peromyscus leucopus) – to understand how disease prevalence and coinfection vary spatio-temporally by utilizing a suite of tools ranging from spatial and ecological modeling to molecular diagnostics, phylogeography and population genetics, as well as transcriptomics and microbial community metabarcoding and metagenomics.


We work very closely with Maria Diuk-Wasser (Columbia U) and Fordham's Vector Ecology Lab at the Calder Center (Armonk, NY).

Plant evolutionary genomics


We work on various aspects of evolutionary and comparative genomics of the seed plants. We are part of the NSF-funded New York Plant Genomics Consortium. Our interests are geared towards gymnosperms for genome and transcriptome sequencing. We also participate in the development of computational tools for phylogenetic analysis of large genomes and their gene families, e.g. OrthologID, RADICAL.


Recently, we started working on comparative transcriptomics of Selaginella spike mosses with NYBG's Barbara Ambrose trying to unravel the evolutionary origin of tissue diversification and cell programming.

Virus evolution


RNA viruses offer a unique way to study evolution. We have been working on endogenous and exogenous retroviruses, e.g. St. Louis Encephalitis Virus, Feline Leukemia Virus, Koala Retrovirus, Gibbon Ape Leukemia Virus, in collaboration with Alex Greenwood (Leibniz Inst, Berlin) and Al Roca (U Illinois, Urbana-Champaign) focusing on temporal diversification patterns and selective pressure detection as they relate to viral protein function. We make full use of natural history collections and archival specimens, as well as ancient DNA techniques.


Prior work includes a phylogenetic characterization of the low-pathogenicity avian influenza virus subtypes circulating in the US – collaboration with Toni Piaggio (USDA). Recently, we started mining the koala genome trying to uncover the antiretroviral repertoire.

Urban biodiversity


The city's highly urbanized environment harbors a mixture of naturally-occuring and introduced or invasive species. We use genetic and metagenomic tools to understand how urbanization affects the distribution and adaptive potential of organisms in the city. We are building a map of the genetic variation among bed bug populations in NYC in an attempt to understand the dynamics of infestation. We are also involved in the Bed Bug Genome Project, where we use a combination of -omic tools. In collaboration with Rob Dunn (NCSU) we have been characterizing the genetic diversity of ants in the city. 


We are using passerine bird species as a system to understand the effects of the urban vs. rural lifestyle with respect to blood parasites and microbiomes.


Free-living microbes are a poorly understood portion of urban biodiversity. In a city-wide collaboration with Chris Mason (Cornell Med) and Jane Carlton (NYU) we investigate the microbial communities colonizing the built environment (PathoMap project). We have become very interested in urban "extreme" environments and study microbial adaptations in heavily polluted sites, e.g. Superfund.


Conservation genetics


In 2007-2011 SOK coordinated the AMNH’s DNA Barcoding Initiative for Conservation (PI: George Amato, funded by the Sloan Foundation), where we characterized the genetic diversity of species of conservation concern (endangered or threatened) and involved in [illegal] trade. Case studies include tuna, sturgeons, sharks, bushmeat, mislabeled animal products in the New York City markets, as well as items confiscated by the authorities. We employ DNA Barcoding as well as DNA sequencing of gene regions that help elucidate relationships of recently diverged species and regional intraspecific variation.


Quantifying the genetic units among African elephants is of paramount importance when drafting conservation and protection policies globally and at the regional and national level. We habe been using mtDNA and nuclear genetic markers to understand the apportionment of genetic variation within and between Loxodonta africana (the savanna elephant) and L. cyclotis, its forest congener. Furthermore, we are analyzing genes that might be of potential functional significance in the divergence of elephants and mammoths using ancient DNA paleogenetics techniques and computational modeling approaches. – In collaboration with Alex Greenwood (Leibniz Inst, Berlin) and Al Roca (U Illinois, Urbana-Champaign)


Recent work includes African vertebrates in collaboration with Evon Hekkala (Fordham).

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