Dr. Michael Sanderson
Program Director
sanderm@email.arizona.edu

Pennie Liebig
Program Coordinator
genomics@email.arizona.edu

IGERT Program in Genomics
University of Arizona
Biosciences West. 328
1041 E. Lowell Street
Tucson, AZ 85721-0088
Tel: 520-626-0988
Fax: 520-621-9190




IGERT Recruitment Program

IGERT.org


IGERT PROGRAM IN GENOMICS FELLOWS


2011-2012 Cohort



David Andrew
Neuroscience

B.A. Neuroscience and Biology, Oberlin College, 2004

I am broadly interested in the evolution of nervous systems and how neuroanatomical characters have changed through evolutionary time. I use arthropods for my study system because of the immense diversity of morphological form among members of this ancient and diverse group. I use large-scale molecular phylogenomics, specifically with sequences derived from expressed sequence tags, and more traditional comparative morphological cladistics to determine trajectories of neuromorphological change.

David graduate in May 2013 and is currently a post-doc at The University of Arizona.



Anam Arik
Entomology and Insect Science

M.S. Entomology, University of Arizona, 2008
B.S. Biochemistry and Molecular Biophysics, University of Arizona, 2007

I am interested in using aspects of genomics to explore how signaling pathways influence diverse physiologies, including reproduction, aging and innate immunity, in disease vectors. I have engineered transgenic lines of mosquitoes with increased insulin signaling in various tissues and I’m trying to identify the molecular basis of how insulin signaling is involved in the regulation of several key physiological processes like lifespan and reproduction.



Noëlle Bittner
Ecology and Evolutionary Biology

B.A. Biological Sciences, Smith College, 2009

I am broadly interested in evolutionary genetics and am currently working on a project to understand the genetic basis of reproductive isolation in two lineages of Mus. To do this, I am sequencing genes involved in genome stability and meiotic sex chromosome inactivation and searching for signatures of selection in wild individuals of house mice. In the future, I will begin work to understand the genes underlying adaptive phenotypes in wild populations of mammals.



Alicia Bolt
Pharmacology and Toxicology

B.S. Human Biology, University of Northern Colorado, 2003

I am interested in identifying the Gene by Environment interactions that contribute to individual variation in response to environmental toxicants. I use genomic approaches to identify candidate genes that are involved in sensitivity to arsenic-induced immunotoxicity in an in vitro model of human populations.

Alicia graduated in May 2012 and is currently a post-doc at McGill University.

Christopher Brownlee
Cell Biology and Anatomy

B.S. General Biology, University of Arizona, 2006

Our lab is using a functional genomics approach in combination with RNAi to silence every Drosophila gene in order to identify genes responsible for the biogenesis of centrosomes; organelles that generate and organize the cell's microtubule cytoskeleton. My project in particular involves characterizing a balance of phosphatase and kinase activities that directly regulates the activity of Polo-like kinase 4 -- a conserved key licensing factor for centrosome assembly. Since cancer cells frequently exhibit centrosome overproduction (or amplification), which in turn promotes chromosomal instability and tumorigenesis, my project will also entail extending our findings to human cancer cells and mining bioinformatic data, such as microarrays and genomes of cancerous cells. Finally, I am currently applying my findings from Drosophila to explain the mechanism by which tumor-causing viruses such as Simian virus 40 promote centrosome amplification.



Daniel DeBlasio
Computer Science

M.S. Computer Science, University of Central Florida, 2009
B.S. Computer Science, University of Central Florida, 2007

My research interests fall into computational approaches to mainly structure based issues. I am interested in modeling biological problems as graphs or trees, then applying computational algorithms to this. I have some background in RNA-Seq assembly and analysis.

Robert (Bob) Fitak
Genetics

B.S. Molecular Genetics, Ohio State University, 2006

I am applying genomic tools and next-generation sequencing to the field of conservation genetics. Conservation geneticists can benefit from genomics to better manage the accrued detrimental variation and lost adaptive variation associated with endangered wildlife. I am currently working on two projects. First, in pumas, I am using 454 pyrosequencing of expressed genes to identify SNPs. I will use the SNP genotypes to address several conservation and ecological concerns. Initially, I will use the SNPs to identify suspected adaptive loci associated with their population expansion in North America, then we will identify the origin and migration pattern of puma populations to improve corridor design in the Southwest. Second, I am examining the genetic effects of the Mexican wolf's unique history (extirpated in 1980, reintroduced in 1998) using a 22k SNP chip developed for the domestic dog. I will quantify the ancestry of Mexican wolves from different captive lineages, dogs, and coyotes, in addition to identifying genes fixed by inbreeding which has plagued the population.



Ariella Gladstein
Ecology and Evolutionary Biology

B.S. Mathematical Biology and Russian, Beloit College, 2011

I am interested in using a combination of computational genomic and linguistic approaches to study human population demographic histories (e.g. founder effect, admixture, population divergence, migration histories). Two populations I am interested in studying are Jewish and Caucasian. These populations are interesting because they have unusual histories. Jewish (as well as Romani) populations have a common origin and have maintained a shared identity, but have lived geographically separated for about two thousand years. In contrast, populations living in the Caucasus Mountains, in southern Russia, seem to have stayed in one place, but have developed/maintained separate languages. The Caucasus region is one of the most linguistically dense regions in the world.



Andrew Gloss
Ecology and Evolutionary Biology

B.S. Biology, University of Notre Dame, 2010

I am interested in the evolution of interactions between plants and herbivorous insects, with a focus on how plants perceive attack by insect herbivores, the resulting activation of chemical defense pathways in the plant, and insect strategies of detoxifying and coping with plant defense compounds.  The ongoing development of an herbivorous Drosophilid fly as a genetic model herbivore of the plant model species Arabidopsis thaliana will allow the identification of specific genes vital to these interactions.  I also plan to continue work at the Rocky Mountain Biological Laboratory on a fly species that has specialized on a wild mustard, both of which are closely related to the organisms I'm studying in the lab.  This will allow me to examine the relevance of processes discovered in a controlled lab environment to a variable natural setting in which plants, insects, bacteria, and fungi interact simultaneously.  Ultimately, I hope to provide insight into how species interactions drive local adapation and patterns of genetic variation within and between natural populations.



Erik Hanschen
Ecology and Evolutionary Biology

B.S. Integrated Sciences, University of British Columbia, 2011

My research focuses on the evolution of multicellularity using Volvocine algae as a model system. I am interested in using a comparative genomics approach to investigate the independent evolution of cellular differentiation from reproductive, flagellated cells to sterile somatic cells and specialized germ cells. As the evolutionary transition to multicellularity requires cooperative behavior, I am also interested in genetic innovations of cooperation, resulting conflicts, and the mechanisms that reconcile these conflicts.



Parris Humphrey
Ecology and Evolutionary Biology

B.A. Biology; Science Technology & Society (STS), Bard College, 2006

I study how and to what extent organisms are environmentally specialized, be they parasites to a hosts, bacteria to a carbon source, or plants to a microhabitat. I use a comparative framework to discover lifestyle changes along lineages and investigate the evolutionary genetics and genomic consequences of phenotypic differentiation. At present I can be found studying the evolution of herbivory in a derived Drosophilid fly lineage (Scaptomyza spp.) that has specialized on wild mustard plants (Cardamine spp.). I also examine this interaction against the backdrop of co-occurring antagonists, including pathogenic bacteria that attack the plant and parasitoid wasps that attack the flies. I am also interested in evolutionary patterns of genomic variation across Bacteria and how both neutral and adaptive processes shape gene repertoires within genomes.



Mana Ohkura
Plant Pathology

M.S. Plant Pathology, Cornell University, 2008
B.S. Biological Sciences, University of California, Davis, 2005

My research focuses on understanding the biology of Aspergillus flavus, an economically important fungus that contaminates food crops with its carcinogenic secondary metabolite known as aflatoxin. In order to do this we are taking a comparative genomics approach to reveal differences between strains that are differentially adapted to the environment and vary in toxin production. Regions of interest highlighted from the genomic analyses will be further characterized using molecular genetic tools.

Ryan Pace
Molecular and Cellular Biology

B.S. Molecular and Cellular Biology, University Arizona, 2010

My research focuses on the evolution and development of arthropod body plans, with the objective of using high throughput technologies to better understand how changes in developmental gene regulatory networks correspond to morphological diversity. In doing so I working with an emerging arthropod model, the two-spotted spider mite Tetranychus urticae, major agricultural pests well known for their broad host range and ability to rapidly evolve resistance to pesticides. With a recently completed genome project, the spider mite genome offers unique insights and tools to use toward increasing understanding of pest control, plant-pest interactions, and arthropod evolution.



Sergei Solonekno
Ecology and Evolutionary Biology

B.S. Cell and Molecular Biology, University of Texas at Austin, 2008

I am a second year graduate student in the laboratory of Dr. Matt Sullivan. My research interests are focused on the application of metagenomic analysis towards the understanding of diverse communities of marine bacteriophages and their microbial hosts. I am currently working on a project to evaluate the compatibility of data generated by several next generation sequencing technologies. My long term interests lie in studying the effects of bacteriophage community composition on bacterial population dynamics, and the evolutionary consequences of coexistence on bacterial and bacteriophage genomes.



Erin Vaughn
Genetics

B.S. Conservation Biology, University of New Mexico, 2008

I am interested in utilizing genomic tools to answer wildlife conservation questions. I am working towards establishing a system of DNA methylation markers as indicators of pollutant exposure in fathead minnow, Pimephales promelas.  Due to the highly complex nature of an epigenetic response, the development of a robust marker system requires measuring methylation and gene expression changes on a genome-wide scale.  Concurrently, I am developing a series of microsatellite markers derived from 454 pyrosequencing data for a threatened population of Florida crested caracara.



Jennifer Wisecaver
Ecology and Evolutionary Biology

B.S. Biological Sciences, Humboldt State University, 2007

My research interests are in the areas of plastid evolution and algal genomics.  As part of my dissertation, I am using a comparative phylogenomics approach to quantify the genetic contribution of Plantae to the chromalveolate algae and evaluate different hypotheses regarding secondary plastid evolution in these algae.  I am also evaluating kleptoplastidy (sequestration of temporary plastids stolen from prey) as a model for understanding the early events in plastid acquisition.

Jennifer graduated in December 2012 and is currently a post-doc at Vanderbilt University.



August Woerner
Computer Science

M.S. Computer Science, University of Arizona, 2011
B.S. Biochemistry, Marlboro College, 2001

My research interests are in population genomics, bioinformatics and computational biology. In general, I am interested in computation from two opposing lines of inquiry: one is the development of novel algorithms to address questions of biological relevance, and the second is the use of such tools (plus a handful of inferential techniques) to conduct full-genome analyses on populations.




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