Kelley Lab Alumni

KELLEY LAB ALUMNI

MASTER'S STUDENTS	LAST KNOWN LOCATION	THESIS TOPIC / PUBLICATION
Kate Wall (2011) Master’s Student Cell and Molecular Biology	Ph.D. Program Microbiology University of California, Davis	Thesis: Microbial diversity in Hawaiian fumaroles.
Krissi Hewitt (2009) Master’s Student Cell and Molecular Biology	University of Oregon	Thesis: Workplace bacterial abundance and diversity in three metropolitan areas
Sujata Sovani (2008) Master’s Student Cell and Molecular Biology	Scripps (UCSD)	Thesis: Diversification of general bacterial porins : elucidating novel structural and functional properties using phylogenetic studies and homology modeling.
Julia Turner (2008) Master’s Student Computational Sciences	Colorado	Thesis: A parallel implementation of the isolation by distance web service Publication: Parallelization and optimization of genetic analyses in isolation by distance web service
Lesley Lee Cagasan (2008) Master’s Student Cell and Molecular Biology	Sequenom Inc., San Diego	Thesis: A culture-independent analysis of bacterial diversity in two "sensitive" human indoor environments Publication: Culture-independent analysis of bacterial diversity in a child-care facility
Sara Tin (2007) Master’s Student Evolutionary Biology	Kelly Scientific Sacramento, CA	Thesis: Phylogeographic patterns of isolation within and among geothermal habitats Publication (unrelated to thesis): Culture-independent analysis of bacterial diversity in a child-care facility
Alexander Poole (2007) Master’s Student Cell and Molecular Biology	Health Sciences Center Denver, CO	Thesis: A novel application of positional weight matrices for transcription factor binding site discovery
Jason Holzman (2006) Master’s Student Evolutionary Biology	Bioneer, Inc. Alameda, CA	Thesis: Genetic structure of the palm seed bark beetle Coccotrypes dactyliperda in California examined at fine and course geographic scales Publications: Inbreeding variability and population structure in the invasive haplodiploid palm-seed borer & Mate availability contributes to maintain the mixed-mating system in a scolytid beetle
Eric Ngan (2006) Master’s Student Computational Sciences	Unknown Company Bay Area, CA	Thesis: Isolation by distance web service with incorporation of DNA data sets Web Site: IBDWS
Dean Ellis (2006) Master’s Student Cell and Molecular Biology	Natural Alternatives International (NAI) San Diego, CA	Thesis: Halophilic Archaea inhabit geothermal vents Publication: Halophilic Archaea determined from geothermal steam vent aerosols
Jayanti Mathur (2005) Master’s Student Cell and Molecular Biology	Genomics Institute of the Novartis Research Foundation San Diego, CA	Thesis: Analysis of ecological and evolutionary determinants of microbial community composition in acidic hydro thermal springs Publication: Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs
Shirin Safaee (2005) Master’s Student Cell and Molecular Biology	Southwestern Community College San Diego, CA	Thesis: Molecular survey of host associated microbial diversity in bighorn sheep Publication: (1) Microbial diversity in bighorn sheep revealed by culture-independent methods (2) Phylogenetic diversity of Pasteurellaceae and horizontal gene transfer of leukotoxin in wild and domestic sheep
UNDERGRADUATES	LAST KNOW LOCATION	PROJECT
Aisha Ahmed	SDSU	Periodontal disease and gum disease
Arman Majidi	SDSU	Periodontal disease and gum disease
Kelly Christian	SDSU	Microbial diversity of Hawaiian steam vent sediments
Eric Alegre PREP student	Arizona State University Computational Biosciences Program	Genomic analysis of Squamates, Application of Phylogenetics to Genome Annotation Eric co-authored a paper on his algorithm in the Journal of Molecular Microbiology and Biotechnology entitled: “Phylogenetic Analysis of General Bacterial Porins: A Phylogenomic Case Study.” Eric has also co-authored a paper in Journal of Virology and two other manuscripts.
Collin McManus (Also Research Technician for 1.5 years)	Touro University Medical School Vallejo, CA	Phylogenetics of the bark beetle genus Dendroctonus
Omar Alemi	UCSD Pharmacy School	Culture-independent analysis of microbiota in bark beetle guts
Cecilie Dahl	Columbia University - School of Public Health New York, NY	PCR amplification and phylogenetic analysis of superoxide dismutase A genes in the Pasteurellaceae
Chris Reid	San Diego	Effects of resource specialization on genetic structure of bark beetles populations. Chris developed molecular genetic tools to study patterns of genetic diversification in bark beetles.
HIGH SCHOOL INTERNS	LAST KNOWN LOCATION	PROJECT
Brad Jensen (2008) High School Intern High Tech High School	HTH Senior	A rapid and accurate method for high-throughput phylogenetic analysis using ancestral sequence reconstructions
Alex Pardes (2008) High School Intern High Tech High School	HTH Senior	Phylogenetic approaches for gene function annotation.
Chris Mitchell (2007) High School Intern High Tech High School	HTH Senior	Application of Alex Poole’s code for prediction of transcription factor binding sites in Ciona intestinalis. Chris and Clarke collaborated on a project that applied Alex Poole’s code from his Master’s thesis to the discovery of new transcription factor binding sites in the sea squirt, an primitive chordate. They also wrote Python scripts to compile and analyze the output data.
Clarke Schulman (2007) High School Intern High Tech High School	HTH Senior	Application of Alex Poole’s code for prediction of transcription factor binding sites in Ciona intestinalis (See above entry)
Jeff Jensen (2004) High School Intern High Tech High School	Stanford University	Isolation by Distance Web Service Jeff created the web interface to the IBDWS software, which has been cited 169 as of 05/24/10.
Ryan (2004) High School Intern High Tech High School	Stanford University	Python GUI for visualization of transcription factor data Ryan created a Python Tkinter GUI that allowed users to scan and visualize transcription factor prediction data.