Past Lab members

Post-doctoral fellows

Thiago Bruce
PhD Genetics

I am Post doc in the Dinsdale Lab. I was born in Brazil and have PhD in Genetics, Msc in Biotechnology and graduate in microbiology (2004). I have genuine interest in topics related to microbial molecular biology. I have been involved in research related to characterization and bioprospecting of microbial diversity. I had opportunity to handle with diverse approaches to characterize microbial communities from a variety of environments, searching for biocatalysts of industrial interest. Currently, I am involved with the Genotype to Phenotype Project. The lack of high-throughput phenotypic data is hindering our ability to describe the metabolic potential of microbes based on their genome annotation and our ability to predict gene complements from phenotypic analyses. The overall goal of this project is to improve our capability to reliably predict phenotype from genotype for microbial life across the bacterial kingdom. This project will result in genomic sequences, annotation and microbial metabolic models.

 

PhD students 

Matthew Haggerty
PhD Ecology, 2017
Microbiome consultant at USC

I am a PhD student in Ecology, I use metagenomics to identify differences in the composition of marine microbial communities in response to the environment. I have used sequence data to identify how microbial communities change with distance and environmental dissimilarity at a global scale. I have also applied these techniques to isolate potential super-heterotrophs implicated in coral reef decline and test the mechanisms regulating kelp decomposition.

 

 Archana Srinivas
PhD Ecology, 2016
Postdoctoral researcher at CSU Northridge

I am a doctoral candidate in the joint doctoral program in ecology hosted by San Diego State University and the University of California, Davis. My dissertation research is an investigation on the role played by siderophores (microbially synthesized iron chelating molecules) in dissimilatory iron reduction (DIR), which is a microbial anaerobic respiratory pathway, in Arctic tundra soils.

 

 

Graduate Students

Reema Maniyar
MS Bioinformatics and Medical Informatics, 2017

My research focuses on developing a pipeline to identify phycotidnaviruses from metagenomes.

 

 

 

 

Bhavya Nalagampalli Papudeshi
MS Bioinformatics and Medical Informatics, 2017
Bioinformatician at National Center for Genome Analysis Support

I am a Bioinformatics graduate student in Dinsdale lab. My research includes optimization of metagenome assembly and binning tools to reconstruct population genomes.

 

 

 

Kristen Aguinaldo
MS Ecology, 2017
Training team lead at Thermo Fisher Scientific

My research focused on Identification and genomic characterization of four novel Rhodobacteracae strains from the Point Loma kelp forest.

 

 

 

Jeremiah Minich
MS Cell and Molecular Biology, 2017
PhD student at UCSD

Research topic: Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

 

 

 

 

 Kevin Walsh
MS Ecology, 2017
Clinical Molecular Technologist at Tempus Inc.

 I have worked in the Dinsdale lab for 5 years working on a variety of metagenomic and sequencing projects. My research looks at benthic macro-organisms and how they interact with microbial communities in the water column on coral reefs, in particular reefs off the coast of North East Brazil.

 

 

Shashank Sathe
MS Bioinformatics and Medical Informatics, 2015
Staff bioinformatics analyst at UCSD

Research topic: The Minimalistic Approach of Plasmid Genomes and Identification of Plasmid Contigs From Within Bacterial Assemblies.

 

 

 

 

 Rohini Singh
MS Bioinformatics and Medical Informatics, 2015

My reseach focused on genome annotation of sea lion.

 

 

 

 Undergraduate Students

Felicia Miller
BS Biology, 2017
Graduate student at Moss landing marine laboratory

 I am currently working on a tide pool project where I am taking samples from two locations, Mission Beach and Ocean Beach. From each location I am taking samples from three different microhabitats, hermit crabs, algae, and the water column and I’ll plating each sample on three different carbon sources, erythritol, cellobiose, and aspartic acid.  My hypothesis is that the     microhabitats that I will sample from will determine the carbon usage rather    than the location, which will infer that the microbial community of each microhabitat is conserved.  I am working under a COAST grant that I was awarded in the fall of 2015.

 

Taylor Cram
BS Biology, 2017

I am currently working with microbial isolates that have been collected from La Jolla, Point Loma, Catalina, and San Diego Bay including both kelp and water samples. We will be plating the individual isolates on sodium alginate plate to see if the bacteria can use alginate as their carbon source.

 

 

Emma Bilings
BS Biology, 2017
Quality control Technician at Sekisui Diagnostics

 

 

 

 

 

 

Natalie Frixione
BS Biology, 2017

 

 

 

 

 

Alejandro Vega
BS Biology, 2016
Graduate student at UC Berkeley

 Since August 2015 I have been the lead researcher under the supervision of Dr. Rob Edwards and Dr. Elizabeth Dinsdale at San Diego State University (SDSU) on a global research project. We have been investigating a newly discovered bacteriophage known as crAssphage, which resides in roughly half the human population across the globe. In order to try to get a better understanding of crAssphage, I am studying the distribution and variance of crAssphage on a temporal and spatial scale. We are also attempting to look at the distribution of crAssphage on a global scale. So far we have contacted 22 potential collaborators to sequence crAssphage from around the globe. If you are interested in helping us out please email alexvega619@gmail.com and raedwards@gmail.com.

 

Mariah Foley
BS Biology, 2016
Graduate student at UC San Francisco

 Investigated the effect of ocean acidification on Rhodolith samples by decalcification techniques. Samples were previously collected, and exposed to varying pCO2 levels.

 

 

Ben Turner
BS Biology, 2015
PhD student at SDSU-UCSD

 

 

 

                             Visiting/Rotation students

 Amanda Alker

I am currently a first year PhD rotation student in the Cell and Molecular Biology (CMB) Joint Doctoral program (JDP) with San Diego State University (SDSU) and University of California San Diego (UCSD). Originally from Florida, most of my previous research incorporated the use of molecular techniques to address both coral and microbial ecology. I was recently awarded the Graduate Research Fellowship funded by the National Science Foundation (NSF), to investigate the underlying mechanisms associated with bacterially-induced metamorphosis in coral larvae. I plan to use metagenomics, comparative genomics, and transcriptomics to elucidate these bacterially-mediated cues.