Former Postdoctoral Researchers
Elke Allers, Ph.D, email@example.com
Elke arrived in January 2009 from the Max Planck Institute in Germany where her PhD thesis work centered upon using fluorescent in situ hybridization (FISH) to identify particular marine microbial groups, and evaluate their physiological responses to experimental manipulations. Her TMPL research furthered FISH towards the high-throughput exploration of novel microbial lineages and phage-host interactions in marine systems. Following her postdoctoral work with TMPL, she worked at Accelerate Diagnostics, from February 2013 – January 2017. She is currently a self-employed scientist/consultant based in Germany.
Nirmala Bardiya, PhD, Postdoctoral Research Associate firstname.lastname@example.org
Nirmala joined the Sullivan lab in December 2016. She has extensive experience in wet lab microbiology, biochemistry and molecular biology approaches for studying and developing genetic tools in a variety of prokaryotes, archaea and eukaryotes. In the Sullivan lab, she is developing genetic tools to understand regulation of the phage infection process in Cellulophaga baltica and to help develop phage-therapy as an alternative to antibiotics. In addition, she is interested in discovering host-phage interactions in marine environments using PhageFISH and Fusion PCR. Nirmala is originally from India and carries scientific experiences from working in India, S. Korea, England, and previous assignments in USA. In the past, she has received several international fellowships including UNDP, British Council-Korea, Brain Korea-21 (KOSEF), and Brain Pool visiting scientist from KOFST. Her hobbies include reading, meditation, and providing care at Mother Teresa’s home.
Jennifer Brum, Ph.D email@example.com
Jenn’s research focused on marine viral community ecology and the myriad ways in which viruses affect Earth’s ecosystem processes. Her projects included (i) ecology of viruses in the Southern Ocean, (ii) investigating viral ecology and the influence of viruses on biogeochemical cycling in the Eastern Tropical North Pacific oxygen minimum zone, (iii) examining the global distribution of viral communities through the Tara Oceans and Malaspina Expeditions, and (iv) exploring hydrothermal vent viral communities on the Mid-Atlantic Ridge. She is currently an Assistant Professor at Louisiana State University in the Department of Oceanography and Coastal Sciences.
Vinh Dang, Ph.D, firstname.lastname@example.org
Vinh finished his PhD in Australia and joined the Sullivan Lab in October 2013. During his time with the lab, he focused on several projects, which are associated with phageFISH and viral tagging. The main project was collaborated with a number of researchers to help quantify nutrient-virus interaction and their impact on marine biogeochemistry by addressing 1) how nutrient availability affect viral infection dynamics and 2) how virally-encoded genes contribute to nutrient uptake during infection. He is currently the Dean of Faculty of Aquaculture at Ha Long University.
Katarzyna Danis-Wlodarczyk, PhD, Postdoctoral Research Associate email@example.com
Kasia’s PhD focused on characterization of lytic bacteriophages infecting Pseudomonas aeruginosa and their peptidoglycan and exopolysaccharide degrading enzymes. She obtained her PhDs in Bioscience Engineering from KU Leuven in Belgium and Biological Sciences, specialization Microbiology, from The University of Wroclaw, Poland. She joined the Sullivan and Wozniak labs in 2018, where she studies phage therapy, characterizing Pseudomonas and Staphylococcus phages.
Li Deng, Ph.D firstname.lastname@example.org
Li arrived in Oct 2008 from the University of Bristol where she studied freshwater cyanophages lfor her PhD. At TMPL, she has focused on three projects: (1) Synechococcus cyanophage population genomics along the Monterey Bay Line67 transect, (2) freshwater cyanophage comparative genomics, and (3) on a flow cytometry “viral tagging” project. Currently, she is a scientist at the Institute of Virology at Helmholtz Zentrum Muenchen, German Research Center for Environmental Health.
Melissa Duhaime, Ph.D email@example.com
Melissa arrived May 2010 from the Max Planck Institute in Germany where her PhD thesis work explored viral genomics and metagenomics. As a post-doc at TMPL from May 2010 to November 2011, Melissa worked on model phage-host systems (Cyanosiphophage P-SS2, Pseudoalteromonas phages) and phage RAST, as well as the development of the linker amplification method. She is currently an Assistant Professor of Ecology and Evolutionary Biology at the University of Michigan. The Duhaime Lab
Joanne Emerson, Ph.D firstname.lastname@example.org
Joanne uses meta-omic, bioinformatic, and ecological techniques to study feedbacks between viral and microbial communities and their influences on biogeochemistry and ecosystem ecology in a variety of environments, particularly soil. She completed her Ph.D. in 2012 in Jill Banfield’s lab at UC Berkeley, where she used metagenomic techniques to study viral population dynamics and community ecology in hypersaline lakes and predicted the environmental impacts of microbial communities in the terrestrial deep subsurface with implications for geologic carbon sequestration. Her first postdoctoral position was in Noah Fierer’s lab at the University of Colorado, Boulder, where she studied bacterial, archaeal, and fungal ecology in the atmosphere and the built environment and developed metagenomic techniques for studying viral assemblages in soil. Recent work as a postdoctoral researcher in Matt Sullivan’s and Virginia Rich’s labs at The Ohio State University has involved studying viral and microbial controls on greenhouse gas emissions in thawing permafrost peatland soils and nearby lake sediments. In the near future, Joanne plans to study virus-host dynamics in a variety of natural and agricultural soils. Joanne’s full profile
Sheri Floge, Ph.D email@example.com
Sheri is interested in how marine microbes interact with one another and their environment, the chemical reactions that mediate such interactions and the resulting impact on global elemental cycles. Her Ph.D. research focused on the impact of virus infections on intact, infected eukaryotic marine microbes and included bioinformatic and flow-cytometric screening for persistent (cryptic) infections and combined molecular, chemical and ecological methods to quantify virus-induced biochemical alterations of phytoplankton cells and the resultant impact on copepod grazing. Sheri joined the Sullivan Lab in August 2014 where her projects include using transcriptomics and metabolomics to explore interactions between model systems of viruses, bacteria, phytoplankton and grazers and developing experimental methodology to quantify the role of marine viruses in trophic transfer of carbon. Sheri’s full profile
Consuelo Gazitua, Ph.D firstname.lastname@example.org
Consuelo obtained her PhD in molecular genetics and microbiology at the Catholic University of Chile, where she studied the contribution of rhizospheric microorganisms in the establishment of pioneer plants over mine tailings. In her first postdoctoral position she moved to the marine environment, specifically to the East Tropical South Pacific oxygen minimum zone, where she studied the composition and activity of pico- and nanoplanktonic communities with especial focus on the eukaryotic fraction. In October 2015 she joined the Sullivan lab, where she studies the viral communities from the ETSP oxygen minimum zones, analyzing its composition and potential role in biogeochemical cycling.
Katherine Hargreaves, Ph.D email@example.com
Katherine is interested in how viruses can modulate their bacterial hosts, and the consequences of infection from both the bacterial and virus perspective. She is motivated by discovery-based science, having obtained her PhD at the University of Leicester during which she isolated phages infecting the medical pathogen Clostridium difficile, from environmental sources. While at Leicester, she used next generation sequencing technologies to study bacterial-virus relationships applying whole genome sequencing and transcriptomic analysis for different infection types. She joined the Sullivan Lab to expand into characterising complex viral communities using the model marine system. Her projects include developing new methods to assign new information to viral sequences of unknown function and affiliation, and to investigate the effects of different bacterial-phage interactions in the biosphere.
Karin Holmfeldt, Ph.D firstname.lastname@example.org
Karin arrived July 2010 from Kalmar University in Sweden where she established a Cellulophaga phage collection from the Baltic Sea for her PhD. As a post-doc at TMPL from July 2010 to June 2012, Karin developed a new environmental model system through genome sequencing, virion structural proteomics of representative isolates, and experimental hypothesis testing. She is now an assistant professor at the Linnaeus University Centre for Ecology and Evolution in Microbial model Systems. Karin’s full profile.
Simon Roux, Ph.D email@example.com
Simon joined the Sullivan Lab in November 2013 from the Université Blaise Pascal (Clermont-Ferrand, France), where his PhD work focused on the bioinformatics anlaysis of viral metagenomes, from the development of tools dedicated to these datasets, to the analysis and meta-analysis of viromes toward a better understanding of the ecology and evolution of viruses. At the Sullivan lab, his main projects again involve both the development of new tools to process viral genomes and metagenomes, and the analysis of viral signal in large-scale genomics and metagenomics datasets. Overall, these different projects all work toward a better understanding of the “viral dark matter”: the incredibly vast and still largely unexplored set of environmental viruses infecting microbes, with special interest in deciphering the extent of viral diversity in nature, the mechanisms shaping the long-term evolutionary history of viral genomes, and the ecological drivers of these communities in aquatic biomes. Currently, he is a research scientist at the DOE Joint Genome Institute. Simon’s full profile
Lindsey Solden, PhD, firstname.lastname@example.org
Lindsey Solden, PhD is a postdoctoral researcher that joined the lab in June 2019. She is focused on the annotation and impact of metabolic genes on viral genomes. In her PhD in Kelly Wrighton’s lab she focused on microbial metabolism in the ruminant gastrointestinal tract, with a particular interest in the coordinated degradation of plant material with carbohydrate active enzymes. Currently, she holds a senior scientist role at Epistemix, Inc.
Former Ph.D Students
Jingjie Du, PhD Student email@example.com
Ann Gregory, Ph.D firstname.lastname@example.org
Ann joined the Sullivan Lab as a technician in August 2010 from her undergraduate degree at Occidental College to learn diverse lab protocols and be exposed to the world of marine viruses. Ann since chose to pursue a PhD, started in August 2012 – her thesis focused on the Population Genomics of 150 cyanophage isolates.
Bonnie Hurwitz, Ph.D email@example.com
As a PhD student from September 2009 to November 2012, Bonnie applied her extensive informatic and databasing experience to TMPL’s large-scale informatics problems. Her thesis focused broadly on “Pacific Ocean viruses” making use of large, highly contextualized metagenomic datasets from from Scripps Pier, Monterey Bay line67, and LineP, but incorporated significant informatic tool development as well as revealing novel biological insight into the sunlit and dark oceans. She is currently an Assistant Professor in the University of Arizona’s Department of Agricultural and Biosystems Engineering. The Hurwitz Lab
Julio Cesar Ignacio-Espinoza, Ph.D firstname.lastname@example.org
Cesar originates from Oaxaca, Mexico and joined the Sullivan Lab in August 2008. He completed a 2 year masters degree in Ecology and Evolutionary Biology, and received his Ph.D. in Molecular & Cellular Biology in December 2014. His research is focused on the ecology and evolution of an abundant ocean viral group, the T4-like viruses. He is currently a postdoctoral researcher at the University of Southern California.
Gareth (Gary) Trubl, Ph.D email@example.com
Gary joined the Sullivan Lab as a graduate student in Spring 2014 being co-advised by Dr. Virginia Rich (since July 2013). His thesis work focuses on the role of viruses in a climate-affected peatland across a thawing permafrost gradient in northern Sweden. He examines viral community structure and their contribution to biogeochemical cycling using ecological methods and meta-omics. Gary is now a postdoctoral researcher at the Lawrence Livermore National Laboratory
Liu Yunxiao, PhD student firstname.lastname@example.org
Yunxiao joined the Sullivan Lab in Spring 2017 after he graduated from Peking University in China. He’s been working on bacterial responses to osmotic shocks as well as culturing uncultivable bacteria during his undergraduate research. He takes particular interest in how bacteria defend themselves against environmental challenges, including phage infections, and how to utilize their stress responses to develop future therapies.