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Lab Members

The Johnston Lab is an interdisciplinary team of microbiologists, synthetic microbiologists, bioinformaticians and engineers.

Group shot of 5 members of the Johnston Lab in white lab coats standing a row between two benches in a wet lab space

Christopher D. Johnston, Ph.D.
Principal Investigator

Martha Zepeda Rivera, Ph.D.
Instructor

As an instructor in the Johnston Lab, I apply computational and bioinformatic tools to large sets of microbial genomes in order to parse and understand their genetic diversity. Trained as a micro- and molecular biologist, I am fascinated by the interactions and capabilities of intratumoral bacteria and how their presence and functions may affect patient treatment and prognosis.

Ping Zhang, Ph.D.
Research Investigator

My work focuses on research and development of protocols for both PacBio long-read and Illumina short-read sequencing technologies. I am excited to support research projects in the labs, contributing to the advancement of microbiome genomic analyses in tumors through my expertise in next generation sequencing.

Heather Bouzek, M.S.
Data Scientist

Rutika Gavate, M.S.
Research Assistant II

I earned my master's in biomedical engineering from Cornell University, where I realized my strongest interest lies in molecular techniques. In the Johnston Lab, I work with genetically engineering microbial strains to better understand how tumor-associated microbes migrate, colonize and persist within tumors. My role involves isolating high-quality DNA and assisting in the development of microbial genetic systems to advance our lab's efforts in engineering microbes for therapeutic applications. Essentially, I spend my days convincing bacteria to do science; some are more cooperative than others!

Kaitlyn N. Lewis, M.S.
Research Assistant II

As a Research Assistant II focused on tumor-infiltrating microbes, I explore how microbial communities within tumor microenvironments influence cancer progression and treatment across various cancer types. Using advanced molecular techniques, I cultivate, identify and analyze these microbes to uncover potential therapeutic targets. My long-term goal is to continue this critical work through a Ph.D. program, where I aim to deepen my understanding of the intricate interactions between microbes and cancer cells. I strive to contribute to the development of novel therapeutic strategies that can improve cancer treatment outcomes.

Joint Members of the Johnston and Bullman Labs

Falk Ponath, Ph.D.
Postdoctoral Fellow

During my Ph.D., I focused on the molecular biology of the cancer-associated microbe Fusobacterium nucleatum, including the development of genetic tools and the investigation of its (post-)transcriptional regulation. As part of the Bullman and Johnston Labs, I am excited to explore how bacteria, including F. nucleatum, shape the tumor microenvironment using spatial technologies. By understanding these interactions between bacteria and host cells, I hope to uncover potential therapeutic strategies to improve cancer treatment. Outside the lab, I enjoy spending time outdoors — whether walking, hiking or running — and discovering the many great restaurants in Houston.

Yousuf Al Farqani, M.S.
Research Assistant II

I completed my master’s at the University of Nebraska-Lincoln, where I researched the effects of liver X receptor activation in obesity and type 2 diabetes, focusing on lipid metabolism and cardiac function. I also studied mitochondrial uncoupling protein gene evolution under oxidative stress as an undergrad, which fueled my interest in metabolic research. Currently, as a Research Assistant II in the Johnston and Bullman Labs in Houston, I investigate the role of Fusobacterium in cancer progression through cell culture maintenance and in vivo cancer models.

Ranjit K. Das, M.S.
Senior Research Assistant

I earned a dual M.S. in biotechnology and molecular biology from INN Norway and The University of Texas Rio Grande Valley. I have experience in molecular biology techniques and strong expertise in working with various mouse models. Throughout my career, I developed an interest in colorectal cancer research. In my current position, I am particularly interested in translational cancer research and am curious about uncovering the role of Fusobacterium in modulating the tumor microenvironment and its implications in cancer progression and therapy. My work primarily focuses on supporting preclinical studies involving murine models, tumor biology and microbiome research. I contribute to experimental design, in vivo animal studies and downstream tissue analysis to advance our understanding of host-microbiome interactions in cancer. Outside of work, I enjoy playing cricket, traveling to new destinations and hiking to explore the outdoors.

Lab Alumni

When people are interested in joining the lab, we invariably ask, “What is your exit strategy? What is your scientific vision for yourself when you leave this lab?”

Because once we figure that out, we can get to work on it. We continue to be especially proud of the lab alumni who have achieved that vision!

Trainees and Staff

Javier Fernandez Juarez, Ph.D.
Now Assistant Professor

Javier joined our synthetic microbiology initiative as a staff research investigator in late 2016, after completing his postdoctoral research in the Church Lab at Harvard. At the Johnston Lab (Cambridge, MA) he sought to expand our SyngenicDNA platforms and create novel synthetic “kill-switch” circuits for biocontainment of engineered organisms.

He successfully transitioned to St. Johns University in 2019 as an Assistant Professor within the Biological Sciences Department. The new Juarez Lab focuses on the construction of whole-cell biosensors that can be applied early detection of pollutants and disease biomarkers. We are super proud of his achievements!

Sean Cotton, M.Eng.
Now Strain Engineer

Sean (the first official alumnus of the Johnston Lab) spent close to 2 years working with us as a staff scientist, figuring out and single-handedly running our PacBio sequencer, honing his synthetic micro skills, and driving our CRISPR projects forward. He began his new career with Synlogic Therapeutics as a Strain Engineer in 2019! We miss him!

Stephany Flores-Ramos, B.A.
Now Graduate Researcher / Paul and Daisy Soros Fellow at UCSD

Stephany joined as a joint research technician between the Johnston and the Lemon Labs at Forsyth Institute. She trained for two years in computational approaches to elucidate the role of Dolosigranulum pigrum as a commensal/health promoting bacterium within the human nasal tract. She performed pan-genomic analysis on nasal isolates and studied its antagonism with Staphylococcus aureus. Steph started grad school enrolled in a Bioinformatics and Systems Biology program at UC San Diego. In 2021 she was awarded The Paul & Daisy Soros Fellowships for New Americans! You can read all about Stephany’s continued success here!

We are very proud of her, and super psyched for her first author D. pigrum pangenome paper

Andy Kempchinsky, B.Sc.
Now Bioengineer / Research Technician II at Fred Hutch Cancer Research Center

Andy joined our lab in Cambridge as a research technician to help out Sean and Arnold with our PacBio SMRTseq efforts. From there he transitioned to a Masters program in Biomedical engineering at Queen Mary University of London in the UK. He studied microbial colonization of plastics and antifouling materials. In 2021, Andy joined our collaborator Dr Bullman’s lab right here at Fred Hutch. You wouldn’t know it from his picture, but he is very happy with his new life on the west coast.