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The Rubin Lab (Fall 2023)

Principal Investigator
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Ben Rubin standing in front of a green background
Ben surfing on a wave!
Ben Rubin, Ph.D.

As a postdoctoral fellow in Professor Jennifer Doudna's lab, Ben and colleagues created technologies that enable CRISPR-Cas editing of microbiomes. The Rubin lab continues to develop this platform while working with collaborators to apply microbial community editing tools to various microbiomes, such as those residing in human guts, cow rumens, and plant roots. Ben is also a co-founder of the non-profit Science Corps and, when not in the lab, tries to spend as much time in the Pacific Ocean as possible. 

Postdoctoral Associates
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Amanda Alker in front of a green background
Amanda hiking!
Amanda Alker

Amanda received a PhD in Biology at San Diego State University/University of California, San Diego in 2022, where she developed modular genetic tools to study diverse marine bacteria and applied them to study bacteria-stimulated metamorphosis in tubeworms and corals. In the Rubin Lab, Amanda will join the BIOME project to work on microbiome editing with support from the Joint BioEnergy Institute. During her postdoc, she will apply microbial community editing techniques to lignin degrading bacterial communities from plant-root microbiomes. Furthermore, she will improve the maintenance and enrichment of successfully edited microbes in this system by developing methods for positive metabolic selection. Outside of the lab, Amanda likes to travel and enjoy outdoor activities like running, surfing, camping and seeing live music.

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Jon Martinson

Jonathan received his PhD in Microbiology at Montana State University in Seth Walk's laboratory where he researched the temporal dynamics of the human gut microbiome with a specific focus on the Enterobacteriaceae. Following his PhD, he joined Will Harcombe's lab at the University of Minnesota where he investigated how ecological interactions impacted gene fitness using synthetic model microbiomes. In the Rubin Lab, Jon will work to understand how microbial genes exacerbate Inflammatory Bowel Disease using microbiome editing techniques. In his free time, Jon enjoys hiking, reading, making terrible electronic music, and coffee.

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Lindsey Pieper

Lindsey earned her PhD in Biomedical Sciences from UCSF in 2023 where she investigated environmental factors impacting gut microbiome driven degradation of azo compounds (eg. food colorings and IBD drug Sulfasalazine). In the Rubin lab, she will be working with the Audacious team to advance microbiome editing. Specifically she is interested in how to select for edits within a community and how these selection techniques could impact community structure and function as a whole. While not in lab, Lindsey can be found spending time with her dog, horseback riding, or reading a novel.

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Bingliang Xie

Bingliang Xie received a Ph.D. in Microbiology from the Institute of Microbiology, Chinese Academy of Sciences in 2023, where he developed gene-targeted methods to cultivate obligate epibiotic bacteria (Candidate Phyla Radiation bacteria) and revealed how interesting CPR can be when interacting with and infecting other microbes as a small parasite. In the Rubin Lab, he contributes to positive metabolic selection projects and is interested in delivering genetic editing tools using various naturally occurring appendages. Outside the lab, Bingliang enjoys coffee, Shostakovich, and running long distances.

Graduate Students
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Sophia Swartz (she/her)

Sophia Swartz received her B.A. in Molecular & Cellular Biology from Harvard University in 2022, where she used confocal microscopy to study the biogeography of various microbial communities ranging from human oral biofilms to plant leaf pathogens to human pores. In the Rubin lab, Sophia will investigate the regulation and integration mechanism of CRISPR-associated transposons to develop and optimize editing tools for non-model microbes. Outside of the lab, Sophia loves to lift, climb, caffeinate, and hike.

Staff
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Leo Song standing in front of an ocean background
Leo scuba-diving
Leo Song

Lab Manager & Research Associate | leosong@berkeley.edu

Leo Song received his B.A. in Molecular & Cell Biology, with an emphasis in Genetics, Genomics, and Development, from the University of California, Berkeley. After joining the lab in the summer of 2022, Leo worked to set up the Rubin Lab space as well as to initiate research activity and manage operation of the lab. He is currently working to advance and optimize CRISPR-Tn based editing technologies for diverse microbial communities. During his spare time, Leo can be found drawing, photographing wildlife and nature, or planning his next backpacking or scuba diving trip.

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A picture of Jigyasa Arora
Jigyasa at a marathon
Jigyasa Arora

Staff Scientist | jarora@berkeley.edu | LinkedIn

Jigyasa received her Ph.D. in Biology from the Okinawa Institute of Science and Technology (OIST), Okinawa, on the beautiful tropical island of Japan.
She bioinformatically examined the host gut microbiome interactions in insects. Statistically, she explored phylogenetic correlations of functional traits, horizontal gene transfers, and co-evolution with the host at evolutionary timescales. In the Rubin Lab, Jigyasa will optimize bioinformatics tools to investigate CRISPR-associated transposons regulation. She will also examine mobile genetic elements (MGEs) and host interactions using machine learning models to inform predictions of unknown proteins or novel functions important for understanding largely unexplored MGEs. In her free time she likes to run and explore the parks of San Francisco with her partner.

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Agnès Oromi-Bosch

Research Associate (Joint with Cress Lab| agnesob@berkeley.edu

Agnès is a microbiologist and synthetic biologist with expertise in developing genome editing tools to transform non-model microorganisms into therapeutic agents. She holds a MSc in Biotechnology from Wageningen University & Research, where her thesis focused on engineering thermophilic bacteria for the production of bio-chemicals. At Caribou Biosciences, she developed a CRISPR-Cas9-based method to engineer anaerobic gut bacteria from the Bacteroides genus into therapeutic candidates for immuno-oncology. At Felix Biotechnology, Agnès worked on a platform to isolate, engineer, and characterize phages targeting multie-drug resistant (MDR) bacteria, and she developed phage candidates for consumer and clinical applications. In September 2023, she joined IGI, where she focuses on strategies to enable efficient CRISPR-based editing of non-model gut bacteria, and uncovering microbe-host interaction mechanisms. Beyond her work, she enjoys “sobremesa” with friends and nature activities such as climbing, trail running, backpacking, and skiing.

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Audrey Glynn, Ph.D.

Senior Program Manager | audrey.glynn@berkeley.edu

Audrey Glynn received a Ph.D. in Microbiology and Immunology from Tulane University, completed her post-doctoral studies with the US Army Medical Research Institute of Infectious Disease, and entered the programmatic side of research during a 2-year AAAS Science and Technology Policy Fellowship with the Office of Naval Research Global. She went on to work for Strategic Analysis, Inc, through which she provided over 8 years of direct support to the DARPA Biological Technologies Office, helping to de-risk and bring novel medical countermeasures to the clinic. Since joining the IGI in late 2021, Audrey provides programmatic and strategic support across multiple IGI projects, including BIOME, the Affordability Task Force, and the Sickle Cell Initiative. When not supporting BiomeForge and other IGI activities, Audrey can be found in the yoga studio, in the kitchen whipping up vegan cuisine, or anywhere reading a good book and sipping a glass of rosé.

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Audrey doing yoga
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Rachel K Evans

Executive Administrative Officer | rachelkevans@berkeley.edu

Rachel K Evans earned a Doctor of Music degree from Indiana University in Bloomington, IN. Before that, she completed a B.A. and M.M. at UCLA. In addition to her passion for performing (and teaching) music, Rachel has worked in a variety of diverse fields, most recently working as a Project Manager in Telecommunications before joining the IGI in early 2022. At IGI Rachel spends most of her time providing administrative support and planning/hosting events.

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Undergraduate Students
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Abby Wang (she/her)

Undergraduate Researcher & Graphic Designer | abbywang@berkeley.edu

Abby is a second-year intended Molecular and Cell Biology major with interests in all-things microbiology, neuroscience, philosophy, and graphic design. At the Rubin Lab, Abby does wetlab experimental work with Amanda and Leo. She also performs various design-related tasks around the lab, including designing and managing this website! Outside of her studies, she enjoys tackling her reading list, museum hopping, and picking up niche hobbies.

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Sarah Hasham (she/her)

Assistant Lab Manager | sarah.hasham@berkeley.edu | LinkedIn

Sarah is a fourth-year undergraduate student completing her BS in Conservation & Resource Studies with a focus in environmental data analysis. She is deeply passionate about sustainability, and hopes to utilize her experience at the lab to dive deeper into the world of microbiology as a tool for climate change mitigation. For the next few months she will be supporting Leo with administrative responsibilities, and will transition into the Lab Manager role after graduating in the spring. Outside of work, Sarah enjoys crocheting, getting creative with second-hand fashion, spending time in nature, and updating her Strava profile with new hikes and runs.

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Christine Corry

Undergraduate Researcher | c.corry@berkeley.edu | LinkedIn

Christine is a second-year intending a double major in Computer Science and Astrophysics and interested in the growing intersection of computer technology and modeling the complexities of the natural world. She works in silico on machine learning models with Jamie and Jigyasa. Christine also participates in research at the NASA Ames Research Center looking into human contributions to safety. In her free time, she loves to play guitar, update her Goodreads, and recenter in nature.

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Danh Tran

Undergraduate Researcher | danht@berkeley.edu

Danh is a current Data Science and MCB student that is interested in the intersection of biology and computational power. He works alongside Jigyasa and Jamie on implementing and research on machine learning models that can help innovate the field of personalized medicine. Outside of the lab, Danh is also in the East Asian Culinary Club as a chef and works to support other social and professional banquets. He also is a big fan of mystery novels and have invested a lot of his time in books from Doyle and Edogawa.

Alumni
Name
Time in Lab
Position
Current Location
Madison Williams
2024
Rotation Student
Nayak Lab
Zoë Chan
2023
Undergraduate Researcher
Sara Smith
2020-2023
Undergraduate Researcher
PhD Student, UCSF Biological and Medical Informatics (BMI)
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