Behind the science: meet the faces of the lab!
We are excited to welcome graduate student and NSF GRFP Fellow Adrienne Cho to the lab! Bringing expertise in microbiology, strain engineering, transcriptomics, and metagenomics, she will be exploring how plasmid ecology can inform microbiome editing efforts.
We had a great day filled with good conversations, beautiful plants, and some much-needed time together outside the lab!
Congratulations to our graduate student (now PhD candidate!) Leo on passing his qualifying exams with flying colors!
We celebrate Sarah's last day in the lab as our wonderful lab manager before she starts her next chapter as a research associate in the Busch Lab at the Salk Institute.
Publication: Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing | Science Advances
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Publication: Generating functional plasmid origins with OriGen | Nucleic Acids Research
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Undergraduate researchers Varsha, Ashley, and Hengyi join the lab this fall! They will be mentored by Lindsey, Bingliang, and Kuang, respectively.
The Rubin and Cress Labs celebrate the start of a busy summer of science together with a rooftop BBQ!
Congratulations to undergraduate researcher Emily Qi (mentored by Jon) for receiving the 2025 UC Berkeley Rose Hills Summer Scholarship! The scholarship awards $5,000 to help support undergraduate students perform intensive research throughout the summer.
A warm welcome to our postdoc Madeline Hayes (co-advised by Brady Cress), joining us from UW-Madison's Microbiology Doctoral Training Program! Madeline will be working with the Joint Bioenergy Institute to improve microbial lignin degradation for sustainable biofuel and chemical production.
The lab takes a field trip to see Jigyasa's feature in the Lawrence Hall of Science's newest Future of Food exhibit!
Amanda is off to start her lab and assistant professor position for Biomedical and Pharmaceutical Sciences in the College of Pharmacy at the University of Rhode Island! We'll miss her dearly and the endless amount of warmth she brought to the lab since day 1.
Jon, Jigyasa, Ben, and Lindsey attend the 2025 Keystone Symposia on Human Microbiome: Diversity, Selection and Adaptation at Banff.
The Rubin and Cress Lab celebrates together at our (belated) annual holiday dinner at Wojia Hunan Cuisine!
We're excited to welcome postdoc Kuang Hu to the Rubin Lab! Kuang will be working on the bioinformatics side of the lab, including the discovery of novel RNA-guided editing tools.
IGI Partners with HBCU Hampton University to Sponsor Summer Research Students | Innovative Genomics Institute
The Rubin Lab was excited to host Hampton University student Alex Mendez this past summer as part of the IGI's participation in the UC-HBCU Initiative.
Sarah Hasham begins her position as the full-time Rubin lab manager! We are excited and lucky to have her on board facilitating the administrative work, organization, and overall support of our lab functions!
We are thrilled to congratulate our stellar lab manager Leo Song on his graduate school decisions and announce that Leo will be continuing with the Rubin Lab as a graduate student through the UC Berkeley Comparative Biochemistry department!
Congratulations to our undergraduate researchers Abby Wang and Danh Tran for receiving the 2024 UC Berkeley Rose Hills Summer Scholarships, which generously awards $5,000 to support undergraduate students in pursuing intensive research over the summer!
Sophia (co-advised by Jennifer Doudna and Brady Cress) has passed her qualifying exam with flying colors! She spectacularly presented her proposal on studying CAST post-transcription complex disassembly. We are endlessly proud of our lab's first PhD candidate and all of her accomplishments!
Christine Corry and Danh Tran join the lab as undergraduate researchers, working with Jigyasa on implementing and research models in the context of microbiome editing.
Sarah Hasham joins the lab as an assistant lab manager, supporting Leo with administrative work before she transitions into the Lab Manager role after graduating in the spring!
The Rubin Lab celebrated the end of the year with the Cress Lab at the annual Doudna Lab holiday party!
The Rubin Lab attended the International Conference on Microbiome Engineering (ICME) 2023, co-chaired by Ben and Brady Cress! We had a great showing at the conference, with presentations from Amanda, Jigyasa, and Jon, and Leo and Sophia giving a fantastic presentation on our lab's work on CAST regulators.
Collaboration Publication: Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species | Nature Communications
Lab members had a blast at the first Rubin and Cress Lab retreat at Point Reyes! Many happy memories were made hiking, hanging out at the beach, kayaking, and cooking together despite the rain.
We are excited to welcome postdoctoral researchers Bingliang Xie, Lindsey Pieper, and Jon Martinson to the lab! They will be investigating positive metabolic selection, advancing microbiome editing with a focus on community dynamics, and exploring microbial genes and their role in Inflammatory Bowel Disease, respectively.
Introducing Precision Microbiome Editing | Innovative Genomics Institute
What exactly is precision microbiome editing, and why is it such an important tool? Ben discusses its exciting applications and how our lab aims to harness microbiome editing in the latest Inside Genomics video from the Innovative Genomics Institute.
The Rubin Lab had a splendid time at the annual Inside IGI Conference! Congratulations to Leo, Sophia, Amanda, Jigyasa, and Abby for scoring second in the best poster contest!
A warm welcome to Agnès Oromi-Bosch, joining the Rubin Lab as a research associate! She will be working jointly with the Cress Lab to develop strategies for enabling efficient CRISPR-based editing of non-model gut bacteria and uncovering microbe-host interaction mechanisms.
Precision Microbiome Editing To Tackle Methane Emissions, by Molly Campbell | Technology Networks
Ben chats about ET-Seq and DART in this article on the work behind CRISPR and precision microbiome editing, the exciting TED Audacious Project, and how we can harness microbiome editing to tackle climate change.
We are honored to announce funding by The Leona M. and Harry B. Helmsley Charitable Trust to UC Berkeley. The generous grant will propel our work on microbiome editing tools, aiding in the understanding of Crohn's disease, with the ultimate goal of creating innovative treatments for this chronic condition.
This project will be co-led by the Cress Lab at the Innovative Genomics Institute at UC Berkeley and is in collaboration with the Devkota Lab at the Cedars-Sinai Medical Center.
The Rubin Lab celebrated the first anniversary of our lab with lunch (missing Amanda and Zoë)! It was an amazing time chatting about the past year of science and community-building, and all the exciting changes ahead!
Leo and Sophia present on CAST regulators at the CRISPR2023 Conference in Würzburg, Germany!
Ben attends the Sequencing to Function: Analysis and Application for the Future (SFA²F) conference in Santa Fe, New Mexico.
Welcome to Jigyasa Arora who is joining the Rubin Lab as a staff scientist! She will be spearheading the bioinformatics side of the lab and working on optimizing tools to investigate the regulation of CRISPR-associated transposon and more.
A warm welcome to our new graduate student Sophia Swartz! She will be working on investigating the regulation and integration mechanism of CRISPR-associated transposons to develop and optimize editing tools for non-model microbes. Sophia is co-advised by Jennifer Doudna and Brady Cress.
Huge congratulations to our undergraduate researcher Sara Smith who will be attending UCSF's Biological and Medical Informatics program later this fall! We are tremendously excited and can't wait to see all the great things she will accomplish in graduate school in the coming years!
Congratulations to undergraduate researcher Abby Wang for receiving a UC Berkeley 2023 Summer Undergraduate Research Fellowship (SURF)! The fellowship will support Abby's research over the summer as she works on projects related to VcDART with the lab.
Precision Microbiome Editing 101 with Brady Cress and Ben Rubin, by Hope Henderson | Innovative Genomics Institute
What is precision microbiome editing? Learn more about microbiomes, why microbiomes matter, and how the lab is tackling creating tools to edit the genes of microbes within their complex, natural environment.
IGI's 'Audacious' New Frontier for CRISPR: Editing Microbiomes for Climate and Health, by Andy Murdock | Innovative Genomics Institute
The Rubin Lab is excited to be part of the initiative headed by Jennifer Doudna and Jill Banfield to use CRISPR genome editing to engineer the microbiome in order to address global problems in climate and human health. This initiative is generously supported by $70 million in funding through the Audacious Project.
Big smiles from the lab's first solo lab meeting!
The lab welcomes Amanda with members of the Cress Lab!
Amanda Alker joins the lab as a postdoctoral researcher. She will be developing microbial community editing techniques and applying them to new systems (such as plant-root microbiomes!).
The Rubin Lab holds its first annual holiday dinner with friends from the Cress Lab! (Also, check out our Twitter launch!)
New Gift Supports Precision Microbiome Editing Technology Development at the IGI, by Andy Murdock | Innovative Genomics Institute
A $2.5 million gift from the Shurl and Kay Curci Foundation supports BIOME's research efforts on developing microbiome editing technology.
The Rubin Lab takes its first group photo featuring all the members of the lab!
Abby Wang joins the Rubin Lab as an undergraduate graphic designer and researcher, designing this website and working on other graphical tasks!
The Rubin Lab sets up its first lab space at the Innovative Genomics Institute Building!
The Rubin Lab starts at UC Berkeley, focusing on the applications of microbiome editing. Its first members are Ben Rubin, Leo Song, and Sara Smith!
From infant poop to trance music, here's a play-by-play of a CRISPR experiment, by Hayden Field | Morning Brew
A fantastic article featuring Ben and colleagues discussing the experimental process and how they employ CRISPR to edit gut microbiomes.
A toolkit for microbial community editing, by Susannah G. Tringe | Nature Reviews Microbiology
An article detailing how microbial community editing works and its current status in research.
A new strategy for editing DNA within microbial communities using CRISPR-Cas9 technology, by Kristina Campbell | Microbiome Times
A conversation with Ben, Brady Cress, and Spencer Diamond on how microbiomes can be edited, the strategies, and its applications for future research.
Genome editing in complex microbial communities, by Immy Mobley | Front Line Genomics
Front Line Genomics covers the new findings and strategies characterized by Ben and colleagues to edit genomes of microorganisms in microbial communities as published in Nature Microbiology.
CRISPR editing within microbial communities, by Linda Koch | Nature Reviews Genetics
A research highlight detailing how the editing approaches ET-seq (environmental transformation sequencing) and DART (DNA-editing all-in-one RNA-guided CRISPR–Cas transposase) were developed and are currently being applied to edit microbiomes.
DART takes aim at community editing, by Connie W. Y. Ha & Suzanne Devkota | Nature Microbiology
DART (DNA-editing all-in-one RNA-guided CRISPR–Cas transposase), one of the methods used to conduct community editing, is explained.
CRISPRing the Microbiome is Just Around the Corner, by Robert Sanders | Innovative Genomics Institute
An article from the Innovative Genomics Institute discussing the exciting applications of CRISPR to modify microbiomes. The article goes into depth on Ben, Brady Cress, and Spencer Diamond's work.
Publication: Species- and site-specific genome editing in complex bacterial communities | Nature Microbiology
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