Principal Investigator

Jennifer A. Doudna
Fax: 510-643-0080
Feel free to use this short bio and picture for announcements.
Jennifer A. Doudna
Principal Investigator

Dr. Jennifer Doudna is a member of the departments of Molecular and Cell Biology and Chemistry at UC Berkeley, the Howard Hughes Medical Institute, and Lawrence Berkeley National Lab, along with the National Academy of Sciences, and the American Academy of Arts and Sciences.

Biographical Highlights:

Feel free to use this short bio and picture for announcements.

Postdoctoral Associates

Alexandra Amen
NIH Kirschstein-NRSA (F32) Postdoctoral Fellowship Awardee
Alexandra Amen

Glioblastoma multiform (GBM) is one of the most common and aggressive forms of brain cancer, but current therapeutic treatments are limited. My research focuses on using the gene-editing CRISPR/Cas9 system in order to first further understanding of genes underlying tumor cell immortality in GBM, and second develop in vivo delivery methods to achieve CRISPR/Cas9 editing of GBM tumor cells, with the ultimate goal of inhibiting tumor growth.

Brady Cress
NIH Kirschstein-NRSA (F32) Postdoctoral Fellowship Awardee
Brady Cress

Diverse CRISPR-Cas systems are now known to function as integral components of the immune repertoire of many microorganisms, with the currently known catalog of systems spanning two of the three domains of life and contributing to the capacity of these bacteria and archaea to thwart viral infection. Eukaryotes conspicuously lack endogenous CRISPR-Cas systems, but it is not yet known if these molecular surveillance complexes can be co-opted to achieve therapeutically relevant inhibition of viral infection in humans through direct interference with the genomes of human viruses. While investigating strategies to improve the therapeutic potential of CRISPR-Cas components, I will also examine our ability to temporally control the editing activity of diverse CRISPR effectors.

Jennifer Hamilton
Jane Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellowship Awardee
Jennifer Hamilton

CRISPR-Cas-based genome editing tools enable the control of gene expression in cells, tissues and whole organisms. Although invaluable for experimental studies, translation of these advances into clinical therapeutics requires delivery of CRISPR-Cas proteins and guide RNA to disease-relevant organs in the body. All current in vivo delivery strategies have drawbacks including ineffective delivery to target tissue, prolonged nuclease expression leading to off-target damage, and clearance of edited cells by adaptive immune responses. I posit that viral infection strategies can be harnessed to overcome the challenges faced by the in vivo delivery of genome editing tools. In the Doudna laboratory, I am applying my background in viral engineering to create the next-generation of CRISPR-Cas delivery vehicles and translate these technologies into therapeutics. By merging virology with bioengineering, I aim to make these revolutionary genome-based treatments accessible to all people who can benefit.

Christine He
Joint with Banfield and Cate Labs
Camille and Henry Dreyfus Environmental Chemistry Fellow
Christine He

The vast majority of microbial diversity remains unexplored due to the inability to cultivate most microbes in a lab. My research focuses on a group of uncultivated bacteria called the candidate phyla radiation (CPR), which comprises over 15% of Domain Bacteria. Currently, almost no experimental characterization of CPR bacteria has been performed and many identified genes have unknown biological function. My work focuses on cultivation, biochemical characterization, and ultimately genetic engineering of CPR bacteria.

Shrutee Jakhanwal
Shrutee Jakhanwal

The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins are an RNA-guided defense mechanism against foreign genetic elements in archaea and bacteria. The first step of CRISPR immunity is acquisition, wherein foreign DNA fragments are detected and integrated into the host cell’s chromosome. The precision of this process is instrumental in maintaining the CRISPR locus and host-genome integrity due to off-target integrations. I am interested in understanding the intricate mechanisms that underline the accuracy of the adaptation process.

Gavin Knott
American Australian Association Fellow
Gavin Knott

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems arose in bacteria and archaea as an adaptive innate immune response to combat viral infection. In Class 2 type II CRISPR systems, the single protein effector Cas9 is guided by a CRISPR-RNA to cleave complementary target sequences within foreign DNA. With biochemical and structural data to define their molecular mechanisms, Cas9 and the Class 2 type V effector, Cpf1, have been readily employed as tools for genome engineering. However, the CRISPR-Cas systems show remarkable diversity across microbial species, with the recent identification of highly divergent class 2 single effectors that share little to no resemblance to Cas9. My research focuses on understanding the molecular mechanisms of the expanding ‘CRISPR universe’ using biochemistry and X-ray crystallography.

Audrone Lapinaite
Human Frontiers Science Program Fellow
Audrone Lapinaite

The discovery of intron-derived RNAs and cytoplasmic intron-retaining transcripts (CIRTs) hints that intronic RNAs, previously regarded as “junk”, play an important role in cellular processes. I aim to unravel the dynamics of intron-derived RNA synthesis, transport and function in vivo by taking on a multi-disciplinary approach: a combination of gene editing technologies with the most advanced tools in biochemistry, structural biology and live cell imaging.

Junjie Liu
Life Sciences Research Fellow, Joint with Nogales Lab
Junjie Liu

Research interest1: LncRNAs play key regulatory roles in various cellular pathways. For example, Host lncRNAs NRON and NEAT1 strongly affect latent infection by exerting a rigorous regulation-cycle on HIV-1 transcripts and proteins. However, detailed 3D structural information is lacking. Leveraging the technical advantages of cryo-EM technology, I’m seeking to establish general methods to help researchers determine the 3D structures of lncRNAs more efficiently.

Research interest2: Various alternative Class2 Cas proteins from different organisms have been characterized that show a number of advantages with respect to SpyCas9. Understanding the structural basis for these special properties of different Cas proteins will greatly benefit the design of an optimized gene-editing tool. Furthermore, anti-CRISPR proteins have been identified as specific and genetically encodable ‘‘off-switches’’ for Cas9 which may help clinical difficulties and safety concerns, but the structural mechanism is yet unknown. I’m interested to explore the guide RNA-binding and DNA-targeting mechanisms for Class2 Cas proteins, and to determine, in atomic detail, how different typeII anti-CRISPR proteins control the activity of Cas9 proteins.

Tina Liu
NIH Kirschstein-NRSA (F32) Postdoctoral Fellowship Awardee
Tina Liu

CRISPR-Cas systems are an ancient and widespread RNA-guided adaptive immune system in bacteria and archaea. My research focuses on how multisubunit Type III CRISPR-Cas complexes target transcriptionally active DNA and RNA of invading phages and plasmids. Using a combination of biochemistry and single-particle electron microscopy, I aim to uncover the mechanism of transcription-coupled target recognition by Type III complexes. Understanding how they find and destroy their targets will provide fundamental insights into RNA-guided immunity in prokaryotes, and could potentially lead to a tool that can detect or target actively expressed genes in heterologous systems, such as eukaryotic cells.

Juliana de Lima Matos
IGI Postdoctoral Fellow
Joint with Staskawicz Lab
Juliana de Lima Matos

My research focuses on understanding how gene editing outcomes in plant cells are influenced by different Cas9-gRNA complex designs and the host DNA repair machinery. In particular, I am working on developing robust CRISPR/Cas9-mediated homology-directed repair (HDR) tools in plant crop species in order to exploit genome engineering beyond producing NHEJ-mediated indel knockouts. Additionally, we are establishing novel delivery methods of CRISPR-Cas9 reagents to overcome the physical barrier imposed by the plant cell wall and thus improve gene editing efficiency and scalability in a transgene-free manner. Finally, we are using comparative and functional genomics to identify, test and deploy genetic engineering of biotic (disease resistance) and abiotic (drought tolerance) stress pathways and traits in plant crop species with emphasis on tomato, rice, and wheat.

Bastian Minkenberg
IGI Postdoctoral Fellow
Bastian Minkenberg

Bastian is a postdoctoral scholar in the Innovative Genomics Institute’s agricultural genomics branch. He started working on genome-editing in the food staple rice during his time as a Beachell-Borlaug International Scholar at Penn State. He now continues his efforts to improve disease resistance and yield of crops at UC Berkeley under supervision of Drs. Jennifer Doudna and Brian Staskawicz. Bastian’s first goal during his time at the Innovative Genomics Institute is to develop tools for precise genome-editing and accelerated plant breeding using advanced plant tissue culture and CRISPR methods. Another interest of him is to develop bioinformatic tools to avoid off-target editing in plants and to increase on-target activity. As ultimate goal, Bastian tries to develop an efficient gene repair system to easily change genetic information in crops to make them healthier and sturdier.

Elizabeth O’Brien
Elizabeth O’Brien

CRISPR-associated systems in bacteria and archaea can specifically bind and cut a sequence of DNA in a programmable, RNA-guided manner. For this reason, CRISPR effector nucleases, particularly Cas9 and Cas12a (AsCas12a) are promising tools for therapeutic genome editing. The challenges of controlling off-target cleavage events and editing outcomes of CRISPR-induced DNA breaks, however, must be overcome to realize their therapeutic potential.
Improved understanding of CRISPR effector behavior in live cells would provide insight into strategies for better control of CRISPR-Cas in human nuclei. A live-cell imaging platform, in which cells stably express nuclease-dead SpyCas9 fused to a HaloTag domain, has been successfully used to visualize Cas9 DNA interrogation in live mouse cell nuclei. Using this CRISPR imaging platform as a foundation, I am working to i) construct stable cell lines expressing WT and nuclease-dead variants of Cas9 and Cas12a, fused to a HaloTag domain for imaging ii) compare binding fidelity and DNA residence time of Cas9 and Cas12a when targeted to the same gene iii) image fluorescently labeled WT CRISPR effectors and human repair enzymes to map the sequence and duration of steps processing CRISPR-induced DNA breaks. Specifically, by measuring the lag time between binding of CRISPR effectors and binding of various individual repair enzymes on target DNA, I will spatiotemporally map substrate transfer from CRISPR-Cas to repair.

Patrick Pausch
Patrick Pausch
Postdoctoral Scholar
Ben Rubin
NIH Kirschstein-NRSA (F32) Postdoctoral Fellowship Awardee
Ben Rubin

CRISPR-Cas in Uncultured Microbes: The large majority of life has never been cultivated within the laboratory. This life can both be mined for new CRISPR-Cas systems and manipulated by these systems to facilitate understanding. My research focuses on the development of genetics, enabled by CRISPR-Cas, in communities of uncultured microorganisms. Secondarily, I look for new CRISPR-CAS and CRISPR-Cas-like defense systems within these same communities.

Haridha Shivram
Haridha Shivram
Postdoctoral Scholar
Elizabeth (Abby) Stahl
Joint with Savage Lab
Elizabeth (Abby) Stahl
Postdoctoral Scholar

Abby is a postdoctoral scholar in the California Institute for Quantitative Biosciences. She began studying the host immune response to bioengineered materials during her time as a graduate student at the University of Pittsburgh McGowan Institute for Regenerative Medicine. She now studies how the immune system responds to Cas proteins and delivery vectors to improve the efficacy of gene editing and to further translate the use of CRISPR systems for in vivo applications.

I-Li Tan

Glioblastoma (GBM) is a deadly disease that most people with this cancer died within two years of diagnosis despite decades of research on finding more effective treatments. With the recent development of CRISPR (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins as easily accessible and programmable means of editing and regulating genes, I propose to directly leverage CRISPR-Cas as a therapeutic modality to eliminate GBM cells. I have two main research focuses 1) use CRISPR-Cas system to dissect mechanisms of tumorigenesis and identify therapeutic targets, and 2) develop in vivo delivery tools to target GBM stem-like cells, the main population responsible for tumor recurrence, using intracranial xenograft model of GBM.

Graduate Students

Basem Al-Shayeb
NSF Fellow
Joint with Banfield Lab
Emeric Charles
Joint with Savage Lab
Josh Cofsky
NSF Fellow
Joint with Kuriyan Lab
Josh Cofsky

While protein structures are commonly represented as a single set of 3D coordinates, most biological macromolecules rely heavily on conformational flexibility to effect their functions in solution. Cas effector complexes in particular undergo dramatic conformational movements during the process of RNA-guided nucleic acid targeting. I am broadly probing the energetic landscape of these dynamic interference complexes to better understand how their nuclease activity is regulated.

Amy R. Eggers
Carolyn Huang
Marco Lobba
Joint with Francis Lab
Arturo Ortega
Joint with the Staskawicz Lab
Arturo Ortega
Graduate Student
Connor Tsuchida
Joint with Wilson Lab
Joy Wang
NSF Fellow

Staff

Enbo Ma
Senior Staff Scientist
510-643-0108
Jen Sabo
Project Scientist
Jen Sabo
Project Scientist
Jinjuan Ye
Technician
510-643-0108
Kaihong Zhou
Lab Manager
510-643-0108
Meredith Triplet
Project Manager
Jonathan Chuck
Lab Assistant
Riley McGarrigle
Lab Assistant
Riley McGarrigle
Lab Assistant
Brittney Thornton
Lab Assistant
Brittney Thornton
Lab Assistant

Adapted by prokaryotic cells as a form of immune response against viral infection, RNA targeting CRISPR systems are currently being investigated for their potential in RNA detection and diagnostic applications.  My research focuses on the biochemical interactions within these CRISPR systems, with a focus on Cas13, which is characterized by two ribonuclease activities that catalyze crRNA processing and ssRNA cleavage.  By researching the binding, processing, and cleavage preferences of these CRISPR systems, I hope to contribute to our understanding of the potential of these systems in vitro.

Undergraduate Students

Charlie Alza
Charlie Alza
Ezra Bisom-Rapp
Ezra Bisom-Rapp
Noah Cheng
Noah Cheng
Swarthmore Undergraduate
Virginia Hsiao
Virginia Hsiao
Mohak Jain
Mohak Jain
Shirley Li
Shirley Li
Casey Mogilevsky
Casey Mogilevsky
Cindy Sandoval Espinoza
Kimberly Tang
Kimberly Tang
Talia Wenger
Talia Wenger
Isaac Witte
Michael Xu
Zeyi Zhou
Zeyi Zhou
YueXin Zhang
YueXin Zhang
Yvette Yao
Yvette Yao

Visiting Scholars

Simon Eitzinger
Simon Eitzinger
Anabel Schweitzer
Anabel Schweitzer

Alumni

Former Postdoctoral Associates

Name
Time In Lab
Position and Location
Fuguo Jiang
2013-2018

Assistant Professor, UT MD Anderson Cancer Center, Jiang Lab

Kyle Watters
2016-2018

Senior Bioengineer, Arbor Biotechnologies

Christof Fellmann
2015-2018

Assistant Adjunct Professor, Department of Cellular & Molecular Pharmacology, School of Medicine, University of California, San Francisco; Staff Research Investigator, Gladstone Institutes

Brett Staahl
2013-2018

Co-founder, Scribe Therapeutics

Chun-Hao Huang
2016-2018
Natalia Orlova
2017-2018

Process Development Scientist, Grifols Therapeutics

David Burstein
2015-2018

Assistant Professor, Tel Aviv University

Stephen Floor
2011-2017

Assistant Professor, UCSF

Mitchell O'Connell
2013-2017
Romain Rouet
2015-2017
April Pawluk
2016-2017
David Taylor
2014-2016

Assistant Professor, University of Texas, Austin

Emine Kaya
2012-2016
Philip Kranzusch
2012-2016

Assistant Professor, Harvard Medical School, Kranzusch Lab

Nathanael Lintner
2011-2016

Senior Scientist, Pfizer

Yun Bai
2011-2015

Assistant Professor, ShanghaiTech

Steven Lin
2012-2015

Assistant Research Fellow, Academica Sinica

Ross Wilson
2010-2015

Principal Investigator, Wilson Lab, UC Berkeley

Ho Young Lee
2008-2013

Scientist at Genentech

Stefanie Mortimer
2009-2013

Senior Manager, Technology Development at Guardant Health

Aaron Brewster
2010-2013

Project Scientist, Berkeley Lab

Martin Jinek
2007-2012

Assistant Professor, Institute of Biochemistry, University of Zurich

Monika Martick
2011-2012

Scientist, Miroculus

Blake Wiedenheft
2007-2012

Assistant Professor, Montana State University

Dipali Sashital
2008-2012

Assistant Professor, Iowa State University

Andrew Mehle
2005-2011

Assistant Professor, Univ. of Wisconsin, Madison

Sandro Ataide
2006-2008

Lecturer, Molecular & Microbial Biosciences, The University of Sydney

Ryuya Fukunaga
2007-2008

Assistant Professor of Biological Chemistry, Johns Hopkins University School of Medicine

Euiyoung Bae
2007-2008

Assistant Professor, Seoul National University

Karin Felderer
2006-2008

Associate Director /Laboratory Leader-Protein Production, MorphoSys AG

Glen Borchert
2007-2008

Assistant Professor, University of Southern Alabama

Wendy V. Gilbert
2004-2008

Associate Professor, MIT

Chris S. Fraser
2003-2008

Assistant Professor, UC Davis

Nik H. Chmiel
2002-2007

Staff Scientist, Bio-Rad Laboratories

Ian J. MacRae
2002-2007
Katrin Karbstein
2003-2006

Associate Professor, The Scripps Research Institute

Rich Spanggord
2002-2006

Senior Scientist, Baxalta, Inc.

Ailong Ke
2002-2005

Associate Professor, Cornell University

Li Chen
2001-2005

Sigma-Aldrich, Shanghai, China

Peter Adams
2000-2002

Research Scientist, NIH

Bidya Sagar
2000-2002

Service Architect,Hitachi Consulting

Jeremy M. Murray
1999-2002

Staff Scientist, Genentech

Benoit Masquida
1999-2000

Research Director, University of Strasbourg, Strasbourg, France

Jeffrey S. Kieft
1998-2001
Robert Batey
1997-2001
Adrian Ferré-D'Amaré
1995-1999

Lab Head, NIH

Sonia DeMorais
1995-1996

Former Graduate Students

Name
Time In Lab
Position and Location
Jorge Bardales Mendieta
2014-18
Addison Wright
2013-18
Lucas Harrington
2015-18

Co-founder, Chief Discovery Officer, Mammoth Biosciences

Janice Chen
2015-18

Co-founder, Chief Research Officer, Mammoth Biosciences

Steven Strutt
2014-2018

Scientist, Spotlight Therapeutics

Akshay Tambe
2013-2017

Scientist, Spotlight Therapeutics

Benjamin Oakes
2014-2017

Entrepreneurial Fellow, Oakes Lab, Innovative Genomics Institute

Kevin Doxzen
2013-2017

Science Media Communications Innovative Genomics Institute

Alexandra Seletsky
2012-2017
Spencer Knight
2014-2017

Data Scientist Forsite Capital

Megan Hochstrasser
2012-2016

Communications Manager Innovative Genomics Institute

James Nunez
2012-2016

Postdoc, Weissman lab, UCSF

Stephen Wilson
2012-2016

Postdoc, Susan Lindquist lab, MIT

Sam Sternberg
2009-2015

Assistant Professor, Columbia University

Mary Anne Kidwell
2009-2014

Consultant, Boston Consulting Group

Cameron Noland
2007-2012

Senior Scientific Researcher, Genentech

Mark Luskus
2011-2012

Freelance Marketer, Boulder Colorado

Rachel Haurwitz
2008-2012

President/CEO, Caribou Biosciences

Bryan Clarkson
2007-2011
Katherine Berry
2006-2011

Assistant Professor, Mount Holyhoke College

Amy Weeks
2008

Postdoctoral Fellow, UCSF

Fai Y. Siu
2003-2008

Postdoc. Research Assoc., R. Stevens Lab, Scripps Research Institute

Eric M. Friedman
2004-2007
Adrian Repic
2003-2006

Resident, Virginia Commonwealth University Department of Radiology

Bunpote Siridechadilok
2002-2006

Research Scientist, Siriraj Hospital, Thailand

Dennis Lullo
2003-2005

Quality Engineer II, Lifecell

Lisa Valdin
2002-2005

Director of Marketing Azure Biosystems, Inc

Kristi Pullen
2001-2002

Staff Scientist, Health Program National Resources Defense Council

Angie Grech
1999-2001

Global Director of Customer Success, LinkedIn Learning

Miguel Talavera
1998-2002

Scientist-Process Development-Attribute Sciences Amgen , Yale U.

Robert Rambo
1997-2003

Principal Beamline Scientist Diamond Light Source, Yale U.

Andrej Luptak
1997-2002

Associate Professor, UC Irvine

Lan Zhang
1997-2002

Principal Scientist, Merck & Co., Inc.

Daniel Battle
1996-2002

Asst. Professor, Ohio State University

Rebecca Hanna
1996-2000

Owner and Proprietor, MadeWithMolecules.com

Elizabeth Doherty
1995-2000

Technical Specialist, Washington DC

Jamie Cate
1994-1997

Prof., UC Berkeley