Principal Investigator

Jennifer A. Doudna
Voice: 510-643-0225
Fax: 510-643-0080
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:

Staff

Enbo Ma
Senior Staff Scientist
510-643-0108
Jinjuan Ye
Technician
510-643-0108
Kaihong Zhou
Lab Manager
510-643-0108
Melanie Leavitt Cantarutti
Senior Project Manager
Meredith Triplet
Project Coordinator
Jonathan Chuck
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.

Cole Urnes
Lab Assistant
Molly Jorgensen
Administrative Assistant
510-643-0113

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
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.

Christof Fellmann
NIH Pathway to Independence Awardee
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.

Fuguo Jiang
Damon Runyon Fellow
Fuguo Jiang

Prokaryotes (Archaea and Bacteria) have evolved a nucleic acid-stimulated immune system that shares similar functions with RNA interference in eukaryotes. CRISPR/Cas system is a microbial nuclease system involved in defense against invading phages and plasmids by integrating spacers from invading genetic elements and subsequently directing the specific cleavage of invasive homologous DNA sequences. My research is focused on the elucidation of the molecular mechanism of the RNA-guided DNA endonuclease Cas9 from the type II CRISPR system. My current research involves in understanding the detailed mechanism by which viral anti-CRISPR proteins inhibit bacterial CRISPR immunity.

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
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.

Kyle Watters
Kyle Watters

In the constant battle between bacteria and phages both have evolved machinery to try to evade the other’s defenses. One system in bacteria and archaea, CRISPR, is used to target mobile genetic elements and prevent them from invading the cell. However, these mobile genetic elements have evolved proteins, or anti-CRISPRs, to thwart CRISPR. I use a combination of bioinformatics (to identify genomes with malfunctioning CRISPR systems) and experiment screening to discover new anti-CRISPR proteins.

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.

Marco Lobba
Joint with Francis Lab

Undergraduate Students

Nami Saghaei
Isaac Witte
Michael Xu
Michael Xu

Many bacteriophage anti-CRISPR proteins inhibit the ability of Cas9 to cleave target DNA. The goals of my research are to determine the inhibition efficiency and binding kinetics of Type II-A anti-CRISPR proteins using various biochemistry methods. Ultimately, the use of anti-CRISPR proteins in vivo may allow us to prevent off-target editing and control editing efficiency.

Visiting Students

Julian Brötzmann

Alumni

Former Postdoctoral Associates

Name
Time In Lab
Position and Location
Brett Staahl
2013-2018
Chun-Hao Huang
2016-2018
Natalia Orlova
2017-2018
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
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