Lab Group Illustration (credit Jennifer Li)

Fraser Lab Members


James Fraser
James Fraser
Principal Investigator
jfraser (at) fraserlab.com
orcid.org/0000-0002-5080-2859
Scholar Citations
@fraser_lab

James was an undergraduate at McGill University, where he worked in the lab of Francois Fagotto on Xenopus developmental biology. During the summers, he returned to his hometown of Toronto and worked in Alan Davidson’s lab on TetR repressor biophysics and bacteriophage genomics.

He moved to California in 2005 to do his PhD in Molecular and Cellular Biology at UC Berkeley. There, he worked with Tom Alber creating biophysical methods to characterize protein side chain flexibility in high resolution X-ray electron density maps. They applied these techniques to study connections between conformational dynamics and enzymatic catalysis, showing that room temperature, but not standard cryogenic, X-ray data collection could reveal the structural basis for critical functional motions.

Near the end of his PhD, he was an EMBO Short-Term Fellow in Dan Tawfik’s lab. Concurrently, he authored the problems and solutions manual for the physical chemistry textbook The Molecules of Life by Kuriyan, Konforti, and Wemmer.

In January 2011, James started his independent career as a QB3 at UCSF Fellow affiliated with the Department of Cellular and Molecular Pharmacology. In January 2013, he was appointed as an Assistant Professor in the Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences (QB3) with promotion to Associate Professor in 2016. The lab is also part of the Macromolecular Structure Group at UCSF and BioXFEL, a Science and Technology Center established by the National Science Foundation. We maintain a deep connection with Beamline 8.3.1., directed by James Holton, at the Advanced Light Source. James is also a Consulting Professor in Photon Science at the Stanford SLAC National Laboratory.

James is a recipient of the NIH Early Independence Award, a Pew Scholar Award, a Searle Scholar Award, and a Packard Fellowship. In addition to all the exciting developments in the lab, James has a long standing interest in teaching computational biology with practical courses (he is the director of the BBC PUBS class and the student-led programming course he developed with Lenny Teytelman and Venky Iyer continues to this day) and with baseball statistics (as explained in this awkward video with Mike Eisen).

Teaching Links:


Lin Liu
Lin Liu
Associate Specialist
lin.liu (at) ucsf.edu
Scholar Citations

Lin was a graduate student at University of Pittsburgh with Angela Gronenborn and Ivet Bahar. Next, Lin was a joint post-doc and Li Foundation fellow between the Kortemme and Fraser labs, using computational and experimental techniques to study the evolution of protein dynamics. Since 2015, she has continued her research in the Fraser lab and has become the key go-to person for its day-to-day operations!


Michael Thompson
Michael Thompson
Postdoc
mct.ucsf (at) gmail.com
Scholar Citations
@mctucsf

Michael was an undergraduate at UC Berkeley, where he was introduced to structural biology and X-ray crystallography as a research assistant in Tom Alber’s laboratory. He received his Ph.D. in 2014 from UCLA, where he worked under the direction of Todd Yeates, investigating structure-function relationships in a key family of proteins that define a widespread class of prokaryotic organelles collectively known as “bacterial microcompartments.” As a postdoc in the Fraser Lab, Michael will examine how amino acid substitutions alter the catalytic rates of enzymes by modifying their conformational ensembles. This work will emphasize the characterization of disease-associated mutations found in human proteases. Additionally, Michael will work on developing experimental methodology for studying conformational heterogeneity and structural dynamics of protein molecules using X-ray free electron lasers (XFELs).

Mike has been supported by a BioXFEL postdoctoral fellowship and is currently supported by a F32 fellowship from NHLBI


Brandi Hudson
Brandi Hudson
Postdoc
brandimhudson (at) gmail.com
http://brandimhudson.com
orcid.org/0000-0003-2288-9157
Scholar Citations

Brandi received her Ph.D. from UC Davis with Dean Tantillo, where she applied computational chemistry to explain complex reaction mechanisms, conformation-activity relationships of potential pharmaceuticals, and non-covalent interactions in small organic molecules. In the Fraser lab, she will use computational and experimental techniques to develop methods to account for conformational ligand heterogeneity and allosteric binding sites.


D. John Lee
D. John Lee
Postdoc
djohnlee (at) fraserlab.com
https://www.linkedin.com/in/djohnlee/
Scholar Citations

John earned his Ph.D. working with Michael Burkart at the University of California, San Diego. His primary focus was the application of protein NMR to the carrier proteins central to fatty acid, polyketide, and non-ribosomal peptide synthetic pathways. In the Fraser lab, he will use structural and computational techniques to explore structural biology and study minor conformational states.


Ben is interested in understanding the role that protein dynamics play in the regulation of biological function. As an undergraduate in Elizabeth Sattely’s lab at Stanford University, he investigated bacterial degradation of the polymer lignin. He is currently a graduate student in James Fraser’s lab at UCSF. His first project involved developing methods for validation of atomic structures solved by high-resolution electron cryomicroscopy. Currently, he is investigating the mechanisms of proteins involved in the allergic immune response to chitin. Outside of research, he is obsessed with finding the perfect cup of coffee, a quest that has included learning to roast his own coffee beans.

Ben is supported by an ARCS Foundation Scholar Award and a UCSF Discovery Fellowship


Justin Biel
Justin Biel
Graduate Student
justin.biel (at) ucsf.edu
orcid.org/0000-0002-0935-8362
Scholar Citations
@thebieldeal

Justin graduated from Oregon State University with a degree in Biochemistry and Biophysics. He conducted research in both the laboratories of Elisar Barbar studying dynein protein interactions, and P. Andrew Karplus conducting structural bioinformatic research on protein structural components from ultra-high resolution protein crystal structures.

Justin is supported by a graduate fellowship from NSF


Erin Thompson
Erin Thompson
Graduate Student
eposs (at) fraserlab.com
@ernpossible

Erin graduated from Drake University with a degree in Biochemistry and Chemistry. As an undergraduate, Erin worked in several labs ranging from exercise physiology to biophysics. In her free time, she enjoys running, hiking, and exploring San Francisco. Erin is supported by a fellowship from the Genentech Foundation


Rahel Woldeyes
Rahel Woldeyes
Graduate Student
rahel.woldeyes (at) ucsf.edu
Scholar Citations
@rahelwoldeyes

Rahel graduated from University of Minnesota – Twin cities with B.S in Biochemistry and Chemistry. As an undergraduate student, she worked in several labs on projects ranging from cell to structural biology. In the Fraser lab, Rahel will be studying the structure-dynamics-function relationships of proteins and protein-ligand complexes using a combination of room temperature X-ray Crystallography and NMR approaches. Furthermore, she will be developing and implementing methods to dissect allostery in drug targets.

Rahel is supported by a graduate fellowship from NSF


Alexander Wolff
Alexander Wolff
Graduate Student
LifeHasOrder (at) gmail.com
http://whywolff.com
Scholar Citations
@LifeHasOrder

Alex earned a B.S. in Kinesiology & Health Promotion, and a M.S. in Molecular Biology, from the University of Wyoming. He worked with Mark Stayton and D. Paul Thomas to elucidate biomarkers in the setting of cardiovascular disease. Alex’s work in the Fraser Lab will focus on the connection between conformational flexibility and protein function; specifically, he will focus on information relay between allosteric sites. He will leverage diffuse X-ray scattering to illuminate these networks, as well as other complementary biophysical techniques.

Alex is supported by a Matilda Edlund Scholarshipand a UCSF Discovery Fellowship


Kazutaka Ito
Kazutaka Ito
Visiting Scientist
ito.kcd (AT) om.asahi-kasei.co.jp

Kazu was a graduate student at Tokyo Institute of Technology, where he studied bacterial metabolism under the guidance of Professor Masaaki Wachi. On completion of his studies, he received his Ph.D. in 2014. Then, he started to work for Asahi Kasei, a pharmaceutical company, where he was introduced to structural biology, especially X-ray crystallography. To study the basics of crystallography, Kazu was sent on loan to the Structural Biology Research Center, which is directed by Professor Toshiya Senda, in KEK for one year. Since August 2017, he has been a visiting researcher in the Fraser Lab. Kazu is interested in conformational heterogeneity and structural dynamics of protein molecules.

Fraser Lab Alumni


Daniel Keedy - Postdoctoral Fellow (A.P. Giannini Foundation)
2012 - 2017
Currently: Assistant Professor @ CUNY


David Mavor - Graduate Student
2012 - 2017
Currently: Postdoctoral Fellow - Bolon Lab @ UMass Medical School


Tomas Lazarou - Visiting Canadian Technician
Spring 2016 - Winter 2016
Currently: Graduate Student - NYU


Andrew VanBenschoten, PhD - Graduate Student
2011 - 2015
Currently: Senior Data Scientist @ Oracle


Lillian Kenner - Specialist
2011 - 2014
Currently: Graduate Student - Frost Lab @ UCSF


Khanh Vuu - Technician
2012 - 2013
Currently: LBL


Avi Samelson - Technician
Summer 2011
Currently: Postdoctoral Fellow - Kampmann Lab @ UCSF (was Graduate Student - Marqusee Lab @ UC Berkeley)