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 Ph.D. 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 Ph.D., he was an EMBO Short-Term Fellow in Dan Tawfiks 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, and Full Professor in 2020. 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 and a Faculty Scientist in the Molecular Biophysics and Integrated Bioimaging Division of Lawrence Berkeley National Lab. James is the Associate Director of the Biophysics Graduate Program.
In addition to all the exciting developments in the lab, James is on the board of ASAPbio and has a long standing interest in teaching computational biology, baseball statistics, and project-based courses. The lab is committed to publishing our code, disseminating our datasets, and posting manuscripts on preprint servers.
Justin graduated from Oregon State University with a degree in Biochemistry and Biophysics. He conducted research in both the laboratories of Dr. Elisar Barbar studying dynein protein interactions, and Dr. P. Andrew Karplus conducting structural bioinformatic research on protein structural components from ultra-high resolution protein crystal structures.
As a graduate student in the Fraser lab, he examined the how conformational heterogeneity changed during directed evolution and revealed minor states that resulted from ligand binding. He was supported by a graduate fellowship from NSF.
As a staff scientist, he is now building up capabilities for high-throughput ligand soaking experiments.
Hector graduated from Rice University with a degree in Biochemistry and Cell Biology. Under the guidance of Dr. George Phillips, he studied the kinetics of BlaC, an enzyme that confers on bacterial pathogens a resistance to a wide range of antibiotics. As an HHMI EXROP fellow, he studied antibody affinity maturation in the Harrison lab at HMS.
His research at UCSF will focus on characterizing ribosomal protection proteins, in complex with the ribosome, using cryo-electron microscopy. When not in the lab, Hector enjoys hiking, exploring beaches, and Latin dance.
Galen’s research interest lies in using structural biology to tackle problems in protein engineering and drug design. He earned his , Ph.D. from the Australian National University, where he worked with Dr. Colin Jackson on the structure, function and evolution of insect enzymes that detoxify organophosphate nerve agents.
Galen joined the Fraser lab as a postdoc in May 2019. He is using recently developed methods in fragment-based drug discovery to guide the design of new inhibitors of an emerging anti-cancer therapeutic target.
Robbie graduated from the University of Miami with a degree in Neuroscience. He studied how transcription factors regulate axon regeneration in the central nervous system as an undergraduate in Dr. Vance Lemmon’s lab.
Robbie is interested in utilizing single-molecule and structural techniques to study interactions between chitin-binding proteins and chitin. When he’s not in lab, Robbie enjoys reading, going to museums, and biking around the city.
Gabby graduated from UC Santa Cruz with a degree in Biochemistry and Molecular Biology. As an undergraduate, she studied the structure and dynamics of telomeres and telomerase under the mentorship of Dr. Michael Stone, where her focus was on developing a high-throughput platform to study telomere lengthening.
In the Fraser Lab, Gabby is interested in studying the allosteric regulation of kinase activity through molecular and structural biology. Outside of lab, she enjoys exploring nature and tries her best to longboard.
Daniel graduated from Stanford, where he worked on single-molecule biophysics with Steven Block.
He joined the Fraser lab in 2020, where he works to improve and expand their computational resources. He’s passionate about open science, open data, and open-source software. Outside of lab, he can usually be found running or playing board games.
John earned his Ph.D. working with Dr. 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.
John is supported by a Kirschstein NRSA (F32) fellowship from NIH/NIAID.
Lin was a graduate student at University of Pittsburgh with Dr. Angela Gronenborn and Dr. 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!
Jen completed her undergraduate degree at Boston University in Biochemistry and Molecular Biology where she studied neurobiology of female rat reproduction under Dr. Mary Erskine. She went on to work as a lab supervisor and in the algae biofuels industry before returning to academia to pursue her Ph.D. at UC San Diego in the lab of Dr. Michael Burkart. In his lab she worked on diverse projects ranging from the use of biochemical probes to understand protein-protein interactions in fatty acid and polyketide synthases to various approaches including metagenomics to explore the biochemical influences on marine atmospheric composition.
In the Fraser lab she seeks to utilize computational approaches to enable high-throughput experiments through automation and pipeline development.
Joey graduated from the University of Texas at Austin with a degree in Biochemistry. He received his PhD in Biochemistry and Cell Biology from Rice University. As a graduate student with George Phillips, his thesis work involved method development of mix-and-inject serial crystallography for structural enzymology using X-ray free electron lasers.
Joey joined the Fraser Lab in June 2020. When he’s not in lab, Joey enjoys discovering new music, reading, and going on long walks around the city.
Jenna graduated from Ursinus College with degrees in Biochemistry and Molecular Biology and in French. While an undergrad, she studied the structure-function relationships of diiron carboxylate enzymes rubrerythrin and symerythrin using the de novo G4DFsc protein model system under the guidance of Dr. Amanda Reig.
Now at UCSF, she studies the interactions between streptogramin antibiotics and the ribosome. When she’s not in the lab, Jenna enjoys climbing, reading, playing squash, and gaming.
Jenna is supported by a graduate fellowship from NSF.
Leah graduated from UC Berkeley with a degree Molecular Cell Biology with emphasis in Biochemistry and Molecular Biology. During undergrad, Leah worked under the guidance of Dr. Ron Zuckermann at LBNL studying peptoids, a class of peptide mimics. Her research focused on controlling structure through side chain to main chain hydrogen bonding.
At UCSF, Leah is working collaboratively with the Fraser and Bondy-Denomy Labs on crystallography of anti-CRISPR proteins. When not in lab, Leah enjoys hikes and exploring the city.
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.
Mike’s longstanding research interest lies in understanding how proteins function by dynamically interconverting between different conformational states. He was introduced to structural biology and X-ray crystallography as an undergraduate at UC Berkeley, where he was a research assistant in Tom Alber’s laboratory. In 2014, he received his Ph.D. in Biochemistry and Molecular Biology from UCLA under the direction of Dr. Todd Yeates. As a graduate student, Mike investigated the role of conformational polymorphism in expanding the functional diversity of 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, he is developing new methods that combine temperature perturbations with static and time-resolved structural measurements to provide detailed insight into the conformational landscapes of biological macromolecules. These new methods are being applied to understand how protein function is modulated by genetic mutations, by interactions with other molecules, and by other physical stimuli.
Since joining the Fraser lab in 2014, Mike has been supported by a postdoctoral fellowship from the BioXFEL Science and Technology Center (NSF), a Kirschstein NRSA (F32) fellowship from NIH/NHLBI, and an Independent Postdoctoral Research Award from the UCSF Program in Breakthrough Biomedical Research (PBBR).
Stephanie graduated from the University of Massachusetts Amherst with a degree in Biochemistry and Molecular Biology. During undergrad, she performed research on pancreas development under Dr. Kimberly Tremblay. She also performed research on economics of the Clean Water Act under Dr. Paul Kolkoswki. Subsequently, she worked as a senior research data specialist and a computational biologist at Dana-Farber Cancer Institute and Broad Institute of MIT and Harvard. There, she worked on many genitourinary translational research projects under Dr. Eliezer Van Allen and Dr. Joaquim Bellmunt. Outside of lab Stephanie enjoys running, reading, gardening, and eating lots of lettuce.
Stephanie is supported by a graduate fellowship from NSF.
Iris enjoys working at the interface of structural biology and scientific computing, primarily developing software expanding the capabilities of cutting-edge instrumentation for X-ray diffraction and electron microscopy. He earned his Ph.D. in chemistry from UC Berkeley working with Drs. Junko Yano, Vittal Yachandra and Nick Sauter at Lawrence Berkeley National Laboratory on discovery of the mechanism of water splitting in oxygenic photosynthesis using X-ray free electron laser (XFEL) diffraction. He worked with the Sauter group to develop XFEL diffraction data processing methods, including the cctbx.xfel program for real-time feedback at XFEL experiments, and with the Yano/Yachandra group to solve several of the first high-resolution room temperature structures and the first high-resolution transient state structures of photosystem II, revealing the sequence of changes at the heterometallic cluster that catalyzes oxygen evolution. As a postdoc with the Fraser group, he is collaborating with the developers of the cisTEM software for macromolecular structure determination by cryo-electron microscopy to improve recovery of flexible molecular motions with this technique. This project aims to determine the mechanism of transcript-dependent but sequence-independent translational efficiency of a pool of naturally occurring, compositionally and conformationally heterogeneous ribosomes, with implications for regulation of the proteome at the stage of translation.
Iris is supported by a Kirschstein NRSA (F32) fellowship from NIH/NIGMS.
Benjamin Barad, Ph.D. - Graduate Student, Biophysics (ARCS Fellow)
2014 - 2019
Subsequently: Postdoctoral Fellow - Grotjahn Lab @ Scripps
Saulo de Oliveira, Ph.D. - Postdoctoral Fellow
2018 - 2019
Subsequently: Bioinformatics Scientist @ Frontier Medicines
Brandi Hudson, Ph.D. - Postdoctoral Fellow
2016 - 2018
Subsequently: Scientist @ Relay Therapeutics
Daniel Keedy, Ph.D. - Postdoctoral Fellow (A.P. Giannini Foundation)
2012 - 2017
Subsequently: Assistant Professor @ CUNY - http://keedylab.org
Lillian Kenner, Ph.D. - Specialist
2011 - 2014
Subsequently: Graduate Student, Biophysics - Frost Lab @ UCSF; now Postdoctoral Fellow - Dueber Lab @ Genentech
Tomas Lazarou - Visiting Technician
2016 - 2016
Subsequently: Graduate Student - Buccella Lab @ NYU
David Mavor, Ph.D. - Graduate Student, Biophysics
2012 - 2017
Subsequently: Postdoctoral Fellow - Bolon Lab @ UMass Medical School
Mario Rodriguez - SRTP Undergraduate
2019 - 2019
Subsequently: Graduate Student @ Scripps
Avi Samelson, Ph.D. - Technician
2011 - 2011
Subsequently: Graduate Student, MCB - Marqussee Lab @ UC Berkeley; now Postdoctoral Fellow - Kampmann Lab @ UCSF
Andrew Van Benschoten, Ph.D. - Graduate Student, Biophysics
2011 - 2015
Subsequently: Senior Data Scientist - Oracle; now Senior Manager, Data Science - Ovative Group
Khanh Vuu - Assistant Specialist
2012 - 2013
Subsequently: Research Associate @ JBEI/LBL
Rahel Woldeyes, Ph.D. - Graduate Student, Chemistry and Chemical Biology (NSF Fellow)
2012 - 2017
Subsequently: Postdoctoral Fellow - Chiu Lab @ SLAC/Stanford
Alexander Wolff, Ph.D. - Graduate Student, Biophysics
2015 - 2020
Subsequently: Medical Writer @ Health Interactions
2016 - 2018
Subsequently: Undergraduate @ San Jose State University
2011 - 2012
Subsequently: Undergraduate @ City College of San Francisco
2015 - 2017
Subsequently: Undergraduate @ San Francisco State University
2014 - 2017
Subsequently: Undergraduate @ UC Davis
2018 - 2019
Subsequently: Undergraduate @ UC Los Angeles
Dan Bolon, Ph.D. - Sabbatical Professor from University of Massachusetts
2014 - 2014
Rocco Caliandro, Ph.D. - Visiting Professor from National Research Council of Italy Institute of Crystallography
2020 - 2020
Roberto Chica, Ph.D. - Sabbatical Professor from University of Ottawa
2018 - 2018
Willow Coyote-Maestas - Visiting Graduate Student (HHMI Gilliam Fellow) from University of Minnesota
Kazutaka Ito, Ph.D. - Visiting Scientist from Asahi Kasei
2017 - 2018