James was an undergraduate at McGill University, where he worked in the lab of Dr. Francois Fagotto on Xenopus developmental biology. During the summers, he returned to his hometown of Toronto and worked in Dr. 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 Dr. 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 Dr. 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, 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 Dr. James Holton, at the Advanced Light Source. James is also 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. His full conflicts of interest are available here.
Angel graduated from San Francisco State University with a Bachelor’s degree in Biochemistry. During undergrad, she worked in Dr. Misty Kuhn’s lab to conduct crystallization trials of uncharacterized Gcn5-related N-acetyltransferases (GNATs) from Pseudomonas aeruginosa.
In the Fraser lab, Angel works with Eric on an oligomeric enzyme, Glutamine Synthetase (GS), to characterize the relationship between oligomeric state and activity as a function of allosteric effectors.
Outside of lab, Angel likes to play video games, go to concerts, and spend time with her partner’s cat Tako.
Pooja received her Ph.D. from the University of Oulu in Finland. Her thesis focused on the structural characterization of mycobacterial membrane proteins using X-ray crystallography and small angle X-ray scattering (SAXS).
In the Fraser lab, Pooja will utilize both X-ray crystallography and cryo-EM to study the drug complexes of tubulin and understand the molecular mechanism of resistance of anti-parasitic drugs.
Outside of lab, Pooja enjoys long walks and board games.
Lena graduated in pharmacy at the Julius-Maximilians-University in Wuerzburg, Germany. During her PhD in biochemistry at the LMU Munich, she focused on the molecular mechanism of chromatin remodeler recruitment in yeast.
In the Fraser lab, Lena is responsible for lab management as well as protein purifications and subsequent assays.
On the weekends you can find her hiking in the forest or mountains or going to the ballet.
Daphne graduated from UCLA with a degree in Biophysics. As an undergraduate, she studied the effects of chaotropes and kosmotropes on protein hydration layers under the guidance of Dr. Giovanni Zocchi.
She discovered her interest in structural biology when she spent a summer working under Dr. Kliment Verba at UCSF, and will pursue structural biology-related projects as a member of the Fraser lab.
Outside of lab, Daphne enjoys exploring San Francisco, playing video games, and reading.
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.
In the Fraser lab, Galen 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.
In the Fraser lab, Robbie is interested in utilizing biochemical and structural techniques to study interactions between chitin-binding proteins and chitin.
When he’s not in lab, Robbie is promoting DEI efforts, reading books (more often tweets), or enjoying a San Francisco park.
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, Gabby enjoys exploring nature and tries her best to longboard.
Eric is interested in understanding how protein conformations impact function and regulation, and, how posttranslational factors that occur throughout a protein’s lifetime further tune function. Eric graduated from the University of Colorado, Boulder with degrees in Biochemistry and Molecular, Cellular, and Development Biology. As an undergraduate, he worked with Dr. Zhongping Tan using chemical biology approaches to study glycosylated proteins. As a graduate student in Dr. Andy Martin’s lab at UC Berkeley, Eric studied how conformations and conformational dynamics of the 26S proteasome influence degradation processes. He also collaborated with Dr. Susan Marqusee’s lab to help illuminate how energetic changes conferred by site-specific ubiquitination on substrate proteins influenced whether, and how, these proteins were degraded by the proteasome.
In the Fraser lab, Eric seeks to understand how protein conformational states influence activity and regulation of metabolic enzymes.
When not in the lab, Eric enjoys spending time at home with his cats, running, skiing, mountain biking, and cooking.
Daniel graduated from Stanford, where he worked on single-molecule biophysics with Dr. Steven Block.
In the Fraser lab, Daniel works to improve and expand the lab’s computational resources. He’s passionate about open science, open data, and open-source software.
Outside of lab, Daniel can usually be found running or playing board games.
Alexis graduated from UC Merced with a degree in Applied Mathematics with emphasis in Computational Biology. During undergrad, she studied prostate cancer heterogenity and used predictive modeling to study cells that undergo Intermittent Androgen Suppression Therapy with Dr. Erica Rutter at UC Merced. Alexis has also completed other projects in prostate cancer and antigen-antibody interactions at Lawrence Livermore National Laboratory and the University of Southern California.
In the Fraser lab, Alexis will use enzymology and structural biology to identify PROSS mutants of mouse Acidic Mammalian Chitinase (mAMCase) that improve expression and solubility in bacteria, and enzyme activity against complex chitin substrates.
When not in the lab, Alexis enjoys playing jazz trumpet, exploring new places, and relaxing at home.
Christian graduated from Arizona State University with degrees in Mathematics and Biochemistry, where he conducted research in the total synthesis of marine natural products with Dr. George Pettit. Afterwards, he attended the University of Michigan for his Ph.D. in Biophysics. In Dr. Randy Stockbridge’s lab, he studied the evolution and function of a number of membrane protein families.
Outside of lab, he enjoys books, music, being outdoors and/or on a bike, and drinking too much coffee.
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 then 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 the Burkart lab, Jen 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, Jen seeks to utilize computational approaches to enable high-throughput experiments through automation and pipeline development.
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.
In the Fraser lab, Jenna 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.
Tushar recently graduated from Department of Chemistry, Universität Hamburg. His research project was carried out in the laboratories of Dr. Arwen Pearson (Center for Free-Electron Laser Science) and Dr. Trevor Forsyth (Institut Laue-Langevin). As a graduate student, he worked on two enzyme systems: E. coli copper amine oxidase (ECAO) and aspartate α-decarboxylase (ADC). In case of ECAO, he explored the effect of two non active site mutations whereas in case of ADC, he studied the effect of binding of a ligand on structure and dynamics of these enzymes. For this, he used a combination of neutron spectroscopy, X-ray/neutron diffraction and molecular dynamics simulations.
In the Fraser lab, Tushar will work on the structural basis of translation stalling using single particle cryo-EM. He will create a predictive model for interactions between nascent peptide motifs, small molecules, and the ribosome.
Ashraya graduated from Anna University, India with a Bachelor of Engineering in Computer Science. She completed her PhD in the Molecular Biophysics Unit at the Indian Insitute of Science in March 2021. During her PhD, Ashraya performed computational studies to understand various aspects of stereochemistry of crystal and cryo-EM protein structures. In the Fraser Lab, Ashraya seeks to develop ensemble modeling methods for cryo-EM and X-ray crystallography.
CJ graduated from UC Berkeley with a degree in Genetics, Genomics and Developmental Biology. As an undergraduate, he studied how somitogenesis is initiated in Xenopus laevis under the mentorship of Dr. Richard Harland.
Outside of lab, CJ enjoys biking, hiking, cooking, and music, and playing guitar.
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 the 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.
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 Alexis Rohou at Genentech to expand on the cisTEM software for macromolecular structure determination by cryo-electron microscopy (cryo-EM). This project aims to improve the quality of reconstructions from particularly difficult datasets, both by reducing overfitting artifacts and by embedding parameters for particle flexibility into the maps themselves. He is also working on tools built on the Computational Crystallographic Toolbox (ccbtx) to detect unmodeled features in electron density such as post-transcriptional modifications (qPTxM) or Hoogsteen base pairs (curiosity). During the COVID-19 pandemic he has served as co-lead of the crystallography subgroup of the Structural Biology Consortium, associated with the QBI Coronavirus Research Group at UCSF, pursuing the discovery of compounds inhibiting SARS-CoV-2 infection.
Outside of lab, Iris enjoys reading, sewing, throwing pottery, learning languages, and his cat Rory. He measures his coffee intake in LD50s.
Iris is supported by a Kirschstein NRSA (F32) fellowship from NIH/NIGMS.
Willow graduated from the Evergreen State College with degrees in Chemistry and Environmental studies. As an undergraduate in Dr. Anitra Ingalls’s lab at the University of Washington, he studied how B vitamins mediate microbial interactions and diversity in the open ocean. For graduate school, Willow did his Ph.D. in Dr. Daniel Schmidt’s lab at the University of Minnesota, where he developed massively parallel sequencing-based methods to study and engineer proteins. Using mutational and insertional scanning methods, Willow found these methods can be useful for identifying regions of a protein involved in functionally meaningful conformational changes, developed mechanistic models for how to assemble protein domains to create useful multi-domain protein tools, and studied the evolution of ion channel regulation.
As an HHMI Hanna Gray and QBI Fellow, Willow is inventing high-throughput sequencing-based biophysics and biochemistry methods for understanding how a genetic, chemical, or physical perturbations alters the trafficking or functional state of receptors. The long-term goal of this work is to build mechanistic holistic models of how receptors break in disease and work in normal physiology
Donovan graduated from CUNY John Jay College with a degree in Cell and Molecular Biology. As an undergraduate, he worked under Dr. Nathan Lents to help develop a computational model that determined an individual’s time of death based on changes in the cadaver’s skin microbiome.
In collaboration with Dr. Willow Coyote-Maestas, he is studying the structure-function relationship of the ESX-3 secretion system in M. smegmatis.
Outside of lab, Donovan enjoys watching movies, gaming, reading, and listening to music. He promises he isn’t ignoring you, he’s just wearing headphones and they’re hidden by his hair.
Donovan is supported by a Kirschstein NRSA (F31) fellowship from NIH/NIGMS.
Justin Biel, Ph.D. - Graduate Student, Biophysics (NSF GRFP)(2014-2019), Staff Scientist (2019-2021)
2014 - 2021
Subsequently: Scientist @ Relay Therapeutics
Erin Thompson, Ph.D. - Graduate Student, Chemistry and Chemical Biology
2015 - 2020
Subsequently: Scientist @ Octant
Michael Thompson, Ph.D. - Postdoctoral Fellow (BioXFEL, F32 NRSA, PBBR Fellow)
2014 - 2020
Subsequently: Assistant Professor @ UC Merced
Alexander Wolff, Ph.D. - Graduate Student, Biophysics (Discovery Fellow, ARCS Scholar)
2015 - 2020
Subsequently: Medical Writer @ Health Interactions; now Specialist - Thompson Lab @ UC Merced
Benjamin Barad, Ph.D. - Graduate Student, Biophysics (Discovery Fellow, ARCS Scholar)
2014 - 2019
Subsequently: Postdoctoral Fellow - Grotjahn Lab @ Scripps
Daniel Keedy, Ph.D. - Postdoctoral Fellow (A.P. Giannini Foundation)
2012 - 2017
Subsequently: Assistant Professor @ City University of New York
David Mavor, Ph.D. - Graduate Student, Biophysics
2011 - 2017
Subsequently: Postdoctoral Fellow - Bolon Lab @ UMass Medical School; now Adjunct Teaching Professor @ Worcester Polytechnic Institute
Rahel Woldeyes, Ph.D. - Graduate Student, Chemistry and Chemical Biology (NSF GRFP)
2012 - 2017
Subsequently: Postdoctoral Fellow - Chiu Lab @ SLAC/Stanford
Andrew Van Benschoten, Ph.D. - Graduate Student, Biophysics
2012 - 2015
Subsequently: Senior Data Scientist - Oracle; now Senior Manager, Data Science - Ovative Group
Lillian Kenner, Ph.D. - Specialist
2011 - 2014
Subsequently: Graduate Student, Biophysics - Frost Lab @ UCSF; now Postdoctoral Fellow - Dueber Lab @ Genentech
Khanh Vuu - Assistant Specialist
2012 - 2013
Subsequently: Research Associate @ JBEI/LBL
Sophia Staggers - BioXFEL Intern
Joanna Maddela - SRTP Undergraduate
Mario Rodriguez - SRTP Undergraduate
Subsequently: Graduate Student @ Scripps
2018 - 2019
Subsequently: Undergraduate @ UC Los Angeles
2016 - 2018
Subsequently: Undergraduate @ San Jose State University
2014 - 2017
Subsequently: Undergraduate @ UC Davis
2015 - 2017
Subsequently: Undergraduate @ San Francisco State University
2011 - 2012
Subsequently: Undergraduate @ City College of San Francisco
Rocco Caliandro, Ph.D. - Visiting Professor
from National Research Council of Italy Institute of Crystallography
Roberto Chica, Ph.D. - Visiting Sabbatical Professor
from University of Ottawa
Kazutaka Ito, Ph.D. - Visiting Scientist
from Asahi Kasei
2017 - 2018
Tomas Lazarou - Visiting Technician
from McMaster University
Dan Bolon, Ph.D. - Visiting Sabbatical Professor
from University of Massachusetts