UCSF

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Craik

Charles S. Craik, PhD
Principal Investigator
[email protected]

Our research interests focus on defining the roles and the mechanisms of enzymes and other challenging proteins in complex biological processes and on developing technologies to facilitate these studies. Current research in the lab is on the chemical biology of post translational modifying enzymes, receptors and membrane transporters. A particular emphasis of our work is on identifying the roles and regulating the activity of proteases and degradative enzyme complexes associated with infectious diseases, neurodegenerative diseases and cancer. We are also developing novel methods to biophysically characterize challenging proteins as well as their complexes. These studies coupled with our global substrate profiling, antibody engineering and noninvasive imaging efforts are providing a better understanding of both the chemical make-up and the biological importance of these critical proteins to aid in the rapid detection, monitoring and control of disease.

Ary

Beatrice Ary
[email protected]

I received my BA in Chemistry concentrating in Biochemistry from Bryn Mawr College. During my undergraduate, I researched the biophysical properties of a human derived peptidic hydrogel for potential applications in medical therapies with Karin Åkerfeldt at Haverford College. My research in the Craik Lab focuses on the host pathogen interface and creating chemical tools to study dynamic protein protein interactions.

Bardine

Conner Bardine
[email protected]

I received my B.S. in Chemistry from Allegheny College working under Dr. Ivelitza Garcia. My undergraduate research focused on DEAD-box proteins, specifically the kinetics and thermodynamics of ATP hydrolysis and RNA binding. While pursuing my PhD in the Craik Lab, I am interested in designing tools for tracking and quantifying biological events utilizing protease-activated probes. Currently, I am developing restricted-interaction-peptides for monitoring immune-activation within the tumor microenvironment with the goal of developing non-invasive biomarkers for tracking responses to cancer immunotherapies.

Bohn

Markus-Frederik Bohn, PhD
[email protected]

I performed my PhD research at UMass Medical School on structure and biochemistry of APOBEC3 enzymes in the lab of Celia Schiffer. Thematically, I am interested in identifying novel therapeutic targets for antiviral strategies at the host-pathogen interface. Methodologically, I work at the interface between structural biology and data analytics, establishing new models for structure-function relationships of enzymatic activity. With my research I hope to elevate molecules that serve analytical, diagnostic, and therapeutic purposes to the next level of precision-engineered tools.

Caiazza

Francesco Caiazza, PhD
[email protected]

I received my MSc in Biology from Roma Tre University, and a PhD in Molecular Medicine from RCSI with Maria Marino and Bryan Harvey, studying the molecular changes associated with steroid signaling in endocrine-dependent tumors. My postdoc training at UCD started with Joe Duffy in the MTCI Consortium to investigate therapeutic targets for triple-negative breast cancer, then in the lab of Liz Ryan and Glen Doherty to work on resistance to targeted therapy in colorectal cancer. I joined the Craik lab in 2016, applying a protease profiling strategy (MSP-MS) to discover proteolytic signatures associated with colon cancer subtypes and progression. I collaborate with Alaunus Biosciences (co-founded by Craik) to leverage the unique protease activity signatures in the tumor microenvironment for development of protease-based diagnostic and therapeutic biomarkers. My interest broadly lies in translational research applied to oncology, at the intersection of the academic and entrepreneurial worlds.

Chung

Dong-Hee Chung, PhD
[email protected]

I received my BA in Chemistry from Kyung Hee University (Seoul, South Korea) and PhD in Chemistry from the University of California, Davis. My PhD research focused on deciphering the mechanism of how substrate and reaction specificities are controlled in two classes of enzymes, chorismate utilizing enzymes and PLP-enzymes. I developed a novel multi-site-specific mutagenesis method to assist in a bioinformatics tool Janus, where key residues predicted to be important for substrate and reaction specificity were randomly mutated. Currently, I am interested in designing next generation phage displayed fab libraries for the rapid identification of high affinity Fabs against specific conformations of transmembrane proteins, proteases involved in various cancers, and DNA. With newly discovered Fabs, I hope to elucidate new fab-target interactions and further utilize them for various applications.

Chuo

Shih-Wei Chuo
[email protected]

I received my PhD in Chemistry at the University of California, Davis with Prof. David B. Goodin. My PhD research involves the use of experimental biochemistry, EPR spectroscopy, and computational techniques to explore the structure-function relationships of cytochromes P450. My research interests are understanding protein-protein and protein-molecule interactions. Currently, I am interested in using structure-guided design and antibody-based tools to expand the understanding of molecular processes in health and diseases.

Connelly

Emily Connelly
[email protected]

I graduated from UC Berkeley with a BS in Bioengineering. My previous research experiences involved elucidating differentiation pathways in adult neural stem cells at UC Berkeley and developing antivirals for chronic Hepatitis B infections at Assembly Biosciences. My graduate work in the Craik lab focuses on host-pathogen interactions in viral systems and cell-based assay development.

Hulce

Kaitlin Hulce
[email protected]

I received my BS in chemistry and biology from Brandeis University. While there, I worked with Dr. Jason Pontrello the synthesis of polymeric glutamine displays to mediate huntingtin protein aggregation and study its role in Huntington’s disease progression. I later worked with Dr. Lizbeth Hedstrom on inhibitor-mediated protein degradation, specifically designing an arginine-linked methotrexate analogue to target dihydrofolate reductase for degradation. I am currently a PhD candidate, working in the Craik Lab to develop Cysteine-targeted inhibitors of herpes virus proteases. My interests are in studying the enzymology and structure-function of this dynamic class of enzymes, as well as in rational inhibitor design to disrupt the herpes viral lifecycle.

Lourenco

André Luiz Lourenço, PhD
[email protected]

I received my BS in development biosciences and my Msc in pathology from the Fluminense Federal University (Rio de Janeiro, Brazil). During my PhD I focused on the development of Restricted-Interaction Peptides (RIPs) for the non-invasive imaging of threatening blood clots in vivo through near-infrared (NIR) fluorescence and positron-emission tomography (PET). My research interests lie in the understanding of disease-associated proteolysis, particularly in cardiovascular diseases and cancer, to proper optimize our RIP technology toward clinical translation.

Rohweder

Peter Rohweder
[email protected]

I received my BA in Chemistry at The College of Wooster in 2016. My undergraduate research focused on the development of synthetic methods for the chiral control of the Ugi multicomponent reaction. In my graduate research, I am interested in the development of safer therapeutics for cancer. Specifically, I am using our recently developed MSP-MS technology for the global characterization of misregulated proteolysis in breast cancer to enable the development of protease activated prodrugs. Additionally, I am interested in using antibody engineering approaches for the development of safer immunotherapies.

Villa

Rudy Villa
[email protected]

I received my BS in Biochemistry and MS in Biochemistry from San Francisco State University. I began conducting research as an undergraduate with the Baird Lab which studies protein structure-function relationships, particularly substrates specificity and inhibition in serine proteases. My masters research project focused on investigating the kinetic and inhibitory functions of previously engineered trypsin variants that displayed a degree of inhibitor resistance with tri-peptides. Through a spectrophotometric assay I monitored the degree of proteolytic and inhibitory effects while using macromolecular /naturally occurring substrates. I joined the Craik lab as a Staff Research Associate 1, where I focus on lab management along with assisting on several research projects.

Wucherer

Kristin Wucherer
[email protected]

I received my BS in Chemistry from Whitworth University. During this time I conducted biochemical research on enzyme therapeutics with Prof. Deanna Ojennus, and biophysical research on transmembrane proteins as an Amgen Summer Scholar. I then earned my PhD degree from UC Berkeley, under the guidance of Matthew B. Francis, where I conducted research on the characterization and application of protein bioconjugation reactions. Here, in my postdoctoral studies, I am using a combination of chemical, biochemical, biophysical, and structural biology techniques to identify, characterize, and optimize therapeutic viral protease inhibitors.

Young
Nicholas Young
[email protected]

I graduated from Penn State with a BS in Chemistry. While there, I worked with Dr. Joseph Cotruvo Jr. on the development of RNA-based fluorescent probes for the detection of transition metals in vivo. After receiving my BS, I worked as a Postbaccalaureate Fellow at the National Institute of Mental Health with Dr. Victor Pike. My research focused on the development of a 11C-trifluoromethylation methodology with an application to developing radiotracers for positron emission tomography (PET). For my graduate work in the Craik Lab, I am interested in the development of diagnostic tools and therapeutics utilizing disease-associated proteolysis.

Kyle Anderson
[email protected]

I received a BS in Biochemistry and a BS in Nanomedicine from Virginia Tech. 
During my undergraduate, I was involved in the preformulation group at AbbVie where I worked on characterizing the stability and biophysical properties of early-stage biologics. I also headed the qualification of a novel microfluidic tangential-flow filtration instrument for measuring viscosity-concentration profiles of biologics. 
For my graduate work in the Craik Lab, I plan to focus on the structural biology of antibody binding interactions and computational antibody design. 

Chayanid (Ing) Ongpipattanakul
 
I received my BS in Biochemistry from UCLA, and PhD in Biochemistry from the University of Illinois at Urbana-Champaign. My PhD research focused on using X-ray crystallography to study enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) and phosphonate natural products. I am broadly interested in using structural biology as an aid to understand protein function.
Joshua Martinez
[email protected]
 
I received a BS from UC Davis where I studied animal biotechnology while working for the School of Veterinary Medicine in multiple research and teaching labs. I then earned my MA in stem cell biology through a collaborative master's research program between UC Davis and CSU Sacramento. My masters research project focused on developing translational in-vitro methods for bioengineering autologous tissue replacements for tracheal transplants. I am working on developing and analyzing translational in-vivo models such as murine pancreatic tumor xenograft and uPAR gene knock-out model. Currently, I am interested in in-vitro analysis, histological profiling, and imaging techniques to validate targets for improved detection, diagnosis, and outcomes for pancreatic lesions.

Patricia Conroy
[email protected]
 

 

I am a general surgery resident at UCSF currently completing a two-year research fellowship under the mentorship of Dr. Kimberly Kirkwood. I am working with Dr. Kirkwood on both translational and health services research projects to validate targets for improved diagnosis and surgical outcomes in pancreatic cystic and solid lesions. Specifically, we are identifying patterns of uPAR expression in pre-malignant pancreatic cysts that may be exploited for diagnosis, risk-stratification for progression to pancreatic adenocarcinoma, and treatment.
Gina Zhu
[email protected]
I graduated with a BS in Molecular, Cellular, and Developmental biology from Yale University. There, I worked at the Yale Stem Cell Center with Dr. Haifan Lin to investigate how the Piwi protein regulates proper stem cell proliferation and differentiation in Drosophila. After receiving my BS, I worked as a Postbaccalaureate Research Fellow at the SENS Research Foundation with Dr. Amit Sharma. I am Dr. Kirkwood’s clinical research coordinator for her studies examining pancreatic cysts. I enroll patients in PANC Cyst, an e-registry for patients with pancreatic cysts, as well as a national ECOG-ACRIN clinical trial to examine surveillance strategies for patients with pancreatic cysts. I collect pancreatic cyst fluid from patients undergoing endoscopic ultrasounds and surgeries at UCSF to be used for protease research by various members of the Craik Lab.

Staff

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Lee-Baird

Marissa Lee-Baird
[email protected]

Faculty support analyst for Charles Craik, Zev Gartner, John Gross, Bo Huang & Brian Shoichet

Alumni

After leaving the Craik Lab, people continue their careers in research and education in a wide variety of ways. They continue learning, teaching, and doing science, often as leaders in their fields, whether in the Bay Area, California, the United States, or internationally. They take with them the many experiences they gathered during their time at UCSF.