Group Leader

Matthew Bogyo
Professor

Bio

Curriculum Vitae

Dr. Bogyo received a B.Sc. degree in Chemistry from Bates College in 1993 and a Ph.D. in Biochemistry from the Massachusetts Institute of Technology in 1997. After completion of his degree he was appointed as a Faculty Fellow in the Department of Biochemistry and Biophysics at the University of California, San Francisco. Dr. Bogyo served as the Head of Chemical Proteomics at Celera Genomics from 2001 to 2003 while maintaining an Adjunct Faculty appointment at UCSF. In the Summer of 2003 Dr. Bogyo joined the Department of Pathology at Stanford Medical School and was appointed as a faculty member in the Department of Microbiology and Immunology in 2004. His interests are focused on the use of chemistry to study the role of proteases in human disease. In particular his laboratory is currently working on understanding the role of cysteine proteases in tumorgenesis and also in the life cycle of human parasites and bacterial pathogens. Dr. Bogyo currently serves on the Editorial Board of Biochemical Journal, Cell Chemical Biology, Molecular and Cellular Proteomics and is an Academic Editor at PLoS One. Dr. Bogyo is a consultant for several biotechnology and pharmaceutical companies in the Bay Area and is a founder and board member of Akrotome Imaging and Facile Therapeutics.

Postdoctoral Fellows

Jiyun Zhu
Postdoctoral Fellow

Bio

Jiyun graduated from Sun Yat-sen University in 2019 with her B.Sc. in Chemical Biology, then she joined the laboratory of Prof. Thomas Meek at Texas A&M University and earned her Ph. D in Biochemistry in 2023. Her thesis focuses on elucidating the catalytic mechanism of the Main protease (Mpro) of SARS-CoV-2 and developing inhibitors targeting Mpro and human cathepsin L, two cysteine protease targets in COVID-19 drug development. Jiyun joined the Bogyo lab in October 2023 and is currently working on exploring the therapeutic potential of inhibitors targeting proteases/hydrolases using high-throughput screening methods combined with enzyme kinetics.

Kristyna Blazkova
Postdoctoral Fellow

Bio

Kristyna completed her B.Sc. in Molecular Biology at Charles University in 2012, followed by an M.Sc. in Virology in 2014, where she conducted research on the use of chemically-modified virus-like particles as targeting agents. After completing her M.Sc., she joined the group of Dr. Petr Bartunek at the Institute of Molecular Genetics to study steroid hormone nuclear receptors in cancer using high-throughput phenotypic screening. Kristyna then pursued her Ph.D. in the Konvalinka lab at the Institute of Organic Chemistry and Biochemistry under the mentorship of Prof. Jan Konvalinka. She focused on ligand discovery using various selection methods and the use of polymer chemistry to target immune receptors in autoimmune diseases and cancer immunotherapy. After completing her Ph.D. in 2022, she joined the Bogyo lab to investigate microbial proteases involved in inflammatory bowel disease.

Shiyu Chen
Postdoctoral Fellow

Bio

Shiyu earned his B.S. in Chemistry from Wuhan University in 2015. He completed his Ph.D. in 2022 at New York University in the lab of Dr. James Canary. His graduate work focused on developing ratiometric fluorescent probes for peroxynitrite and manganese. Shiyu joined the Bogyo lab in Aug 2022 and is currently working on protease activated probes for preclinical applications.

Emily Woods
Postdoctoral Fellow

Bio

Emily completed her Ph.D. (2017) and M.D. (2020) through the Emory University Medical Scientist Training Program. She did her Ph.D. work in the lab of Dr. Shonna McBride. Her thesis work primarily focused on genetic mechanisms of the Clostridioides difficile response to host-produced antimicrobials. She subsequently continued her medical training as an Internal Medicine resident at Stanford University (2020-2023). Emily joined the Bogyo lab in July 2023 and is interested in developing in vivo imaging techniques for bacterial infections.

Sijie Wang
Postdoctoral Fellow

Bio

Sijie earned his B.E. in Pharmaceutical Engineering from East China University of Science and Technology in 2014. During his master study in 2014-2016 at University of Southern California, he conducted cancer research under Dr. Pin Wang. In 2016, he joined Dr. Casey Krusemark's lab and Dr. Emily Dykhuizen's lab at Purdue University. His graduate work focused on the development of chemical probes using DNA-encoded libraries to study target functions in cancer. In addition, he also developed cyclic imine-based warheads for selective bioconjudgation of tyrosine and tryptophan. After he earned his Ph.D. in 2022, he joined Bogyo lab as a postdoctoral fellow. He is currently working on the development of covalent cyclic peptidic inhibitors using phage display and mRNA display, as well as developing novel warheads for covalent drug development. 

Jeyun Jo
Postdoctoral Fellow

Bio

Jeyun received his Pharm.D. from Pusan National University in 2016 and completed his Ph.D. research in the laboratory of Prof. Hwayoung Yun at the same university in 2021. His thesis studies focused on the first total synthesis of anmindenol A and optimization of 2-anilinopyrimidine-based selective inhibitors against TNBC cells. After working as a senior research scientist at Chong Kun Dang for a year, Jeyun joined the Bogyo lab as a postdoctoral fellow in May of 2022. He is currently working on the development of highly selective inhibitors and probes targeting specific serine hydrolases in pathogenic bacteria and parasites.

Tulsi Upadhyay
Postdoctoral Fellow

Bio

Tulsi received her B.Sc. degree in Biotechnology (2009) from Mohanlal Sukhadiya University Udaipur and her M.Sc.degree in Biotechnology (2011) from H. N. B. Garhwal University Srinagar, India. She then joined the Department of Mathematics, Maulana Azad National Institute of Technology Bhopal, India to pursue M. Tech in Bioinformatics (2014). She worked under the guidance of Prof. K.R. Paradasni and Prof. Neeru Adlakha to identify riboswitches in Clostridium difficile and their small-molecule binders using an in silico approach. In January 2015, she started her Ph. D. work in the laboratory of Dr. Ishu Saraogi at the Indian Institute of Science Education and Research, Bhopal. Her thesis focused on studying essential structural features that regulate protein-protein interaction in the bacterial Hsp70 system and the identification of small molecule inhibitors of DnaK. Tulsi joined the Bogyo lab in March 2022. Her current interest is in characterizing the function of serine hydrolases in pathogenic bacteria and developing selective inhibitors using diverse chemical libraries and phage-display approaches.

Nichole Pedowitz
Postdoctoral Fellow

Bio

Nikki graduated from the University of Maryland in 2016 where she earned a B.S. (cum laude) in Chemistry and Biological Sciences. She performed undergraduate research in physical organic chemistry in Prof. Daniel Falvey's lab where she studied photo releasable protecting groups. She went on to earn a Ph.D. in Chemistry from the University of Southern California in 2021 under the mentorship of Prof. Matthew Pratt. Her graduate work centered around the posttranslational modification O-GlcNAcylation. During her time in the Pratt lab, Nikki developed selective inhibitors of O-GlcNAc modifications and investigated its role in fibroblast contraction. Nikki joined the Bogyo lab in October of 2021 and is interested in using covalent inhibitors to investigate the role of key enzymes in mammalian immune responses.

PhD Students

Franco Faucher
Ph.D. Student Department of Chemistry

Bio

Franco graduated from the University of California Berkeley with a B.S. in Chemistry and a minor in Biological Engineering in 2019. At Berkeley, he worked under the guidance of Dr. Gabor Somorjai working in the field of surface science while developing supported metal nanoparticle based heterogeneous catalysts. Franco also spent time researching in the Vision Science Program studying lipid circuits and immune response with Dr. Karsten Gronert. While at UC Berkeley, he completed a summer internship at Genentech synthesizing antibacterial small molecules and improving synthetic routes. In the Bogyo lab, Franco is interested in developing covalent cyclic peptide inhibitors for future use as therapeutics, imaging agents, and biological tools. Franco is a National Science Foundation Graduate Research Fellowship Program scholar and is also ChEM-H Chemical Biology Interface fellowship trainee.

John Bennett
PhD. Student Department of Chemistry

Bio

John graduated from Colgate University in 2019 with a Bachelors of Arts (Summa Cum Laude) in Biochemistry and Classical Studies. His undergraduate research with Dr. Ernie Nolen focused on the chemistry of oxazolidinones as intermediates in unnatural amino acid synthesis to develop C-linked peptidoglycans. During his time at Colgate, he also had the opportunity to work with Dr. Kenneth Jacobson at the NIDDK where he synthesized a library of antagonists for the P2Y14 receptor. In the Bogyo Lab, John is interested in using chemical probes to study how environmental factors alter serine hydrolase activity in pathogenic bacteria.

Undergraduates

Philip Ipock
Undergraduate Researcher

Our Team