Matthew Bogyo
Associate Professor
mbogyo[at]stanford.edu
Ph.D. MIT
B.S. Bates College
Curriculum Vitae
short form

Biography: Dr. Bogyo received his Ph.D. in Chemistry 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 the human parasites, Plasmodium falciparum and Toxoplasma gondii. Dr. Bogyo currently serves on the Editorial Board of Biochemical Journal, Chemistry and Biology. Molecular and Cellular Proteomics and Drug Discovery Today: Technologies. Dr. Bogyo is a consultant for several biotechnology and pharmaceutical companies in the Bay Area.

Edgar Deu Sandoval
Postdoctoral Fellow
edgardeu[at]stanford.edu
B.Sc.
Ph.D. University of California, Berkeley
short form

Biography: Edgar received a BS in organic chemistry and chemical engineering from the Insitut Quimic de Sarria in Barcelona, Spain, in 2000. He joined the research group of Prof. Jack Kirsch at UC Berkeley in the Fall of 2000, where he earned his PhD degree in Comparative Biochemistry in 2007. Edgar's research as a graduate student focused on the thermodynamic characterization of protein stability and protein-protein interactions of large oligomeric enzymes. He also work on protein engineering projects, and was able to design a hybrid aminotransferase enzyme with dual substrate specificity and allosteric communication between its two active sites. He joined the Bogyo lab in the summer of 2007 and is interested in the development of new antimalarial drugs that inhibit essential protease in the Plasmodium falciparum parasite.

Aimee Shen
Postdoctoral Fellow
ashen2[at]stanford.edu
B.S. University of Alberta
Ph.D. Harvard University
short form

Biography: Dr. Shen received a Bachelors of Science degree with honors in microbiology with a minor in English in 2001 from the University of Alberta. In 2006, she completed her Ph.D. studies in the laboratory of Dr. Darren Higgins at Harvard Medical School. Her thesis work focused on 5'UTR mediated regulation of virulence gene expression and elucidating the molecular mechanism underlying temperature-dependent regulation of flagellar gene expression in the facultative intracellular pathogen Listeria monocytogenes. She joined the Bogyo Lab in April 2007 and is currently working on determining how the Apicomplexan parasite Toxoplasma gondii inhibits intrinsic apoptotic signaling.

Margot Paulick
Postdoctoral Fellow
mpaulick[at]stanford.edu
B.S. University of Wisconsin-Madison
Ph.D. University of California, Berkeley
short form

Biography: Margot received her B.S. degree in chemistry from the University of Wisconsin-Madison in 2000.  She then moved 2000 miles across the country to the University of California-Berkeley where she earned her Ph.D. in chemistry in the laboratory of Professor Carolyn Bertozzi.  During her graduate studies, she developed a chemical approach that enables the investigation of the biological functions of the GPI anchor, a glycolipid structure that anchors modified proteins in the cell membrane.  Margot joined the Bogyo lab in the winter of 2007 and is interested in using activity-based probes to understand the functions of serine proteases involved in cancer.

Paul Bowyer
Postdoctoral Fellow
pwbowyer[at]stanford.edu
B.S.
Ph.D. Imperial College of London
short form

Biography: Dr. Bowyer received his Masters of Science degree in chemistry with honours in 2001 from Imperial College London during which he completed an industrial year placement at Zeneca Agrochemicals. He completed his Wellcome Trust funded Ph.D, ’Studies on the N-myristoyltransferase of Plasmodium falciparum’ in 2006 under the guidance of Prof. D. Smith, Dr. K. Brown, Prof. R. Leatherbarrow and Prof. A. Holder in the Division of Cell and Molecular Biology at Imperial College London. In March 2007 he joined the Bogyo Lab and is currently working on the cathepsins of Toxoplasma gondii in addition to development of novel chemical probes of protease activity in P. falciparum.

Fangfang Yin
Postdoctoral Fellow
fyin[at]stanford.edu
B.Sc. Anhui University
Ph.D. Cornell Univsersity School of Medicine
short form

Biography: Dr. Yin received her Bachelor of Science degree with honors in Biochemistry from Anhui University, China in 1999. She completed her doctorate studies at Cornell Medical School in 2008. Her graduate work focused on the in vivo functions of a gene named progranulin in inflammation and neurodegeneration. She joined the Bogyo lab in January 2009 and is currently working on elucidating the roles of proteases in immune responses using mouse models of diseases.

Victoria Albrow
Postdoctoral Fellow
valbrow[at]stanford.edu
B.S. University of Nottingham
Ph.D. University of Nottingham
short form

Biography: Dr. Albrow received her Masters of Science degree in chemistry with honours in 2002 from The University of Nottingham, England where she also completed her Ph.D. studies in 2006 in the laboratory of Prof. S. Woodward. Her thesis work involved the design and synthesis of novel chiral ferrocenyl ligands and their application in the conjugate addition of organoalanes to enones. She joined the Bogyo Lab in March 2007 and is currently focused on the effects of isocoumarin-based compounds on the Apicomplexan parasite Toxoplsma gondii.

Jiyoun Lee
Postdoctoral Fellow
jiyounlee[at]stanford.edu
B.S./M.S. Seoul National University
Ph.D. Northwestern University
short form

Biography: Dr. Lee received her Bachelor of Science degree in pharmacy and Masters of Science degree in medicinal chemistry in 2000 under the guidance of Prof. Jeewoo Lee at Seoul National University, Korea. After finishing her Master’s studies on the development of vanilloid receptor ligands as novel analgesics, she joined the laboratory of Prof. Thomas Meade in the department of chemistry at Northwestern University and completed her Ph.D. studies in 2006. Her thesis work focused on the development of transition metal and lanthanide complexes as molecular probes, particularly receptor-targeted MRI contrast agents. After briefly working in the laboratory of Prof. Chris Chang in the department of chemistry at UC Berkeley, she joined the Bogyo lab in December 2007. Her current project involves the development of activity-based probes for lysosomal proteases and their applications for in vivo imaging.

Aaron Puri
Graduate Student, Chemical and Systems Biology
awpuri[at]stanford.edu
B.A. University of Chicago
short form

Biography:

Beth Ponder
Graduate Student, Microbiology and Immunology
eponder[at]stanford.edu
B.S. Lafayette College
short form

Biography: Elizabeth earned her B.S. degree in Biochemistry from Lafayette College in 2004. Her undergraduate studies focused on the effects of Echinostoma caproni and Schistosoma mansoni parasite infections on simple metabolite profiles in snail intermediate hosts and factors affecting shed parasite survival. Elizabeth enrolled in the Stanford Microbiology and Immunology Ph.D. program in the fall of 2004 and is currently working on a thesis project using small molecule inhibitors to understand the role of cysteine proteases in the life cycle of the human malaria parasite, Plasmodium falciparum.

Laura Edgington
Graduate Student, Cancer Biology
laurae1[at]stanford.edu
B.A. Transylvania University
short form

Biography: .

Mark Rice
Research Consultant
mjrice[at]stanford.edu
B.S.E. U.W. Seattle
Ph.D. U.C. Berkeley
short form

Biography: Dr. Rice received his bachelors degrees in Chemical Engineering and Bioengineering at the University of Washington in Seattle. At the University of California, Berkeley, he completed his Ph.D. studies working on computational studies on the catalytic activity of zeolites. Since 1999, he has worked as a computation chemist, supporting structure based drug design at Axys Pharmaceuticals (acquired by Celera) and Millenium Pharmaceuticals. In the Bogyo lab, Dr. Rice is offering computational and modeling support on several protease projects.

Carolyn Phillips
Graduate Student, Microbiology and Immunology
phillica[at]stanford.edu
B.A. West Virginia Univ.
short form

Biography: Carolyn earned her B.A. degree in Biology at West Virginia University in 2002. Prior to enrolling at in the Ph.D. program at Stanford in 2003, Carolyn was awarded a pre-IRTA Fellowship to work for 1 year at the NIH . Her project was focused on applying yeast genetics to study protein trafficking. She is currently working on a thesis project in the Bogyo Lab to define the functional roles of cysteine proteases in the human parasite, Toxoplasma gondii using small molecule inhibitors and probes.

Galia Blum
Postdoctoral Fellow
galia[at]stanford.edu
B.Sc. Hebrew Univ. of Jerusalem
Ph.D. Hebrew Univ. of Jerusalem
short form

Biography: Dr. Blum received her B.Sc. in Chemistry from the Hebrew University of Jerusalem, Israel 1994. She carried out her doctoral studies at the Hebrew University of Jerusalem, in the laboratory of Professor Alexander Levitzki, for this work she was awarded the Polack prize for excellence in studies and research from the Institute of Life Sciences, The Hebrew University of Jerusalem. Her research focused on Development of potent inhibitors of Insulin-like Growth Factor 1 receptor as anti cancer drugs. Dr. Blum received her Ph.D. in the spring of 2003 and has been a postdoctoral researcher at Stanford University in the laboratory of Professor Matthew Bogyo since this time. Her postdoctoral work involves organic synthesis, protein biochemistry, enzymology and fluorescent imaging to investigate protease activity associated with human pathologies.

Zhimou Yang
Postdoctoral Fellow
yangzm[at]stanford.edu
B.S. Nanjing University
Ph.D. Hong Kong Univ. of Sci. & Tech.
short form

Biography: Dr. Yang received his B.Sc. in Polymer Science from the Nanjing University of Nanjing, China in 2001. He carried out his doctoral studies in the department of Chemistry of the Hong Kong University of Science and Technology, in the laboratory of Professor Bing Xu. His research focused on design, synthesis, enzymatic regulation, and biological Applications of molecular hydrogels. Dr. Yang received his Ph.D. in the August of 2006 and now is a postdoctoral researcher at Stanford University in the laboratory of Professor Matthew Bogyo. His postdoctoral work involves in organic synthesis, protein labeling, enzymology and fluorescent imaging to probe protease activity.

Alicia Berger
Graduate Student, Cancer Biology
bergera[at]stanford.edu
B.A. U.C. Boulder
short form

Biography: Alicia earned her B.A. degree in Molecular Biology and Biochemistry at University of Colorado, Boulder in 2003. During her undgraduate studies she worked in several research laboratories working on projects related to apoptosis, environmental microbiology and RNAi. She started as a Ph.D student in the Cancer Biology Program at Stanford in the Fall of 2003. She is currently working on a thesis project to develop and apply small molecule probes of caspases.

Steven Verhelst
Postdoctoral Fellow
verhelst[at]stanford.edu
M.S. Leiden University
Ph.D. Leiden University
short form

Website: http://www.wzw.tum.de/verhelst

Biography: Dr. Verhelst commenced his studies in chemistry, during which he did two internships. The first one, at the Leiden Institute of Chemistry under supervision of Prof. Dr. J. H. van Boom and Dr. H. S. Overkleeft, concerned the design and synthesis of novel sugar amino acids as conformationally rescricted dipeptide isosters. The second internship was performed at Harvard Medical School in the group of Prof. Dr. H. L. Ploegh and was directed towards the synthesis and evaluation of several protease inhibitors. He received his Masters degree in Chemistry cum laude from Leiden University. He carried out a Ph.D. in bio-organic synthesis under the supervision of Prof. Dr. J. H. van Boom, Prof. Dr. C. A. A. van Boeckel and Dr. G. A. van der Marel. His work involved the synthesis of analogs of aminoglycoside antibiotics. He received his Ph.D. from Leiden University in 2004. Currently, he is employed a post-doctoral fellow at Stanford University in the group of Dr. M. Bogyo, where he is working on the synthesis of serine and cysteine protease activity-based probes and their application as proteomic tools.

Shirin Arastu Kapur
Postdoctoral Fellow
shirinak[at]stanford.edu
B.S. Moravian College
Ph.D. Oregon Health & Sciences Univ.
short form

Biography: Dr. Kapur received a Bachelors of Science degree in chemistry with a minor in Biology in 1997 from Moravian College. She completed her Ph.D. studies in 2004 in the laboratory of Dr. Buddy Ullman at Oregon Health and Sciences University. Her thesis work was focused on functional studies of the inosine/guanosine nucleoside transporter from Leishmania donovani. She joined the Bogyo Lab in June 2004 and is currently working on functional studies of serine proteases in the human malaria parasite Plasmodium falciparum.

Amir Masoud Sadaghiani
Research Associate
feengil[at]stanford.edu
B.S. U.C. Davis
short form

Biography: Mr. Sadaghiani received a Bachelor of Science degree in Biochemistry and Molecular Cellular Biology from the University of California, Davis in 2003. During his undergraduate studies he worked as a Research Associate in the laboratory of Dr. Robert Fairclough in the Department of Neurology at UC Davis. Mr. Sadaghiani joined the laboratory of Dr. Matthew Bogyo at Stanford University in October 2004. He is currently working on the design and synthesis of libraries of small molecule protease inhibitors.

Marko Fonovic
Postdoctoral Fellow
mfonovic[at]stanford.edu
B.S. Univ. Ljubljana
Ph.D. Univ. Ljubljana
short form

Biography: Dr. Fonovic received a Bachelors of Science degree in chemistry from University of Ljubljana in 1998. He earned his Ph.D. in biochemistry and molecular biology in 2004 at the same university, working at Jozef Stefan Institute under the guidance of Prof. Dr. Vito Turk and Assist. Prof. Dr. Boris Turk. In 1999, he worked three months in Dr. Dieter Brömmes lab, at Mount Sinai School of Medicine, New York cloning, expressing and characterizing novel human cysteine proteases. In 2004 he joined the research group of Assist. Prof. Dr. Matthew Bogyo at Stanford Universitiy School of Medicine, where he is working on proteomic analysis of proteases in complex samples and the study of host-parasite interactions of Toxoplasma gondii.

Fang Yuan
Postdoctoral Fellow
chemyuanfang@yahoo.com
B.S. Jilin University
M.S. Nankai University
Ph.D. Nanjing University
short form

Biography: Dr. Yuan conducted his graduate work at Nanjing University in organometallic synthesis, asymmetric catalysis and multi-step organic synthesis. Dr. Yuan then worked as a post-doc in Professor Bing Xu at the Hong Kong University of Science and Technology. In the Xu Lab, he synthesized oligopeptides using solution and solid-phase chemistries, characterizing gelation rules by changing the peptide structures.

Kelly B. Sexton
Postdoctoral Fellow
kellymb[at]stanford.edu
B.S. Univ. Georgia
Ph.D. U.C. San Diego
short form

Biography: Dr. Sexton received her B.S. in Biochemistry and Molecular Biology from the University of Georgia in 1999. She carried out her doctoral studies at the University of California, San Diego, where she worked in the laboratory of Professor Guy S. Salvesen at the Burnham Institute in La Jolla. From 2002 until 2004 she was funded by a dissertation fellowship from the California Breast Cancer Research Foundation. Her research focused on investigating the mechanisms of initiator caspase activation. For this work she was awarded the Molecular Pathology Excellence in Research Award in 2003. Dr. Sexton received her Ph.D. in the Fall of 2004 and has been a postdoctoral researcher at Stanford University in the laboratory of Professor Matthew Bogyo since this time. Her postdoctoral work involves the integration of protein biochemistry, enzymology and chemical proteomics to investigate pathways associated with human pathologies.

Daisuke Kato
Research Associate
daisukek[at]stanford.edu
B.S. U.C. Davis
short form

Biography: Mr. Kato received a Bachelors of Science degree in Biotechnology with a special emphasis in Biochemistry from the University of California, Davis in 2002. While working towards his undergraduate degree Mr. Kato worked as a Research Assistant in the Department of Biochemistry at UC Davis Medical School where he investigated the molecular mechanisms of polysialylation associated with human cancer metastasis and neural development. In 2003, Mr Kato joined the laboratory of Dr. Matthew Bogyo at Stanford University as Research Associate. While at the Boygo Lab, he worked on the synthesis and application of novel activity based probes for proteases. Currently, he is attending graduate school at the Scripts Research Institute.

Christine Yang
Undergraduate Researcher
christine.yang[at]stanford.edu
short form

Biography: Christine is a junior at Stanford University. She joined the Bogyo Lab in the Spring of 2004. She is currently working on the analysis of falcipain I knockout of the malaria parasite Plasmodium falciparum.