University
of California, San Francisco Prepared: 8/19/10
CURRICULUM VITAE
Name: Matthew
P. Jacobson
Position: Associate
Professor and Vice Chair, Department of Pharmaceutical Chemistry
Associate
Professor, WOS, Department of Bioengineering and Therapeutic Sciences
School
of Pharmacy
Member: Graduate
Group in Biophysics
Chemistry
and Chemical Biology Graduate Program
Graduate
Program in Biological and Medical Informatics
Program
in Biological Sciences
Program
in Quantitative Biology
Integrative
Program in Complex Biological Systems
California Institute for Quantitative Biosciences
Address: UCSF
MC 2240
Genentech
Hall Room N472C
600
16th Street
San
Francisco, CA 94158-2517
Voice: 415-514-9811
FAX: 415-502-4222
Email: matt.jacobson@ucsf.edu
Web: http://jacobsonlab.org
1989-1993 Stanford University, Stanford,
CA B.S.,
Honors Chemistry
1994-1999 MIT, Cambridge, MA Ph.D. Physical
Chemistry
1999-2000 University of Oxford, England,
UK Post-Doctoral Physical
Chemistry
2000-2002 Columbia University, New York,
NY Post-Doctoral
Computational
Biology
1999-2000 University College, Oxford Research
Lecturer Physical
Chemistry
2002-2007 University of California, San
Francisco Assistant
Professor Pharmaceutical Chemistry
2007- University
of California, San Francisco Associate
Professor Pharmaceutical Chemistry
2007- University
of California, San Francisco Vice
Chair Pharmaceutical
Chemistry
2008- University
of California, San Francisco Associate
Professor Bioengineering and
(WOS) Therapeutic
Sciences
FELLOWSHIPS,
HONORS AND AWARDS
1989 David
Starr Jordan Scholar, Stanford University
1993 Phi
Beta Kappa, Stanford University
1993 American
Institute of Chemists Graduation Award, Stanford University
1995-1998 National Defense Science and
Engineering Graduate Fellow
1997 Rao Prize, for Òoutstanding student talkÓ at the
International Symposium on Molecular Spectroscopy (Ohio State University)
1998-1999 Fannie and John Hertz Fellow
1999-2000 EPSRC (Engineering and Physical
Sciences Research Council, U.K.) Visiting Fellow
2000 Air
Force Research Laboratory, Space Vehicles Directorate ÒTeam Publication of the
Year AwardÓ (See peer-reviewed publications, #10).
2000-2002 National Science Foundation
Postdoctoral Fellowship in Biological Informatics
2004 NSF
CAREER Award
2004 Alfred
P. Sloan Research Fellowship
2006 UCSF
School of Pharmacy DeanÕs Recognition for Excellence in Teaching
KEYWORDS/AREAS OF INTEREST
Physical
chemistry, protein structure prediction, homology modeling, rational drug
design, protein phosphorylation, electrostatics, quantum mechanics, statistical
mechanics, thermodynamics.
PROFESSIONAL
ACTIVITIES
PROFESSIONAL ORGANIZATION MEMBERSHIPS
American
Chemical Society
SERVICE TO PROFESSIONAL PUBLICATIONS
Ongoing Reviewer
for: Science, Nature, PNAS,
Structure, JACS, Chemistry, Biochemistry, PLOS Computational Biology, Journal
of Molecular Biology, Journal of Biological Chemistry, Protein Science, Journal
of Computational Chemistry, Journal of Physical Chemistry, Journal of Chemical
Physics, Journal of Computer-Aided Molecular Design, Journal of Chemical
Information and Modeling, Molecular and Cellular Proteomics, Journal of
Proteomics Research, Journal of Chemical Theory and Computation, Biomacromolecules, ChemMedChem,
Biopolymers, Nucleic Acids Research, Chemistry and Biology, Journal of
Medicinal Chemistry, Biophysical Journal, Biochimica
et Biophysica Acta.
2003-2006 Faculty of
1000 Reviewer, ÒBiomacromolecule-Ligand InteractionsÓ
section
2005- Editorial
Advisory Board, Chemical Biology and Drug Design
2006- Editorial
Advisory Board, Chemistry Central Journal (an open access journal)
2006 Guest,
Annual Reviews of Physical Chemistry Editorial Committee Planning Meeting
2007 Guest
Associate Editor, PLOS Computational Biology
2007-2010 Associate
Editor, PLOS Computational Biology
INTERNATIONAL
2000 CECAM
Workshop on Highly Excited Polyatomic Molecules, Lyon, France
2006 Canadian
Computational Chemistry Conference
2007 Academica Sinica, Taipei, Taiwan
2007 Gordon
Research Conference:
Computer-Aided Drug Design
2008 Gordon
Research Conference: Computational
Chemistry
2009 U.
Regensburg, Germany
2009 U.
Dusseldorf, Germany
2009 Barcelona
Supercomputer Center, Spain
2010 Caribbean
Meeting on Structure Biology of Drug Discovery
NATIONAL
1998 Air
Force Office of Sponsored Research Contractors' Meeting, Monterey, California
1998 ITAMP
Workshop on Quantum Nonintegrability, Harvard
University
1998 ACS
National Meeting, Boston, MA. Speaker and Session Chair, ÒSpecial
Topics in High-Resolution SpectroscopyÓ
2002 SIAM
Life Sciences Conference, Symposium on Multiscale
Modeling, Boston, MA
2003 NIGMS
ÒHigh Accuracy Comparative Modeling WorkshopÓ, Bethesda, MD
2006 ACS
National Meeting, Atlanta, GA
2006 ACS
National Meeting, San Francisco, CA
2007 ACS
National Meeting, speaker and session chair, Chicago, IL
2007 Protein
Society National Meeting, Boston, MA
2008 Keystone
Symposium on Computer-Aided Drug Design
2008 ICAM
Frontiers of Science Workshop, UCSD
2009 ASBMB
National Meeting, New Orleans, LA
2010 Telluride
Symposium on Phosphoryl Transfer, Telluride, CO
2010 ACS
National Meeting, San Francisco, CA
2010 Cold
Spring Harbor blood-brain barrier meeting
2010 ACS
National Meeting, Boston, MA
2011 Winter
Enzyme Mechanisms Conference, FL
2011 Peptalk, ÒAntibodies for the 21st CenturyÓ, San
Diego, CA
2011 Keystone
Conference on Evolution of Phosphoregulation
OTHER INVITED PRESENTATIONS
1998 Molecular
Optics and Spectroscopy Seminar Series, MIT
1999 Algebraic
Methods in Molecular Physics Conference, University of Washington
1999 Oxford
University Theoretical Chemistry Seminar
2001 Stanford
University Physical Chemistry Seminar
2001 Northwestern
University Chemistry Seminar
2001 Cornell
University Chemistry Seminar
2001 University
of California (Berkeley) Chemistry Seminar
2001 MIT
Chemistry Seminar
2001 New
York University Chemistry Seminar
2001 University
of Colorado (Boulder) Chemistry Seminar
2002 University
of California (San Francisco) Pharmaceutical Chemistry Seminar
2002 University
of Texas (Austin) Chemistry Seminar
2002 University
of Illinois (Urbana-Champaign) Chemistry Seminar
2002 University
of Chicago Chemistry Seminar
2002 Graduate
Group in Biophysics Retreat, UCSF, faculty speaker selected by students
2004 World Molecular Engineering Network
Conference, Los Cabos, Mexico
2004 Chiron
Corporation
2004 Center
for Computational Biology, Washington University, St. Louis, MO
2004 UCSF
Seminars in Quantitative Biology
2004 UCSF
Biophysics/CCB retreat, Asilomar, CA (conference
organizer and speaker)
2004 eCheminfo, ÒApplications of Cheminformatics
and Modelling to Drug DiscoveryÓ
2005 Center
for Computational Biology and Bioinformatics, U. Pittsburgh
2005 UC
Santa Cruz Chemistry Seminar
2005 Biogen, Cambridge, MA
2005 Genentech,
South San Francisco, CA
2005 Biological
and Medical Informatics Graduate Group Retreat, faculty speaker
2006 University
of Minnesota, New Frontiers in Drug Discovery: The Power of Chemical Library
Development and Screening
2006 Schrodinger
UsersÕ Summit, panelist and invited speaker
2006 Amgen,
South San Francisco, CA
2006 Novartis,
Emeryville, CA
2006 Theravance, South San Francisco, CA
2006 Arizona
State University, Biological Physics Seminar
2006 University
of Illinois, Urbana-Champaign, Chemical Biology Lecture Series
2007 Sanibel
Symposium, University of Florida
2007 Columbia
University, Department of Chemistry seminar series
2007 Rochester
University, Department of Chemistry seminar series
2007 Wyeth,
Pearl River, NJ
2007 Ensemble
Discovery, Cambridge, MA
2008 NIH
Workshop on Applications of Protein Models in Biomedical Research
2008 Schrodinger
Inc. Regional User Symposium
2009 Biosciences
and Biotechnology Division Seminar Series, Lawrence Livermore National
Laboratory
2010 U.
Texas Biophysics Seminar, Austin, TX
2010 Genentech,
South San Francisco, CA
2010 San
Jose State University, Department of Chemistry
2010 Indiana
University, Center for Computational Biology and Bioinformatics
2010 Schrodinger
User Group Meeting, South San Francisco, CA
2010 Vertex,
Cambridge, MA
GOVERNMENT AND OTHER PROFESSIONAL SERVICE
2004 Congressionally
Directed Medical Research Programs Teleconference
Reviewer
(Chronic
Myelogenous Leukemia Review Panel)
2004 U.S.
Civilian Research and Development Foundation Reviewer
2006 ACS
Petroleum Research Fund Peer
review
2006 NIH
Mail Reviewer Peer
review
2007 NIH
DDR study section Ad-hoc
reviewer
2007 St.
Jude, Dept. of Structural Biology SAB
member
2007-2010 NSF Mail Reviewer Peer
review
2007 NIH
SCORE review panel (ZMG1 MBRS-3) Peer
review
2008 U.S.-Israel
Binational Science Foundation Peer
review
2008 NIH
MSFE review panel Peer
review
2008 Defense
Threat Reduction Agency Basic Sciences Peer
review
2009 Israel
Science Foundation Peer
review
2009 ICREA
(Catalan Institute of Research) Promotion
review
2009 NIH
Challenge Grant panel Peer
review
2009 Wellcome Trust/DBT India Alliance Peer
review
2009 NIH
Special Emphasis Panel (Biophysics) Peer
review
2010 NIH
MSFD study section Ad-hoc
member
2010 NWO
(Netherlands) Peer
review
CONSULTING
2003- Schrodinger
Inc. SAB
member
2007 Novartis Consultant
2005, 2007 D. E. Shaw
Research Consultant
2007-2008 Genepharm Inc. SAB
member
SABBATICAL VISITORS HOSTED
2006 Chris
Oostenbrink Vrije Universitet, Amsterdam
2008 Pradipta Bandyopadhyay Jawaharlal
Nehru University, New Delhi, India
2008 Evangelos
Coutsias University
of New Mexico
UNIVERSITY
AND PUBLIC SERVICE
UNIVERSITY SERVICE
2005-2006 Chair, School of Pharmacy
Faculty Council
2005-2006 Member, UCSF Academic Senate Coordinating
Committee
2005-2006 Member, UCSF Academic Senate Executive
Committee
2005-2006 Member ex officio, Academic Planning and Budget Committee
2005-2006 Member, ChancellorÕs Council
2006 Member, Task Force Reviewing Proposed Changes to APM 220
2006 Member,
Task Force Reviewing Proposed Changes to APM 700, 710, 711, and 080
2007 Reviewer,
Packard Foundation Fellowships (internal competition)
2007 Reviewer,
Burroughs-Wellcome Career Award (internal
competition)
2009 Faculty
Mentoring Award Selection Committee
2009 Reviewer,
Keck Foundation Program in Medical Sciences (internal competition)
2009 Postdoc bootcamp, mock interview
session
SCHOOL OF PHARMACY
2003-2004 Student Welfare Committee
2004, 2008 Admissions Interviewer
2004-2006 Member, Faculty Council
2004-2005 Strategic Planning Committee
2005-2007 Taskforce on Underrepresented
Minorities
2007 Software
income policy taskforce
DEPARTMENTAL SERVICE
2003-2004 Department of Pharmaceutical
Chemistry Faculty
Search Committee
2006-2007 Department of Pharmaceutical
Chemistry Faculty
Search Committee
2007-2008 Department of Pharmaceutical
Chemistry Department
Chair Search Committee
2007-2009 Department of Pharmaceutical
Chemistry Chair,
Faculty Search Committee
2010- Dept.
of Bioengineering and Therapeutic Sciences Faculty
Search Committee
GRADUATE PROGRAMS
2003, 2006 Chemistry and Chemical Biology
Graduate Program Admissions
Committee
2004-now Chemistry and Chemical
Biology Graduate Program Curriculum
Committee
2003 Graduate
Group in Biophysics Admissions
Committee
2004-now Graduate Group in
Biophysics Curriculum
Committee
2004-2005 Graduate Group in Biophysics Organizer,
Asilomar Retreat
2006- Graduate
Group in Biophysics Executive
Committee
2007-2008 Chemistry and Chemical Biology
Graduate Program Student
Advisor
2008- Graduate
Group in Biophysics Director
2008- PIBS Executive
Committee
2010- Quantitative
Biosciences Consortium (QBC) Vice
Chair
SUMMARY
OF SERVICE ACTIVITIES
My
early service activities were largely in support of the graduate programs in
which I participate, especially the Graduate Group in Biophysics. I served as Chair of the School of
Pharmacy Faculty Council for 2005-2006, which of course involved me in the
activities of a ridiculous number of Academic Senate committees. Beginning in 2008, I agreed to serve as
Director of the Graduate Group in Biophysics, and a Vice Chair in my
department.
TEACHING
and MENTORING
FORMAL SCHEDULED CLASSES
FOR UCSF STUDENTS
|
Q |
Year |
Number |
Title |
Contribution |
Units |
Class
Size |
|
F |
2002-03 |
Chemistry 111 |
Physical Chemistry |
Lab instructor (8 labs) |
4 |
123 |
|
W |
2002-03 |
Biophysics 206 |
Computation of Biological Molecules |
Course director, sole lecturer (10 lectures), developed
syllabus |
2 |
25 |
|
S |
2002-03 |
Chemistry 262 |
Quantum Mechanics |
Course director, sole lecturer (20 lectures), developed
syllabus |
3 |
6 |
|
F |
2003-04 |
Chemistry 111 |
Physical Chemistry |
Lecturer (14 lectures); lab instructor (8 labs) |
4 |
123 |
|
F |
2003-04 |
Biochem
200A |
Macromolecules |
1 lecture |
3 |
~50 |
|
S |
2003-04 |
Biophysics 206 |
Computation of Biological Molecules |
Course director, lecturer (13 lectures); developed
syllabus |
3 |
20 |
|
F |
2004-05 |
Chemistry 111 |
Physical Chemistry |
Course director, lecturer (15 lectures) |
4 |
123 |
|
F |
2004-05 |
Biochem
200A |
Macromolecules |
1 lecture |
3 |
~50 |
|
W |
2004-05 |
Medicine 170.09 |
Current Topics in Medical Science |
1 lecture |
2 |
20 |
|
S |
2004-05 |
Biophysics 206 |
Computation of Biological Molecules |
Course director, lecturer (14 lecture hours) |
3 |
8 |
|
F |
2005-06 |
Chemistry 111 |
Physical Chemistry |
Course director, lecturer (15 lectures) |
4 |
123 |
|
F |
2006-07 |
Biophysics 204 |
Macromolecular Interactions |
Lecturer (13.5 contact hours) |
4 |
20 |
|
W |
2006-07 |
BMI 206 |
Computational Biology |
Co-director, Lectures (12 contact hours) |
4 |
20 |
|
W |
2006-07 |
BBC Journal Club |
BBC Journal Club |
Facilitator (12 contact hours) |
1 |
30 |
|
F |
2007-08 |
Biophysics 204 |
Macromolecular Interactions |
Lecturer (18 contact hours) |
4 |
32 |
|
S |
2007-08 |
Biophysics 206 |
Computation of Biological Molecules |
Course director, ~14 lecture hours |
3 |
10 |
|
F |
2008-09 |
Biophysics 204 |
Macromolecular Interactions |
Lecturer (18 contact hours) |
4 |
30 |
|
S |
2008-09 |
Mini course |
Molecular simulations: membranes and membrane proteins |
Director: ~24 contact hours |
3 |
10 |
|
F |
2009-10 |
Biophysics 204 |
Macromolecular Interactions |
Lecturer (8 lecture hours) |
4 |
30 |
|
F |
2009-10 |
PC 111 |
Physical Chemistry (PharmD) |
Director: ~24 lecture hours |
4.5 |
123 |
|
S |
2009-10 |
Mini course |
Modeling spatial organization in cells |
Director: ~20 contact hours |
3 |
7 |
PREDOCTORAL STUDENTS
SUPERVISED OR MENTORED
|
Dates |
Name |
Program
or School |
Role |
Current
Position |
|
2002-2006 |
Sergio
Wong |
Biophysics/PQB |
PhD
advisor |
Postdoc, LLNL |
|
2002-2006 |
Hod Greeley |
Columbia
University |
Joint
research advisor |
Samsung |
|
2003-2008 |
Eli
Groban |
Biophysics/PQB |
PhD
advisor |
LS9 |
|
2003-now |
Benjamin
Sellers |
Biophysics/PQB |
PhD
advisor |
Genentech |
|
2003-2008 |
Jerome
Nilmeier |
Biophysics/PQB |
PhD
advisor |
Postdoc, UCB |
|
2004-2008 |
Arjun Narayanan |
Biophysics |
PhD
advisor |
Postdoc, Yale |
|
2004-2008 |
Nima Fayazmanesh |
MSTP/Biophysics |
PhD
advisor |
UCSF
medical school |
|
Dinah Zaghi |
Stern College |
Undergraduate student |
Technician, UCLA |
|
|
2005-2007 |
Laura
Dominguez |
UNAM/UCSF |
Exchange
program advisor |
PhD
student, UNAM |
|
Summer
2006 |
Reina
Eisner |
Stern
College |
Undergraduate
student |
|
|
2004- |
Victor
Kenyon |
UCSC
Chemistry |
Mentor |
|
|
2006- |
Colin
Smith |
BMI
(Bioinformatics) |
PhD
advisor |
|
|
2006- |
Chris
McClendon |
Biophysics |
PhD
advisor |
|
|
2008 |
Francesca
Milletti |
Universitˆ degli Studi di Perugia |
Exchange program |
Roche |
|
Summer
2008 |
Ying
Ye |
U. Illinois Chicago |
SRTP
student |
|
|
2009 |
Alrun Koller |
U. Kiel (Germany) |
Exchange
program |
PhD
student, Germany |
|
2008- |
Monica
Tremont |
Biophysics |
PhD
advisor |
|
|
2009-2010 |
Jona Mijalkovic |
U. Leiden |
Exchange
program |
|
|
2009-2010 |
Daisuke
Kuroda |
U. Kyoto |
Exchange
program |
|
POSTDOCTORAL FELLOWS
SUPERVISED OR MENTORED
|
Dates |
Name |
Position |
Faculty
Role |
Current
Position |
|
2002-2006 |
Katarzyna Bernacki |
NSF
Postdoctoral Fellow |
Research
advisor |
Consultant,
Campbell Alliance |
|
2003-now |
Chakrapani Kalyanaraman |
Assistant
Research Chemist |
Research
advisor |
|
|
2003-2005 |
Ilya
Chorny |
Sloan
Postdoctoral Fellow |
Research
advisor |
Founder,
Simprota |
|
2003-2007 |
Niu Huang |
Postdoctoral
researcher |
Research
advisor |
Assistant
Professor, National Institute of Biological Science, Beijing |
|
2003-2006 |
Song
Ling |
Postdoctoral
researcher |
Supervisor |
System
administrator |
|
2003-2004 |
Michael
Gonzales |
Postdoc, MSI |
Mentor |
Life
Sciences Program Director, Texas Advanced Computing Center |
|
2006-2007 |
Gabriela
Barreiro |
Postdoctoral
researcher |
Research
advisor |
Research
scientist, Pfizer |
|
2008- |
Salma Rafi |
Postdoctoral
researcher |
Research
advisor |
|
|
2008- |
Lan Hua |
Postdoctoral
researcher |
Research
advisor |
|
|
2009- |
Siegfried
Leung |
Postdoctoral
researcher |
Research
advisor |
|
|
2009- |
Michael
Chimenti |
Postdoctoral
researcher |
Research
advisor |
|
|
2009- |
Lena
Dolghih |
Postdoctoral
researcher |
Research
advisor |
|
|
2009- |
Adam
Steeves |
Postdoctoral
researcher |
Research
advisor |
|
|
2010- |
Suwen Zhao |
Postdoctoral
researcher |
Research
advisor |
|
TEACHING NARRATIVE
In my first year as a UCSF
professor, I developed 2 new courses for PhD students: Biophysics 206 (Computation of
Biological Molecules) and Chemistry 262 (Quantum Mechanics). These courses were
previously taught by the late Peter Kollman,
but I developed new curricula from scratch. In 2009. I also created a new
mini-course on molecular modeling, focused on membranes and membrane proteins. Starting in 2006, I am a lecturer in Biophysics 204, a part
of the core curriculum for 3 graduate programs. The goal of these lectures is to introduce the PhD students
to key concepts in molecular simulations, and to encourage them to think
critically about simulations and how to productively combine them with wet lab
experiments. Student participation
in my graduate courses has included the Graduate Group in Biophysics, Chemistry
and Chemical Biology, Biological and Medical Informatics, MSTP, Tetrad, Oral
and Craniofacial Sciences, and Neuroscience.
Finally, also in 2009, I
revamped the physical chemistry curriculum for the PharmD
students, which we now teach as PC 111.
The major changes include more focused and relevant topics from
thermodynamics and kinetics, a new section on drug discovery, and
computer-based exercises. I previously
served as an instructor and director of the ÒoldÓ physical chemistry course, Chemistry
111.