University of
California, San Francisco Prepared: 9/30/2008
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://jacobson.compbio.ucsf.edu
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
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 “outstanding student talk” 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 “Team Publication of the Year
Award” (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 Dean’s 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,
Protein Science, Journal of Computational Chemistry, Journal of Physical
Chemistry,
2003-2006 Faculty of
1000 Reviewer, “Biomacromolecule-Ligand Interactions”
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- 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
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, “Special Topics in High-Resolution Spectroscopy”
2002 SIAM
Life Sciences Conference, Symposium on Multiscale
Modeling, Boston, MA
2003 NIGMS
“High Accuracy Comparative Modeling Workshop”, 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
2007 Gordon Research Conference: Computer-Aided Drug Design
2008 Keystone
Symposium on Computer-Aided Drug Design
2008 Gordon
Research Conference: Computational
Chemistry
2008 ICAM
Frontiers of Science Workshop, UCSD
2009 ASBMB
National Meeting, New Orleans, LA
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,
“Applications of Cheminformatics and Modelling to Drug Discovery”
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
Users’ 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
GOVERNMENT
2004 Congressionally
Directed Medical Research Programs Teleconference
Reviewer
(Chronic
Myelogenous Leukemia Review Panel)
2004 U.S.
Civilian Research and Development Foundation Reviewer
2006
2006 NIH Mail
Reviewer Peer
review
2007 NIH
2007 St. Jude, Dept. of Structural
Biology
2007 NSF Mail Reviewer Peer
review
2007 NIH SCORE review panel (ZMG1
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
CONSULTING
2003- Schrodinger
Inc.
2007 Novartis Consultant
2005, 2007 D. E. Shaw
Research Consultant
2007- Genepharm Inc.
SABBATICAL
VISITORS HOSTED
2006
2008 Pradipta
Bandyopadhyay Jawaharlal
Nehru University, New Delhi, India
2008 Evangelos Coutsias University
of New Mexico
2008-2009 Calvin Chen China
Medical University, Taiwan
UNIVERSITY
UNIVERSITY
SERVICE
UCSF CAMPUS-
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, Chancellor’s 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)
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- Department of Pharmaceutical
Chemistry Department
Chair Search Committee
2007- Department of Pharmaceutical
Chemistry Chair,
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- Chemistry and Chemical Biology
Graduate Program Student
Advisor
2008- Graduate Group in Biophysics Director
2008- PIBS Executive
Committee
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, and the School of Pharmacy, where I have been a member of
several different committees. I served
as Chair of the School of Pharmacy Faculty Council for 2005-2006, which of
course involved me in the activities of several Academic Senate
committees. Beginning in 2008, I have
agreed to serve as Director of the Graduate Group in Biophysics.
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 |
|
Computational
Biology |
Co-director,
Lectures (12 contact hours) |
4 |
20 |
|
W |
2006-07 |
|
|
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 |
PREDOCTORAL STUDENTS SUPERVISED OR MENTORED
|
Dates |
Name |
Program or School |
Role |
Current Position |
|
2002-2006 |
|
Biophysics/PQB |
PhD advisor |
Postdoc, UCSD |
|
2002-2006 |
|
Columbia University |
Joint research advisor |
|
|
2003-2008 |
|
Biophysics/PQB |
PhD advisor |
LS9 |
|
2003-now |
Benjamin Sellers |
Biophysics/PQB |
PhD advisor |
|
|
2003-now |
|
Biophysics/PQB |
PhD advisor |
|
|
2004-now |
|
Biophysics |
PhD advisor |
|
|
2004-now |
|
|
PhD advisor |
UCSF medical school |
|
|
Stern College |
Undergraduate student |
Technician, UCLA |
|
|
2005-2007 |
|
|
Exchange program advisor |
PhD student, |
|
Summer 2006 |
Reina Eisner |
Stern College |
Undergraduate student |
|
|
2004- |
Victor Kenyon |
UCSC Chemistry |
Mentor |
|
|
2006- |
Colin Smith |
|
PhD advisor |
|
|
2006- |
Chris McClendon |
Biophysics |
PhD advisor |
|
|
2008 |
Francesca Milletti |
Università degli
Studi di Perugia |
Exchange
program |
|
|
Summer 2008 |
Ying Ye |
U. Illinois Chicago |
SRTP student |
|
POSTDOCTORAL FELLOWS SUPERVISED OR MENTORED
|
Dates |
Name |
Position |
Faculty Role |
Current Position |
|
2002-2006 |
|
NSF Postdoctoral Fellow |
Research advisor |
Genentech |
|
2003-now |
Chakrapani Kalyanaraman |
Assistant Research Chemist |
Research advisor |
|
|
2003-2005 |
|
Sloan Postdoctoral Fellow |
Research advisor |
Postdoc, UCSF |
|
2003-2007 |
|
Postdoctoral researcher |
Research advisor |
Assistant Professor, National Institute of
Biological Science, Beijing |
|
2003-2006 |
|
Postdoctoral researcher |
Research advisor |
System administrator |
|
2003-2004 |
Michael Gonzales |
Postdoc, |
Mentor |
Life Sciences Program Director, Texas
Advanced Computing Center |
|
2006-2007 |
|
Postdoctoral researcher |
Research advisor |
Research scientist, Pfizer |
|
2008- |
Salma Rafi |
Postdoctoral researcher |
Research advisor |
|
|
2008- |
Lan Hua |
Postdoctoral researcher |
Research advisor |
|
OTHER TEACHING
1995 Author
of textbook, “Laser Experiments for Beginners”
2000 External
Tutor, Advanced Physical Chemistry, Keble College, University of Oxford
2003-2004 Faculty coach for PIBS Journal Club (6
students)
2005- Faculty coach for
2003 Invited speaker at “CCB Chats”: Successful transitions from postdoc to professor
2004-2005 Joint mentor for GREAT fellowship
applications: 3 Biophysics students
2003- Oral examination committees:
Chemistry and Chemical Biology (6
students, chair of 1 committee); Bioengineering (1 student); Oral and
Craniofacial Sciences (1 student); Biophysics (8 students, chair of 4 committees);
Biological and Medical Informatics (6 students; chair of 1 committee);
Pharmaceutical Sciences and Pharmacogenomics (1 student)
2003- Thesis committees (other than my
own students): Chemistry and Chemical Biology (5 students); Biophysics (3
students); Oral and Craniofacial Sciences (1 student);
2005 Nominated for Postdoctoral
Scholar’s Association Outstanding Mentorship Award
2006- Faculty coach, 2nd
year talk for
2008 Speaker at UCSF Scientific
Leadership and Management Course
SUMMARY OF
TEACHING
2003-2004 Total hours
of teaching (including preparation): 222
Formal
class or course teaching hours: 69
Mentoring
hours: ~500
2004-2005 Total hours
of teaching (including preparation): 120
Formal
class or course teaching hours: 31
Mentoring
hours: ~500
2005-2006 Total hours
of teaching (including preparation): 60
Formal
class or course teaching hours: 15
Mentoring
hours: ~500
2006-2007 Total hours
of teaching (including preparation): 50
Formal
class or course teaching hours: 13.5
Mentoring
hours: ~500
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.
My goal in teaching Biophysics 206 is to deepen understanding of physics-based
approaches to biomolecular modeling, for a broad array of students. Course attendance, including many
post-doctoral researchers auditing the course, has ranged between 10-30. Student participation has included the
Graduate Group in Biophysics, Chemistry and Chemical Biology, Biological and
Medical Informatics, and
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.
My other
teaching responsibility is Chemistry 111 (Physical Chemistry), a required
course for first-year PharmD students (123
students). This course contains a
laboratory component, and during my first two years I was the instructor for
one lab section. During 2003-2005, I
also assumed responsibility for teaching half of the lectures for the course,
as well as associated responsibilities of setting/grading exams, holding office
hours, and course management. During
2004 and 2005, I was course director. I
have invested considerable effort into continuously updating the curriculum to
make it more responsive to the students’ needs and interests. During 2005, I revamped the examination schedule,
created a new computer-based laboratory, and added new material on
pharmaceutically relevant applications of physical chemistry. I will be course director of a new version
of the class beginning in Fall 2009, pending approval of the proposed curriculum
changes, which put greater emphasis on pharmaceutical applications.