Debra
S. Goldberg, Ph.D.
§
Computational
molecular biology
§
Algorithms
for noisy and error-prone data
§
Graph
theory
§
Comparative
genomics
§
Combinatorics
§
Discrete
mathematics
§
Genomic
network analysis
Ph.D.
Applied Mathematics 2001
M.S. Applied
Mathematics 2000
Advisors: Jon Kleinberg (Computer
Science) and
Susan McCouch (Plant Breeding & Genetics)
Dissertation: Algorithms for constructing
comparative genome maps.
M.S.
Computer Science 1988
Advisor: James Hagler (Mathematics
and Computer Science)
Thesis: Algorithms and
constructions related to combinatorial design of maximal families of k-tuples.
B.S.
Biology 1984
Advisor: Jeffrey Powell (Biology)
Senior Project: A computer simulation of an original
mathematical model of nucleic and mitochondrial DNA based on observations of
populations of Drosophila.
Harvard Medical School, Research
Fellow 2001-2005
Dr.
Frederick Roth (advisor), Department of Biological Chemistry & Molecular
Pharmacology
Dr.
Marc Vidal (co-mentor), Department of Genetics, Dana Farber Cancer Institute
Developed graph-theoretic algorithms to enhance understanding of diverse types
of large-scale genomic data, such as protein-protein interaction networks. Integrated protein interaction, gene expression,
and gene knockdown phenotype data and exploited the small-world and other
topological properties of genomic networks to make interaction and function
predictions.
Cornell University, Doctoral Research,
Center for Applied Mathematics 1996-2001
Dr.
Jon Kleinberg (advisor), Department of Computer Science
Dr.
Susan McCouch (advisor), Department of Plant Breeding & Genetics
Provided a rigorous mathematical framework for the construction of comparative
genome maps with the goal of identifying common ancestral chromosome
fragments. Developed broadly applicable
models that balance parsimony and accuracy using dynamic programming
techniques. Applied methods to
rice-maize, rice-sorghum, and human-mouse comparisons.
TRW Space & Defense, Aurora, CO, Senior Member of Technical Staff 1988-1996
Research and development. Designed,
implemented, tested, and maintained signal processing algorithms to gain
insights from noisy data. Responsible to
keep system operational 24 hours a day.
Wrote portions of proposals considered critical to company activities.
The Johns Hopkins School of Medicine,
Research Programmer 1985-1986
Dr.
Dean Wong (supervisor), Department of Nuclear Medicine
Analyzed data from human Positron Emission Tomography (PET) scan studies. Assisted with the design of theoretical
models of brain biochemistry.
The Johns Hopkins School of Medicine, Sr. Lab Technician 1984-1985
Dr.
Marshall Plaut (supervisor), Department of Clinical Immunology
Studied human macrophages. Responsible
for all phases of the cycle for in-vitro research, including experimental
design, specimen collection, cell culture, analysis and reporting of results,
and subsequent redesign and refinement of procedures.
Yale University, Undergraduate Research 1984
Dr.
Jeffrey Powell, Biology Department
Senior project: developed an original
mathematical model of nucleic and mitochondrial DNA inheritance in Drosophila
and wrote a computer simulation.
Yale University, Undergraduate Research 1983
Dr.
Steven Handel, Biology Department
Independent research project: grew controlled replicate plants in a greenhouse
and performed statistical analysis.
Yale School of Medicine, Lab Technician 1980-1982
Department of Dermatology, part-time.
Rockefeller University, High School Extern 1979
Lab Technician: one semester, full-time.
Ran polyacrylamide gel electrophoresis experiments.
Cornell University,
Department of Computer Science, Lecturer 2000
Data Structures. Senior-level
class. 5 lectures/week. Managed 2 TAs.
On course evaluations, averaged less than 2.1 for question ”How did the
teaching skills of the instructor in this course compare with other
instructors? (1) very favorably (5) very
unfavorably”
Some completions to the statement “The aspects of this course I valued
most were:”
- “Teaching was very good, I
learned a lot.”
- “Great instructor and great
TAs. HWs have the right level of
difficulty, though it’s a rush in summer.”
- “Clear presentation of
material.”
- “The obvious engagement of the
instructor in the material, the availability of help.”
- “The homework and quizzes kept me
on track and get [sic] a good understanding of the course.”
A complete list of comments and average scores available upon request.
Cornell University,
Department of Computer Science, Teaching
Assistant
Introduction to Computer Programming (Java) 1999
Discrete Structures; Introduction to Computer Programming
(C++) 1996-1997
TRW Space & Defense, Aurora, CO, Senior
Member of Technical Staff
Organized and taught a class on signal processing algorithms. 1995-1996
Led development, teaching of 12-day software maintenance class for customers. 1988-1990
University of Denver, Department of Mathematics and Computer Science,
Teaching Assistant 1987-1988
Taught Core Computer Lab; Taught Calculus III problem sessions.
University of Denver, Computing and Information Resources, User Consultant 1988
Prepared and taught classes on the use of commonly used software and assisted
university computer users.
Sylvan Learning Center, Littleton, CO, Tutor 1986-1988
Basic skills, SAT preparation, enrichment.
Elementary and high school students.
Yale University, Department of Computer Science, Tutor 1984
Introduction to Computer Programming (Pascal)
Harvard Medical School, Research Fellow 2001-2005
Hired and managed an undergraduate research assistant.
TRW Space & Defense, Aurora, CO, Senior Member of Technical Staff 1988-1996
Managed maintenance and upgrade group for software required to operate 24 hours
a day.
Group Lead, design and implementation of new signal processing algorithms.
Coordinator for a 500-page volume of a proposal for recompetition of
company’s major contract.
Factory Direct Sales, Littleton, CO, M.I.S.
Manager 1986-1987
Supervised all aspects of data processing department responsible for all
programming needs of the company.
1.
L Zhang, OD King, SL Wong, DS
Goldberg, AHY Tong, G Lesage, B Andrews, H Bussey, C Boone, FP
Roth. Motifs, themes and thematic
maps of an integrated S. cerevisiae
network. (in review)
2.
SL Wong, LV Zhang, AHY Tong, Z Li, DS Goldberg, OD King, G Lesage, M Vidal, B
Andrews, H Bussey, C Boone, FP Roth. Combining
biological networks to predict genetic interactions. Proceedings
of the National Academy of Sciences 101: 15682-15687 (2004).
3.
J-DJ Han, N Bertin, T Hao, DS
Goldberg, GF Berriz, LV Zhang, D Dupuy, AJM Walhout, ME Cusick, FP
Roth, M Vidal. Evidence for
dynamically organized modularity in the yeast protein-protein interaction
network. Nature 430: 88-93 (2004).
4.
AHY Tong*, G Lesage*, GD Bader, H Ding, H Xu, X Xin, J
Young, GF Berriz, RL Brost, M Chang, Y Chen, X Cheng, G Chua, H Friesen, DS Goldberg, J Haynes, C Humphries, G He, S
Hussein, L Ke, N Krogan, Z Li, JN Levinson, H Lu, P Ménard, C Munyana, AB
Parsons, O Ryan, R Tonikian, T Roberts, A-M Sdicu, J Shapiro, B Sheikh, B
Suter, SL Wong, LV Zhang, H Zhu, CG Burd, S Munro, C Sander, J Rine, J
Greenblatt, M Peter, A Bretscher, G Bell, FP Roth, GW Brown, B Andrews, H
Bussey C Boone. Global mapping of the
yeast genetic interaction network. Science 303: 808-813 (2004).
5.
S Li*, CM Armstrong*, N Bertin*, H Ge*, S Milstein*, M
Boxem*, P-O Vidalain*, J-DJ Han*, A Chesneau*, T Hao, DS Goldberg, N Li, M Martinez, J-F Rual, P
Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J
Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose,
H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S van den
Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC
Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill, M Vidal. A map of the interactome network of the
metazoan C. elegans. Science,
303: 540-543 (2004).
6.
DS Goldberg, FP Roth. Assessing
experimentally derived interactions in a small world. Proceedings
of the National Academy of Sciences 100:4372-4376 (2003).
7.
D Goldberg, S McCouch, J Kleinberg. Constructing
Comparative Genome Maps with Unresolved Marker Order. Proceedings of the Pacific Symposium on Biocomputing
(PSB) (2002).
8.
D Goldberg. Algorithms for constructing
comparative genome maps. Ph.D.
thesis (2001).
9.
D Goldberg, S McCouch, J Kleinberg. Algorithms for Constructing Comparative Maps.
in D Sankoff and JH Nadeau, editors, Comparative
Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map
Alignment and the Evolution of Gene Families, Vol. 1 of Series in Computational Biology,
Dordrecht, NL. Kluwer Academic
Press (2000).
10.
DM Post, ME Conners, DS
Goldberg. Prey preference
of mobile predators and the stability of partially linked food webs. Ecology
81:8-14 (2000).
11. DS Goldberg. Algorithms and Constructions
Related to Combinatorial Design of Maximal Families of k-tuples Master's
thesis (1988)
12. DF Wong, A Gjedde, HN Wagner, Jr., RF Dannals, L Tune, C
Tamminga, L O’Tuama, J Williams, DS
Goldberg, J Links. In Vivo
Quantification of Absolute D2 Dopamine Receptor Density Using Positron Emission
Tomography: Preliminary Human Studies.
[Abstract] J Nucl Med., 27:954 (1986).
13. DF Wong, G Wand, H Zacur, DS
Goldberg, J Williams, L O’Tuama, E Broussolle, RF Dannals, JM
Links, HN Wagner, Jr. The Effect of
the Menstrual Cycle on Dopamine Receptor Binding of c11-3-N-Methylspiperone. [Abstract]
J Nucl Med., 27:1010
(1986).
* These authors contributed
equally to this work
1.
K Gunsalus*, H Ge*, AJ Schetter*, DS Goldberg*, J-DJ Han, T Hao, N Bertin, N Li, J Huang,
L-S Chuang, R Mani, AA Hyman, B Sönnichsen, CJ Echeverri, FP Roth, M Vidal,
F Piano. Predictive models of
molecular machines involved in C. elegans early
embryogenesis. (in review)
3.
DS Goldberg, G Franklin, FP Roth. Breaking
the power law: improved model selection reveals increased network complexity.
(submitted)
* These authors contributed
equally to this work
National Science Foundation 2003-2005
Postdoctoral Research Fellowship in Interdisciplinary Informatics
Starter grants for those taking tenure-track positions
Engineering Graduate Research Symposium, Cornell University 2001
Oral Presentation Award Winner
Cornell University
Department of Computer Science 1999-2000
Outstanding Teaching Assistant Award
National Science Foundation 1998-99
Training Grant DEB-9602229: Evolution from DNA to the Organism: The interface
between evolutionary biology and the mathematical sciences.
National Science Foundation 1997-98
Training Grant BIR-9113307: Dynamics of heterogeneous ecological and
evolutionary systems.
AAUW Educational Foundation 1997-98
Research and Projects Career Development Grant
What can
we learn from the topology of inaccurate biological networks?
Georgia Institute of Technology, Applied Mathematics Seminar, Atlanta, GA, March 2005.
Data
Assessment and Function Prediction Using Inaccurate Network Data
Rocky Mountain Regional Bioinformatics Conference, Aspen, CO, December 2004.
A model
selection approach to classify the topology of biological networks
BioPathways, Glasgow, UK, July 2004.
Gaining
biological insight from genomic network topology
Society of Industrial and Applied Mathematics (SIAM) Conference on the Life
Sciences, Portland, OR, July 2004.
Interactome
networks
ORFeome Meeting, Boston, MA, December
2003.
Using
small-world network topology to refine experimentally-derived networks
Tufts University, Electrical Engineering and Computer Science Department,
Medford, MA, October 2002.
Constructing
Comparative Maps with Unresolved Marker Order
Pacific Symposium on Biocomputing, Lihue, HI,
January 2002.
DeCAL: An Open Source System for Constructing Comparative Maps
Bioinformatics Open Source Conference, Copenhagen, Denmark, July 2001.
Automated Construction of Genomic Comparative Maps
Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, July 2001.
Harvard Medical School, Boston, MA, June
2001.
Engineering Graduate Research Symposium, Cornell University, Ithaca, NY,
March 2001.
DIMACS Workshop on Whole Genome Comparison, Piscataway, NJ, March 2001.
Plant and Animal Genome IX Conference, San Diego, CA, January 2001.
Algorithms for Constructing Comparative Maps
Cornell University,
Mathematical Sciences Seminar, Ithaca, NY,
October 2000.
Tel Aviv University, School of Computer Science, Tel Aviv, Israel, October 2000.
Conference on Gene Order Dynamics, Comparative Maps and Multigene Families,
Sainte-Adèle,
Canada, September 2000.
Prey preference by mobile predators and the stability of partially
linked food webs.
Ecological Society of America (ESA) Annual Meeting, Albuquerque, NM, August 1997.
Comparative genome map algorithms were featured in:
Cornell
Chronicle, January 18, 2001.
Cornell
press release, December 21, 2000.
EurekAlert, December 21, 2000.
GenomeWeb,
December 26, 2000.
bioresearch
online, December 27, 2000.
ScienceDaily,
January 1, 2001.
Bioinform, January 2001.
Technology
Research News, February 14, 2001.
Genome Technology, March 2001.
International Society for Computational Biology 2004-current
Vice-Chair, inaugural Student Council
Reviewer
Nucleic Acid Research 2003-2004
Bioinformatics 2003
Advisory Committee on the Status of Women (ACSW); Cornell University 2000-2001
Elected to represent graduate students on this committee comprised primarily of
Cornell faculty
and staff. The mission of ACSW is to
advise Cornell Administration
and educate the University community on women’s issues, and to advocate
for equality for women.
Engineering Graduate Student Association (EGSA); Cornell University 1999-2001
Organized professional seminars and social activities.
Williams Elementary School 2002-current
Regularly posted mathematical puzzles at “Dr. Deb’s Puzzle
Corner”
Led activities for Mathematics Awareness Month
Expanding Your Horizons in Math, Science, and Engineering; Cornell University 1999-2001
Chairman, Science Resources and Books Committee 1999
Chairman, Evaluations Committee 2000
Workshop co-leader: Computational Genomics 2000,
2001
Workshop co-leader: Mathematics 2001
Kids on Campus; Cornell University 1997
Organized mathematical activities at the Center for Applied Mathematics.
Girls, Inc., Science, Math, And Relevant Technology (SMART)
program 1993-1994.
Volunteer, leading weekly science and math activities for girls in grades 1-8.
International Society for
Computational Biology (ISCB)
American Mathematical Society (AMS)
Association for Computing
Machinery (ACM)
Society for Industrial and Applied
Mathematics (SIAM)
American Association of University
Women (AAUW)
Frederick Roth, Ph.D. (Postdoctoral Advisor) (617) 432-3551 fritz_roth@hms.harvard.edu
Assistant Professor, Department of Biological Chemistry and Molecular
Pharmacology
Harvard Medical School, 250 Longwood Ave., SGM-322, Boston, MA 02115
Marc Vidal, Ph.D. (Postdoctoral Co-Mentor) (617) 632-5180 Marc_Vidal@dfci.harvard.edu
Associate Professor, Department of Genetics
Dana Farber Cancer Institute, Smith 858, 44 Binney St., Boston, MA 02115
Jon Kleinberg, Ph.D. (Doctoral Advisor) (607) 255-3600 kleinber@cs.cornell.edu
Associate Professor, Department of Computer Science
Cornell
University, 5134 Upson Hall, Ithaca, NY 14853
Susan McCouch, Ph.D. (Doctoral Advisor) (607) 255-0420 srm4@cornell.edu
Professor, Department of Plant Breeding & Genetics
Cornell University,
162 Emerson Hall, Ithaca, NY 14853
David Schwartz, Ph.D. (Teaching Advisor) (607) 255-5395 dis@cs.cornell.edu
Lecturer, Department of Computer Science
Cornell University,
5137 Upson Hall, Ithaca, NY 14853