Curriculum Vitae
ADAM MARGOLIN
(917)414-7709
Department of Biomedical Informatics, PhD Candidate
GPA:
3.9/4.0
Honors
IBM PhD Fellowship, 2006
National Science Foundation Fellowship Competition, Honorable Mention, 2004
Qualifying exam passed with honors
Oral Exam 2 passed with honors
Master of Philosophy in Biomedical Informatics ------ September, 2006
School of Engineering and Applied Sciences, Masters in Computer Information Technology------ December, 2002
Honors
Summa Cum Laude
Cum Laude
Dean’s List 2000-2001, 2001-2002
Intern, Functional Genomics and Systems Biology Group. Developed an algorithm that uses ChIP-on-chip data to identify genomic regions bound by a transcription factor. Used this method to elucidate transcriptional targets and regulatory programs associated with the NOTCH proto-oncogene in T-cell acute lymphoblastic leukemia.
Intern, Functional Genomics and Systems Biology Group. Researched genetic networks inference algorithms to identify regulatory hubs that are disregulated in cancerous phenotypes. Developed an in vivo experimental methodology for detecting differential regulation of gene combinations identified by this method.
PhD Candidate. Reverse Engineering of Gene Regulatory Networks: Developed ARACNE, a novel, information-theoretic algorithm for the reverse engineering of gene regulatory networks from microarray data. ARACNE employs three variable mutual information analysis to construct high fidelity probabilistic gene regulatory topologies as adirected graphs. ARACNE has been used to reconstruct a complex regulatory network in human B cells, representing the first reported genome‑wide mammalian network inferred from microarray expression profiles.
Forward Engineering of Gene Regulatory Networks: Developed a software platform for the simulation of biochemical networks using massively parallel computation. This platform is used to generate simulated microarray datasets that enable the comparative benchmarking of reverse engineering algorithms.
University of
Pennsylvania, Abramson Cancer Research Institute,
Bioinformatics
Application Developer.
Designed and developed CGHAnalyzer, a java application incorporating
novel algorithms for analysis of array based genome copy number data. CGHAnalyzer allows discontinuous probe data
values from array-based genome copy number assays to be converted to
statistically-based estimates of complete genome copy number profiles. This
technique allows analytic units other than the array clones, such as genes or
genomic regions, to be used for data abstraction and pattern classification
within large data sets, and enables comparison between experiments performed
using different assays.
Developer. Designed and developed GeoGrapher, a java application for analysis and visualization of gene expression data stored in NCBI’s Gene Expression Omnibus database. The program allows for multi-experiment data mining with reference to gene expression level and different measures of gene expression variability and statistical associations across experiments.
EGenomics, Inc.,
Bear Stearns & Co.,
Inc.,
High Yield Bonds Analyst and Programmer.
Programming Jobs: Researched, developed, and published a model to estimate fair value of emerging market bonds. Developed predictive algorithm and analysis software to model future risk and performance of these bonds.
Analyst Work:
Served as keynote speaker, when my boss was incapacitated, at a conference in
Bear Stearns &
Co., Inc.,
Programmer (Treasury Department). Developed analytic software for volume analysis, P/E analysis, and future growth projections to determine suitable candidates for Dividend Re-Investment Plans. Created automated $45 million end-of-month allocation report. Created software and databases to determine interest rate adjustments, hard-to-borrow adjustments, and short rebates. Analyzed changes in company’s profit and loss reports.
Marketing Assistant. Created relational database based on promotional and ticketing surveys given to fans. Prepared marketing analysis reports. Organized and led groups during games, including anthem singers, player appearances, specialty groups, and auction winners.
Teaching Assistant,
Introduction to Biophysical Modeling,
Teaching Assistant, Computational
Biology,
1. Palomero, T., W. Lim, D.
Odom, M. Sulis, P. Real, J. O’Neal, D. Neuberg, A. Margolin, A. Weng, J.
Aster, F. Sigaux, J. Soulier,
A. Look, R. Young, A. Califano, and A. Ferrando, NOTCH1 directly regulates
MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl
Acad Sci, 2006. 103(48).
2. Wang, K., I. Nemenman,
K. Basso, A. Margolin, N. Banerjee, R. Dalla-Favera, and A. Califano. Genome-wide identification of modulators of cellular networks in
human B lymphocytes. in Proceedings of
the 10th Annual International Conference on Research in Computational Molecular
Biology (RECOMB). 2006.
3. Palomero, T., D.T. Odom,
J. O'Neil, A.A. Ferrando, A. Margolin, D.S. Neuberg,
S.S. Winter, R.S. Larson, W. Li, X.S. Liu, R.A. Young, and A.T. Look, Transcriptional
regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic
leukemia. Blood, 2006. 108(3): p. 986-92.
4. Margolin, A.A., K. Wang,
W.K. Lim, M. Kustagi, I. Nemenman, and A. Califano, Reverse Engineering
Cellular Networks. Nature Protocols, 2006. 1(2):
p. 662-671.
5. Margolin, A.A., I.
Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla Favera, and A. Califano, ARACNE:
an algorithm for the reconstruction of gene regulatory networks in a mammalian
cellular context. BMC Bioinformatics, 2006. 7 Suppl 1: p. S7.
6. Li, C.M., A.A. Margolin,
M. Salas, L. Memeo, M. Mansukhani,
H. Hibshoosh, M. Szabolcs,
A. Klinakis, and B. Tycko, PEG10 is a c-MYC target gene in cancer cells.
Cancer Res, 2006. 66(2):
p. 665-72.
7. Mosse,
Y.P., J. Greshock, A. Margolin, T. Naylor, K. Cole, D. Khazi,
G. Hii, C. Winter, S. Shahzad,
M.U. Asziz, J.A. Biegel,
B.L. Weber, and J.M. Maris, High-resolution
detection and mapping of genomic DNA alterations in neuroblastoma.
Genes Chromosomes Cancer, 2005. 43(4): p.
390-403.
8. Margolin, A.A. and M.N. Stojanovic, Boolean calculations made easy (for ribozymes). Nat Biotechnol,
2005. 23(11): p. 1374-6.
9. Margolin, A.A., J.
Greshock, and B.L. Weber, CGH data analysis, in Encyclopedia of
Genetics, Genomics, Proteomics and Bioinformatics, L.B. Jorde,
et al., Editors. 2005, Wiley & Sons Ltd:
10. Margolin, A.A., J.
Greshock, T.L. Naylor, Y. Mosse, J.M. Maris, G. Bignell, A.I. Saeed, J. Quackenbush, and B.L.
Weber, CGHAnalyzer: a stand-alone software
package for cancer genome analysis using array-based DNA copy number data. Bioinformatics, 2005. 21(15): p. 3308-11.
11. Basso, K., A.A.
Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera,
and A. Califano, Reverse engineering of regulatory networks in human B
cells. Nat Genet, 2005. 37(4): p. 382-90.
12. Margolin, A.A.,
13. Li, C.M., C.E. Kim, A.A.
Margolin, M. Guo, J. Zhu, J.M. Mason, T.W. Hensle, V.V. Murty, P.E. Grundy,
E.R. Fearon, V. D'Agati,
J.D. Licht, and B. Tycko, CTNNB1 mutations and overexpression of Wnt/beta-catenin
target genes in WT1-mutant Wilms' tumors. Am J Pathol, 2004. 165(6): p.
1943-53.
14. Greshock, J., T.L.
Naylor, A. Margolin, S. Diskin, S.H. Cleaver, P.A. Futreal, P.J. deJong, S. Zhao, M.
Liebman, and B.L. Weber, 1-Mb resolution
array-based comparative genomic hybridization using a BAC clone set optimized
for cancer gene analysis. Genome Res,
2004. 14(1): p. 179-87.
Margolin, A. A., I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla Favera and A. Califano (2005). ARACNE: An Algorithm for the Reconstruction of Accurate Cellular Networks. Keystone Symposium in Systems Biology.
Wang, K., I. Nemenman, K. Basso, A. A. Margolin, N. Banerjee, R. Dalla-Favera and A. Califano (2005). Conditional network analysis: exploring network dynamics and identifying key modulator genes from gene expression data. Intelligent Systems in Molecular Biology.
T.L. Naylor, J.D. Greshock, S.H. Cleaver, B.J. Baxter, A. Margolin, M.L. Liebman, R. Wooster, P.A. Futreal, M.R Stratton, B.L. Weber. (2002) Novel Approaches to Visualizing and Analyzing Array-Based Comparative Genomic Hybridization Data. Annual Meeting of the American Society of Human Genetics.
J. Greshock, T.L. Naylor, S.H. Cleaver, M.R. Gererro, A. Margolin, M.L. Liebman, B.L. Weber. (2002) Genomic Profiling of Primary Breast Cancers and Cell Lines Using Array CGH.. Annual Meeting of the American Society of Human Genetics.
OTHER INTERESTS / AFFILIATIONS
Fluent in Spanish, Brazilian Jiu-Jitsu, Traditional Chinese Qigong, electric guitar, athletics, philosophical and technical reading