Adam Margolin's Home Page

Hello! Welcome to my home page.

I'm a PhD student in the Department of Biomedical Informatics at Columbia University. My research interests are designing molecular nanocomputers for cancer diagnosis and therapy and development of computational methods for the inference of genetic regulatory networks in cancer cells.

When I'm not in the lab, I'm usually training in Brazilian jiu-jitsu, listening to music, or reading about some scientific, philosophical or spiritual interest of the moment. Below are some of those scientific interests.

PUBLICATIONS

Margolin, A. A., K. Wang, W. K. Lim, I. Nemenman and A. Califano (2006). "Reverse engineering cellular networks." Nature Protocols 1(2): p. 662-671.

Palomero, T., W. K. Lim, D. Odom, A. A. Margolin, M. L. Sulis, P. J. Real, J. O'Neal, D. Neuberg, J. C. Aster, F. Sigaux, J. Soulier, A. T. Look, R. Young, A. Califano and A. Ferrando (2006). "NOTCH1 directly regulates MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci 103(48).

Margolin, A. A., I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla Favera and A. Califano (2006). "ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context." BMC Bioinformatics 7 Suppl 1: S1-7. PDF

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 (2006). "Transcriptional regulatory networks downstream of TAL1/SCL in t-cell acute lymphoblastic leukemia." Blood.

Li, C. M., A. A. Margolin, M. Salas, L. Memeo, M. Mansukhani, H. Hibshoosh, M. Szabolcs, A. Klinakis and B. Tycko (2006). "PEG10 is a c-MYC target gene in cancer cells." Cancer Res 66(2): 665-72. PDF

Basso, K., A. A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera and A. Califano (2005). "Reverse engineering of regulatory networks in human B cells." Nat Genet 37(4): 382-90. PDF
Selected as a Faculty 1000 of Biology key paper

Margolin, A. A. and M. N. Stojanovic (2005). "Boolean calculations made easy (for ribozymes)." Nat Biotechnol 23(11): 1374-6. PDF

Margolin, A. A., J. Greshock and B. L. Weber (2005). CGH data analysis. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. L. B. Jorde, P. F. R. Little, M. J. Dunn and S. Subramaniam. Chichester, Wiley & Sons Ltd: 3193-3201.

Margolin, A. A., J. Greshock, T. L. Naylor, Y. Mosse, J. M. Maris, G. Bignell, A. I. Saeed, J. Quackenbush and B. L. Weber (2005). "CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data." Bioinformatics 21(15): 3308-11.

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 (2005). "High-resolution detection and mapping of genomic DNA alterations in neuroblastoma." Genes Chromosomes Cancer 43(4): 390-403.

Wang, K., I. Nemenman, K. Basso, A. Margolin, N. Banerjee, R. Dalla-Favera and A. Califano (2005). Genome-wide identification of modulators of cellular networks in human B lymphocytes. Intelligent Systems in Molecular Biology, Detroit, MI.

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 (2004). "1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis." Genome Res 14(1): 179-87.

Margolin, A. A., I. Nemenman, C. Wiggins, G. Stolovitzky and A. Califano (2004). On the reconstruction of interaction networks with applications to transcriptional regulation. Neural Information Processing Systems, Whistler, BC, Canada.

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 (2004). "CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors." Am J Pathol 165(6): 1943-53.