Adam Margolin

Professor

  • 10732 Citations
  • 32 h-Index
20042019
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Research Output 2004 2019

  • 10732 Citations
  • 32 h-Index
  • 59 Article
  • 11 Conference contribution
  • 2 Comment/debate
  • 1 Editorial
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Article
2018
3 Citations (Scopus)

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Nov 6 2018, In : Genome Biology. 19, 1, 1 p.

Research output: Contribution to journalArticle

Crowdsourcing
Benchmarking
tumor
benchmarking
genome
15 Citations (Scopus)

Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy

Medler, T. R., Murugan, D., Horton, W., Kumar, S., Cotechini, T., Forsyth, A. M., Leyshock, P., Leitenberger, J. J., Kulesz-Martin, M., Margolin, A., Werb, Z. & Coussens, L., Oct 8 2018, In : Cancer Cell. 34, 4, p. 561-578.e6

Research output: Contribution to journalArticle

Complement C5a
Carcinogenesis
Macrophages
T-Lymphocytes
Drug Therapy
4 Citations (Scopus)

Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer

Xu, C., Nikolova, O., Basom, R. S., Mitchell, R. M., Shaw, R., Moser, R. D., Park, H., Gurley, K. E., Kao, M. C., Green, C. L., Schaub, F. X., Diaz, R. L., Swan, H. A., Jang, I. S., Guinney, J., Gadi, V. K., Margolin, A., Grandori, C., Kemp, C. J. & Méndez, E., Jun 15 2018, In : Clinical Cancer Research. 24, 12, p. 2828-2843 16 p.

Research output: Contribution to journalArticle

Precision Medicine
Head and Neck Neoplasms
Small Interfering RNA
Neoplasms
Pharmaceutical Preparations
1 Citation (Scopus)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Sendorek, D. H., Caloian, C., Ellrott, K., Bare, J. C., Yamaguchi, T. N., Ewing, A. D., Houlahan, K. E., Norman, T. C., Margolin, A., Stuart, J. M. & Boutros, P. C., Jan 31 2018, In : BMC Bioinformatics. 19, 1, 28.

Research output: Contribution to journalArticle

Nucleotides
Contamination
Leakage
Genome
Genes
4 Citations (Scopus)

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism

Davis, R. J., Gonen, M., Margineantu, D. H., Handeli, S., Swanger, J., Hoellerbauer, P., Paddison, P. J., Gu, H., Raftery, D., Grim, J. E., Hockenbery, D. M., Margolin, A. & Clurman, B. E., May 22 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 21, p. 5462-5467 6 p.

Research output: Contribution to journalArticle

Mutation
Neoplasms
Ubiquitin-Protein Ligases
Mitochondrial Genes
Atlases
2 Citations (Scopus)

Population-level distribution and putative immunogenicity of cancer neoepitopes

Wood, M. A., Paralkar, M., Paralkar, M. P., Nguyen, A., Struck, A. J., Ellrott, K., Margolin, A., Nellore, A. & Thompson, R., Apr 13 2018, In : BMC Cancer. 18, 1, 414.

Research output: Contribution to journalArticle

Demography
Peptides
Neoplasms
Genome
Atlases

Valection: Design optimization for validation and verification studies

Cooper, C. I., Yao, D., Sendorek, D. H., Yamaguchi, T. N., P'ng, C., Houlahan, K. E., Caloian, C., Fraser, M., Ellrott, K., Margolin, A., Bristow, R. G., Stuart, J. M. & Boutros, P. C., Sep 25 2018, In : BMC Bioinformatics. 19, 1, 339.

Research output: Contribution to journalArticle

Verification and Validation
Validation Studies
Software
Programming Languages
Technology
2017
2 Citations (Scopus)

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gonen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 25 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C. & Margolin, A., 2017, (Accepted/In press) In : Cell Systems.

Research output: Contribution to journalArticle

Benchmarking
Cell Line
Genes
Neoplasms
Publications
6 Citations (Scopus)

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

Palpant, N. J., Wang, Y., Hadland, B., Zaunbrecher, R. J., Redd, M., Jones, D., Pabon, L., Jain, R., Epstein, J., Ruzzo, W. L., Zheng, Y., Bernstein, I., Margolin, A. & Murry, C. E., Aug 15 2017, In : Cell Reports. 20, 7, p. 1597-1608 12 p.

Research output: Contribution to journalArticle

Hematopoiesis
Mesoderm
Chromatin
Stem Cells
Endothelial cells
4 Citations (Scopus)

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies

Nikolova, O., Moser, R., Kemp, C., Gonen, M. & Margolin, A., May 1 2017, In : Bioinformatics. 33, 9, p. 1362-1369 8 p.

Research output: Contribution to journalArticle

Pharmacological Biomarkers
Biomarkers
Cancer
Drugs
Genes
91 Citations (Scopus)

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

Tsujikawa, T., Kumar, S., Borkar, R. N., Azimi, V., Thibault, G., Chang, Y. H., Balter, A., Kawashima, R., Choe, G., Sauer, D., El Rassi, E., Clayburgh, D., Kulesz-Martin, M., Lutz, E. R., Zheng, L., Jaffee, E. M., Leyshock, P., Margolin, A., Mori, M. T., Gray, J. & 2 others, Flint, P. & Coussens, L., Apr 4 2017, In : Cell Reports. 19, 1, p. 203-217 15 p.

Research output: Contribution to journalArticle

Tumors
Immunohistochemistry
Tissue
Biomarkers
Papillomaviridae
2016
32 Citations (Scopus)

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

Salomonis, N., Dexheimer, P. J., Omberg, L., Schroll, R., Bush, S., Huo, J., Schriml, L., Ho Sui, S., Keddache, M., Mayhew, C., Shanmukhappa, S. K., Wells, J., Daily, K., Hubler, S., Wang, Y., Zambidis, E., Margolin, A., Hide, W., Hatzopoulos, A. K., Malik, P. & 3 others, Cancelas, J. A., Aronow, B. J. & Lutzko, C., Jul 12 2016, In : Stem Cell Reports. 7, 1, p. 110-125 16 p.

Research output: Contribution to journalArticle

Cytology
Induced Pluripotent Stem Cells
Stem cells
Cell Biology
Stem Cells
2015
107 Citations (Scopus)

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Ewing, A. D., Houlahan, K. E., Hu, Y., Ellrott, K., Caloian, C., Yamaguchi, T. N., Bare, J. C., P'Ng, C., Waggott, D., Sabelnykova, V. Y., Kellen, M. R., Norman, T. C., Haussler, D., Friend, S. H., Stolovitzky, G., Margolin, A., Stuart, J. M. & Boutros, P. C., Jun 30 2015, In : Nature Methods. 12, 7, p. 623-630 8 p.

Research output: Contribution to journalArticle

Crowdsourcing
Benchmarking
Tumors
Nucleotides
Genes
140 Citations (Scopus)

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Sperber, H., Mathieu, J., Wang, Y., Ferreccio, A., Hesson, J., Xu, Z., Fischer, K. A., Devi, A., Detraux, D., Gu, H., Battle, S. L., Showalter, M., Valensisi, C., Bielas, J. H., Ericson, N. G., Margaretha, L., Robitaille, A. M., Margineantu, D., Fiehn, O., Hockenbery, D. & 7 others, Blau, C. A., Raftery, D., Margolin, A., Hawkins, R. D., Moon, R. T., Ware, C. B. & Ruohola-Baker, H., Nov 27 2015, In : Nature Cell Biology. 17, 12, p. 1523-1535 13 p.

Research output: Contribution to journalArticle

Nicotinamide N-Methyltransferase
Metabolome
Epigenomics
Methionine
Human Development
24 Citations (Scopus)

The NIH BD2K center for big data in translational genomics

Paten, B., Diekhans, M., Druker, B., Friend, S., Guinney, J., Gassner, N., Guttman, M., James Kent, W., Mantey, P., Margolin, A., Massie, M., Novak, A. M., Nothaft, F., Pachter, L., Patterson, D., Smuga-Otto, M., Stuart, J. M., Van't Veer, L., Wold, B. & Haussler, D., 2015, In : Journal of the American Medical Informatics Association. 22, 6, p. 1143-1147 5 p.

Research output: Contribution to journalArticle

Genomics
Insurance Pools
Software
Genome
Benchmarking
2014
129 Citations (Scopus)

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

Yuan, Y., Van Allen, E. M., Omberg, L., Wagle, N., Amin-Mansour, A., Sokolov, A., Byers, L. A., Xu, Y., Hess, K. R., Diao, L., Han, L., Huang, X., Lawrence, M. S., Weinstein, J. N., Stuart, J. M., Mills, G., Garraway, L. A., Margolin, A., Getz, G. & Liang, H., 2014, In : Nature Biotechnology. 32, 7, p. 644-652 9 p.

Research output: Contribution to journalArticle

Proteomics
Tumors
Genes
Neoplasms
MicroRNAs

Cancer genomics: Moving from unknown unknown to known unknown

Margolin, A., Jan 29 2014, In : Science Translational Medicine. 6, 221

Research output: Contribution to journalArticle

Genomics
Neoplasms
37 Citations (Scopus)

Functional kinomics identifies candidate therapeutic targets in head and neck cancer

Moser, R., Xu, C., Kao, M., Annis, J., Lerma, L. A., Schaupp, C. M., Gurley, K. E., Jang, I. S., Biktasova, A., Yarbrough, W. G., Margolin, A., Grandori, C., Kemp, C. J. & Méndez, E., Aug 15 2014, In : Clinical Cancer Research. 20, 16, p. 4274-4288 15 p.

Research output: Contribution to journalArticle

Head and Neck Neoplasms
Phosphotransferases
RNA Interference
Therapeutics
G2 Phase Cell Cycle Checkpoints
28 Citations (Scopus)

Global optimization of somatic variant identification in cancer genomes with a global community challenge

Boutros, P. C., Ewing, A. D., Ellrott, K., Norman, T. C., Dang, K. K., Hu, Y., Kellen, M. R., Suver, C., Bare, J. C., Stein, L. D., Spellman, P., Stolovitzky, G., Friend, S. H., Margolin, A. & Stuart, J. M., 2014, In : Nature Genetics. 46, 4, p. 318-319 2 p.

Research output: Contribution to journalArticle

DNA Mutational Analysis
Crowdsourcing
High-Throughput Screening Assays
Genetic Databases
Human Genome
609 Citations (Scopus)

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Hoadley, K. A., Yau, C., Wolf, D. M., Cherniack, A. D., Tamborero, D., Ng, S., Leiserson, M. D. M., Niu, B., McLellan, M. D., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., Van'T Veer, L. J., Lopez-Bigas, N., Laird, P. W. & 12 others, Raphael, B. J., Ding, L., Robertson, A. G., Byers, L. A., Mills, G., Weinstein, J. N., Van Waes, C., Chen, Z., Collisson, E. A., Benz, C. C., Perou, C. M. & Xia, Z., Aug 14 2014, In : Cell. 158, 4, p. 929-944 16 p.

Research output: Contribution to journalArticle

Tissue
Urinary Bladder Neoplasms
Neoplasms
Genes
Data Mining
5 Citations (Scopus)

Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting

Neto, E. C., Bare, J. C. & Margolin, A., 2014, In : PLoS One. 9, 10, p. e107957

Research output: Contribution to journalArticle

Computational Biology
Experiments
Sample Size
Gene expression
Signal to noise ratio
55 Citations (Scopus)

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.

Jang, I. S., Neto, E. C., Guinney, J., Friend, S. H. & Margolin, A., 2014, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 63-74 12 p.

Research output: Contribution to journalArticle

Pharmacogenetics
Research Design
Cell Line
Pharmaceutical Preparations
Neoplasms
16 Citations (Scopus)
Pharmacogenetics
Cell Line
Efficiency
Neoplasms
Bayes Theorem

To catch a pre-leukemia

Margolin, A., Mar 5 2014, In : Science Translational Medicine. 6, 226, 226ec40.

Research output: Contribution to journalArticle

Leukemia
26 Citations (Scopus)

Toward better benchmarking: challenge-based methods assessment in cancer genomics

Boutros, P. C., Margolin, A., Stuart, J. M., Califano, A. & Stolovitzky, G., 2014, In : Genome Biology. 15, 9, p. 462 1 p.

Research output: Contribution to journalArticle

Crowdsourcing
Benchmarking
benchmarking
technological development
assessment method
2013
77 Citations (Scopus)

ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens

Shao, D. D., Tsherniak, A., Gopal, S., Weir, B. A., Tamayo, P., Stransky, N., Schumacher, S. E., Zack, T. I., Beroukhim, R., Garraway, L. A., Margolin, A., Root, D. E., Hahn, W. C. & Mesirov, J. P., Apr 2013, In : Genome Research. 23, 4, p. 665-678 14 p.

Research output: Contribution to journalArticle

RNA Interference
Phenotype
Genes
Oncogenes
Libraries
1 Citation (Scopus)

Cancer therapeutics: Best informed by genes or genomes?

Margolin, A., May 8 2013, In : Science Translational Medicine. 5, 184, 184ec77.

Research output: Contribution to journalArticle

Genome
Genes
Neoplasms
Therapeutics
59 Citations (Scopus)

Enabling transparent and collaborative computational analysis of 12 tumor types within the Cancer Genome Atlas

Omberg, L., Ellrott, K., Yuan, Y., Kandoth, C., Wong, C., Kellen, M. R., Friend, S. H., Stuart, J., Liang, H. & Margolin, A., Oct 2013, In : Nature Genetics. 45, 10, p. 1121-1126 6 p.

Research output: Contribution to journalArticle

Atlases
Genome
Neoplasms
Synapses
Software

Genomics of T-ALL reveals a weapon of an evasive foe

Margolin, A., Mar 27 2013, In : Science Translational Medicine. 5, 178, 178ec52.

Research output: Contribution to journalArticle

Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Weapons
Genomics
15 Citations (Scopus)

hARACNe: Improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

Jang, S., Margolin, A. & Califano, A., Aug 6 2013, In : Interface Focus. 3, 4

Research output: Contribution to journalArticle

Reverse engineering
Transcription factors
Transcription Factors
Information Theory
Dissection
47 Citations (Scopus)

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

Bilal, E., Dutkowski, J., Guinney, J., Jang, I. S., Logsdon, B. A., Pandey, G., Sauerwine, B. A., Shimoni, Y., Moen Vollan, H. K., Mecham, B. H., Rueda, O. M., Tost, J., Curtis, C., Alvarez, M. J., Kristensen, V. N., Aparicio, S., Børresen-Dale, A. L., Caldas, C., Califano, A., Friend, S. H. & 4 others, Ideker, T., Schadt, E. E., Stolovitzky, G. A. & Margolin, A., May 2013, In : PLoS Computational Biology. 9, 5, e1003047.

Research output: Contribution to journalArticle

Survival Analysis
Breast Cancer
breast neoplasms
cancer
Breast Neoplasms
2 Citations (Scopus)

Oncogenic driver mutations: Neither tissue-specific nor independent

Margolin, A., Dec 4 2013, In : Science Translational Medicine. 5, 214, 214ec200.

Research output: Contribution to journalArticle

Mutation

Single-molecule imaging: It takes two to make a RAF signal right

Margolin, A., Nov 13 2013, In : Science Translational Medicine. 5, 211, 211ec187.

Research output: Contribution to journalArticle

Single Molecule Imaging
60 Citations (Scopus)

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

Margolin, A., Bilal, E., Huang, E., Norman, T. C., Ottestad, L., Mecham, B. H., Sauerwine, B., Kellen, M. R., Mangravite, L. M., Furia, M. D., Vollan, H. K. M., Rueda, O. M., Guinney, J., Deflaux, N. A., Hoff, B., Schildwachter, X., Russnes, H. G., Park, D., Vang, V. O., Pirtle, T. & 10 others, Youseff, L., Citro, C., Curtis, C., Kristensen, V. N., Hellerstein, J., Friend, S. H., Stolovitzky, G., Aparicio, S., Caldas, C. & Børresen-Dale, A. L., Apr 17 2013, In : Science Translational Medicine. 5, 181, 181re1.

Research output: Contribution to journalArticle

Molecular Models
Breast Neoplasms
Genome
Gene Expression
1 Citation (Scopus)

The bionic cancer-resistant extracellular matrix of the naked mole-rat

Margolin, A., Jul 31 2013, In : Science Translational Medicine. 5, 196, 196ec125.

Research output: Contribution to journalArticle

Mole Rats
Bionics
Extracellular Matrix
Neoplasms
1778 Citations (Scopus)

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N., Collisson, E. A., Mills, G., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A., Chuah, E. & 316 others, Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 2013, In : Nature Genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journalArticle

Atlases
Genome
Neoplasms
Epigenomics
RNA

The enemy of the enemy of my enemy is a therapeutic target

Margolin, A., Jun 19 2013, In : Science Translational Medicine. 5, 190, 190ec100.

Research output: Contribution to journalArticle

Therapeutics
2012

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., J.Wilson, C., Lehár, J., Kryukov, G. V., Sonkin, D., Reddy, A., Liu, M., Murray, L., Berger, M. F., Monahan, J. E., Morais, P., Meltzer, J., Korejwa, A., Jané-Valbuena, J., Mapa, F. A. & 41 others, Thibault, J., Bric-Furlong, E., Raman, P., Shipway, A., Engels, I. H., Cheng, J., Yu, G. K., Yu, J., Aspesi, P., de Silva, M., Jagtap, K., Jones, M. D., Wang, L., Hatton, C., Palescandolo, E., Gupta, S., Mahan, S., Sougnez, C., Onofrio, R. C., Liefeld, T., MacConaill, L., Winckler, W., Reich, M., Li, N., Mesirov, J. P., Gabriel, S. B., Getz, G., Ardlie, K., Chan, V., Myer, V. E., Weber, B. L., Porter, J., Warmuth, M., Finan, P., Harris, J. L., Meyerson, M., Golub, T. R., Morrissey, M. P., Sellers, W. R., Schlegel, R. & Garraway, L. A., Nov 28 2012, (Accepted/In press) In : Nature.

Research output: Contribution to journalArticle

104 Citations (Scopus)

Chemical Genomics Identifies Small-Molecule MCL1 Repressors and BCL-xL as a Predictor of MCL1 Dependency

Wei, G., Margolin, A., Haery, L., Brown, E., Cucolo, L., Julian, B., Shehata, S., Kung, A. L., Beroukhim, R. & Golub, T. R., Apr 17 2012, In : Cancer Cell. 21, 4, p. 547-562 16 p.

Research output: Contribution to journalArticle

Repressor Proteins
Genomics
Anthracyclines
Patient Selection
Half-Life
2832 Citations (Scopus)

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., Reddy, A., Liu, M., Murray, L., Berger, M. F., Monahan, J. E., Morais, P., Meltzer, J., Korejwa, A., Jané-Valbuena, J., Mapa, F. A. & 41 others, Thibault, J., Bric-Furlong, E., Raman, P., Shipway, A., Engels, I. H., Cheng, J., Yu, G. K., Yu, J., Aspesi, P., De Silva, M., Jagtap, K., Jones, M. D., Wang, L., Hatton, C., Palescandolo, E., Gupta, S., Mahan, S., Sougnez, C., Onofrio, R. C., Liefeld, T., MacConaill, L., Winckler, W., Reich, M., Li, N., Mesirov, J. P., Gabriel, S. B., Getz, G., Ardlie, K., Chan, V., Myer, V. E., Weber, B. L., Porter, J., Warmuth, M., Finan, P., Harris, J. L., Meyerson, M., Golub, T. R., Morrissey, M. P., Sellers, W. R., Schlegel, R. & Garraway, L. A., Mar 29 2012, In : Nature. 483, 7391, p. 603-607 5 p.

Research output: Contribution to journalArticle

Encyclopedias
Drug Design
Cell Line
Neoplasms
Topoisomerase Inhibitors
2010
131 Citations (Scopus)

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells

Basso, K., Saito, M., Sumazin, P., Margolin, A., Wang, K., Lim, W. K., Kitagawa, Y., Schneider, C., Alvarez, M. J., Califano, A. & Dalla-Favera, R., Feb 4 2010, In : Blood. 115, 5, p. 975-984 10 p.

Research output: Contribution to journalArticle

Germinal Center
B-Lymphocytes
Genes
Cells
Reverse engineering
26 Citations (Scopus)

Multivariate dependence and genetic networks inference

Margolin, A., Wang, K., Califano, A. & Nemenman, I., Nov 2010, In : IET Systems Biology. 4, 6, p. 428-440 13 p.

Research output: Contribution to journalArticle

Genetic Network
Genes
Gene
Pathway
Target
2009
58 Citations (Scopus)

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

Margolin, A., Palomero, T., Sumazin, P., Califano, A., Ferrando, A. A. & Stolovitzky, G., Jan 6 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 1, p. 244-249 6 p.

Research output: Contribution to journalArticle

Oncogenes
Transcription Factors
Transcription Factor 3
Gene Regulatory Networks
Gene Expression Profiling
38 Citations (Scopus)

Empirical bayes analysis of quantitative proteomics experiments

Margolin, A., Ong, S. E., Schenone, M., Gould, R., Schreiber, S. L., Carr, S. A. & Golub, T. R., Oct 14 2009, In : PLoS One. 4, 10, e7454.

Research output: Contribution to journalArticle

Proteomics
proteomics
quantitative analysis
Statistical Data Interpretation
statistical analysis
160 Citations (Scopus)

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

Wang, K., Saito, M., Bisikirska, B. C., Alvarez, M. J., Lim, W. K., Rajbhandari, P., Shen, Q., Nemenman, I., Basso, K., Margolin, A., Klein, U., Dalla-Favera, R. & Califano, A., Sep 2009, In : Nature Biotechnology. 27, 9, p. 829-837 9 p.

Research output: Contribution to journalArticle

Transcription factors
Human Activities
Modulators
B-Lymphocytes
Transcription Factors
215 Citations (Scopus)

Identifying the proteins to which small-molecule probes and drugs bind in cells

Ong, S. E., Schenone, M., Margolin, A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L. & Carr, S. A., Mar 24 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 12, p. 4617-4622 6 p.

Research output: Contribution to journalArticle

Pharmaceutical Preparations
Proteins
Immunophilins
Proteomics
Action Potentials
2007
2 Citations (Scopus)

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding

Margolin, A., Palomero, T., Ferrando, A. A., Califano, A. & Stolovitzky, G., Nov 20 2007, In : BMC Bioinformatics. 8, SUPPL. 8, S2.

Research output: Contribution to journalArticle

Transcription Factors

Erratum: NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth (Proceedings of the National Academy of Sciences of the United States of America (2006) 103, 48, (18261-18266) DOI: 10.1073/pnas.0606108103)

Palomero, T., Wei, K. L., Odom, D. T., Sulis, M. L., Real, P. J., Margolin, A., Barnes, K. C., O'Neil, J., Neuberg, D., Weng, A. P., Aster, J. C., Sigaux, F., Soulier, J., Look, A. T., Young, R. A., Califano, A. & Ferrando, A. A., Mar 6 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 10, p. 4240 1 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Growth
2006
1398 Citations (Scopus)

ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context

Margolin, A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R. D. & Califano, A., Mar 20 2006, In : BMC Bioinformatics. 7, SUPPL.1, S7.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Gene Regulatory Network
Microarrays
Genes
Reverse engineering
520 Citations (Scopus)

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

Palomero, T., Wei, K. L., Odom, D. T., Sulis, M. L., Real, P. J., Margolin, A., Barnes, K. C., O'Neil, J., Neuberg, D., Weng, A. P., Aster, J. C., Sigaux, F., Soulier, J., Look, A. T., Young, R. A., Califano, A. & Ferrando, A. A., Nov 28 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 48, p. 18261-18266 6 p.

Research output: Contribution to journalArticle

Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Gene Regulatory Networks
Growth
T-Cell Leukemia
Gene Expression