Adam Margolin

Professor

  • 11817 Citations
  • 32 h-Index
20042019

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2018

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, 188.

Research output: Contribution to journalArticle

8 Scopus citations

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

24 Scopus citations

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

6 Scopus citations

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. A., Stuart, J. M. & Boutros, P. C., Jan 31 2018, In : BMC bioinformatics. 19, 1, 28.

Research output: Contribution to journalArticle

1 Scopus citations

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

5 Scopus citations

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

10 Scopus citations

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. A., Bristow, R. G., Stuart, J. M. & Boutros, P. C., Sep 25 2018, In : BMC bioinformatics. 19, 1, 339.

Research output: Contribution to journalArticle

2 Scopus citations
2017

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

7 Scopus citations

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

9 Scopus citations

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

4 Scopus citations

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

113 Scopus citations
2016

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

38 Scopus citations
2015

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. 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

120 Scopus citations

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. 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

155 Scopus citations

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

27 Scopus citations
2014

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. B., Garraway, L. A., Margolin, A. A., Getz, G. & Liang, H., Jul 2014, In : Nature biotechnology. 32, 7, p. 644-652 9 p.

Research output: Contribution to journalArticle

148 Scopus citations

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. 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

41 Scopus citations

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

The Cancer Genome Atlas Research Network, Aug 14 2014, In : Cell. 158, 4, p. 929-944 16 p.

Research output: Contribution to journalArticle

672 Scopus citations

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. A., Oct 7 2014, In : PloS one. 9, 10, e107957.

Research output: Contribution to journalArticle

6 Scopus citations

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

27 Scopus citations
2013

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. A., Root, D. E., Hahn, W. C. & Mesirov, J. P., Apr 1 2013, In : Genome Research. 23, 4, p. 665-678 14 p.

Research output: Contribution to journalArticle

77 Scopus citations

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

Open Access
17 Scopus citations

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. A., May 1 2013, In : PLoS computational biology. 9, 5, e1003047.

Research output: Contribution to journalArticle

52 Scopus citations

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

Margolin, A. 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

71 Scopus citations
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

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

Wei, G., Margolin, A. 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

116 Scopus citations

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., 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

3100 Scopus citations
2010

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. 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

136 Scopus citations

Multivariate dependence and genetic networks inference

Margolin, A. A., Wang, K., Califano, A. & Nemenman, I., Nov 1 2010, In : IET Systems Biology. 4, 6, p. 428-440 13 p.

Research output: Contribution to journalArticle

27 Scopus citations
2009

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

Margolin, A. 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

59 Scopus citations

Empirical bayes analysis of quantitative proteomics experiments

Margolin, A. 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

40 Scopus citations

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. A., Klein, U., Dalla-Favera, R. & Califano, A., Sep 1 2009, In : Nature biotechnology. 27, 9, p. 829-837 9 p.

Research output: Contribution to journalArticle

170 Scopus citations

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

Ong, S. E., Schenone, M., Margolin, A. 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

223 Scopus citations
2007

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

Margolin, A. 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

2 Scopus citations
2006

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

Margolin, A. 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

1473 Scopus citations

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

540 Scopus citations

PEG10 is a c-MYC target gene in cancer cells

Li, C. M., Margolin, A. A., Salas, M., Memeo, L., Mansukhani, M., Hibshoosh, H., Szabolcs, M., Klinakis, A. & Tycko, B., Jan 15 2006, In : Cancer Research. 66, 2, p. 665-672 8 p.

Research output: Contribution to journalArticle

62 Scopus citations

Reverse engineering cellular networks

Margolin, A. A., Wang, K., Lim, W. K., Kustagi, M., Nemenman, I. & Califano, A., Jul 1 2006, In : Nature protocols. 1, 2, p. 662-671 10 p.

Research output: Contribution to journalArticle

246 Scopus citations

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia

Palomero, T., Odom, D. T., O'Neil, J., Ferrando, A. A., Margolin, A., Neuberg, D. S., Winter, S. S., Larson, R. S., Li, W., Liu, X. S., Young, R. A. & Look, A. T., Aug 1 2006, In : Blood. 108, 3, p. 986-992 7 p.

Research output: Contribution to journalArticle

55 Scopus citations
2005

CGHAnalyzer: A stand-alone software package for cancer genome analysis using array-based DNA copy number data

Margolin, A. A., Greshock, J., Naylor, T. L., Mosse, Y., Maris, J. M., Bignell, G., Saeed, A. I., Quackenbush, J. & Weber, B. L., Aug 1 2005, In : Bioinformatics. 21, 15, p. 3308-3311 4 p.

Research output: Contribution to journalArticle

25 Scopus citations

High-resolution detection and mapping of genomic DNA alterations in neuroblastoma

Mosse, Y. P., Greshock, J., Margolin, A., Naylor, T., Cole, K., Khazi, D., Hii, G., Winter, C., Shahzad, S., Asziz, M. U., Biegel, J. A., Weber, B. L. & Maris, J. M., Aug 1 2005, In : Genes Chromosomes and Cancer. 43, 4, p. 390-403 14 p.

Research output: Contribution to journalArticle

75 Scopus citations

Reverse engineering of regulatory networks in human B cells

Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R. & Califano, A., Apr 1 2005, In : Nature genetics. 37, 4, p. 382-390 9 p.

Research output: Contribution to journalArticle

974 Scopus citations
2004

1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

Greshock, J., Naylor, T. L., Margolin, A., Diskin, S., Cleaver, S. H., Futreal, P. A., deJong, P. J., Zhao, S., Liebman, M. & Weber, B. L., Jan 1 2004, In : Genome Research. 14, 1, p. 179-187 9 p.

Research output: Contribution to journalArticle

96 Scopus citations

CTNNB1 mutations and overexpression of Wnt/β-catenin target genes in WT1-mutant wilms' tumors

Li, C. M., Kim, C. E., Margolin, A. A., Guo, M., Zhu, J., Mason, J. M., Hensle, T. W., Murty, V. V. V. S., Grundy, P. E., Fearon, E. R., D'Agati, V., Licht, J. D. & Tycko, B., Dec 2004, In : American Journal of Pathology. 165, 6, p. 1943-1953 11 p.

Research output: Contribution to journalArticle

98 Scopus citations