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
2019

Erratum: Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (Nature (2012) 483 7391 (603-607))

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., Jan 1 2019, In : Nature. 565, 7738

Research output: Contribution to journalComment/debate

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
2 Citations (Scopus)

SHIFT: Speedy histopathological-To-immunofluorescent translation of whole slide images using conditional generative adversarial networks

Burlingame, E. A., Margolin, A., Gray, J. & Chang, Y. H., Jan 1 2018, Medical Imaging 2018: Digital Pathology. SPIE, Vol. 10581. 1058105

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hematoxylin
Eosine Yellowish-(YS)
chutes
Coloring Agents
Imaging techniques

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
1 Citation (Scopus)

Breast cancer histopathology image analysis pipeline for tumor purity estimation

Azimi, V., Chang, Y. H., Thibault, G., Smith, J., Tsujikawa, T., Kukull, B., Jensen, B., Corless, C., Margolin, A. & Gray, J., Jun 15 2017, 2017 IEEE 14th International Symposium on Biomedical Imaging, ISBI 2017. IEEE Computer Society, p. 1137-1140 4 p. 7950717

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Image analysis
Tumors
Pipelines
Breast Neoplasms
Neoplasms
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
93 Citations (Scopus)

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., Barnell, E. K., Wagner, A. H., Skidmore, Z. L., Wollam, A., Liu, C. J., Jones, M. R., Bilski, R. L., Lesurf, R., Feng, Y. Y., Shah, N. M. & 25 others, Bonakdar, M., Trani, L., Matlock, M., Ramu, A., Campbell, K. M., Spies, G. C., Graubert, A. P., Gangavarapu, K., Eldred, J. M., Larson, D. E., Walker, J. R., Good, B. M., Wu, C., Su, A. I., Dienstmann, R., Margolin, A., Tamborero, D., Lopez-Bigas, N., Jones, S. J. M., Bose, R., Spencer, D. H., Wartman, L. D., Wilson, R. K., Mardis, E. R. & Griffith, O. L., Jan 31 2017, In : Nature Genetics. 49, 2, p. 170-174 5 p.

Research output: Contribution to journalComment/debate

Crowdsourcing
Knowledge Bases
Neoplasms
6 Citations (Scopus)

Deep learning based Nucleus Classification in pancreas histological images

Chang, Y. H., Thibault, G., Madin, O., Azimi, V., Meyers, C., Johnson, B., Link, J., Margolin, A. & Gray, J., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 672-675 4 p. 8036914

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Pancreas
Learning
Tumors
Neoplasms
Explosions

Integrative analysis on histopathological image for identifying cellular heterogeneity

Chang, Y. H., Thibault, G., Johnson, B., Margolin, A. & Gray, J., 2017, Medical Imaging 2017: Digital Pathology. SPIE, Vol. 10140. 101400T

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Spatial Analysis
Lymphocytes
Spatial distribution
Tumors
lymphocytes
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

Multiplexed immunohistochemistry image analysis using sparse coding

Chang, Y. H., Tsujikawa, T., Margolin, A., Coussens, L. & Gray, J., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 4046-4049 4 p. 8037744

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Image analysis
Immunohistochemistry
Tissue
Biomarkers
Tumors
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
6 Citations (Scopus)

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics

Chang, Y. H., Thibault, G., Azimi, V., Johnson, B., Jorgens, D., Link, J., Margolin, A. & Gray, J., Oct 13 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-October. p. 1175-1178 4 p. 7590914

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Statistics
Tissue
Chemical analysis
Spatial Analysis
Hematoxylin
2015

Cancer panomics: Computational methods and nfrastructure for integrative analysis of cancer highthroughput "omics" data

Brunak, S., De La Vega, F. M., Margolin, A., Raphael, B. J., Rätsch, G. & Stuart, J. M., 2015, In : Unknown Journal. p. 8-9 2 p.

Research output: Contribution to journalEditorial

Computational methods
Neoplasms
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
4 Citations (Scopus)

Stepwise group sparse regression (SGSR): Gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

Jang, I. S., Dienstmann, R., Margolin, A. & Guinney, J., 2015, 20th Pacific Symposium on Biocomputing, PSB 2015. Stanford University, p. 32-43 12 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Cells
Aberrations
Linear regression
Pharmacogenetics
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
12 Citations (Scopus)

Kernelized Bayesian transfer learning

Gonen, M. & Margolin, A., 2014, Proceedings of the National Conference on Artificial Intelligence. AI Access Foundation, Vol. 3. p. 1831-1839 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Tumors
Cells
Experiments
Object recognition
Gene expression
40 Citations (Scopus)

Localized data fusion for kernel k-means clustering with application to cancer biology

Gonen, M. & Margolin, A., 2014, Advances in Neural Information Processing Systems. January ed. Neural information processing systems foundation, Vol. 2. p. 1305-1313 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Data fusion
Learning algorithms
Biomarkers
Bioinformatics
Computer vision
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