Adam A. Margolin, Ph.D. - Publications

Oregon Health and Science University, Portland, OR 
Cancer, Gene regulatory models, Computational Biology

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, Kellen MR, Chen K, ... ... Margolin AA, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology. 19: 188. PMID 30400818 DOI: 10.1186/s13059-018-1539-5  0.44
2018 Xu C, Nikolova O, Basom R, Mitchell RM, Shaw R, Moser R, Park H, Gurley KE, Kao M, Green CL, Schaub FX, Diaz RL, Swan HA, Jang IS, Guinney J, ... ... Margolin AA, et al. Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29599409 DOI: 10.1158/1078-0432.CCR-17-1339  0.4
2017 Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, ... ... Margolin AA, et al. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. PMID 28988802 DOI: 10.1016/j.cels.2017.09.004  0.44
2016 Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, ... ... Margolin AA, et al. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Molecular Cancer Research : McR. PMID 27401613 DOI: 10.1158/1541-7786.MCR-16-0090  0.96
2015 Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, ... ... Margolin AA, et al. The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nature Cell Biology. PMID 26571212 DOI: 10.1038/ncb3264  0.96
2015 Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/jamia/ocv047  0.96
2015 Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, Kellen MR, Norman TC, Haussler D, Friend SH, ... ... Margolin AA, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods. PMID 25984700 DOI: 10.1038/nmeth.3407  0.96
2015 Jang IS, Dienstmann R, Margolin AA, Guinney J. Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 32-43. PMID 25592566  0.4
2014 Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biology. 15: 462. PMID 25314947 DOI: 10.1186/s13059-014-0462-7  0.96
2014 Chaibub Neto E, Bare JC, Margolin AA. Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting. Plos One. 9: e107957. PMID 25289666 DOI: 10.1371/journal.pone.0107957  0.96
2014 Moser R, Xu C, Kao M, Annis J, Lerma LA, Schaupp CM, Gurley KE, Jang IS, Biktasova A, Yarbrough WG, Margolin AA, Grandori C, Kemp CJ, Méndez E. Functional kinomics identifies candidate therapeutic targets in head and neck cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 4274-88. PMID 25125259 DOI: 10.1158/1078-0432.CCR-13-2858  0.96
2014 Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, ... ... Margolin AA, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 158: 929-44. PMID 25109877 DOI: 10.1016/j.cell.2014.06.049  0.96
2014 Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, ... ... Margolin AA, et al. Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nature Biotechnology. 32: 644-52. PMID 24952901 DOI: 10.1038/nbt.2940  0.96
2014 Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics. 46: 318-9. PMID 24675517 DOI: 10.1038/ng.2932  0.96
2014 Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA. Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 63-74. PMID 24297534  0.96
2014 Neto EC, Jang IS, Friend SH, Margolin AA. The Stream algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27-38. PMID 24297531  0.96
2014 Margolin AA. To catch a pre-leukemia Science Translational Medicine. 6. DOI: 10.1126/scitranslmed.3008713  0.96
2014 Margolin AA. Cancer genomics: Moving from unknown unknown to known unknown Science Translational Medicine. 6: 221ec20. DOI: 10.1126/scitranslmed.3008434  0.96
2014 Gönen M, Margolin AA. Kernelized Bayesian transfer learning Proceedings of the National Conference On Artificial Intelligence. 3: 1831-1839.  0.96
2014 Gönen M, Margolin AA. Localized data fusion for kernel k-means clustering with application to cancer biology Advances in Neural Information Processing Systems. 2: 1305-1313.  0.96
2013 Jang IS, Margolin A, Califano A. hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus. 3: 20130011. PMID 24511376 DOI: 10.1098/rsfs.2013.0011  0.96
2013 Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nature Genetics. 45: 1121-6. PMID 24071850 DOI: 10.1038/ng.2761  0.96
2013 Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, ... ... Margolin AA, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. Plos Computational Biology. 9: e1003047. PMID 23671412 DOI: 10.1371/journal.pcbi.1003047  0.96
2013 Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Science Translational Medicine. 5: 181re1. PMID 23596205 DOI: 10.1126/scitranslmed.3006112  0.96
2013 Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Research. 23: 665-78. PMID 23269662 DOI: 10.1101/gr.143586.112  0.96
2013 Margolin AA. Oncogenic driver mutations: Neither tissue-specific nor independent Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3008075  0.96
2013 Margolin AA. Single-molecule imaging: It takes two to make a RAF signal right Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3007774  0.96
2013 Margolin AA. The bionic cancer-resistant extracellular matrix of the naked mole-rat Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3007045  0.96
2013 Margolin AA. The enemy of the enemy of my enemy is a therapeutic target Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3006748  0.96
2013 Margolin AA. Cancer therapeutics: Best informed by genes or genomes? Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3006450  0.96
2013 Margolin AA. Genomics of T-ALL reveals a weapon of an evasive foe Science Translational Medicine. 5. DOI: 10.1126/scitranslmed.3006150  0.96
2012 Wei G, Margolin AA, Haery L, Brown E, Cucolo L, Julian B, Shehata S, Kung AL, Beroukhim R, Golub TR. Chemical genomics identifies small-molecule MCL1 repressors and BCL-xL as a predictor of MCL1 dependency. Cancer Cell. 21: 547-62. PMID 22516262 DOI: 10.1016/j.ccr.2012.02.028  0.96
2012 Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 483: 603-7. PMID 22460905 DOI: 10.1038/nature11003  0.96
2012 Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, J.Wilson C, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, et al. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Nature. DOI: 10.1038/nature11735  0.96
2010 Margolin AA, Wang K, Califano A, Nemenman I. Multivariate dependence and genetic networks inference. Iet Systems Biology. 4: 428-40. PMID 21073241 DOI: 10.1049/iet-syb.2010.0009  0.96
2010 Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 115: 975-84. PMID 19965633 DOI: 10.1182/blood-2009-06-227017  0.96
2009 Margolin AA, Ong SE, Schenone M, Gould R, Schreiber SL, Carr SA, Golub TR. Empirical Bayes analysis of quantitative proteomics experiments. Plos One. 4: e7454. PMID 19829701 DOI: 10.1371/journal.pone.0007454  0.96
2009 Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology. 27: 829-39. PMID 19741643 DOI: 10.1038/nbt.1563  0.96
2009 Ong SE, Schenone M, Margolin AA, Li X, Do K, Doud MK, Mani DR, Kuai L, Wang X, Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub TR, Gould RJ, et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 4617-22. PMID 19255428 DOI: 10.1073/pnas.0900191106  0.96
2009 Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proceedings of the National Academy of Sciences of the United States of America. 106: 244-9. PMID 19118200 DOI: 10.1073/pnas.0806445106  0.96
2007 Margolin AA, Califano A. Theory and limitations of genetic network inference from microarray data. Annals of the New York Academy of Sciences. 1115: 51-72. PMID 17925348 DOI: 10.1196/annals.1407.019  0.96
2007 Margolin AA, Palomero T, Ferrando AA, Califano A, Stolovitzky G. ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-S2  0.96
2006 Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nature Protocols. 1: 662-71. PMID 17406294 DOI: 10.1038/nprot.2006.106  0.96
2006 Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, Look AT, Young RA, et al. 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. 103: 18261-6. PMID 17114293 DOI: 10.1073/pnas.0606108103  0.96
2006 Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Bmc Bioinformatics. 7: S7. PMID 16723010 DOI: 10.1186/1471-2105-7-S1-S7  0.96
2006 Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA, Look AT. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood. 108: 986-92. PMID 16621969 DOI: 10.1182/blood-2005-08-3482  0.96
2006 Li CM, Margolin AA, Salas M, Memeo L, Mansukhani M, Hibshoosh H, Szabolcs M, Klinakis A, Tycko B. PEG10 is a c-MYC target gene in cancer cells. Cancer Research. 66: 665-72. PMID 16423995 DOI: 10.1158/0008-5472.CAN-05-1553  0.96
2006 Wang K, Nemenman I, Banerjee N, Margolin AA, Califano A. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 348-362.  0.96
2005 Margolin AA, Stojanovic MN. Boolean calculations made easy (for ribozymes). Nature Biotechnology. 23: 1374-6. PMID 16273066 DOI: 10.1038/nbt1105-1374  0.96
2005 Margolin AA, Greshock J, Naylor TL, Mosse Y, Maris JM, Bignell G, Saeed AI, Quackenbush J, Weber BL. CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics (Oxford, England). 21: 3308-11. PMID 15905276 DOI: 10.1093/bioinformatics/bti500  0.96
2005 Mosse YP, Greshock J, Margolin A, Naylor T, Cole K, Khazi D, Hii G, Winter C, Shahzad S, Asziz MU, Biegel JA, Weber BL, Maris JM. High-resolution detection and mapping of genomic DNA alterations in neuroblastoma Genes Chromosomes and Cancer. 43: 390-403. PMID 15892104 DOI: 10.1002/gcc.20198  0.96
2005 Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nature Genetics. 37: 382-90. PMID 15778709 DOI: 10.1038/ng1532  0.96
2004 Li CM, Kim CE, Margolin AA, Guo M, Zhu J, Mason JM, Hensle TW, Murty VV, Grundy PE, Fearon ER, D'Agati V, Licht JD, Tycko B. CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors. The American Journal of Pathology. 165: 1943-53. PMID 15579438  0.96
2004 Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis Genome Research. 14: 179-187. PMID 14672980 DOI: 10.1101/gr.1847304  0.96
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