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Adam A. Margolin, Ph.D. - Publications

Affiliations: 
Oregon Health and Science University, Portland, OR 
Area:
Cancer, Gene regulatory models, Computational Biology
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60/119 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 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. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. PMID 30559381 DOI: 10.1038/S41586-018-0722-X  0.378
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  0.552
2018 Wagner A, Walsh B, Sonkin D, Dienstmann R, Li XS, Beckmann JS, Mayfield G, Tamborero D, Lopez-Bigas N, Goecks J, Margolin A, Griffith M, Griffith O. 4. Coordinating variant interpretation knowledgebases improves clinical interpretation of genomic variants in cancers Cancer Genetics and Cytogenetics. 37. DOI: 10.1016/J.Cancergen.2018.04.065  0.346
2017 Nikolova O, Moser R, Kemp C, Onen MG, Margolin AA. Modeling Gene-Wise Dependencies Improves the Identification of Drug Response Biomarkers in Cancer Studies. Bioinformatics (Oxford, England). PMID 28082455 DOI: 10.1093/Bioinformatics/Btw836  0.33
2017 Griffith O, Griffith M, Tamborero D, Wagner A, Krysiak K, Fitz CDV, Chakravarty D, Cerami E, Elemento O, Schultz N, Margolin A, Lopez-Bigas N. Global integration of knowledgebases for clinical interpretation of cancer variants F1000research. 6. DOI: 10.7490/F1000Research.1113918.1  0.315
2017 Griffith OL, Griffith M, Tamborero D, Wagner AH, Krysiak K, Fitz CDV, Chakravarty D, Cerami E, Elemento O, Schultz N, Margolin A, Lopez-Bigas N. Abstract 2608: Global integration of knowledgebases for clinical interpretation of cancer variants Cancer Research. 77: 2608-2608. DOI: 10.1158/1538-7445.Am2017-2608  0.315
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  0.542
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  0.371
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  0.616
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  0.551
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  0.345
2014 Gönen M, Margolin AA. Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. Bioinformatics (Oxford, England). 30: i556-63. PMID 25161247 DOI: 10.1093/Bioinformatics/Btu464  0.342
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  0.559
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  0.401
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  0.326
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  0.581
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  0.533
2014 Ferte C, Chaibub Neto E, Commo F, Nikolova O, Jang iS, Gonen M, Lacroix L, Koubi-Pick V, Angevin E, Besse B, Ducreux M, Hollebecque A, Massard C, Margolin A, Friend SH, et al. Joint cell-line and patient modeling of drug sensitivity reveals novel molecular biomarkers for targeted and conventional chemotherapy. Journal of Clinical Oncology. 32: 2565-2565. DOI: 10.1200/Jco.2014.32.15_Suppl.2565  0.574
2014 Nikolova OH, Gönen M, Dienstmann R, Jang IS, Moser R, Cermelli S, Xu C, Mitchell RM, Mendez E, Grandori C, Kemp C, Friend S, Guinney J, Margolin A. Abstract 5323: Integrated computational cell-line modeling of drug sensitivity and high-throughput siRNA screening reveals novel molecular biomarkers for conventional chemotherapy Cancer Research. 74: 5323-5323. DOI: 10.1158/1538-7445.Am2014-5323  0.62
2014 Margolin AA. To catch a pre-leukemia Science Translational Medicine. 6. DOI: 10.1126/Scitranslmed.3008713  0.301
2014 Margolin AA. Cancer genomics: Moving from unknown unknown to known unknown Science Translational Medicine. 6: 221ec20. DOI: 10.1126/Scitranslmed.3008434  0.363
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  0.691
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  0.373
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  0.646
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  0.375
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  0.416
2013 Ferté C, Neto EC, Sun C, Noecker C, Commo F, Nikolova O, Jang IS, Gonen M, Besse B, André F, Angevin E, Lacroix L, Mazoyer C, Hollebecque A, Massard C, ... Margolin A, et al. Abstract A130: Joint cell-line (CCLE, Sanger) and patient (TCGA) modeling of drug sensitivity reveals novel molecular biomarkers for targeted therapy and conventional chemotherapy. Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Targ-13-A130  0.614
2013 Moser R, Xu C, Kao M, Jang IS, Gurley K, Margolin A, Grandori C, Mendez E, Kemp C. Abstract PR05: Construction of synthetic lethal networks for p53 tumor suppressor pathways identifies candidate therapeutic targets for metastatic, chemotherapy resistant HNSCC Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-Pr05  0.573
2013 Margolin AA. Oncogenic driver mutations: Neither tissue-specific nor independent Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3008075  0.347
2013 Margolin AA. Single-molecule imaging: It takes two to make a RAF signal right Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3007774  0.363
2013 Margolin AA. Co-opting a Tumor Predator to Provide Life Support Science Translational Medicine. 5: 202ec149-202ec149. DOI: 10.1126/Scitranslmed.3007484  0.3
2013 Margolin AA. The enemy of the enemy of my enemy is a therapeutic target Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3006748  0.324
2013 Margolin AA. Cancer therapeutics: Best informed by genes or genomes? Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3006450  0.412
2013 Margolin AA. Genomics of T-ALL reveals a weapon of an evasive foe Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3006150  0.38
2013 Lopez-Bigas N, Cline M, Broom B, Margolin A, Omberg L, Weinstein J, Axton M. Thread 4: Data discovery, transparency and visualization Nature Genetics. DOI: 10.1038/Ng.2789  0.323
2013 Reimand J, Bader G, Margolin A, Gonzalez-Perez A, Tamborero D, Lopez-Bigas N, Weinstein J, Stuart J, Axton M. Thread 2: Network models Nature Genetics. 1-1. DOI: 10.1038/Ng.2787  0.325
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  0.304
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  0.449
2012 Margolin AA, Jang IS, Friend S. Abstract IA15: Predicting drug sensitivity from cancer cell lines Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-Ia15  0.627
2012 Stransky N, Kryukov GV, Caponigro G, Barretina J, Venkatesan K, Margolin AA, Wilson CJ, Lehar J, Jones MD, Palescandolo E, Sougnez C, Onofrio RC, MacConaill L, Ardlie K, Golub TR, et al. Abstract 5114: Integrative analysis of the Cancer Cell Line Encyclopedia reveals genetic and transcriptional predictors of compound sensitivity Cancer Research. 72: 5114-5114. DOI: 10.1158/1538-7445.Am2012-5114  0.484
2011 Barretina J, Stransky N, Caponigro G, Kim S, Margolin A, Venkhatesan K, Kryukov G, Berger M, Monahan J, Morais P, Meltzer J, Mahan S, Sonkin D, Raman P, Jones M, et al. Abstract 5455: Integrative analysis of the Cancer Cell Line Encyclopedia reveals genetic and transcriptional predictors of compound sensitivity Cancer Research. 71: 5455-5455. DOI: 10.1158/1538-7445.Am2011-5455  0.459
2011 Wei G, Margolin A, Brown E, Cucolo L, Stransky N, Barretina J, Garraway L, Beroukhim R. Abstract 13: Chemical genomics identifies MCL1 repressors and resistance mechanism Cancer Research. 71: 13-13. DOI: 10.1158/1538-7445.Am2011-13  0.447
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  0.703
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  0.566
2010 Venkatesan K, Stransky N, Margolin A, Reddy A, Raman P, Sonkin D, Jones M, Wilson C, Kim S, Warmuth M, Sellers W, Lehar J, Barretina J, Caponigro G, Garraway L, et al. Prediction of drug response using genomic signatures from the Cancer Cell Line Encyclopedia Clinical Cancer Research. 16. DOI: 10.1158/Diag-10-Pr2  0.452
2010 Du J, Bernasconi P, He F, Julian B, Mani DR, Margolin A, Ross K, Clauser K, Finn SP, Beroukhim R, Burns M, Peng X, Hieronymus H, Maglathlin R, Lewis TA, et al. Abstract 5559: Proteomic identification of activated, essential tyrosine kinases in human cancers Cancer Research. 70: 5559-5559. DOI: 10.1158/1538-7445.Am10-5559  0.406
2010 Stransky N, Venkatesan K, Barretina J, Caponigro G, Margolin A, Morrissey M, Raman P, Getz G, Berger M, Johannessen C, Callahan A, Morais P, Mahan S, Gupta S, Onofrio R, et al. Abstract PR4: Integrative analysis of genomic and pharmacologic data from the Cancer Cell Line Encyclopedia Clinical Cancer Research. 16. DOI: 10.1158/1078-0432.Tcmusa10-Pr4  0.469
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  0.347
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  0.7
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  0.339
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  0.587
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  0.581
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  0.571
2007 Palomero T, Wei KL, 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. 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) Proceedings of the National Academy of Sciences of the United States of America. 104. DOI: 10.1073/Pnas.0700840104  0.508
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  0.72
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  0.549
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  0.709
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  0.345
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.  0.472
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  0.595
Low-probability matches (unlikely to be authored by this person)
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  0.299
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 DOI: 10.1016/S0002-9440(10)63246-4  0.298
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  0.295
2015 Stuart J, Boutros P, Lee AY, Ellrott K, Margolin A, Dang K, Houlahan K, Bare C, Guinney J, Espiritu S, Hu Y, Norman T, Ewing A, Stein L, Caloian C, et al. Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detection F1000research. 4. DOI: 10.7490/F1000Research.1111147.1  0.285
2013 Margolin AA. The bionic cancer-resistant extracellular matrix of the naked mole-rat Science Translational Medicine. 5. DOI: 10.1126/Scitranslmed.3007045  0.273
2018 Davis RJ, Gönen M, Margineantu DH, Handeli S, Swanger J, Hoellerbauer P, Paddison PJ, Gu H, Raftery D, Grim JE, Hockenbery DM, Margolin AA, Clurman BE. Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735700 DOI: 10.1073/Pnas.1718338115  0.263
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  0.261
2012 Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin A, Kim S, Wilson C, Lehar J, Kryukov G, Murray L, Morrissey M, Sellers W, Schlegel R, Garraway L. 22 The Cancer Cell Line Encyclopedia - Using Preclinical Models to Predict Anticancer Drug Sensitivity European Journal of Cancer. 48: S5-S6. DOI: 10.1016/S0959-8049(12)70726-8  0.256
2018 Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC. Germline contamination and leakage in whole genome somatic single nucleotide variant detection. Bmc Bioinformatics. 19: 28. PMID 29385983 DOI: 10.1186/S12859-018-2046-0  0.255
2020 Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, ... ... Margolin AA, et al. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature Genetics. PMID 32246132 DOI: 10.1038/S41588-020-0603-8  0.252
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  0.252
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  0.244
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  0.242
2016 Salomonis N, Dexheimer PJ, Omberg L, Schroll R, Bush S, Huo J, Schriml L, Ho Sui S, Keddache M, Mayhew C, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, ... ... Margolin A, et al. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cell from the Progenitor Cell Biology Consortium. Stem Cell Reports. PMID 27293150 DOI: 10.1016/J.Stemcr.2016.05.006  0.237
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  0.234
2017 Palpant NJ, Wang Y, Hadland B, Zaunbrecher RJ, Redd M, Jones D, Pabon L, Jain R, Epstein J, Ruzzo WL, Zheng Y, Bernstein I, Margolin A, Murry CE. Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis. Cell Reports. 20: 1597-1608. PMID 28813672 DOI: 10.1016/J.Celrep.2017.07.067  0.217
2013 Margolin A, Weinstein J, Stuart J, Axton M. Thread 5: Future directions Nature Genetics. 1-1. DOI: 10.1038/Ng.2790  0.213
2017 Palpant N, Wang Y, Hadland B, Zaunbrecher R, Redd M, Pabon L, Jain R, Epstein J, Zheng Y, Bernstein I, Margolin A, Murry C. Epigenetic and transcriptional analysis of mesoderm progenitor cells identifies HOPX as a novel regulator of hemogenic endothelium Mechanisms of Development. 145: S101. DOI: 10.1016/J.Mod.2017.04.263  0.213
2017 Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, ... ... Margolin AA, et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 49: 170-174. PMID 28138153 DOI: 10.1038/Ng.3774  0.202
2013 Gonzalez-Perez A, Tamborero D, Lopez-Bigas N, Margolin A, Ding L, Gordenin D, Axton M. Thread 1: Mutational drivers Nature Genetics. 1-1. DOI: 10.1038/Ng.2786  0.201
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  0.2
2017 Young Hwan Chang, Thibault G, Madin O, Azimi V, Meyers C, Johnson B, Link J, Margolin A, Gray JW. Deep learning based Nucleus Classification in pancreas histological images. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2017: 672-675. PMID 29059962 DOI: 10.1109/EMBC.2017.8036914  0.2
2018 Medler TR, Murugan D, Horton W, Kumar S, Cotechini T, Forsyth AM, Leyshock P, Leitenberger JJ, Kulesz-Martin M, Margolin AA, Werb Z, Coussens LM. Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy. Cancer Cell. 34: 561-578.e6. PMID 30300579 DOI: 10.1016/J.Ccell.2018.09.003  0.2
2020 Lopez G, Egolf LE, Giorgi FM, Diskin SJ, Margolin AA. Svpluscnv: analysis and visualization of complex structural variation data. Bioinformatics (Oxford, England). PMID 33051644 DOI: 10.1093/bioinformatics/btaa878  0.198
2018 Heath AP, Raman P, Zhu Y, Lilly JV, Taylor D, Storm PB, Waanders AJ, Volchenboum S, Stein L, Ellrott K, Margolin A, Davis-Dusenbery B, Grossman R, Ferretti V, Mueller S, et al. TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS Neuro-Oncology. 20: i186-i186. DOI: 10.1093/Neuonc/Noy059.715  0.193
2005 Margolin AA, Stojanovic MN. Boolean calculations made easy (for ribozymes). Nature Biotechnology. 23: 1374-6. PMID 16273066 DOI: 10.1038/Nbt1105-1374  0.189
2017 Azimi V, Chang YH, Thibault G, Smith J, Tsujikawa T, Kukull B, Jensen B, Corless C, Margolin A, Gray JW. BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION. Proceedings. Ieee International Symposium On Biomedical Imaging. 2017: 1137-1140. PMID 30364881 DOI: 10.1109/ISBI.2017.7950717  0.184
2017 Young Hwan Chang, Tsujikawa T, Margolin A, Coussens LM, Gray JW. Multiplexed immunohistochemistry image analysis using sparse coding. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2017: 4046-4049. PMID 29060785 DOI: 10.1109/EMBC.2017.8037744  0.176
2023 Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. Bmc Genomics. 24: 349. PMID 37365517 DOI: 10.1186/s12864-023-09424-z  0.165
2023 Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. Research Square. PMID 36824803 DOI: 10.21203/rs.3.rs-2140339/v1  0.165
2017 Tsujikawa T, Kumar S, Borkar RN, Azimi V, Thibault G, Chang YH, Balter A, Kawashima R, Choe G, Sauer D, El Rassi E, Clayburgh DR, Kulesz-Martin MF, Lutz ER, Zheng L, ... ... Margolin AA, et al. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis. Cell Reports. 19: 203-217. PMID 28380359 DOI: 10.1016/J.Celrep.2017.03.037  0.158
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  0.15
2018 Wood MA, Paralkar M, Paralkar MP, Nguyen A, Struck AJ, Ellrott K, Margolin A, Nellore A, Thompson RF. Population-level distribution and putative immunogenicity of cancer neoepitopes. Bmc Cancer. 18: 414. PMID 29653567 DOI: 10.1186/S12885-018-4325-6  0.144
2016 Young Hwan Chang, Thibault G, Azimi V, Johnson B, Jorgens D, Link J, Margolin A, Gray JW. Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2016: 1175-1178. PMID 28324942 DOI: 10.1109/EMBC.2016.7590914  0.142
2016 Chang YH, Thibault G, Azimi V, Johnson B, Jorgens D, Link J, Margolin A, Gray JW, Young Hwan Chang, Thibault G, Azimi V, Johnson B, Jorgens D, Link J, Margolin A, ... ... Margolin A, et al. Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2016: 1175-1178. PMID 28226710 DOI: 10.1109/EMBC.2016.7590914  0.142
2018 Burlingame EA, Margolin AA, Gray JW, Chang YH. SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. Proceedings of Spie--the International Society For Optical Engineering. 10581. PMID 30283195 DOI: 10.1117/12.2293249  0.134
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.  0.132
2017 Chang YH, Thibault G, Johnson B, Margolin A, Gray JW. Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity. Proceedings of Spie--the International Society For Optical Engineering. 10140. PMID 30364826 DOI: 10.1117/12.2250428  0.125
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  0.122
2018 Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P'ng C, Houlahan KE, Caloian C, Fraser M, Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC. Valection: design optimization for validation and verification studies. Bmc Bioinformatics. 19: 339. PMID 30253747 DOI: 10.1186/S12859-018-2391-Z  0.121
2007 Beitel M, Genova M, Schuman-Olivier Z, Arnold R, Avants SK, Margolin A. Reflections by inner-city drug users on a Buddhist-based spirituality-focused therapy: a qualitative study. The American Journal of Orthopsychiatry. 77: 1-9. PMID 17352579 DOI: 10.1037/0002-9432.77.1.1  0.082
2010 Amaro H, Magno-Gatmaytan C, Meléndez M, Cortés DE, Arevalo S, Margolin A. Addiction treatment intervention: An uncontrolled prospective pilot study of spiritual self-schema therapy with Latina women Substance Abuse. 31: 117-125. PMID 20408063 DOI: 10.1080/08897071003641602  0.077
2007 Copenhaver MM, Lee IC, Margolin A. Successfully integrating an HIV risk reduction intervention into a community-based substance abuse treatment program. The American Journal of Drug and Alcohol Abuse. 33: 109-20. PMID 17366251 DOI: 10.1080/00952990601087463  0.067
2009 Zak A, Sallacan-Ecker L, Margolin A, Genut M, Tenne R. Insight into the growth mechanism of ws2 nanotubes in the scaled-up fluidized-bed reactor Nano. 4: 91-98. DOI: 10.1142/S1793292009001551  0.066
2011 Zak A, Sallacan-Ecker L, Margolin A, Feldman Y, Popovitz-Biro R, Albu-Yaron A, Genut M, Tenne R. Scaling up of the WS2 nanotubes synthesis Fullerenes Nanotubes and Carbon Nanostructures. 19: 18-26. DOI: 10.1080/1536383X.2010.488594  0.057
2011 Copenhaver MM, Lee IC, Margolin A, Bruce RD, Altice FL. Testing an optimized community-based human immunodeficiency virus (HIV) risk reduction and antiretroviral adherence intervention for HIV-infected injection drug users. Substance Abuse. 32: 16-26. PMID 21302180 DOI: 10.1080/08897077.2011.540466  0.052
2009 Torosian SD, Regan PM, Doran T, Taylor MA, Margolin A. A refrigeration temperature of 4 degrees C does not prevent static growth of Yersinia pestis in heart infusion broth. Canadian Journal of Microbiology. 55: 1119-24. PMID 19898555 DOI: 10.1139/w09-060  0.051
2007 Margolin A, Schuman-Olivier Z, Beitel M, Arnold RM, Fulwiler CE, Avants SK. A preliminary study of spiritual self-schema (3-S(+)) therapy for reducing impulsivity in HIV-positive drug users. Journal of Clinical Psychology. 63: 979-99. PMID 17828761 DOI: 10.1002/Jclp.20407  0.048
2006 Margolin A, Beitel M, Schuman-Olivier Z, Avants SK. A controlled study of a spirituality-focused intervention for increasing motivation for HIV prevention among drug users. Aids Education and Prevention : Official Publication of the International Society For Aids Education. 18: 311-22. PMID 16961448 DOI: 10.1521/Aeap.2006.18.4.311  0.044
2009 Zak A, Sallacan-Ecker L, Margolin A, Genut M, Tenne R. Large scale synthesis of WS2 nanotubes as building block for new nanocomposites 6th International Conference On Condition Monitoring and Machinery Failure Prevention Technologies 2009. 2: 1325-1332.  0.04
2013 Halpert B, Margolin A, Drangai L. The case for nano solid-based lubricants as EP additives Nlgi Spokesman. 77: 29-30.  0.039
2012 Barak A, Margolin A, Shiloh A. Automatic resource-centric process migration for MPI Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7490: 163-172. DOI: 10.1007/978-3-642-33518-1_21  0.038
2009 Torosian SD, Regan PM, Taylor MA, Margolin A. Detection of Yersinia pestis over time in seeded bottled water samples by cultivation on heart infusion agar. Canadian Journal of Microbiology. 55: 1125-9. PMID 19898556 DOI: 10.1139/w09-061  0.033
2009 Rosentsveig R, Margolin A, Gorodnev A, Popovitz-Biro R, Feldman Y, Rapoport L, Novema Y, Naveh G, Tenne R. Synthesis of fullerene-like MoS2 nanoparticles and their tribological behavior Journal of Materials Chemistry. 19: 4368-4374. DOI: 10.1039/B820927H  0.031
2014 Gönen M, Margolin AA. Kernelized Bayesian transfer learning Proceedings of the National Conference On Artificial Intelligence. 3: 1831-1839.  0.031
2014 Diloyan G, Margolin A, Drangai L, Gururajan G. Novel fullerene-like inorganic nanoparticles of tungsten disulfide (if WS2) as a superior lubricant Society of Tribologists and Lubrication Engineers Annual Meeting and Exhibition 2014. 2: 573-579.  0.03
2009 Margolin A. Publication Error Journal of the Association of Nurses in Aids Care. 20: 159. PMID 19427591 DOI: 10.1016/j.jana.2009.04.001  0.014
2008 Margolin A, Deepak FL, Popovitz-Biro R, Bar-Sadan M, Feldman Y, Tenne R. Fullerene-like WS2 nanoparticles and nanotubes by the vapor-phase synthesis of WCln and H2S Nanotechnology. 19. DOI: 10.1088/0957-4484/19/9/095601  0.01
2008 Lalonde J, Margolin A. Immobilization of enzymes Enzyme Catalysis in Organic Synthesis: Second Edition. 163-184. DOI: 10.1002/9783527618262.ch6  0.01
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