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 |
0.617 |
|
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 |
0.534 |
|
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 |
0.575 |
|
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 |
0.621 |
|
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 |
0.647 |
|
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 |
0.704 |
|
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 |
0.567 |
|
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 |
0.701 |
|
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 |
0.34 |
|
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 |
0.721 |
|
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 |
|
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