Journal papers (Last updated: November 2016)
1. Şenbabaoğlu Y, Gejman R, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. (2016) Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant mRNA signatures. Genome Biology. 17(231) doi: 10.1186/s13059-016-1092-z. PDF1. PDF2. XLS1.
2. Mandal R, Şenbabaoğlu Y, Desrichard A, Havel JJ, Dalin MG, Riaz N, Lee K, Ganly I, Hakimi AA, Chan TA, Morris LGT. (2016) The head and neck cancer immune landscape and its immunotherapeutic implications. JCI Insight. 1(17):e89829. doi:10.1172/jci.insight.89829.
3. Şenbabaoğlu Y, Sümer SO, Sánchez-Vega F, Bemis D, Ciriello G, Schultz N, Sander C. (2016) A multi-method approach for proteomic network inference in 11 human cancers. PLOS Comp Biol. doi: 10.1371/journal.pcbi.1004765.
With accompanying web application ProtNet
4. {Chen F, Zhang Y}, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond J, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ (2016) Multilevel Genomics-based Taxonomy of Renal Cell Carcinoma. Cell Reports. 14(10):2476-89. doi: 10.1016/j.celrep.2016.02.024.
5. Reznik E, Miller ML, Senbabaoglu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C. (2016) Mitochondrial DNA Copy Number Variation Across Human Cancers. eLife. 2016;5:e10769.
6. Morris LGT, Riaz N, Desrichard A, Şenbabaoğlu Y, Hakimi AA, Makarov V, Reis-Filho JS, Chan TA. (2016) Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. Oncotarget. doi: 10.18632/oncotarget.7067
7. Sandhu R, Georgiou T, Reznik E, Zhu L, Kolesov I, Senbabaoglu Y, Tannenbaum A. (2015) Graph Curvature for Differentiating Cancer Networks. Scientific Reports. 5:12323
8. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2015) Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 372(26):2481-98
9. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2015) Genomic Classification of Cutaneous Melanoma. Cell. 161(7):1681-96.
10. D’Angelo RC, Ouzounova M, Davis A, Choi D, Tchuenkam SM, Kim G, Luther T, Quraishi AA, Şenbabaoğlu Y, Conley S, Clouthier SG, Hassan KA, Wicha MS, Korkaya H. (2015) Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity. Molecular Cancer Therapeutics. doi: 10.1158/1535-7163.MCT-14-0228
11. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell. 159(3).
12. Şenbabaoğlu Y, Michailidis G, Li JZ. (2014) Critical limitations of consensus clustering in class discovery. Scientific Reports. 4:6207 doi: 10.1038/srep06207. [See related blog post]
13. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 513(7517)
14. 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, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network (including Şenbabaoğlu Y), Benz CC, Perou CM, Stuart JM. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.
Cell. 158(4):929-44.
15. Ciriello G, Miller ML, Aksoy BA, Şenbabaoğlu Y, Schultz N, and Sander C. (2013) Emerging landscape of oncogenic signatures across human cancers. Nature Genetics. 45(10)
16. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics. 45(10)
17. {Lim N, Şenbabaoğlu Y}, Michailidis G, d’Alché-Buc F. (2013) OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks. Bioinformatics. 29(11) [Code available here]
18. Li B, Şenbabaoğlu Y, Peng W, Yang M, Xu J, Li JZ. (2012) Genomic estimates of aneuploid content in glioblastoma multiforme and improved classification. Clin Cancer Res. 18(20)
19. Zhang NR, Şenbabaoğlu Y, Li JZ. (2010) Joint estimation of DNA copy number from multiple platforms. Bioinformatics. 26(2)
2. Mandal R, Şenbabaoğlu Y, Desrichard A, Havel JJ, Dalin MG, Riaz N, Lee K, Ganly I, Hakimi AA, Chan TA, Morris LGT. (2016) The head and neck cancer immune landscape and its immunotherapeutic implications. JCI Insight. 1(17):e89829. doi:10.1172/jci.insight.89829.
3. Şenbabaoğlu Y, Sümer SO, Sánchez-Vega F, Bemis D, Ciriello G, Schultz N, Sander C. (2016) A multi-method approach for proteomic network inference in 11 human cancers. PLOS Comp Biol. doi: 10.1371/journal.pcbi.1004765.
With accompanying web application ProtNet
4. {Chen F, Zhang Y}, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond J, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ (2016) Multilevel Genomics-based Taxonomy of Renal Cell Carcinoma. Cell Reports. 14(10):2476-89. doi: 10.1016/j.celrep.2016.02.024.
5. Reznik E, Miller ML, Senbabaoglu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C. (2016) Mitochondrial DNA Copy Number Variation Across Human Cancers. eLife. 2016;5:e10769.
6. Morris LGT, Riaz N, Desrichard A, Şenbabaoğlu Y, Hakimi AA, Makarov V, Reis-Filho JS, Chan TA. (2016) Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. Oncotarget. doi: 10.18632/oncotarget.7067
7. Sandhu R, Georgiou T, Reznik E, Zhu L, Kolesov I, Senbabaoglu Y, Tannenbaum A. (2015) Graph Curvature for Differentiating Cancer Networks. Scientific Reports. 5:12323
8. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2015) Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 372(26):2481-98
9. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2015) Genomic Classification of Cutaneous Melanoma. Cell. 161(7):1681-96.
10. D’Angelo RC, Ouzounova M, Davis A, Choi D, Tchuenkam SM, Kim G, Luther T, Quraishi AA, Şenbabaoğlu Y, Conley S, Clouthier SG, Hassan KA, Wicha MS, Korkaya H. (2015) Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity. Molecular Cancer Therapeutics. doi: 10.1158/1535-7163.MCT-14-0228
11. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell. 159(3).
12. Şenbabaoğlu Y, Michailidis G, Li JZ. (2014) Critical limitations of consensus clustering in class discovery. Scientific Reports. 4:6207 doi: 10.1038/srep06207. [See related blog post]
13. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 513(7517)
14. 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, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network (including Şenbabaoğlu Y), Benz CC, Perou CM, Stuart JM. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.
Cell. 158(4):929-44.
15. Ciriello G, Miller ML, Aksoy BA, Şenbabaoğlu Y, Schultz N, and Sander C. (2013) Emerging landscape of oncogenic signatures across human cancers. Nature Genetics. 45(10)
16. The Cancer Genome Atlas Research Network (including Şenbabaoğlu Y). (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics. 45(10)
17. {Lim N, Şenbabaoğlu Y}, Michailidis G, d’Alché-Buc F. (2013) OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks. Bioinformatics. 29(11) [Code available here]
18. Li B, Şenbabaoğlu Y, Peng W, Yang M, Xu J, Li JZ. (2012) Genomic estimates of aneuploid content in glioblastoma multiforme and improved classification. Clin Cancer Res. 18(20)
19. Zhang NR, Şenbabaoğlu Y, Li JZ. (2010) Joint estimation of DNA copy number from multiple platforms. Bioinformatics. 26(2)
acknowledged in
1. De Henau et al. (2016) Overcoming resistance to checkpoint blockade therapy by targeting PI3Kγ in myeloid cells. Nature. doi:10.1038/nature20554
2. Hoekenga et al. (2003) Identification and Characterization of Aluminum Tolerance Loci in Arabidopsis (Landsberg erecta × Columbia) by Quantitative Trait Locus Mapping. A Physiologically Simple But Genetically Complex Trait. Plant Physiology. doi:10.1104/pp.103.023085
2. Hoekenga et al. (2003) Identification and Characterization of Aluminum Tolerance Loci in Arabidopsis (Landsberg erecta × Columbia) by Quantitative Trait Locus Mapping. A Physiologically Simple But Genetically Complex Trait. Plant Physiology. doi:10.1104/pp.103.023085
Pre-prints
1. Yasin Şenbabaoğlu, Selçuk Onur Sümer, Giovanni Ciriello, Nikolaus Schultz, Chris Sander (2015) A multi-method approach for proteomic network inference in 11 human cancers. bioRxiv doi: 10.1101/015214
2. Yasin Senbabaoglu, Andrew G Winer, Ron S Gejman, Ming Liu, Augustin Luna, Irina Ostrovnaya, Nils Weinhold, William Lee, Samuel D Kaffenberger, Ying Bei Chen, Martin H Voss, Jonathan A Coleman, Paul Russo, Victor E Reuter, Timothy A Chan, Emily H Cheng, David A Scheinberg, Ming O Li, James J Hsieh, Chris Sander, Ari Hakimi (2015) The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression. bioRxiv doi: 10.1101/025908
3. Ed Reznik, Martin Miller, Yasin Senbabaoglu, Nadeem Riaz, William Lee, Chris Sander (2015) Mitochondrial DNA Copy Number Variation Across Human Cancers. _bioRxiv doi: 10.1101/021535.
4. Yasin Şenbabaoğlu, George Michailidis, Jun Z Li. (2014) A reassessment of consensus clustering for class discovery. bioRxiv doi: 10.1101/002642
2. Yasin Senbabaoglu, Andrew G Winer, Ron S Gejman, Ming Liu, Augustin Luna, Irina Ostrovnaya, Nils Weinhold, William Lee, Samuel D Kaffenberger, Ying Bei Chen, Martin H Voss, Jonathan A Coleman, Paul Russo, Victor E Reuter, Timothy A Chan, Emily H Cheng, David A Scheinberg, Ming O Li, James J Hsieh, Chris Sander, Ari Hakimi (2015) The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression. bioRxiv doi: 10.1101/025908
3. Ed Reznik, Martin Miller, Yasin Senbabaoglu, Nadeem Riaz, William Lee, Chris Sander (2015) Mitochondrial DNA Copy Number Variation Across Human Cancers. _bioRxiv doi: 10.1101/021535.
4. Yasin Şenbabaoğlu, George Michailidis, Jun Z Li. (2014) A reassessment of consensus clustering for class discovery. bioRxiv doi: 10.1101/002642
Conference Papers
1. Lim N, Şenbabaoğlu Y, Michailidis G, d’Alché-Buc F. (2013) Boosting an operator-valued kernel model and application to network inference. Proceedings of the 30th International Conference on Machine Learning, Atlanta, Georgia, USA
Abstracts
1. Mandal R, Senbabaoglu Y, Desrichard A, Havel JJ, Lee K, Chan TA, Morris LGT. The immune infiltrative landscape of HNSCC and its prognostic implications. The New York Head and Neck Society Meeting 2016. Winner of 1st place.
2. Kowanetz M, Senbabaoglu Y, Koeppen H, Chaft J, Rudin C, Zou W, Nickles D, Desai R, Nakamura R, Sandler A, Amler L, Hegde PS, Rizvi N, Hellmann M. Spatiotemporal effects on Programmed Death-Ligand 1 (PD-L1) expression and immunophenotype of non-small cell lung cancer (NSCLC). WCLC 2015
3. Winer A, Şenbabaoğlu Y, Gejman R, Ostrovnaya I, Kaffenberger SD, Voss MH, Coleman JA, Russo P, Hsieh J, Sander C, Hakimi AA. The immune landscape of renal cell carcinoma and its association with intratumoral clonality. GU ASCO 2016
4. Winer A, Şenbabaoğlu Y, Kaffenberger S, Coleman J, Russo P, Hsieh J, Sander C, Hakimi A. Tumor purity and immune cell infiltration as prognostic risk predictors for clear cell renal cell carcinoma. GU ASCO 2015.
5. Winer A, Şenbabaoğlu Y, Kaffenberger S, Weinhold N, Bemis D, Coleman J, Russo P, Hsieh J, Sander C, Hakimi A. Tumor purity and immune cell infiltration as a prognostic risk predictor for clear cell renal cell carcinoma. SUO 2014.
(Selected for one of 4 oral presentations, awarded a travel grant.)
6. Şenbabaoğlu Y, Zhang N, Absher D, Sherlock G, Myers RM, Li J. MP-CBS: a new method for multi-platform integrated analysis of copy number variation (CNV). ASHG 2008.
2. Kowanetz M, Senbabaoglu Y, Koeppen H, Chaft J, Rudin C, Zou W, Nickles D, Desai R, Nakamura R, Sandler A, Amler L, Hegde PS, Rizvi N, Hellmann M. Spatiotemporal effects on Programmed Death-Ligand 1 (PD-L1) expression and immunophenotype of non-small cell lung cancer (NSCLC). WCLC 2015
3. Winer A, Şenbabaoğlu Y, Gejman R, Ostrovnaya I, Kaffenberger SD, Voss MH, Coleman JA, Russo P, Hsieh J, Sander C, Hakimi AA. The immune landscape of renal cell carcinoma and its association with intratumoral clonality. GU ASCO 2016
4. Winer A, Şenbabaoğlu Y, Kaffenberger S, Coleman J, Russo P, Hsieh J, Sander C, Hakimi A. Tumor purity and immune cell infiltration as prognostic risk predictors for clear cell renal cell carcinoma. GU ASCO 2015.
5. Winer A, Şenbabaoğlu Y, Kaffenberger S, Weinhold N, Bemis D, Coleman J, Russo P, Hsieh J, Sander C, Hakimi A. Tumor purity and immune cell infiltration as a prognostic risk predictor for clear cell renal cell carcinoma. SUO 2014.
(Selected for one of 4 oral presentations, awarded a travel grant.)
6. Şenbabaoğlu Y, Zhang N, Absher D, Sherlock G, Myers RM, Li J. MP-CBS: a new method for multi-platform integrated analysis of copy number variation (CNV). ASHG 2008.
Grants
1. Computational analyst in Department of Surgery Faculty Research Award to Ari Hakimi MD. Awarded Dec 2014.
2. Co-investigator in SPORE grant “Identifying genomic predictors of disease progression in papillary microcarcinoma of the thyroid". Awarded Feb 2014.
2. Co-investigator in SPORE grant “Identifying genomic predictors of disease progression in papillary microcarcinoma of the thyroid". Awarded Feb 2014.
Thesis
"Developing and Applications of Statistical Methods for High-Dimensional Biological Data Analysis" (please email for pdf)
