Chris Sander - Publications

Computational Biology Center Memorial Sloan Kettering Cancer Center, Rockville Centre, NY, United States 

171 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
2020 Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Systems. PMID 33373583 DOI: 10.1016/j.cels.2020.11.013  0.32
2020 Reguant R, Antipin Y, Sheridan R, Dallago C, Diamantoukos D, Luna A, Sander C, Gauthier NP. AlignmentViewer: Sequence Analysis of Large Protein Families. F1000research. 9. PMID 33123346 DOI: 10.12688/f1000research.22242.2  0.32
2020 Nyman E, Stein RR, Jing X, Wang W, Marks B, Zervantonakis IK, Korkut A, Gauthier NP, Sander C. Perturbation biology links temporal protein changes to drug responses in a melanoma cell line. Plos Computational Biology. 16: e1007909. PMID 32667922 DOI: 10.1371/journal.pcbi.1007909  0.32
2019 Stiffler MA, Poelwijk FJ, Brock KP, Stein RR, Riesselman A, Teyra J, Sidhu SS, Marks DS, Gauthier NP, Sander C. Protein Structure from Experimental Evolution. Cell Systems. PMID 31838147 DOI: 10.1016/j.cels.2019.11.008  0.32
2019 Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, ... ... Sander C, et al. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. Iscience. 21: 664-680. PMID 31733513 DOI: 10.1016/j.isci.2019.10.059  0.6
2019 Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, ... ... Sander C, et al. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Research. PMID 31647099 DOI: 10.1093/nar/gkz946  0.56
2019 Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nature Communications. 10: 3682. PMID 31417090 DOI: 10.1038/s41467-019-11610-1  0.4
2019 Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Inferring protein 3D structure from deep mutation scans. Nature Genetics. PMID 31209393 DOI: 10.1038/s41588-019-0432-9  0.32
2019 Xu J, Reznik E, Lee HJ, Gundem G, Jonsson P, Sarungbam J, Bialik A, Sanchez-Vega F, Creighton CJ, Hoekstra JG, Zhang L, Sajjakulnukit P, Kremer D, Tolstyka ZP, Casuscelli J, ... ... Sander C, et al. Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma. Elife. 8. PMID 30924768 DOI: 10.7554/eLife.38986  0.64
2018 Ebhardt HA, Root A, Liu Y, Gauthier NP, Sander C, Aebersold R. Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. Npj Systems Biology and Applications. 4: 26. PMID 29977602 DOI: 10.1038/s41540-018-0064-1  0.32
2018 Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, ... ... Sander C, et al. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 173: 321-337.e10. PMID 29625050 DOI: 10.1016/j.cell.2018.03.035  0.32
2018 Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports. 23: 172-180.e3. PMID 29617658 DOI: 10.1016/j.celrep.2018.03.046  0.32
2018 Reznik E, Luna A, Aksoy BA, Liu EM, La K, Ostrovnaya I, Creighton CJ, Hakimi AA, Sander C. A Landscape of Metabolic Variation across Tumor Types. Cell Systems. PMID 29396322 DOI: 10.1016/j.cels.2017.12.014  0.64
2017 Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, et al. CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database : the Journal of Biological Databases and Curation. 2017. PMID 29220450 DOI: 10.1093/database/bax054  0.32
2017 Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, ... ... Sander C, et al. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Reports. 19: 2878-2880. PMID 28658632 DOI: 10.1016/j.celrep.2017.06.008  0.64
2017 Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, ... ... Sander C, et al. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Reports. 18: 2780-2794. PMID 28297679 DOI: 10.1016/j.celrep.2017.02.033  0.64
2017 Gao J, Chang MT, Johnsen HC, Gao SP, Sylvester BE, Sumer SO, Zhang H, Solit DB, Taylor BS, Schultz N, Sander C. 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. Genome Medicine. 9: 4. PMID 28115009 DOI: 10.1186/s13073-016-0393-x  0.32
2017 Reznik E, Wang Q, La K, Schultz N, Sander C. Mitochondrial respiratory gene expression is suppressed in many cancers. Elife. 6. PMID 28099114 DOI: 10.7554/eLife.21592  0.64
2016 Okada T, Lee AY, Qin LX, Agaram N, Mimae T, Shen Y, O'Connor R, López-Lago MA, Craig A, Miller ML, Agius P, Molinelli E, Socci ND, Crago AM, Shima F, ... Sander C, et al. Integrin-α10 dependency identifies RAC and RICTOR as therapeutic targets in high-grade myxofibrosarcoma. Cancer Discovery. PMID 27577794 DOI: 10.1158/2159-8290.CD-15-1481  0.32
2016 Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, ... ... Sander C, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID 27453469 DOI: 10.1016/j.cell.2016.06.041  1
2016 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 JA, ... ... Sander C, et al. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Reports. PMID 26947078 DOI: 10.1016/j.celrep.2016.02.024  1
2016 Şenbabaoğlu Y, Sümer SO, Sánchez-Vega F, Bemis D, Ciriello G, Schultz N, Sander C. A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. Plos Computational Biology. 12: e1004765. PMID 26928298 DOI: 10.1371/journal.pcbi.1004765  0.32
2016 Reznik E, Miller ML, Şenbabaoğlu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C. Mitochondrial DNA copy number variation across human cancers. Elife. 5. PMID 26901439 DOI: 10.7554/eLife.10769  1
2016 Landa I, Ibrahimpasic T, Boucai L, Sinha R, Knauf JA, Shah RH, Dogan S, Ricarte-Filho JC, Krishnamoorthy GP, Xu B, Schultz N, Berger MF, Sander C, Taylor BS, Ghossein R, et al. Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. The Journal of Clinical Investigation. PMID 26878173 DOI: 10.1172/JCI85271  0.64
2016 Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, ... ... Sander C, et al. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 29: 104-116. PMID 26766592 DOI: 10.1016/j.ccell.2015.12.004  0.64
2015 Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. Cell Systems. 1: 197-209. PMID 27135912 DOI: 10.1016/j.cels.2015.08.014  0.64
2015 Luna A, Babur Ö, Aksoy BA, Demir E, Sander C. PaxtoolsR: Pathway Analysis in R Using Pathway Commons. Bioinformatics (Oxford, England). PMID 26685306 DOI: 10.1093/bioinformatics/btv733  1
2015 Luna A, Rajapakse VN, Sousa FG, Gao J, Schultz N, Varma S, Reinhold W, Sander C, Pommier Y. rcellminer: Exploring Molecular Profiles and Drug Response of the NCI-60 Cell Lines in R. Bioinformatics (Oxford, England). PMID 26635141 DOI: 10.1093/bioinformatics/btv701  1
2015 Gauthier NP, Reznik E, Gao J, Sumer SO, Schultz N, Sander C, Miller ML. MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. Nucleic Acids Research. PMID 26590264 DOI: 10.1093/nar/gkv1132  1
2015 Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, ... ... Sander C, et al. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 163: 506-19. PMID 26451490 DOI: 10.1016/j.cell.2015.09.033  1
2015 Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C. Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. Elife. 4. PMID 26284497 DOI: 10.7554/eLife.04640  1
2015 Stein RR, Marks DS, Sander C. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. Plos Computational Biology. 11: e1004182. PMID 26225866 DOI: 10.1371/journal.pcbi.1004182  1
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/nmeth.3440  0.88
2015 Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nature Methods. PMID 26121406 DOI: 10.1038/nmeth.3455  1
2015 Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. PMID 26097198 DOI: 10.1002/pmic.201500004  0.64
2015 Reznik E, Sander C. Extensive decoupling of metabolic genes in cancer. Plos Computational Biology. 11: e1004176. PMID 25961905 DOI: 10.1371/journal.pcbi.1004176  0.64
2015 Babur Ö, Gönen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E. Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome Biology. 16: 45. PMID 25887147 DOI: 10.1186/s13059-015-0612-6  1
2015 Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proceedings of the National Academy of Sciences of the United States of America. 112: 5413-8. PMID 25858953 DOI: 10.1073/pnas.1419956112  0.64
2015 Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, Miller ML, Rekhtman N, Moreira AL, Ibrahim F, Bruggeman C, ... ... Sander C, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science (New York, N.Y.). 348: 124-8. PMID 25765070 DOI: 10.1126/science.aaa1348  0.64
2015 Sousa FG, Matuo R, Tang SW, Rajapakse VN, Luna A, Sander C, Varma S, Simon PH, Doroshow JH, Reinhold WC, Pommier Y. Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity. Dna Repair. 28: 107-15. PMID 25758781 DOI: 10.1016/j.dnarep.2015.01.011  0.64
2015 Erson-Omay EZ, Ça?layan AO, Schultz N, Weinhold N, Omay SB, Özduman K, Köksal Y, Li J, Serin Harmanc? A, Clark V, Carrión-Grant G, Baranoski J, Ça?lar C, Barak T, Co?kun S, ... ... Sander C, et al. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis. Neuro-Oncology. PMID 25740784 DOI: 10.1093/neuonc/nov027  1
2015 Hakimi AA, Tickoo SK, Jacobsen A, Sarungbam J, Sfakianos JP, Sato Y, Morikawa T, Kume H, Fukayama M, Homma Y, Chen YB, Sankin AI, Mano R, Coleman JA, Russo P, ... ... Sander C, et al. TCEB1-mutated renal cell carcinoma: a distinct genomic and morphological subtype. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. 28: 845-53. PMID 25676555 DOI: 10.1038/modpathol.2015.6  0.64
2015 Wanjala J, Taylor BS, Chapinski C, Hieronymus H, Wongvipat J, Chen Y, Nanjangud GJ, Schultz N, Xie Y, Liu S, Lu W, Yang Q, Sander C, Chen Z, Sawyers CL, et al. Identifying actionable targets through integrative analyses of GEM model and human prostate cancer genomic profiling. Molecular Cancer Therapeutics. 14: 278-88. PMID 25381262 DOI: 10.1158/1535-7163.MCT-14-0542-T  0.32
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes Nature Methods. 12: 615-621. DOI: 10.1038/nmeth.3440  1
2015 Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains Cell Systems. 1: 197-209. DOI: 10.1016/j.cels.2015.08.014  1
2014 Kaushik P, Molinelli EJ, Miller ML, Wang W, Korkut A, Liu W, Ju Z, Lu Y, Mills G, Sander C. Spatial normalization of reverse phase protein array data. Plos One. 9: e97213. PMID 25501559 DOI: 10.1371/journal.pone.0097213  0.36
2014 Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nature Genetics. 46: 1160-5. PMID 25261935 DOI: 10.1038/ng.3101  1
2014 Shinbrot E, Henninger EE, Weinhold N, Covington KR, Göksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Research. 24: 1740-50. PMID 25228659 DOI: 10.1101/gr.174789.114  0.64
2014 Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/bioinformatics/btu458  1
2014 Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E. Integrating biological pathways and genomic profiles with ChiBE 2. Bmc Genomics. 15: 642. PMID 25086704 DOI: 10.1186/1471-2164-15-642  1
2014 Hieronymus H, Schultz N, Gopalan A, Carver BS, Chang MT, Xiao Y, Heguy A, Huberman K, Bernstein M, Assel M, Murali R, Vickers A, Scardino PT, Sander C, Reuter V, et al. Copy number alteration burden predicts prostate cancer relapse. Proceedings of the National Academy of Sciences of the United States of America. 111: 11139-44. PMID 25024180 DOI: 10.1073/pnas.1411446111  0.32
2014 Rendleman J, Antipin Y, Reva B, Adaniel C, Przybylo JA, Dutra-Clarke A, Hansen N, Heguy A, Huberman K, Borsu L, Paltiel O, Ben-Yehuda D, Brown JR, Freedman AS, Sander C, et al. Genetic variation in DNA repair pathways and risk of non-Hodgkin's lymphoma. Plos One. 9: e101685. PMID 25010664 DOI: 10.1371/journal.pone.0101685  0.32
2014 Oricchio E, Ciriello G, Jiang M, Boice MH, Schatz JH, Heguy A, Viale A, de Stanchina E, Teruya-Feldstein J, Bouska A, McKeithan T, Sander C, Tam W, Seshan VE, Chan WC, et al. Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. The Journal of Experimental Medicine. 211: 1379-91. PMID 24913233 DOI: 10.1084/jem.20132120  0.32
2014 Aksoy BA, Demir E, Babur Ö, Wang W, Jing X, Schultz N, Sander C. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics (Oxford, England). 30: 2051-9. PMID 24665131 DOI: 10.1093/bioinformatics/btu164  0.32
2014 Voss MH, Hakimi AA, Pham CG, Brannon AR, Chen YB, Cunha LF, Akin O, Liu H, Takeda S, Scott SN, Socci ND, Viale A, Schultz N, Sander C, Reuter VE, et al. Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 1955-64. PMID 24622468 DOI: 10.1158/1078-0432.CCR-13-2345  0.32
2014 Gao J, Ciriello G, Sander C, Schultz N. Collection, integration and analysis of cancer genomic profiles: from data to insight. Current Opinion in Genetics & Development. 24: 92-8. PMID 24584084 DOI: 10.1016/j.gde.2013.12.003  0.32
2014 Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E. Pattern search in BioPAX models. Bioinformatics (Oxford, England). 30: 139-40. PMID 24045775 DOI: 10.1093/bioinformatics/btt539  0.32
2013 Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, ... Sander C, et al. Perturbation biology: inferring signaling networks in cellular systems. Plos Computational Biology. 9: e1003290. PMID 24367245 DOI: 10.1371/journal.pcbi.1003290  0.32
2013 Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. Plos Computational Biology. 9: e1003388. PMID 24348232 DOI: 10.1371/journal.pcbi.1003388  0.32
2013 Li L, Shen C, Nakamura E, Ando K, Signoretti S, Beroukhim R, Cowley GS, Lizotte P, Liberzon E, Bair S, Root DE, Tamayo P, Tsherniak A, Cheng SC, Tabak B, ... ... Sander C, et al. SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell. 24: 738-50. PMID 24332042 DOI: 10.1016/j.ccr.2013.10.025  0.32
2013 Hakimi AA, Furberg H, Zabor EC, Jacobsen A, Schultz N, Ciriello G, Mikklineni N, Fiegoli B, Kim PH, Voss MH, Shen H, Laird PW, Sander C, Reuter VE, Motzer RJ, et al. An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. Journal of the National Cancer Institute. 105: 1862-70. PMID 24285872 DOI: 10.1093/jnci/djt310  0.32
2013 Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. Plos One. 8: e80306. PMID 24265805 DOI: 10.1371/journal.pone.0080306  0.32
2013 Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, ... ... Sander C, et al. The somatic genomic landscape of glioblastoma. Cell. 155: 462-77. PMID 24120142 DOI: 10.1016/j.cell.2013.09.034  1
2013 Ciriello G, Sinha R, Hoadley KA, Jacobsen AS, Reva B, Perou CM, Sander C, Schultz N. The molecular diversity of Luminal A breast tumors. Breast Cancer Research and Treatment. 141: 409-20. PMID 24096568 DOI: 10.1007/s10549-013-2699-3  1
2013 Jacobsen A, Silber J, Harinath G, Huse JT, Schultz N, Sander C. Analysis of microRNA-target interactions across diverse cancer types. Nature Structural & Molecular Biology. 20: 1325-32. PMID 24096364 DOI: 10.1038/nsmb.2678  1
2013 Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nature Genetics. 45: 1127-33. PMID 24071851 DOI: 10.1038/ng.2762  1
2013 Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics. 45: 1113-20. PMID 24071849 DOI: 10.1038/ng.2764  1
2013 Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Using biological pathway data with paxtools. Plos Computational Biology. 9: e1003194. PMID 24068901 DOI: 10.1371/journal.pcbi.1003194  1
2013 Miller ML, Molinelli EJ, Nair JS, Sheikh T, Samy R, Jing X, He Q, Korkut A, Crago AM, Singer S, Schwartz GK, Sander C. Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. Science Signaling. 6: ra85. PMID 24065146 DOI: 10.1126/scisignal.2004014  1
2013 Pflugfelder A, Kochs C, Blum A, Capellaro M, Czeschik C, Dettenborn T, Dill D, Dippel E, Eigentler T, Feyer P, Follmann M, Frerich B, Ganten MK, Gärtner J, Gutzmer R, ... ... Sander C, et al. Malignant melanoma S3-guideline "diagnosis, therapy and follow-up of melanoma". Journal Der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : Jddg. 11: 1-116, 1-126. PMID 24028775 DOI: 10.1111/ddg.12113_suppl  0.32
2013 Reich-Schupke S, Alm J, Altmeyer P, Bachter D, Bayerl C, Beissert S, Bieber T, Böhmer J, Dill D, Dippel E, Dücker P, Effendy I, El Gammal S, Elsner P, Enk A, ... ... Sander C, et al. [Phlebology in German departments of dermatology. An analysis on behalf of the German Society of Phlebology]. Der Hautarzt; Zeitschrift FüR Dermatologie, Venerologie, Und Verwandte Gebiete. 64: 685-94. PMID 24022632 DOI: 10.1007/s00105-013-2623-0  0.32
2013 Rodchenkov I, Demir E, Sander C, Bader GD. The BioPAX Validator. Bioinformatics (Oxford, England). 29: 2659-60. PMID 23918249 DOI: 10.1093/bioinformatics/btt452  1
2013 Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, ... ... Sander C, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/nmeth.2562  1
2013 Iyer G, Al-Ahmadie H, Schultz N, Hanrahan AJ, Ostrovnaya I, Balar AV, Kim PH, Lin O, Weinhold N, Sander C, Zabor EC, Janakiraman M, Garcia-Grossman IR, Heguy A, Viale A, et al. Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 31: 3133-40. PMID 23897969 DOI: 10.1200/JCO.2012.46.5740  1
2013 Domcke S, Sinha R, Levine DA, Sander C, Schultz N. Evaluating cell lines as tumour models by comparison of genomic profiles. Nature Communications. 4: 2126. PMID 23839242 DOI: 10.1038/ncomms3126  1
2013 Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C, Miller ML. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nature Methods. 10: 768-73. PMID 23817070 DOI: 10.1038/nmeth.2529  1
2013 Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C. PiHelper: an open source framework for drug-target and antibody-target data. Bioinformatics (Oxford, England). 29: 2071-2. PMID 23766416 DOI: 10.1093/bioinformatics/btt345  1
2013 Ho AS, Kannan K, Roy DM, Morris LG, Ganly I, Katabi N, Ramaswami D, Walsh LA, Eng S, Huse JT, Zhang J, Dolgalev I, Huberman K, Heguy A, Viale A, ... ... Sander C, et al. The mutational landscape of adenoid cystic carcinoma. Nature Genetics. 45: 791-8. PMID 23685749 DOI: 10.1038/ng.2643  1
2013 Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, Takeda S, Voss MH, Tickoo SK, Reuter VE, Russo P, Cheng EH, Sander C, Motzer RJ, et al. Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 19: 3259-67. PMID 23620406 DOI: 10.1158/1078-0432.CCR-12-3886  1
2013 Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling. 6: pl1. PMID 23550210 DOI: 10.1126/scisignal.2004088  1
2013 Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N. Using MEMo to discover mutual exclusivity modules in cancer. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.17. PMID 23504936 DOI: 10.1002/0471250953.bi0817s41  1
2013 Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proceedings of the National Academy of Sciences of the United States of America. 110: 4245-50. PMID 23431203 DOI: 10.1073/pnas.1208949110  1
2013 Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne PH, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. The Journal of Pathology. 229: 99-110. PMID 22899370 DOI: 10.1002/path.4087  1
2012 Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nature Biotechnology. 30: 1072-80. PMID 23138306 DOI: 10.1038/nbt.2419  1
2012 Mitsiades N, Sung CC, Schultz N, Danila DC, He B, Eedunuri VK, Fleisher M, Sander C, Sawyers CL, Scher HI. Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors. Cancer Research. 72: 6142-52. PMID 22971343 DOI: 10.1158/0008-5472.CAN-12-1335  1
2012 Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M, Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, et al. Genome sequencing identifies a basis for everolimus sensitivity. Science (New York, N.Y.). 338: 221. PMID 22923433 DOI: 10.1126/science.1226344  1
2012 Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discovery. 2: 401-4. PMID 22588877 DOI: 10.1158/2159-8290.CD-12-0095  1
2012 Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 149: 1607-21. PMID 22579045 DOI: 10.1016/j.cell.2012.04.012  1
2012 Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell. 149: 693-707. PMID 22541438 DOI: 10.1016/j.cell.2012.02.057  1
2012 Shen R, Mo Q, Schultz N, Seshan VE, Olshen AB, Huse J, Ladanyi M, Sander C. Integrative subtype discovery in glioblastoma using iCluster. Plos One. 7: e35236. PMID 22539962 DOI: 10.1371/journal.pone.0035236  1
2012 Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, ... ... Sander C, et al. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. Plos One. 7: e34546. PMID 22479643 DOI: 10.1371/journal.pone.0034546  1
2012 Silber J, Jacobsen A, Ozawa T, Harinath G, Pedraza A, Sander C, Holland EC, Huse JT. miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis. Plos One. 7: e33844. PMID 22479456 DOI: 10.1371/journal.pone.0033844  1
2012 Hanrahan AJ, Schultz N, Westfal ML, Sakr RA, Giri DD, Scarperi S, Janakiraman M, Janikariman M, Olvera N, Stevens EV, She QB, Aghajanian C, King TA, Stanchina Ed, Spriggs DR, ... ... Sander C, et al. Genomic complexity and AKT dependence in serous ovarian cancer. Cancer Discovery. 2: 56-67. PMID 22328975 DOI: 10.1158/2159-8290.CD-11-0170  1
2012 Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Research. 22: 398-406. PMID 21908773 DOI: 10.1101/gr.125567.111  1
2012 Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... ... Sander C, et al. The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) Nature Biotechnology. 30: 365. DOI: 10.1038/nbt0412-365c  1
2011 Taylor BS, DeCarolis PL, Angeles CV, Brenet F, Schultz N, Antonescu CR, Scandura JM, Sander C, Viale AJ, Socci ND, Singer S. Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discovery. 1: 587-97. PMID 22328974 DOI: 10.1158/2159-8290.CD-11-0181  1
2011 Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. Plos One. 6: e28766. PMID 22163331 DOI: 10.1371/journal.pone.0028766  1
2011 Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences of the United States of America. 108: E1293-301. PMID 22106262 DOI: 10.1073/pnas.1111471108  1
2011 Hoell JI, Larsson E, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T. RNA targets of wild-type and mutant FET family proteins. Nature Structural & Molecular Biology. 18: 1428-31. PMID 22081015 DOI: 10.1038/nsmb.2163  1
2011 Mankoo PK, Shen R, Schultz N, Levine DA, Sander C. Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. Plos One. 6: e24709. PMID 22073136 DOI: 10.1371/journal.pone.0024709  1
2011 Lipchina I, Elkabetz Y, Hafner M, Sheridan R, Mihailovic A, Tuschl T, Sander C, Studer L, Betel D. Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes & Development. 25: 2173-86. PMID 22012620 DOI: 10.1101/gad.17221311  1
2011 Somwar R, Erdjument-Bromage H, Larsson E, Shum D, Lockwood WW, Yang G, Sander C, Ouerfelli O, Tempst PJ, Djaballah H, Varmus HE. Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proceedings of the National Academy of Sciences of the United States of America. 108: 16375-80. PMID 21930909 DOI: 10.1073/pnas.1113554108  1
2011 Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, et al. Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell. 20: 173-86. PMID 21840483 DOI: 10.1016/j.ccr.2011.07.013  1
2011 Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Research. 39: e118. PMID 21727090 DOI: 10.1093/nar/gkr407  1
2011 Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, Decarolis PL, Khanin R, O'Connor R, Mihailovic A, Taylor BS, Sheridan R, Gimble JM, Viale A, Crago A, Antonescu CR, ... Sander C, et al. Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Research. 71: 5659-69. PMID 21693658 DOI: 10.1158/0008-5472.CAN-11-0890  1
2011 Palaskas N, Larson SM, Schultz N, Komisopoulou E, Wong J, Rohle D, Campos C, Yannuzzi N, Osborne JR, Linkov I, Kastenhuber ER, Taschereau R, Plaisier SB, Tran C, Heguy A, ... ... Sander C, et al. 18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Research. 71: 5164-74. PMID 21646475 DOI: 10.1158/0008-5472.CAN-10-4633  1
2011 Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, et al. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nature Genetics. 43: 668-72. PMID 21642991 DOI: 10.1038/ng.855  1
2011 Jörnsten R, Abenius T, Kling T, Schmidt L, Johansson E, Nordling TE, Nordlander B, Sander C, Gennemark P, Funa K, Nilsson B, Lindahl L, Nelander S. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Molecular Systems Biology. 7: 486. PMID 21525872 DOI: 10.1038/msb.2011.17  1
2011 Schultz N, Marenstein DR, De Angelis DA, Wang WQ, Nelander S, Jacobsen A, Marks DS, Massagué J, Sander C. Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2. Silence. 2: 3. PMID 21401928 DOI: 10.1186/1758-907X-2-3  1
2011 Clegg NJ, Couto SS, Wongvipat J, Hieronymus H, Carver BS, Taylor BS, Ellwood-Yen K, Gerald WL, Sander C, Sawyers CL. MYC cooperates with AKT in prostate tumorigenesis and alters sensitivity to mTOR inhibitors. Plos One. 6: e17449. PMID 21394210 DOI: 10.1371/journal.pone.0017449  1
2011 Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucleic Acids Research. 39: D411-9. PMID 21071423 DOI: 10.1093/nar/gkq1105  1
2011 Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Research. 39: D685-90. PMID 21071392 DOI: 10.1093/nar/gkq1039  1
2010 Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Molecular Systems Biology. 6: 433. PMID 21081925 DOI: 10.1038/msb.2010.89  1
2010 Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... ... Sander C, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/nbt.1666  1
2010 Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biology. 11: R90. PMID 20799968 DOI: 10.1186/gb-2010-11-8-r90  1
2010 Brill E, Gobble R, Angeles C, Lagos-Quintana M, Crago A, Laxa B, Decarolis P, Zhang L, Antonescu C, Socci ND, Taylor BS, Sander C, Koff A, Singer S. ZIC1 overexpression is oncogenic in liposarcoma. Cancer Research. 70: 6891-901. PMID 20713527 DOI: 10.1158/0008-5472.CAN-10-0745  1
2010 Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, Decarolis PL, Shah K, Socci ND, Weir BA, Ho A, Chiang DY, Reva B, Mermel CH, Getz G, Antipin Y, ... ... Sander C, et al. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nature Genetics. 42: 715-21. PMID 20601955 DOI: 10.1038/ng.619  1
2010 Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, ... ... Sander C, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell. 18: 11-22. PMID 20579941 DOI: 10.1016/j.ccr.2010.05.026  1
2010 Babur O, Demir E, Gönen M, Sander C, Dogrusoz U. Discovering modulators of gene expression. Nucleic Acids Research. 38: 5648-56. PMID 20466809 DOI: 10.1093/nar/gkq287  1
2010 Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Molecular Systems Biology. 6: 363. PMID 20404830 DOI: 10.1038/msb.2010.24  1
2010 Xavier JB, Sander C. Principle of system balance for drug interactions. The New England Journal of Medicine. 362: 1339-40. PMID 20375413 DOI: 10.1056/NEJMcibr1001270  1
2010 Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. Plos One. 5: e8918. PMID 20169195 DOI: 10.1371/journal.pone.0008918  1
2010 Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, ... ... Sander C, et al. NetPath: a public resource of curated signal transduction pathways. Genome Biology. 11: R3. PMID 20067622 DOI: 10.1186/gb-2010-11-1-r3  1
2010 Babur O, Dogrusoz U, Demir E, Sander C. ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics (Oxford, England). 26: 429-31. PMID 20007251 DOI: 10.1093/bioinformatics/btp665  1
2010 Veeriah S, Taylor BS, Meng S, Fang F, Yilmaz E, Vivanco I, Janakiraman M, Schultz N, Hanrahan AJ, Pao W, Ladanyi M, Sander C, Heguy A, Holland EC, Paty PB, et al. Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nature Genetics. 42: 77-82. PMID 19946270 DOI: 10.1038/ng.491  1
2009 Mu P, Han YC, Betel D, Yao E, Squatrito M, Ogrodowski P, de Stanchina E, D'Andrea A, Sander C, Ventura A. Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes & Development. 23: 2806-11. PMID 20008931 DOI: 10.1101/gad.1872909  1
2009 Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E. Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron. 63: 803-17. PMID 19778509 DOI: 10.1016/j.neuron.2009.05.029  1
2009 Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, ... ... Sander C, et al. The Systems Biology Graphical Notation. Nature Biotechnology. 27: 735-41. PMID 19668183 DOI: 10.1038/nbt.1558  1
2009 Chitale D, Gong Y, Taylor BS, Broderick S, Brennan C, Somwar R, Golas B, Wang L, Motoi N, Szoke J, Reinersman JM, Major J, Sander C, Seshan VE, Zakowski MF, et al. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene. 28: 2773-83. PMID 19525976 DOI: 10.1038/onc.2009.135  1
2009 Veeriah S, Brennan C, Meng S, Singh B, Fagin JA, Solit DB, Paty PB, Rohle D, Vivanco I, Chmielecki J, Pao W, Ladanyi M, Gerald WL, Liau L, Cloughesy TC, ... ... Sander C, et al. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proceedings of the National Academy of Sciences of the United States of America. 106: 9435-40. PMID 19478061 DOI: 10.1073/pnas.0900571106  1
2009 Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology. 27: 549-55. PMID 19465925 DOI: 10.1038/nbt.1543  1
2009 King JC, Xu J, Wongvipat J, Hieronymus H, Carver BS, Leung DH, Taylor BS, Sander C, Cardiff RD, Couto SS, Gerald WL, Sawyers CL. Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nature Genetics. 41: 524-6. PMID 19396167 DOI: 10.1038/ng.371  1
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, ... ... Sander C, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/j.molonc.2008.11.003  1
2009 Pratilas CA, Taylor BS, Ye Q, Viale A, Sander C, Solit DB, Rosen N. (V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proceedings of the National Academy of Sciences of the United States of America. 106: 4519-24. PMID 19251651 DOI: 10.1073/pnas.0900780106  1
2009 Yi R, Pasolli HA, Landthaler M, Hafner M, Ojo T, Sheridan R, Sander C, O'Carroll D, Stoffel M, Tuschl T, Fuchs E. DGCR8-dependent microRNA biogenesis is essential for skin development. Proceedings of the National Academy of Sciences of the United States of America. 106: 498-502. PMID 19114655 DOI: 10.1073/pnas.0810766105  1
2008 Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, ... ... Sander C, et al. Introducing meta-services for biomedical information extraction. Genome Biology. 9: S6. PMID 18834497 DOI: 10.1186/gb-2008-9-s2-s6  1
2008 Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, et al. A specificity map for the PDZ domain family. Plos Biology. 6: e239. PMID 18828675 DOI: 10.1371/journal.pbio.0060239  1
2008 Taylor BS, Barretina J, Socci ND, Decarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. Functional copy-number alterations in cancer. Plos One. 3: e3179. PMID 18784837 DOI: 10.1371/journal.pone.0003179  1
2007 Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, ... ... Sander C, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/nprot.2007.324  1
2007 Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B. From bytes to bedside: data integration and computational biology for translational cancer research. Plos Computational Biology. 3: e12. PMID 17319736 DOI: 10.1371/journal.pcbi.0030012  0.56
2006 Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. Bmc Bioinformatics. 7: 497. PMID 17101041 DOI: 10.1186/1471-2105-7-497  0.56
2006 Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Research. 34: D504-6. PMID 16381921 DOI: 10.1093/nar/gkj126  1
2005 Cary MP, Bader GD, Sander C. Pathway information for systems biology. Febs Letters. 579: 1815-20. PMID 15763557 DOI: 10.1016/j.febslet.2005.02.005  1
2004 Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, ... ... Sander C, et al. Global mapping of the yeast genetic interaction network. Science (New York, N.Y.). 303: 808-13. PMID 14764870 DOI: 10.1126/science.1091317  1
2004 Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, ... ... Sander C, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/nbt926  1
2003 Berriz GF, King OD, Bryant B, Sander C, Roth FP. Characterizing gene sets with FuncAssociate. Bioinformatics (Oxford, England). 19: 2502-4. PMID 14668247 DOI: 10.1093/bioinformatics/btg363  1
2003 Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, ... ... Sander C, et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (Oxford, England). 19: 717-26. PMID 12691983 DOI: 10.1093/bioinformatics/btg077  1
1998 Dodge C, Schneider R, Sander C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Research. 26: 313-5. PMID 9399862 DOI: 10.1093/nar/26.1.313  1
1997 Andrade MA, Daruvar A, Casari G, Schneider R, Termier M, Sander C. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome. Yeast (Chichester, England). 13: 1363-74. PMID 9392081 DOI: 10.1002/(SICI)1097-0061(199711)13:14<1363::AID-YEA182>3.0.CO;2-8  1
1997 Andrade M, Casari G, de Daruvar A, Sander C, Schneider R, Tamames J, Valencia A, Ouzounis C. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Computer Applications in the Biosciences : Cabios. 13: 481-3. PMID 9283767 DOI: 10.1093/bioinformatics/13.4.481  1
1997 Rost B, Schneider R, Sander C. Protein fold recognition by prediction-based threading. Journal of Molecular Biology. 270: 471-80. PMID 9237912 DOI: 10.1006/jmbi.1997.1101  1
1997 Schneider R, de Daruvar A, Sander C. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 25: 226-30. PMID 9016541 DOI: 10.1093/nar/25.1.226  1
1996 Casari G, De Daruvar A, Sander C, Schneider R. Bioinformatics and the discovery of gene function. Trends in Genetics : Tig. 12: 244-5. PMID 8763493 DOI: 10.1016/0168-9525(96)30057-7  1
1996 Schneider R, Sander C. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 24: 201-5. PMID 8594579 DOI: 10.1093/nar/24.1.201  1
1995 Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. Challenging times for bioinformatics. Nature. 376: 647-8. PMID 7651513 DOI: 10.1038/376647a0  1
1995 Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Molecular Microbiology. 16: 955-67. PMID 7476192 DOI: 10.1111/j.1365-2958.1995.tb02321.x  1
1994 Rost B, Sander C, Schneider R. Redefining the goals of protein secondary structure prediction. Journal of Molecular Biology. 235: 13-26. PMID 8289237 DOI: 10.1016/S0022-2836(05)80007-5  1
1994 Göbel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 18: 309-17. PMID 8208723 DOI: 10.1002/prot.340180402  1
1994 Rost B, Sander C, Schneider R. PHD--an automatic mail server for protein secondary structure prediction. Computer Applications in the Biosciences : Cabios. 10: 53-60. PMID 8193956 DOI: 10.1093/bioinformatics/10.1.53  1
1994 Sander C, Schneider R. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 22: 3597-9. PMID 7937066  1
1994 Scharf M, Schneider R, Casari G, Bork P, Valencia A, Ouzounis C, Sander C. GeneQuiz: a workbench for sequence analysis. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 348-53. PMID 7584411  1
1993 Holmes KC, Sander C, Valencia A. A new ATP-binding fold in actin, hexokinase and Hsc70. Trends in Cell Biology. 3: 53-9. PMID 14731729 DOI: 10.1016/0962-8924(93)90161-S  1
1993 Rost B, Schneider R, Sander C. Progress in protein structure prediction? Trends in Biochemical Sciences. 18: 120-3. PMID 8493721 DOI: 10.1016/0968-0004(93)90017-H  1
1993 Ouzounis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. Journal of Molecular Biology. 232: 805-25. PMID 8355272 DOI: 10.1006/jmbi.1993.1433  1
1993 Sander C, Schneider R. The HSSP data base of protein structure-sequence alignments. Nucleic Acids Research. 21: 3105-9. PMID 8332531  1
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature. 358: 287. PMID 1641000 DOI: 10.1038/358287a0  1
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science : a Publication of the Protein Society. 1: 1677-90. PMID 1304897 DOI: 10.1002/pro.5560011216  1
1992 Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Science : a Publication of the Protein Society. 1: 409-17. PMID 1304348 DOI: 10.1002/pro.5560010313  1
1991 Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 9: 56-68. PMID 2017436 DOI: 10.1002/prot.340090107  1
1980 Lifson S, Sander C. Specific recognition in the tertiary structure of beta-sheets of proteins. Journal of Molecular Biology. 139: 627-39. PMID 7411635 DOI: 10.1016/0022-2836(80)90052-2  1
1979 Lifson S, Sander C. Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature. 282: 109-11. PMID 503185 DOI: 10.1038/282109a0  1
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