The Nikolaus Schultz Lab: Publications


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, Taylor BS, Sawyers CL. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A. 2014 Jul 14.

Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, Pico AR. BridgeDb app: unifying identifier mapping services for Cytoscape. F1000Research 2014, 3:148.

Al-Ahmadie H, Iyer G, Hohl M, Asthana S, Inagaki A, Schultz N, Hanrahan AJ, Scott SN, Brannon AR, McDermott GC, Pirun M, Ostrovnaya I, Kim P, Socci ND, Viale A, Schwartz GK, Reuter V, Bochner BH, Rosenberg JE, Bajorin DF, Berger MF, Petrini JH, Solit DB, Taylor BS. Synthetic lethality in ATM-deficient RAD50-mutant tumors underlie outlier response to cancer therapy. Cancer Discov. 2014 Jun 16. pii: CD-14-0380.

The Cancer Genome Atlas Research Network. Comprehensive Molecular Characterization of Gastric Adenocarcinoma. Nature. Published online 23 July 2014.

The Cancer Genome Atlas Research Network. Comprehensive Molecular Profiling of Lung Adenocarcinoma. Nature. In press.

Ortiz B, Fabius AW, Wu WH, Pedraza A, Brennan CW, Schultz N, Pitter KL, Bromberg JF, Huse JT, Holland EC, Chan TA. Loss of the tyrosine phosphatase PTPRD leads to aberrant STAT3 activation and promotes gliomagenesis. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8149-54

Chen C, Liu Y, Rappaport AR, Kitzing T, Schultz N, Zhao Z, Shroff AS, Dickins RA, Vakoc CR, Bradner JE, Stock W, LeBeau MM, Shannon KM, Kogan S, Zuber J, Lowe SW. MLL3 Is a Haploinsufficient 7q Tumor Suppressor in Acute Myeloid Leukemia. Cancer Cell. 2014 May 12;25(5):652-65.

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, Russo P, Cheng EH, Motzer RJ, Berger MF, Hsieh JJ. Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy. Clin Cancer Res. 2014 Apr 1;20(7):1955-64.

Aksoy BA, Demir E, Babur O, Wang W, Jing X, Schultz N, Sander C. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics. 2014 Jul 15;30(14):2051-9.

Jelinic P, Mueller JJ, Olvera N, Dao F, Scott SN, Shah R, Gao J, Schultz N, Gonen M, Soslow RA, Berger MF, Levine DA. Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. Nat Genet. 2014 May;46(5):424-6.

The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-22.

Nissan MH, Pratilas CA, Jones AM, Ramirez R, Won H, Liu C, Tiwari S, Kong L, Hanrahan AJ, Yao Z, Merghoub T, Ribas A, Chapman PB, Yaeger R, Taylor BS, Schultz N, Berger MF, Rosen N, Solit DB. Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence. Cancer Res. 2014 Apr 15;74(8):2340-50.

Gao J, Ciriello G, Sander C, Schultz N. Collection, Integration and Analysis of Cancer Genomic Profiles: From Data to Insight. Curr Opin Genet Dev. 2014 Feb 26;24C:92-98.

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, Jacobsen A, Hakimi AA, Schultz N, Ciriello G, Sander C, Hsieh JJ, Kaelin WG Jr. SQSTM1 Is a Pathogenic Target of 5q Copy Number Gains in Kidney Cancer. Cancer Cell. 2013 Dec 9;24(6):738-50.

Hakimi A, 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, Hsieh JJ, Russo P. An Epidemiologic and Genomic Investigation Into the Obesity Paradox in Renal Cell Carcinoma. J Natl Cancer Inst. 2013 Dec 18;105(24):1862-70.

Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013 Sep 26;45(10):1127-1133.

The Cancer Genoma Atlas Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10;155(2):462-77.

The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-20.

Ciriello G, Sinha R, Hoadley KA, Jacobsen AS, Jing X, Wang WQ, Reva B, Perou CM, Sander C, Schultz N. The molecular diversity of Luminal A breast tumors. Breast Cancer Res Treat. 2013 Oct;141(3):409-20.

Akrami R, Jacobsen A, Reimers J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and somatic DNA-level alteration. PLoS One. 2013 Nov 12;8(11):e80306.

Jacobsen A, Silber J, Harinath G, Huse JT, Schultz N, Sander C. Analysis of microRNA target interactions across diverse cancer types. Nat Struct Mol Biol. 2013 Nov;20(11):1325-32.

Iyer G, Al-Ahmadie H, Schultz N, Hanrahan AJ, Ostrovnaya I, Balar A, Kim P, Lin O, Weinhold N, Sander C, Zabor EC, Janakiraman M, Garcia-Grossman I, Heguy A, Viale A, Bochner BI, Reuter VE, Bajorin DF, Milowsky MI, Taylor BS, Solit DB. Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol. 2013 Sep 1;31(25):3133-3140

Domcke S, Sinha R, Levine DA, Sander C, Schultz N. Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun. 2013 Jul 9;4:2126.

Danila DC, Anand A, Schultz N, Heller G, Wan M, Sung CC, Dai C, Khanin R, Fleisher M, Lilja H, Scher HI. Analytic and Clinical Validation of a Prostate Cancer–Enhanced Messenger RNA Detection Assay in Whole Blood as a Prognostic Biomarker for Survival. Eur Urol. 2013 Jul 26. pii: S0302-2838(13)00721-5.

The Cancer Genome Atlas Research Network. Integrative Analysis of Genomic and Molecular Alterations in Clear Cell Renal Cell Carcinoma. Nature. 2013 Jul 4;499(7456):43-9.

Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, Takeda S, Voss MH, Tickoo SK, Reuter VE, Sander C, Russo P, Cheng EH, Motzer RJ, Hsieh JJ. Adverse Outcomes in Clear Cell Renal Cell Carcinoma with Mutations of 3p21 Epigenetic Regulators BAP1 and SETD2. Clin Cancer Res. 2013 Jun 15;19(12):3259-67.

Ho AS, Kannan K, Morris LGT, Ganly I, Katabi N, Dolgalev I, Eng S, Huberman K, Heguy A, Viale A, Drobnjak M, Leversha MA, Singh B, Iyer G, Leemans CR, Bloemena E, Ferris RL, Seethala RR, Gross BE, Liang Y, Sinha R, Rice CE, Gong Y, Turcan S, Ramaswami D, Schultz N, Kim S, Chiosea S, Shah JP, Sander C, Lee W, Chan TA. Mutational Landscape of Adenoid Cystic Carcinoma Reveals Driving Pathways and Therapeutic Targets. Nat Genet. 2013 Jul;45(7):791-8.

Duijf PH, Schultz N, Benezra R. Cancer cells preferentially lose small chromosomes. Int J Cancer. Int J Cancer. 2013 May 15;132(10):2316-26.

The Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Endometrial Carcinoma. Nature. 2013 May 2;497(7447):67-73.

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. Sci Signal. 2013 Apr 2;6(269):pl1.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N. Using MEMo to Discover Mutual Exclusivity Modules in Cancer. Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit8.17.

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. Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4245-50.

Garg K, Levine DA, Olvera N, Dao F, Bisogna M, Secord AA, Berchuck A, Cerami E, Schultz N, Soslow RA. BRCA1 Immunohistochemistry in a Molecularly Characterized Cohort of Ovarian High-Grade Serous Carcinomas. Am J Surg Pathol. 2013 Jan;37(1):138-46.

Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne P, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-Silenced and Non-Silenced Subgroups of Hypermutated Colorectal Carcinomas Have Distinct Mutational Landscapes. J Pathol. 2013 Jan;229(1):99-110.

Bazzoli E, Pulvirenti T, Oberstadt MC, Perna F, Wee B, Schultz N, Huse JT, Fomchenko EI, Voza F, Tabar V, Brennan CW, DeAngelis LM, Nimer SD, Holland EC, Squatrito M. MEF promotes stemness in the pathogenesis of gliomas. Cell Stem Cell. 2012 Dec 7;11(6):836-44.

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 Res. 2012 Dec 1;72(23):6142-52.

Squatrito M, Vanoli F, Schultz N, Jasin M, Holland EC. 53BP1 is a haploinsufficient tumor suppressor and protects cells from radiation response in glioma. Cancer Res. 2012 Oct 15;72(20):5250-60.

The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25.

The Cancer Genome Atlas Research Network. Comprehensive Molecular Portraits of Human Breast Tumors. Nature. 2012 Sep 23;490(7418):61-70.

Comerford SA, Schultz N, Hinnant EA, Klapproth S, Hammer RE. Comparative analysis of SV40 17kT and LT function in vivo demonstrates that LT’s C-terminus rapidly re-programs hepatic gene expression and is required for tumorigenesis in the liver. Oncogenesis. 2012; 1, e28.

The Cancer Genome Atlas Research Network. Comprehensive Molecular Characterization of Human Colon and Rectal Cancer. Nature. 2012 Jul 18;487(7407):330-7.

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 Discov. 2012 May;2(5):401-4.

Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, Zhang J, Luo W, Hicks J, Zender L, Wang XW, Powers S, Wigler M, Lowe SW. A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci U S A. 2012 May 22;109(21):8212-7.

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. 2012;7(4):e35236.

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, Gibbs RA, Sander C, Hayes DN, Gunaratne PH; Cancer Genome Atlas Research Network. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012;7(3):e34546.

Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2012;22(2):398-406.

Hanrahan AJ, Schultz N, Westfal ML, Sakr RA, Giri DD, Scarperi S, Janikariman M, Olvera N, Stevens EV, She QB, Aghajanian C, King TA, de Stanchina E, Spriggs DR, Heguy A, Taylor BS, Sander C, Rosen N, Levine DA, Solit DB. Genomic complexity and AKT-dependence in serous ovarian cancer. Cancer Discov. 2012;2(1):56-67.

Mellinghoff IK, Schultz N, Mischel PS, Cloughesy TF. Will Kinase Inhibitors Make it as Glioblastoma Drugs? Curr Top Microbiol Immunol. 2012;355:135-69.

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. 2011; 6(11): e24709.

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 Discov. 2011;1(7):587-597.

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, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC. Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell. 2011 Aug 16;20(2):173-86.

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, Wu H, Sander C, Phelps ME, Brennan C, Port E, Huse JT, Graeber TG, Mellinghoff IK. 18F-fluorodeoxy-glucose positron emission tomography (18FDG-PET) marks basal-like human breast cancer with MYC overexpression. Cancer Res. 2011 Aug 1;71(15):5164-74.

The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15.

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 TGFβ pathway and reveal microRNA regulation of TGFBR2. Silence. 2011;2(1):3.

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 Res. 2011;39(Database issue):D685-90.

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, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010;18(1):11-22.

Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS One. 2010;5(2):e8918.

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, Mischel PS, Liau L, Cloughesy TF, Mellinghoff IK, Solit DB, Chan TA. Somatic mutations of the Parkinson’s disease–associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet. 2010;42(1):77-82.

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, Mischel PS, Sander C, Taylor B, Schultz N, Major J, Heguy A, Fang F, Mellinghoff IK, Chan TA. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A. 2009;106(23):9435-40.

The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455(7216):1061-8.

Diederichs S, Bäumer N, Schultz N, Hamra FK, Schrader MG, Sandstede ML, Berdel WE, Serve H, Müller-Tidow C.  Global post-natal changes in cyclin expression pattern in testis development are reversed in tumorigenesis. Int J Cancer 2005;116(2):207-17.

Garbers DL, Schultz N, Wu Z, Hamra FK. Spermatogonial cells in the rat and mouse. In: Lanza, R., ed. Handbook of Stem Cells, Volume 1: Embryonic. San Diego: Academic Press, 2004:179-186.

Hamra FK, Schultz N, Chapman KM, Grellhesl DM, Cronkhite JY, Hammer RE, Garbers DL.  Defining the spermatogonial stem cell. Dev Biol 2004;269(2):393-410.

Schultz N, Hamra FK and Garbers DL.  A multitude of genes expressed solely in meiotic or post-meiotic spermatogenic cells offers a myriad of contraceptive targets. Proc Natl Acad Sci U S A 2003; 100:12201-6.