Paul Spellman – Molecular Biology Institute

Email: pspellman@mednet.ucla.edu

I work to apply genomic and computational technologies to improve human health with a primary emphasis on improving outcomes for people with cancer. The work in our lab works at all phases from technology/method development, to application of technologies to answer critical questions in cancer biology, to population studies to understand the impact of genetic variation of disease, and to implementation trials that directly impact health. Current funded research focuses on systematic analysis of genetic and gene regulation information in clinical cohorts as part of the Genome Data Analysis Network and a clinical trial implementing genetic health screening for hereditary breast and ovarian cancer and Lynch syndromes. Other areas of interest include polygenic risk implementation and modeling, precision medicine, and understanding the molecular biology of cellular replication.

Research Interests:

Cancer, Genetics, Genomics, Precision Medicine, Computational Biology,

Publications:

Baker TM, Lai S, Lynch AR, Lesluyes T, Yan H, Ogilvie HA, Verfaillie A, Dentro S, Bowes AL, Pillay N, Flanagan AM, Swanton C, Spellman PT, Tarabichi M, Van Loo P. The History of Chromosomal Instability in Genome-Doubled Tumors. Cancer Discov. 2024 Oct 04; 14(10):1810-1822. view on PubMed

Ak Ç, Sayar Z, Thibault G, Burlingame EA, Kuykendall MJ, Eng J, Chitsazan A, Chin K, Adey AC, Boniface C, Spellman PT, Thomas GV, Kopp RP, Demir E, Chang YH, Stavrinides V, Eksi SE. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment. iScience. 2024 Sep 20; 27(9):110668. view on PubMed

Thayer M, Heskett MB, Smith LG, Spellman PT, Yates PA. ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins. Elife. 2024 Jun 18; 13. view on PubMed

Vermehren-Schmaedick A, Peto M, Wagoner W, Chiotti KE, Ramsey E, Wang X, Rakshe S, Minnier J, Sears R, Spellman P, Luoh SW. Mutation of SIVA, a candidate metastasis gene identified from clonally related bilateral breast cancers, promotes breast cancer cell spread in vitro and in vivo. PLoS One. 2024; 19(5):e0302856. view on PubMed

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Liu W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2024 Apr 23; 43(4):113063. view on PubMed

Marín-Aguilera M, Jares P, Sanfeliu E, Villacampa G, Hernández-Lllán E, Martínez-Puchol AI, Shankar S, González-Farré B, Waks AG, Brasó-Maristany F, Pardo F, Manning DK, Abery JA, Curaba J, Moon L, Gordon O, Galván P, Wachirakantapong P, Castillo O, Nee CM, Blasco P, Senevirathne TH, Sirenko V, Martínez-Sáez O, Aguirre A, Krop IE, Li Z, Spellman P, Metzger Filho O, Polyak K, Michaels P, Puig-Butillé JA, Vivancos A, Matito J, Buckingham W, Perou CM, Villagrasa-González P, Prat A, Parker JS, Paré L. Analytical validation of HER2DX genomic test for early-stage HER2-positive breast cancer. ESMO Open. 2024 Mar; 9(3):102903. view on PubMed

Li Z, Metzger Filho O, Viale G, dell'Orto P, Russo L, Goyette MA, Kamat A, Yardley DA, Gupta Abramson V, Arteaga CL, Spring LM, Chiotti K, Halsey C, Waks AG, King TA, Lester SC, Bellon JR, Winer EP, Spellman PT, Krop IE, Polyak K. HER2 heterogeneity and treatment response-associated profiles in HER2-positive breast cancer in the NCT02326974 clinical trial. J Clin Invest. 2024 Feb 01; 134(7). view on PubMed

Zhang Z, Shafer A, Johnson-Camacho K, Adey A, Anur P, Brown KA, Conrad C, Crist R, Farris PE, Harrington CA, Marriott LK, Mitchell A, O'Roak B, Serrato V, Richards CS, Spellman PT, Shannon J. Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project. J Clin Transl Sci. 2024; 8(1):e32. view on PubMed

O'Brien TD, Potter AB, Driscoll CC, Goh G, Letaw JH, McCabe S, Thanner J, Kulkarni A, Wong R, Medica S, Week T, Buitrago J, Larson A, Camacho KJ, Brown K, Crist R, Conrad C, Evans-Dutson S, Lutz R, Mitchell A, Anur P, Serrato V, Shafer A, Marriott LK, Hamman KJ, Mulford A, Wiszniewski W, Sampson JE, Adey A, O'Roak BJ, Harrington CA, Shannon J, Spellman PT, Richards CS. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon. Am J Hum Genet. 2023 08 03; 110(8):1249-1265. view on PubMed

Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics. 2023 Jun 26; 24(1):349. view on PubMed

Goldman EA, Spellman PT, Agarwal A. Defining clonal hematopoiesis of indeterminate potential: evolutionary dynamics and detection under aging and inflammation. Cold Spring Harb Mol Case Stud. 2023 04; 9(2). view on PubMed

Ren T, Chen C, Danilov AV, Liu S, Guan X, Du S, Wu X, Sherman MH, Spellman PT, Coussens LM, Adey AC, Mills GB, Wu LY, Xia Z. Supervised learning of high-confidence phenotypic subpopulations from single-cell data. bioRxiv. 2023 Mar 25. view on PubMed

Boniface CT, Spellman PT. Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response. Pathol Oncol Res. 2023; 29:1611133. view on PubMed

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023 Feb; 614(7948):E42. view on PubMed

Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun. 2022 10 22; 13(1):6301. view on PubMed

Boniface CT, Spellman PT. Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response. Pathol Oncol Res. 2022; 28:1610103. view on PubMed

Roskams-Hieter B, Kim HJ, Anur P, Wagner JT, Callahan R, Spiliotopoulos E, Kirschbaum CW, Civitci F, Spellman PT, Thompson RF, Farsad K, Naugler WE, Ngo TTM. Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies. NPJ Precis Oncol. 2022 Apr 25; 6(1):28. view on PubMed

Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med. 2022 02 15; 3(2):100525. view on PubMed

Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun. 2021 12 15; 12(1):7292. view on PubMed

Sun D, Guan X, Moran AE, Wu LY, Qian DZ, Schedin P, Dai MS, Danilov AV, Alumkal JJ, Adey AC, Spellman PT, Xia Z. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data. Nat Biotechnol. 2022 04; 40(4):527-538. view on PubMed

Heskett MB, Spellman PT, Thayer MJ. Differential Allelic Expression among Long Non-Coding RNAs. Noncoding RNA. 2021 Oct 22; 7(4). view on PubMed

Labrie M, Li A, Creason A, Betts C, Keck J, Johnson B, Sivagnanam S, Boniface C, Ma H, Blucher A, Chang YH, Chin K, Vuky J, Guimaraes AR, Downey M, Lim JY, Gao L, Siex K, Parmar S, Kolodzie A, Spellman PT, Goecks J, Coussens LM, Corless CL, Bergan R, Gray JW, Mills GB, Mitri ZI. Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ Precis Oncol. 2021 Oct 19; 5(1):92. view on PubMed

Lindner JR, Davidson BP, Song Z, Maier CS, Minnier J, Stevens JF, Ferencik M, Taqui S, Belcik JT, Moccetti F, Layoun M, Spellman P, Turker MS, Tavori H, Fazio S, Raber J, Bobe G. Plasma Lipidomic Patterns in Patients with Symptomatic Coronary Microvascular Dysfunction. Metabolites. 2021 Sep 22; 11(10). view on PubMed

Minnier J, Rajeevan N, Gao L, Park B, Pyarajan S, Spellman P, Haskell SG, Brandt CA, Luoh SW. Polygenic Breast Cancer Risk for Women Veterans in the Million Veteran Program. JCO Precis Oncol. 2021 07; 5. view on PubMed

Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren MJ, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME, SMC-RNA Challenge Participants, Stolovitzky G, Guinney J, Boutros PC, Stuart JM, Ellrott K. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Syst. 2021 08 18; 12(8):827-838.e5. view on PubMed

Janiszewska M, Stein S, Metzger Filho O, Eng J, Kingston NL, Harper NW, Rye IH, Aleckovic M, Trinh A, Murphy KC, Marangoni E, Cristea S, Oakes B, Winer EP, Krop IE, Russnes HG, Spellman PT, Bucher E, Hu Z, Chin K, Gray JW, Michor F, Polyak K. The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2+ breast cancer. JCI Insight. 2021 06 08; 6(11). view on PubMed

Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, Vaca Jacome AS, Peckner R, Christianson KE, Jaffe JD, Spellman PT, Aslan JE, Sander C, Demir E. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns (N Y). 2021 Jun 11; 2(6):100257. view on PubMed

Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021 04 15; 184(8):2239-2254.e39. view on PubMed

Matsumoto T, Wakefield L, Peters A, Peto M, Spellman P, Grompe M. Proliferative polyploid cells give rise to tumors via ploidy reduction. Nat Commun. 2021 01 28; 12(1):646. view on PubMed

Boniface C, Deig C, Halsey C, Kelley T, Heskett MB, Thomas CR, Spellman PT, Nabavizadeh N. The Feasibility of Patient-Specific Circulating Tumor DNA Monitoring throughout Multi-Modality Therapy for Locally Advanced Esophageal and Rectal Cancer: A Potential Biomarker for Early Detection of Subclinical Disease. Diagnostics (Basel). 2021 Jan 05; 11(1). view on PubMed

Naffar-Abu Amara S, Kuiken HJ, Selfors LM, Butler T, Leung ML, Leung CT, Kuhn EP, Kolarova T, Hage C, Ganesh K, Panayiotou R, Foster R, Rueda BR, Aktipis A, Spellman P, Ince TA, Xiu J, Oberley M, Gatalica Z, Navin N, Mills GB, Bronson RT, Brugge JS. Transient commensal clonal interactions can drive tumor metastasis. Nat Commun. 2020 11 16; 11(1):5799. view on PubMed

Zhao W, Li J, Chen MM, Luo Y, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NT, Davies MA, Herlyn M, Muranen T, Zervantonakis IK, von Euw E, Schultz A, Kumar SV, Korkut A, Spellman PT, Akbani R, Slamon DJ, Gray JW, Brugge JS, Lu Y, Mills GB, Liang H. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell. 2020 12 14; 38(6):829-843.e4. view on PubMed

Wagner JT, Kim HJ, Johnson-Camacho KC, Kelley T, Newell LF, Spellman PT, Ngo TTM. Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples. Sci Rep. 2020 10 05; 10(1):16456. view on PubMed

Berlow NE, Grasso CS, Quist MJ, Cheng M, Gandour-Edwards R, Hernandez BS, Michalek JE, Ryan C, Spellman P, Pal R, Million LS, Renneker M, Keller C. Deep Functional and Molecular Characterization of a High-Risk Undifferentiated Pleomorphic Sarcoma. Sarcoma. 2020; 2020:6312480. view on PubMed

Heskett MB, Smith LG, Spellman P, Thayer MJ. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. RNA. 2020 06; 26(6):724-738. view on PubMed

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. view on PubMed

Heskett MB, Sanborn JZ, Boniface C, Goode B, Chapman J, Garg K, Rabban JT, Zaloudek C, Benz SC, Spellman PT, Solomon DA, Cho RJ. Multiregion exome sequencing of ovarian immature teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components. Mod Pathol. 2020 06; 33(6):1193-1206. view on PubMed

Butler TM, Boniface CT, Johnson-Camacho K, Tabatabaei S, Melendez D, Kelley T, Gray J, Corless CL, Spellman PT. Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer. Cold Spring Harb Mol Case Stud. 2019 04; 5(2). view on PubMed

Cassetta L, Fragkogianni S, Sims AH, Swierczak A, Forrester LM, Zhang H, Soong DYH, Cotechini T, Anur P, Lin EY, Fidanza A, Lopez-Yrigoyen M, Millar MR, Urman A, Ai Z, Spellman PT, Hwang ES, Dixon JM, Wiechmann L, Coussens LM, Smith HO, Pollard JW. Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets. Cancer Cell. 2019 04 15; 35(4):588-602.e10. view on PubMed

Rozanov D, Cheltsov A, Nilsen A, Boniface C, Forquer I, Korkola J, Gray J, Tyner J, Tognon CE, Mills GB, Spellman P. Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity. PLoS One. 2019; 14(3):e0205623. view on PubMed

Slansky JE, Spellman PT. Alternative Splicing in Tumors - A Path to Immunogenicity? N Engl J Med. 2019 02 28; 380(9):877-880. view on PubMed

Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Neutral tumor evolution? Nat Genet. 2018 12; 50(12):1630-1633. view on PubMed

Risom T, Langer EM, Chapman MP, Rantala J, Fields AJ, Boniface C, Alvarez MJ, Kendsersky ND, Pelz CR, Johnson-Camacho K, Dobrolecki LE, Chin K, Aswani AJ, Wang NJ, Califano A, Lewis MT, Tomlin CJ, Spellman PT, Adey A, Gray JW, Sears RC. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun. 2018 09 19; 9(1):3815. view on PubMed

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19; 23(12):3698. view on PubMed

Cornforth MN, Anur P, Wang N, Robinson E, Ray FA, Bedford JS, Loucas BD, Williams ES, Peto M, Spellman P, Kollipara R, Kittler R, Gray JW, Bailey SM. Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. Radiat Res. 2018 07; 190(1):88-97. view on PubMed

Okunieff P, Casey-Sawicki K, Lockney NA, Hoppe BS, Enderling H, Pinnix C, Welsh J, Krishnan S, Yothers G, Brown M, Knox S, Bristow R, Spellman P, Mitin T, Nabavizadeh N, Jaboin J, Manning HC, Feng F, Galbraith S, Solanki AA, Harkenrider MM, Tuli R, Decker RH, Finkelstein SE, Hsu CC, Ha CS, Jagsi R, Shumway D, Daly M, Wang TJC, Fitzgerald TJ, Laurie F, Marshall DT, Raben D, Constine L, Thomas CR, Kachnic LA. Report from the SWOG Radiation Oncology Committee: Research Objectives Workshop 2017. Clin Cancer Res. 2018 08 01; 24(15):3500-3509. view on PubMed

Wang Y, Dorrell C, Naugler WE, Heskett M, Spellman P, Li B, Galivo F, Haft A, Wakefield L, Grompe M. Long-Term Correction of Diabetes in Mice by In Vivo Reprogramming of Pancreatic Ducts. Mol Ther. 2018 05 02; 26(5):1327-1342. view on PubMed

Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Cancer Genome Atlas Network, Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 2018 02 12; 33(2):244-258.e10. view on PubMed

Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 2018 03 30; 176:13-23. view on PubMed

Korkola JE, Collisson EA, Heiser LM, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, Gray JW. Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. PLoS One. 2017; 12(10):e0186551. view on PubMed

Guo Q, Minnier J, Burchard J, Chiotti K, Spellman P, Schedin P. Physiologically activated mammary fibroblasts promote postpartum mammary cancer. JCI Insight. 2017 03 23; 2(6):e89206. view on PubMed

Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, Wood KW, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Erratum to: Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Breast Cancer Res. 2017 02 09; 19(1):17. view on PubMed

Butler TM, Spellman PT, Gray J. Circulating-tumor DNA as an early detection and diagnostic tool. Curr Opin Genet Dev. 2017 Feb; 42:14-21. view on PubMed

Hill SM, Nesser NK, Johnson-Camacho K, Jeffress M, Johnson A, Boniface C, Spencer SE, Lu Y, Heiser LM, Lawrence Y, Pande NT, Korkola JE, Gray JW, Mills GB, Mukherjee S, Spellman PT. Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling. Cell Syst. 2017 01 25; 4(1):73-83.e10. view on PubMed

Van Hook K, Wang Z, Chen D, Nold C, Zhu Z, Anur P, Lee HJ, Yu Z, Sheppard B, Dai MS, Sears R, Spellman P, Lopez CD. ΔN-ASPP2, a novel isoform of the ASPP2 tumor suppressor, promotes cellular survival. Biochem Biophys Res Commun. 2017 Jan 22; 482(4):1271-1277. view on PubMed

Fu X, Jeselsohn R, Pereira R, Hollingsworth EF, Creighton CJ, Li F, Shea M, Nardone A, De Angelis C, Heiser LM, Anur P, Wang N, Grasso CS, Spellman PT, Griffith OL, Tsimelzon A, Gutierrez C, Huang S, Edwards DP, Trivedi MV, Rimawi MF, Lopez-Terrada D, Hilsenbeck SG, Gray JW, Brown M, Osborne CK, Schiff R. FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer. Proc Natl Acad Sci U S A. 2016 10 25; 113(43):E6600-E6609. view on PubMed

Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Breast Cancer Res. 2016 07 01; 18(1):70. view on PubMed

Munson DJ, Egelston CA, Chiotti KE, Parra ZE, Bruno TC, Moore BL, Nakano TA, Simons DL, Jimenez G, Yim JH, Rozanov DV, Falta MT, Fontenot AP, Reynolds PR, Leach SM, Borges VF, Kappler JW, Spellman PT, Lee PP, Slansky JE. Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):8272-7. view on PubMed

Fei SS, Mitchell AD, Heskett MB, Vocke CD, Ricketts CJ, Peto M, Wang NJ, Sönmez K, Linehan WM, Spellman PT. Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours. Nat Commun. 2016 05 13; 7:11588. view on PubMed

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 2016 Apr; 13(4):310-8. view on PubMed

Lue HW, Cole B, Rao SA, Podolak J, Van Gaest A, King C, Eide CA, Wilmot B, Xue C, Spellman PT, Heiser LM, Tyner JW, Thomas GV. Src and STAT3 inhibitors synergize to promote tumor inhibition in renal cell carcinoma. Oncotarget. 2015 Dec 29; 6(42):44675-87. view on PubMed

Fleyshman D, Cheney P, Ströse A, Mudambi S, Safina A, Commane M, Purmal A, Morgan K, Wang NJ, Gray J, Spellman PT, Issaeva N, Gurova K. ARTIK-52 induces replication-dependent DNA damage and p53 activation exclusively in cells of prostate and breast cancer origin. Cell Cycle. 2016; 15(3):455-70. view on PubMed

Ivanov M, Baranova A, Butler T, Spellman P, Mileyko V. Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. BMC Genomics. 2015; 16 Suppl 13:S1. view on PubMed

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 09; 6:10001. view on PubMed

Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14; 374(2):135-45. view on PubMed

Butler TM, Johnson-Camacho K, Peto M, Wang NJ, Macey TA, Korkola JE, Koppie TM, Corless CL, Gray JW, Spellman PT. Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease. PLoS One. 2015; 10(8):e0136407. view on PubMed

Sanborn JZ, Chung J, Purdom E, Wang NJ, Kakavand H, Wilmott JS, Butler T, Thompson JF, Mann GJ, Haydu LE, Saw RP, Busam KJ, Lo RS, Collisson EA, Hur JS, Spellman PT, Cleaver JE, Gray JW, Huh N, Murali R, Scolyer RA, Bastian BC, Cho RJ. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination. Proc Natl Acad Sci U S A. 2015 Sep 01; 112(35):10995-1000. view on PubMed

Korkola JE, Collisson EA, Heiser M, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, Gray JW. Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. PLoS One. 2015; 10(7):e0133219. view on PubMed

Liu Y, Yasukawa M, Chen K, Hu L, Broaddus RR, Ding L, Mardis ER, Spellman P, Levine DA, Mills GB, Shmulevich I, Sood AK, Zhang W. Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma. JAMA Oncol. 2015 Jul; 1(4):486-94. view on PubMed

Grasso CS, Tang Y, Truffaux N, Berlow NE, Liu L, Debily MA, Quist MJ, Davis LE, Huang EC, Woo PJ, Ponnuswami A, Chen S, Johung TB, Sun W, Kogiso M, Du Y, Qi L, Huang Y, Hütt-Cabezas M, Warren KE, Le Dret L, Meltzer PS, Mao H, Quezado M, van Vuurden DG, Abraham J, Fouladi M, Svalina MN, Wang N, Hawkins C, Nazarian J, Alonso MM, Raabe EH, Hulleman E, Spellman PT, Li XN, Keller C, Pal R, Grill J, Monje M. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nat Med. 2015 Jul; 21(7):827. view on PubMed

Rozanov D, Cheltsov A, Sergienko E, Vasile S, Golubkov V, Aleshin AE, Levin T, Traer E, Hann B, Freimuth J, Alexeev N, Alekseyev MA, Budko SP, Bächinger HP, Spellman P. TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response. PLoS One. 2015; 10(6):e0129566. view on PubMed

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW. Erratum to: Modeling precision treatment of breast cancer. Genome Biol. 2015 May 12; 16:95. view on PubMed

Rozanov D, Spellman P, Savinov A, Strongin AY. A humanized leucine zipper-TRAIL hybrid induces apoptosis of tumors both in vitro and in vivo. PLoS One. 2015; 10(4):e0122980. view on PubMed

Chang H, Zhou Y, Borowsky A, Barner K, Spellman P, Parvin B. Stacked Predictive Sparse Decomposition for Classification of Histology Sections. Int J Comput Vis. 2015 May; 113(1):3-18. view on PubMed

Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep. 2014 Nov 20; 9(4):1228-34. view on PubMed

Fu X, Creighton CJ, Biswal NC, Kumar V, Shea M, Herrera S, Contreras A, Gutierrez C, Wang T, Nanda S, Giuliano M, Morrison G, Nardone A, Karlin KL, Westbrook TF, Heiser LM, Anur P, Spellman P, Guichard SM, Smith PD, Davies BR, Klinowska T, Lee AV, Mills GB, Rimawi MF, Hilsenbeck SG, Gray JW, Joshi A, Osborne CK, Schiff R. Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase. Breast Cancer Res. 2014 Sep 11; 16(5):430. view on PubMed

Zhou Y, Chang H, Barner K, Spellman P, Parvin B. Classification of Histology Sections via Multispectral Convolutional Sparse Coding. Conf Comput Vis Pattern Recognit Workshops. 2014 Jun; 2014:3081-3088. view on PubMed

Spellman PT, Gray JW. Detecting cancer by monitoring circulating tumor DNA. Nat Med. 2014 May; 20(5):474-5. view on PubMed

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. Nat Genet. 2014 Apr; 46(4):318-319. view on PubMed

Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014; 5:3156. view on PubMed

Griffith OL, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW. A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med. 2013; 5(10):92. view on PubMed

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, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. view on PubMed

Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P. Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics. 2013 Dec 15; 29(24):3113-20. view on PubMed

Luoh SW, Ramsey B, Hanlon Newell A, Troxell M, Hu Z, Chin K, Spellman P, Olson S, Keenan E. HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression. Springerplus. 2013; 2:386. view on PubMed

Rhee JK, Kim K, Chae H, Evans J, Yan P, Zhang BT, Gray J, Spellman P, Huang TH, Nephew KP, Kim S. Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. Nucleic Acids Res. 2013 Oct; 41(18):8464-74. view on PubMed

Chang H, Borowsky A, Spellman P, Parvin B. Classification of Tumor Histology via Morphometric Context. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2013 Jun 23; 2013. view on PubMed

Kodigepalli KM, Anur P, Spellman P, Sims PJ, Nanjundan M. Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells. Mol Cancer. 2013 Apr 26; 12:32. view on PubMed

Nayak N, Chang H, Borowsky A, Spellman P, Parvin B. CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING. Proc IEEE Int Symp Biomed Imaging. 2013 Apr; 2013. view on PubMed

Pharoah PD, Tsai YY, Ramus SJ, Phelan CM, Goode EL, Lawrenson K, Buckley M, Fridley BL, Tyrer JP, Shen H, Weber R, Karevan R, Larson MC, Song H, Tessier DC, Bacot F, Vincent D, Cunningham JM, Dennis J, Dicks E, Australian Cancer Study, Australian Ovarian Cancer Study Group, Aben KK, Anton-Culver H, Antonenkova N, Armasu SM, Baglietto L, Bandera EV, Beckmann MW, Birrer MJ, Bloom G, Bogdanova N, Brenton JD, Brinton LA, Brooks-Wilson A, Brown R, Butzow R, Campbell I, Carney ME, Carvalho RS, Chang-Claude J, Chen YA, Chen Z, Chow WH, Cicek MS, Coetzee G, Cook LS, Cramer DW, Cybulski C, Dansonka-Mieszkowska A, Despierre E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Edwards R, Ekici AB, Fasching PA, Fenstermacher D, Flanagan J, Gao YT, Garcia-Closas M, Gentry-Maharaj A, Giles G, Gjyshi A, Gore M, Gronwald J, Guo Q, Halle MK, Harter P, Hein A, Heitz F, Hillemanns P, Hoatlin M, Høgdall E, Høgdall CK, Hosono S, Jakubowska A, Jensen A, Kalli KR, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Konecny GE, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee N, Lee J, Leminen A, Lim BK, Lissowska J, Lubinski J, Lundvall L, Lurie G, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, Menon U, Modugno F, Moysich KB, Nakanishi T, Narod SA, Ness RB, Nevanlinna H, Nickels S, Noushmehr H, Odunsi K, Olson S, Orlow I, Paul J, Pejovic T, Pelttari LM, Permuth-Wey J, Pike MC, Poole EM, Qu X, Risch HA, Rodriguez-Rodriguez L, Rossing MA, Rudolph A, Runnebaum I, Rzepecka IK, Salvesen HB, Schwaab I, Severi G, Shen H, Shridhar V, Shu XO, Sieh W, Southey MC, Spellman P, Tajima K, Teo SH, Terry KL, Thompson PJ, Timorek A, Tworoger SS, van Altena AM, van den Berg D, Vergote I, Vierkant RA, Vitonis AF, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wik E, Winterhoff B, Woo YL, Wu AH, Yang HP, Zheng W, Ziogas A, Zulkifli F, Goodman MT, Hall P, Easton DF, Pearce CL, Berchuck A, Chenevix-Trench G, Iversen E, Monteiro AN, Gayther SA, Schildkraut JM, Sellers TA. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet. 2013 Apr; 45(4):362-70, 370e1-2. view on PubMed

Chang H, Nayak N, Spellman PT, Parvin B. Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching. Med Image Comput Comput Assist Interv. 2013; 16(Pt 2):91-8. view on PubMed

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, van't Veer LJ, Spellman PT, Gray JW. Modeling precision treatment of breast cancer. Genome Biol. 2013; 14(10):R110. view on PubMed

Chang H, Zhou Y, Spellman P, Parvin B. Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology. Proc IEEE Int Conf Comput Vis. 2013; 169-176. view on PubMed

Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M, Cancer Genome Atlas Research Network. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25. view on PubMed

Ordinario E, Han HJ, Furuta S, Heiser LM, Jakkula LR, Rodier F, Spellman PT, Campisi J, Gray JW, Bissell MJ, Kohwi Y, Kohwi-Shigematsu T. ATM suppresses SATB1-induced malignant progression in breast epithelial cells. PLoS One. 2012; 7(12):e51786. view on PubMed

Chang H, Han J, Borowsky A, Loss L, Gray JW, Spellman PT, Parvin B. Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association. IEEE Trans Med Imaging. 2013 Apr; 32(4):670-82. view on PubMed

Sadanandam A, Lal A, Benz SC, Eppenberger-Castori S, Scott G, Gray JW, Spellman P, Waldman F, Benz CC. Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? Breast Cancer Res Treat. 2012 Dec; 136(3):693-703. view on PubMed

Chang H, Han J, Spellman PT, Parvin B. Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme. IEEE Trans Biomed Eng. 2012 Dec; 59(12):3460-7. view on PubMed

Petrillo LA, Wolf DM, Kapoun AM, Wang NJ, Barczak A, Xiao Y, Korkaya H, Baehner F, Lewicki J, Wicha M, Park JW, Spellman PT, Gray JW, Van't Veer L, Esserman LJ. Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors. Breast Cancer Res Treat. 2012 Oct; 135(3):913-22. view on PubMed

Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics. 2012 Nov 01; 28(21):2804-10. view on PubMed

Daemen A, Wolf DM, Korkola JE, Griffith OL, Frankum JR, Brough R, Jakkula LR, Wang NJ, Natrajan R, Reis-Filho JS, Lord CJ, Ashworth A, Spellman PT, Gray JW, van't Veer LJ. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Res Treat. 2012 Sep; 135(2):505-17. view on PubMed

Collisson EA, Trejo CL, Silva JM, Gu S, Korkola JE, Heiser LM, Charles RP, Rabinovich BA, Hann B, Dankort D, Spellman PT, Phillips WA, Gray JW, McMahon M. A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma. Cancer Discov. 2012 Aug; 2(8):685-93. view on PubMed

Hill SM, Neve RM, Bayani N, Kuo WL, Ziyad S, Spellman PT, Gray JW, Mukherjee S. Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. BMC Bioinformatics. 2012 May 11; 13:94. view on PubMed

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. view on PubMed

Corless CL, Spellman PT. Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discov. 2012 Jan; 2(1):23-4. view on PubMed

Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B. Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinformatics. 2011 Dec 20; 12:484. view on PubMed

Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L, Pennypacker S, Zou Y, Sharma M, North JP, Vemula SS, Mauro TM, Neuhaus IM, Leboit PE, Hur JS, Park K, Huh N, Kwok PY, Arron ST, Massion PP, Bale AE, Haussler D, Cleaver JE, Gray JW, Spellman PT, South AP, Aster JC, Blacklow SC, Cho RJ. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc Natl Acad Sci U S A. 2011 Oct 25; 108(43):17761-6. view on PubMed

Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2724-9. view on PubMed

Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RC, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov. 2011 Jul; 1(2):137-43. view on PubMed

Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011 Aug 01; 27(15):2038-46. view on PubMed

Han J, Chang H, Loss L, Zhang K, Baehner FL, Gray JW, Spellman P, Parvin B. COMPARISON OF SPARSE CODING AND KERNEL METHODS FOR HISTOPATHOLOGICAL CLASSIFICATION OF GLIOBASTOMA MULTIFORME. Proc IEEE Int Symp Biomed Imaging. 2011 Jun 09; 2011:711-714. view on PubMed

Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, Feiler HS, Ko AH, Olshen AB, Danenberg KL, Tempero MA, Spellman PT, Hanahan D, Gray JW. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 2011 Apr; 17(4):500-3. view on PubMed

Spellman P, Gray J. A new treasure in the breast cancer gene hunt. Nat Med. 2011 Apr; 17(4):422-3. view on PubMed

Nabavizadeh N, Klifa C, Newitt D, Lu Y, Chen YY, Hsu H, Fisher C, Tokayasu T, Olshen AB, Spellman P, Gray JW, Hylton N, Park CC. Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI. Integr Biol (Camb). 2011 Apr; 3(4):490-6. view on PubMed

Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP. Unifying gene expression measures from multiple platforms using factor analysis. PLoS One. 2011 Mar 11; 6(3):e17691. view on PubMed

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res. 2010 Jul; 8(7):961-74. view on PubMed

Nautiyal S, Carlton VE, Lu Y, Ireland JS, Flaucher D, Moorhead M, Gray JW, Spellman P, Mindrinos M, Berg P, Faham M. High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12587-92. view on PubMed

Loss LA, Sadanandam A, Durinck S, Nautiyal S, Flaucher D, Carlton VE, Moorhead M, Lu Y, Gray JW, Faham M, Spellman P, Parvin B. Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinformatics. 2010 Jun 04; 11:305. view on PubMed

International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Cross A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Gardiner BA, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Himmelbaue H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, et al. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. view on PubMed

Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN, Cancer Genome Atlas Research Network. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010 Jan 19; 17(1):98-110. view on PubMed

Kuo WL, Das D, Ziyad S, Bhattacharya S, Gibb WJ, Heiser LM, Sadanandam A, Fontenay GV, Hu Z, Wang NJ, Bayani N, Feiler HS, Neve RM, Wyrobek AJ, Spellman PT, Marton LJ, Gray JW. A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. BMC Med. 2009 Dec 14; 7:77. view on PubMed

Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009; 4(8):1184-91. view on PubMed

Heiser LM, Wang NJ, Talcott CL, Laderoute KR, Knapp M, Guan Y, Hu Z, Ziyad S, Weber BL, Laquerre S, Jackson JR, Wooster RF, Kuo WL, Gray JW, Spellman PT. Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol. 2009; 10(3):R31. view on PubMed

Wang Y, Carlton VE, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Med Genomics. 2009 Feb 19; 2:8. view on PubMed

Bengtsson H, Ray A, Spellman P, Speed TP. A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics. 2009 Apr 01; 25(7):861-7. view on PubMed

Mirzoeva OK, Das D, Heiser LM, Bhattacharya S, Siwak D, Gendelman R, Bayani N, Wang NJ, Neve RM, Guan Y, Hu Z, Knight Z, Feiler HS, Gascard P, Parvin B, Spellman PT, Shokat KM, Wyrobek AJ, Bissell MJ, McCormick F, Kuo WL, Mills GB, Gray JW, Korn WM. Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Res. 2009 Jan 15; 69(2):565-72. view on PubMed

Hodgson JG, Yeh RF, Ray A, Wang NJ, Smirnov I, Yu M, Hariono S, Silber J, Feiler HS, Gray JW, Spellman PT, Vandenberg SR, Berger MS, James CD. Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts. Neuro Oncol. 2009 Oct; 11(5):477-87. view on PubMed

Durinck S, Bullard J, Spellman PT, Dudoit S. GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics. 2009 Jan 06; 10:2. view on PubMed

Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP. Sparse combinatorial inference with an application in cancer biology. Bioinformatics. 2009 Jan 15; 25(2):265-71. view on PubMed

Brown LA, Kalloger SE, Miller MA, Shih IeM, McKinney SE, Santos JL, Swenerton K, Spellman PT, Gray J, Gilks CB, Huntsman DG. Amplification of 11q13 in ovarian carcinoma. Genes Chromosomes Cancer. 2008 Jun; 47(6):481-9. view on PubMed

Press JZ, De Luca A, Boyd N, Young S, Troussard A, Ridge Y, Kaurah P, Kalloger SE, Blood KA, Smith M, Spellman PT, Wang Y, Miller DM, Horsman D, Faham M, Gilks CB, Gray J, Huntsman DG. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer. 2008 Jan 22; 8:17. view on PubMed

Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 2007 Oct; 25(10):1127-33. view on PubMed

Kenny PA, Lee GY, Myers CA, Neve RM, Semeiks JR, Spellman PT, Lorenz K, Lee EH, Barcellos-Hoff MH, Petersen OW, Gray JW, Bissell MJ. The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression. Mol Oncol. 2007 Jun; 1(1):84-96. view on PubMed

Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M. Analysis of molecular inversion probe performance for allele copy number determination. Genome Biol. 2007; 8(11):R246. view on PubMed

Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 2006 Dec; 10(6):515-27. view on PubMed

Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41. view on PubMed

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489. view on PubMed

Brun S, Vidal S, Spellman P, Takahashi K, Tricoire H, Lemaitre B. The MAPKKK Mekk1 regulates the expression of Turandot stress genes in response to septic injury in Drosophila. Genes Cells. 2006 Apr; 11(4):397-407. view on PubMed

Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24. view on PubMed

Jones AR, Pizarro A, Spellman P, Miller M, FuGE Working Group. FuGE: Functional Genomics Experiment Object Model. OMICS. 2006; 10(2):179-84. view on PubMed

Spellman P. A status report on MAGE. Bioinformatics. 2005 Sep 01; 21(17):3459-60. view on PubMed

Vodovar N, Vinals M, Liehl P, Basset A, Degrouard J, Spellman P, Boccard F, Lemaitre B. Drosophila host defense after oral infection by an entomopathogenic Pseudomonas species. Proc Natl Acad Sci U S A. 2005 Aug 09; 102(32):11414-9. view on PubMed

Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Submission of microarray data to public repositories. PLoS Biol. 2004 Sep; 2(9):E317. view on PubMed

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, MGED Society. Standards for microarray data: an open letter. Environ Health Perspect. 2004 Aug; 112(12):A666-7. view on PubMed

Spellman PT, Sherlock G. Final words: cell age and cell cycle are unlinked. Trends Biotechnol. 2004 Jun; 22(6):277-8. view on PubMed

Spellman PT, Sherlock G. Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends Biotechnol. 2004 Jun; 22(6):270-3. view on PubMed

Pile LA, Spellman PT, Katzenberger RJ, Wassarman DA. The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolism. J Biol Chem. 2003 Sep 26; 278(39):37840-8. view on PubMed

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data. The underlying principles of scientific publication. Bioinformatics. 2002 Nov; 18(11):1409. view on PubMed

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data (MGED) Society. Standards for microarray data. Science. 2002 Oct 18; 298(5593):539. view on PubMed

Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ, Brazma A. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23; 3(9):RESEARCH0046. view on PubMed

Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 2002; 1(1):5. view on PubMed

De Gregorio E, Spellman PT, Tzou P, Rubin GM, Lemaitre B. The Toll and Imd pathways are the major regulators of the immune response in Drosophila. EMBO J. 2002 Jun 03; 21(11):2568-79. view on PubMed

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec; 29(4):365-71. view on PubMed

Spellman PT. The future of publishing microarray data. Brief Bioinform. 2001 Dec; 2(4):316-8. view on PubMed

De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc Natl Acad Sci U S A. 2001 Oct 23; 98(22):12590-5. view on PubMed

George RA, Woolley JP, Spellman PT. Ceramic capillaries for use in microarray fabrication. Genome Res. 2001 Oct; 11(10):1780-3. view on PubMed

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 01; 29(1):152-5. view on PubMed

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000 Dec; 11(12):4241-57. view on PubMed

Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 2000 Jul 06; 406(6791):90-4. view on PubMed

Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000 Mar; 24(3):227-35. view on PubMed

Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 08; 95(25):14863-8. view on PubMed

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998 Dec; 9(12):3273-97. view on PubMed

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