Paul Thomas Spellman

Title(s)Professor, Medicine
SchoolMedicine
ORCID ORCID Icon0000-0002-4810-0022 Additional info
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    Title(s)Professor, Human Genetics


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    MIT, Cambridge, MASB02/1995Biology
    Stanford University SoM, StanfordPhD04/2000Genetics
    UC Berkeley, Berkeley12/2003Gene Regulation/Genomics

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    Collapse Overview
    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.
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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. The History of Chromosomal Instability in Genome-Doubled Tumors. Cancer Discov. 2024 Oct 04; 14(10):1810-1822. 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. PMID: 38943574; PMCID: PMC7616501.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment. iScience. 2024 Sep 20; 27(9):110668. 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. PMID: 39246442; PMCID: PMC11379676.
      View in: PubMed   Mentions:
    3. ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins. Elife. 2024 Jun 18; 13. Thayer M, Heskett MB, Smith LG, Spellman PT, Yates PA. PMID: 38896448; PMCID: PMC11186638.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. 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. Vermehren-Schmaedick A, Peto M, Wagoner W, Chiotti KE, Ramsey E, Wang X, Rakshe S, Minnier J, Sears R, Spellman P, Luoh SW. PMID: 38722955; PMCID: PMC11081324.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    5. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2024 Apr 23; 43(4):113063. 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. PMID: 38578829.
      View in: PubMed   Mentions: 1     Fields:    
    6. Analytical validation of HER2DX genomic test for early-stage HER2-positive breast cancer. ESMO Open. 2024 Mar; 9(3):102903. 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. PMID: 38452436; PMCID: PMC10937240.
      View in: PubMed   Mentions: 4  Translation:Humans
    7. 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). 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. PMID: 38300710; PMCID: PMC10977978.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCTClinical Trials
    8. 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. 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. PMID: 38384895; PMCID: PMC10880011.
      View in: PubMed   Mentions:
    9. Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon. Am J Hum Genet. 2023 08 03; 110(8):1249-1265. 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. PMID: 37506692; PMCID: PMC10432140.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    10. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics. 2023 Jun 26; 24(1):349. 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. PMID: 37365517; PMCID: PMC10291816.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. Defining clonal hematopoiesis of indeterminate potential: evolutionary dynamics and detection under aging and inflammation. Cold Spring Harb Mol Case Stud. 2023 04; 9(2). Goldman EA, Spellman PT, Agarwal A. PMID: 36889927; PMCID: PMC10240836.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    12. Supervised learning of high-confidence phenotypic subpopulations from single-cell data. bioRxiv. 2023 Mar 25. 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. PMID: 36993424; PMCID: PMC10055361.
      View in: PubMed   Mentions:
    13. Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response. Pathol Oncol Res. 2023; 29:1611133. Boniface CT, Spellman PT. PMID: 36969563; PMCID: PMC10035571.
      View in: PubMed   Mentions:    Fields:    
    14. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. Res Sq. 2023 Feb 16. 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. PMID: 36824803; PMCID: PMC9949261.
      View in: PubMed   Mentions:
    15. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023 Feb; 614(7948):E42. 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. PMID: 36697833; PMCID: PMC9931577.
      View in: PubMed   Mentions: 2     Fields:    
    16. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun. 2022 10 22; 13(1):6301. Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. PMID: 36273230; PMCID: PMC9588035.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    17. Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response. Pathol Oncol Res. 2022; 28:1610103. Boniface CT, Spellman PT. PMID: 35665409; PMCID: PMC9160182.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    18. 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. 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. PMID: 35468987; PMCID: PMC9038724.
      View in: PubMed   Mentions: 21  
    19. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med. 2022 02 15; 3(2):100525. 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. PMID: 35243422; PMCID: PMC8861971.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    20. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun. 2021 12 15; 12(1):7292. Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. PMID: 34911933; PMCID: PMC8674326.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    21. Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data. Nat Biotechnol. 2022 04; 40(4):527-538. Sun D, Guan X, Moran AE, Wu LY, Qian DZ, Schedin P, Dai MS, Danilov AV, Alumkal JJ, Adey AC, Spellman PT, Xia Z. PMID: 34764492; PMCID: PMC9010342.
      View in: PubMed   Mentions: 128     Fields:    Translation:Humans
    22. Differential Allelic Expression among Long Non-Coding RNAs. Noncoding RNA. 2021 Oct 22; 7(4). Heskett MB, Spellman PT, Thayer MJ. PMID: 34698262; PMCID: PMC8544735.
      View in: PubMed   Mentions: 2  
    23. Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ Precis Oncol. 2021 Oct 19; 5(1):92. 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. PMID: 34667258; PMCID: PMC8526613.
      View in: PubMed   Mentions: 12  
    24. Plasma Lipidomic Patterns in Patients with Symptomatic Coronary Microvascular Dysfunction. Metabolites. 2021 Sep 22; 11(10). 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. PMID: 34677363; PMCID: PMC8540191.
      View in: PubMed   Mentions: 5  
    25. Polygenic Breast Cancer Risk for Women Veterans in the Million Veteran Program. JCO Precis Oncol. 2021 07; 5. Minnier J, Rajeevan N, Gao L, Park B, Pyarajan S, Spellman P, Haskell SG, Brandt CA, Luoh SW. PMID: 34381935; PMCID: PMC8345920.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    26. 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. 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. PMID: 34146471; PMCID: PMC8376800.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    27. The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2+ breast cancer. JCI Insight. 2021 06 08; 6(11). 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. PMID: 33886505; PMCID: PMC8262355.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    28. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns (N Y). 2021 Jun 11; 2(6):100257. 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. PMID: 34179843; PMCID: PMC8212145.
      View in: PubMed   Mentions: 39  
    29. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021 04 15; 184(8):2239-2254.e39. 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. PMID: 33831375; PMCID: PMC8054914.
      View in: PubMed   Mentions: 199     Fields:    Translation:Humans
    30. Proliferative polyploid cells give rise to tumors via ploidy reduction. Nat Commun. 2021 01 28; 12(1):646. Matsumoto T, Wakefield L, Peters A, Peto M, Spellman P, Grompe M. PMID: 33510149; PMCID: PMC7843634.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    31. 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). Boniface C, Deig C, Halsey C, Kelley T, Heskett MB, Thomas CR, Spellman PT, Nabavizadeh N. PMID: 33466369; PMCID: PMC7824834.
      View in: PubMed   Mentions: 8  
    32. Transient commensal clonal interactions can drive tumor metastasis. Nat Commun. 2020 11 16; 11(1):5799. 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. PMID: 33199705; PMCID: PMC7669858.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    33. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell. 2020 12 14; 38(6):829-843.e4. 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. PMID: 33157050; PMCID: PMC7738392.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    34. Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples. Sci Rep. 2020 10 05; 10(1):16456. Wagner JT, Kim HJ, Johnson-Camacho KC, Kelley T, Newell LF, Spellman PT, Ngo TTM. PMID: 33020547; PMCID: PMC7536441.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    35. Deep Functional and Molecular Characterization of a High-Risk Undifferentiated Pleomorphic Sarcoma. Sarcoma. 2020; 2020:6312480. 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. PMID: 32565715; PMCID: PMC7285280.
      View in: PubMed   Mentions: 5  
    36. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. RNA. 2020 06; 26(6):724-738. Heskett MB, Smith LG, Spellman P, Thayer MJ. PMID: 32144193; PMCID: PMC7266157.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    37. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. 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. PMID: 32025013; PMCID: PMC7054212.
      View in: PubMed   Mentions: 436     Fields:    Translation:HumansCells
    38. 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. Heskett MB, Sanborn JZ, Boniface C, Goode B, Chapman J, Garg K, Rabban JT, Zaloudek C, Benz SC, Spellman PT, Solomon DA, Cho RJ. PMID: 31911616; PMCID: PMC7286805.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    39. 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). Butler TM, Boniface CT, Johnson-Camacho K, Tabatabaei S, Melendez D, Kelley T, Gray J, Corless CL, Spellman PT. PMID: 30833418; PMCID: PMC6549569.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    40. 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. 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. PMID: 30930117; PMCID: PMC6472943.
      View in: PubMed   Mentions: 435     Fields:    Translation:HumansCells
    41. Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity. PLoS One. 2019; 14(3):e0205623. Rozanov D, Cheltsov A, Nilsen A, Boniface C, Forquer I, Korkola J, Gray J, Tyner J, Tognon CE, Mills GB, Spellman P. PMID: 30908483; PMCID: PMC6433232.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    42. Alternative Splicing in Tumors - A Path to Immunogenicity? N Engl J Med. 2019 02 28; 380(9):877-880. Slansky JE, Spellman PT. PMID: 30811916.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    43. Neutral tumor evolution? Nat Genet. 2018 12; 50(12):1630-1633. 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. PMID: 30374075; PMCID: PMC6548558.
      View in: PubMed   Mentions: 38     Fields:    Translation:Humans
    44. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun. 2018 09 19; 9(1):3815. 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. PMID: 30232459; PMCID: PMC6145927.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansAnimalsCells
    45. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19; 23(12):3698. 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. PMID: 29925010.
      View in: PubMed   Mentions: 115     Fields:    
    46. Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. Radiat Res. 2018 07; 190(1):88-97. 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. PMID: 29749794; PMCID: PMC6055522.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    47. Report from the SWOG Radiation Oncology Committee: Research Objectives Workshop 2017. Clin Cancer Res. 2018 08 01; 24(15):3500-3509. 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. PMID: 29661779.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansPHPublic Health
    48. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 04 03; 23(1):313-326.e5. 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. PMID: 29617669; PMCID: PMC6075733.
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    49. Long-Term Correction of Diabetes in Mice by In Vivo Reprogramming of Pancreatic Ducts. Mol Ther. 2018 05 02; 26(5):1327-1342. Wang Y, Dorrell C, Naugler WE, Heskett M, Spellman P, Li B, Galivo F, Haft A, Wakefield L, Grompe M. PMID: 29550076; PMCID: PMC5993989.
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    50. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 2018 02 12; 33(2):244-258.e10. 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. PMID: 29438696; PMCID: PMC5994906.
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    51. 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. 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. PMID: 29331515; PMCID: PMC5999401.
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    52. Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. PLoS One. 2017; 12(10):e0186551. 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. PMID: 29020035; PMCID: PMC5636161.
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    53. Physiologically activated mammary fibroblasts promote postpartum mammary cancer. JCI Insight. 2017 03 23; 2(6):e89206. Guo Q, Minnier J, Burchard J, Chiotti K, Spellman P, Schedin P. PMID: 28352652; PMCID: PMC5358521.
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    54. 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. 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. PMID: 28183333; PMCID: PMC5301377.
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    55. Circulating-tumor DNA as an early detection and diagnostic tool. Curr Opin Genet Dev. 2017 Feb; 42:14-21. Butler TM, Spellman PT, Gray J. PMID: 28126649.
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    56. Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling. Cell Syst. 2017 01 25; 4(1):73-83.e10. 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. PMID: 28017544; PMCID: PMC5279869.
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    57. ΔN-ASPP2, a novel isoform of the ASPP2 tumor suppressor, promotes cellular survival. Biochem Biophys Res Commun. 2017 Jan 22; 482(4):1271-1277. 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. PMID: 27939881; PMCID: PMC5237613.
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    58. 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. 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. PMID: 27791031; PMCID: PMC5087040.
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    59. 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. 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. PMID: 27368372; PMCID: PMC4930593.
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    60. 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. 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. PMID: 27307436; PMCID: PMC4961128.
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    61. Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours. Nat Commun. 2016 05 13; 7:11588. Fei SS, Mitchell AD, Heskett MB, Vocke CD, Ricketts CJ, Peto M, Wang NJ, Sönmez K, Linehan WM, Spellman PT. PMID: 27174753; PMCID: PMC4869254.
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    62. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 2016 Apr; 13(4):310-8. 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. PMID: 26901648; PMCID: PMC4854847.
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    63. Src and STAT3 inhibitors synergize to promote tumor inhibition in renal cell carcinoma. Oncotarget. 2015 Dec 29; 6(42):44675-87. 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. PMID: 26625308; PMCID: PMC4792584.
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    64. 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. 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. PMID: 26694952; PMCID: PMC4943693.
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    65. Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. BMC Genomics. 2015; 16 Suppl 13:S1. Ivanov M, Baranova A, Butler T, Spellman P, Mileyko V. PMID: 26693644; PMCID: PMC4686799.
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    66. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 09; 6:10001. 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. PMID: 26647970; PMCID: PMC4682041.
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    67. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14; 374(2):135-45. 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. PMID: 26536169; PMCID: PMC4775252.
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    68. Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease. PLoS One. 2015; 10(8):e0136407. Butler TM, Johnson-Camacho K, Peto M, Wang NJ, Macey TA, Korkola JE, Koppie TM, Corless CL, Gray JW, Spellman PT. PMID: 26317216; PMCID: PMC4552879.
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    69. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination. Proc Natl Acad Sci U S A. 2015 Sep 01; 112(35):10995-1000. 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. PMID: 26286987; PMCID: PMC4568214.
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    70. Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. PLoS One. 2015; 10(7):e0133219. 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. PMID: 26181325; PMCID: PMC4504492.
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    71. 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. 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. PMID: 26181259; PMCID: PMC4608536.
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    72. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nat Med. 2015 Jul; 21(7):827. 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. PMID: 26151328.
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    73. 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. 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. PMID: 26075913; PMCID: PMC4468210.
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    74. Erratum to: Modeling precision treatment of breast cancer. Genome Biol. 2015 May 12; 16:95. 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. PMID: 25962591; PMCID: PMC4426644.
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    75. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nat Med. 2015 Jun; 21(6):555-9. 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. PMID: 25939062; PMCID: PMC4862411.
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    76. A humanized leucine zipper-TRAIL hybrid induces apoptosis of tumors both in vitro and in vivo. PLoS One. 2015; 10(4):e0122980. Rozanov D, Spellman P, Savinov A, Strongin AY. PMID: 25849628; PMCID: PMC4388654.
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    77. Stacked Predictive Sparse Decomposition for Classification of Histology Sections. Int J Comput Vis. 2015 May; 113(1):3-18. Chang H, Zhou Y, Borowsky A, Barner K, Spellman P, Parvin B. PMID: 27721567; PMCID: PMC5051579.
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    78. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep. 2014 Nov 20; 9(4):1228-34. 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. PMID: 25456125; PMCID: PMC4254608.
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    79. 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. 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. PMID: 25212826; PMCID: PMC4303114.
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    80. Classification of Histology Sections via Multispectral Convolutional Sparse Coding. Conf Comput Vis Pattern Recognit Workshops. 2014 Jun; 2014:3081-3088. Zhou Y, Chang H, Barner K, Spellman P, Parvin B. PMID: 25554749; PMCID: PMC4279924.
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    81. Detecting cancer by monitoring circulating tumor DNA. Nat Med. 2014 May; 20(5):474-5. Spellman PT, Gray JW. PMID: 24804754.
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    82. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet. 2014 Apr; 46(4):318-319. 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. PMID: 24675517; PMCID: PMC4035501.
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    83. Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014; 5:3156. 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. PMID: 24448499; PMCID: PMC4025965.
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    84. A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med. 2013; 5(10):92. Griffith OL, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW. PMID: 24112773; PMCID: PMC3961800.
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    85. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. 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. PMID: 24120142; PMCID: PMC3910500.
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    86. Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics. 2013 Dec 15; 29(24):3113-20. Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P. PMID: 24064421; PMCID: PMC3842754.
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    87. HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression. Springerplus. 2013; 2:386. Luoh SW, Ramsey B, Hanlon Newell A, Troxell M, Hu Z, Chin K, Spellman P, Olson S, Keenan E. PMID: 24102037; PMCID: PMC3791222.
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    88. 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. Rhee JK, Kim K, Chae H, Evans J, Yan P, Zhang BT, Gray J, Spellman P, Huang TH, Nephew KP, Kim S. PMID: 23887935; PMCID: PMC3794600.
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    89. Classification of Tumor Histology via Morphometric Context. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2013 Jun 23; 2013. Chang H, Borowsky A, Spellman P, Parvin B. PMID: 24319324; PMCID: PMC3850786.
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    90. 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. Kodigepalli KM, Anur P, Spellman P, Sims PJ, Nanjundan M. PMID: 23621864; PMCID: PMC3644492.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    91. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet. 2013 Apr; 45(4):362-70, 370e1-2. 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. PMID: 23535730; PMCID: PMC3693183.
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    92. CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING. Proc IEEE Int Symp Biomed Imaging. 2013 Apr; 2013. Nayak N, Chang H, Borowsky A, Spellman P, Parvin B. PMID: 24319533; PMCID: PMC3850768.
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    93. Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology. Proc IEEE Int Conf Comput Vis. 2013; 169-176. Chang H, Zhou Y, Spellman P, Parvin B. PMID: 24770492; PMCID: PMC3998824.
      View in: PubMed   Mentions: 5  
    94. Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching. Med Image Comput Comput Assist Interv. 2013; 16(Pt 2):91-8. Chang H, Nayak N, Spellman PT, Parvin B. PMID: 24579128; PMCID: PMC3998828.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    95. Modeling precision treatment of breast cancer. Genome Biol. 2013; 14(10):R110. 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. PMID: 24176112; PMCID: PMC3937590.
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    96. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25. 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. PMID: 23257362; PMCID: PMC3533304.
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    97. ATM suppresses SATB1-induced malignant progression in breast epithelial cells. PLoS One. 2012; 7(12):e51786. 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. PMID: 23251624; PMCID: PMC3519734.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    98. Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association. IEEE Trans Med Imaging. 2013 Apr; 32(4):670-82. Chang H, Han J, Borowsky A, Loss L, Gray JW, Spellman PT, Parvin B. PMID: 23221815; PMCID: PMC3728287.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    99. 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. Sadanandam A, Lal A, Benz SC, Eppenberger-Castori S, Scott G, Gray JW, Spellman P, Waldman F, Benz CC. PMID: 23104223; PMCID: PMC3511697.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    100. Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme. IEEE Trans Biomed Eng. 2012 Dec; 59(12):3460-7. Chang H, Han J, Spellman PT, Parvin B. PMID: 22987497; PMCID: PMC3728286.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    101. Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors. Breast Cancer Res Treat. 2012 Oct; 135(3):913-22. 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. PMID: 22941572; PMCID: PMC3873871.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    102. Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics. 2012 Nov 01; 28(21):2804-10. Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. PMID: 22923301; PMCID: PMC3476330.
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    103. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Res Treat. 2012 Sep; 135(2):505-17. 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. PMID: 22875744; PMCID: PMC3429780.
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    104. A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma. Cancer Discov. 2012 Aug; 2(8):685-93. 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. PMID: 22628411; PMCID: PMC3425446.
      View in: PubMed   Mentions: 155     Fields:    Translation:HumansAnimalsCells
    105. Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. BMC Bioinformatics. 2012 May 11; 13:94. Hill SM, Neve RM, Bayani N, Kuo WL, Ziyad S, Spellman PT, Gray JW, Mukherjee S. PMID: 22578440; PMCID: PMC3503557.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    106. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012; 7(3):e34546. 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. PMID: 22479643; PMCID: PMC3315571.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    107. Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discov. 2012 Jan; 2(1):23-4. Corless CL, Spellman PT. PMID: 22585165.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    108. Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinformatics. 2011 Dec 20; 12:484. Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B. PMID: 22185703; PMCID: PMC3271112.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    109. 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. 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. PMID: 22006338; PMCID: PMC3203814.
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    110. 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. 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. PMID: 22003129; PMCID: PMC3286973.
      View in: PubMed   Mentions: 283     Fields:    Translation:HumansCells
    111. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov. 2011 Jul; 1(2):137-43. 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. PMID: 21984974; PMCID: PMC3187561.
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    112. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011 Aug 01; 27(15):2038-46. Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. PMID: 21666266; PMCID: PMC3137217.
      View in: PubMed   Mentions: 71     Fields:    Translation:Humans
    113. 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. Han J, Chang H, Loss L, Zhang K, Baehner FL, Gray JW, Spellman P, Parvin B. PMID: 23243485; PMCID: PMC3521607.
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    114. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 2011 Apr; 17(4):500-3. 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. PMID: 21460848; PMCID: PMC3755490.
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    115. A new treasure in the breast cancer gene hunt. Nat Med. 2011 Apr; 17(4):422-3. Spellman P, Gray J. PMID: 21475233.
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    116. Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI. Integr Biol (Camb). 2011 Apr; 3(4):490-6. 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. PMID: 21416100; PMCID: PMC3698966.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    117. Unifying gene expression measures from multiple platforms using factor analysis. PLoS One. 2011 Mar 11; 6(3):e17691. Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP. PMID: 21436879; PMCID: PMC3059153.
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    118. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res. 2010 Jul; 8(7):961-74. 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. PMID: 20605923; PMCID: PMC2911965.
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    119. 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. Nautiyal S, Carlton VE, Lu Y, Ireland JS, Flaucher D, Moorhead M, Gray JW, Spellman P, Mindrinos M, Berg P, Faham M. PMID: 20616066; PMCID: PMC2906552.
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    120. Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinformatics. 2010 Jun 04; 11:305. Loss LA, Sadanandam A, Durinck S, Nautiyal S, Flaucher D, Carlton VE, Moorhead M, Lu Y, Gray JW, Faham M, Spellman P, Parvin B. PMID: 20525369; PMCID: PMC2903569.
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    121. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. 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, et al. PMID: 20393554; PMCID: PMC2902243.
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    122. 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. 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. PMID: 20129251; PMCID: PMC2818769.
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    123. A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. BMC Med. 2009 Dec 14; 7:77. 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. PMID: 20003408; PMCID: PMC2803786.
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    124. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009; 4(8):1184-91. Durinck S, Spellman PT, Birney E, Huber W. PMID: 19617889; PMCID: PMC3159387.
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    125. Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol. 2009; 10(3):R31. 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. PMID: 19317917; PMCID: PMC2691002.
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    126. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Med Genomics. 2009 Feb 19; 2:8. 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. PMID: 19228381; PMCID: PMC2649948.
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    127. 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. Bengtsson H, Ray A, Spellman P, Speed TP. PMID: 19193730; PMCID: PMC2660872.
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    128. 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. 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. PMID: 19147570; PMCID: PMC2737189.
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    129. Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts. Neuro Oncol. 2009 Oct; 11(5):477-87. 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. PMID: 19139420; PMCID: PMC2765338.
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    130. GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics. 2009 Jan 06; 10:2. Durinck S, Bullard J, Spellman PT, Dudoit S. PMID: 19123956; PMCID: PMC2629762.
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    131. Sparse combinatorial inference with an application in cancer biology. Bioinformatics. 2009 Jan 15; 25(2):265-71. Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP. PMID: 19038985; PMCID: PMC2639004.
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    132. Amplification of 11q13 in ovarian carcinoma. Genes Chromosomes Cancer. 2008 Jun; 47(6):481-9. Brown LA, Kalloger SE, Miller MA, Shih IeM, McKinney SE, Santos JL, Swenerton K, Spellman PT, Gray J, Gilks CB, Huntsman DG. PMID: 18314909.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    133. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer. 2008 Jan 22; 8:17. 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. PMID: 18208621; PMCID: PMC2245962.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansCells
    134. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 2007 Oct; 25(10):1127-33. 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. PMID: 17921998.
      View in: PubMed   Mentions: 36     Fields:    
    135. 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. 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. PMID: 18516279; PMCID: PMC2391005.
      View in: PubMed   Mentions: 496     Fields:    Translation:HumansCells
    136. Analysis of molecular inversion probe performance for allele copy number determination. Genome Biol. 2007; 8(11):R246. 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. PMID: 18028543; PMCID: PMC2258201.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    137. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41. 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. PMID: 17157792.
      View in: PubMed   Mentions: 614     Fields:    Translation:HumansCells
    138. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 2006 Dec; 10(6):515-27. 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. PMID: 17157791; PMCID: PMC2730521.
      View in: PubMed   Mentions: 1743     Fields:    Translation:HumansCells
    139. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489. 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. PMID: 17087822; PMCID: PMC1687205.
      View in: PubMed   Mentions: 108     Fields:    Translation:Humans
    140. 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. Brun S, Vidal S, Spellman P, Takahashi K, Tricoire H, Lemaitre B. PMID: 16611243.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    141. Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. PMID: 16511469.
      View in: PubMed   Mentions: 6     Fields:    
    142. FuGE: Functional Genomics Experiment Object Model. OMICS. 2006; 10(2):179-84. Jones AR, Pizarro A, Spellman P, Miller M, FuGE Working Group. PMID: 16901224.
      View in: PubMed   Mentions: 6     Fields:    
    143. A status report on MAGE. Bioinformatics. 2005 Sep 01; 21(17):3459-60. Spellman P. PMID: 16116036.
      View in: PubMed   Mentions: 1     Fields:    
    144. 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. Vodovar N, Vinals M, Liehl P, Basset A, Degrouard J, Spellman P, Boccard F, Lemaitre B. PMID: 16061818; PMCID: PMC1183552.
      View in: PubMed   Mentions: 195     Fields:    Translation:AnimalsCells
    145. Submission of microarray data to public repositories. PLoS Biol. 2004 Sep; 2(9):E317. 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. PMID: 15340489; PMCID: PMC514887.
      View in: PubMed   Mentions: 40     Fields:    
    146. Standards for microarray data: an open letter. Environ Health Perspect. 2004 Aug; 112(12):A666-7. 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. PMID: 15345376; PMCID: PMC1277123.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    147. Final words: cell age and cell cycle are unlinked. Trends Biotechnol. 2004 Jun; 22(6):277-8. Spellman PT, Sherlock G. PMID: 15158055.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    148. Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends Biotechnol. 2004 Jun; 22(6):270-3. Spellman PT, Sherlock G. PMID: 15158053.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    149. 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. Pile LA, Spellman PT, Katzenberger RJ, Wassarman DA. PMID: 12865422.
      View in: PubMed   Mentions: 49     Fields:    Translation:AnimalsCells
    150. The underlying principles of scientific publication. Bioinformatics. 2002 Nov; 18(11):1409. 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. PMID: 12424109.
      View in: PubMed   Mentions: 10     Fields:    
    151. Standards for microarray data. Science. 2002 Oct 18; 298(5593):539. 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. PMID: 12387284.
      View in: PubMed   Mentions: 42     Fields:    
    152. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23; 3(9):RESEARCH0046. 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. PMID: 12225585; PMCID: PMC126871.
      View in: PubMed   Mentions: 135     Fields:    
    153. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 2002; 1(1):5. Spellman PT, Rubin GM. PMID: 12144710; PMCID: PMC117248.
      View in: PubMed   Mentions: 206     Fields:    Translation:AnimalsCells
    154. The Toll and Imd pathways are the major regulators of the immune response in Drosophila. EMBO J. 2002 Jun 03; 21(11):2568-79. De Gregorio E, Spellman PT, Tzou P, Rubin GM, Lemaitre B. PMID: 12032070; PMCID: PMC126042.
      View in: PubMed   Mentions: 332     Fields:    Translation:AnimalsCells
    155. The future of publishing microarray data. Brief Bioinform. 2001 Dec; 2(4):316-8. Spellman PT. PMID: 11808743.
      View in: PubMed   Mentions: 1     Fields:    
    156. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec; 29(4):365-71. 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. PMID: 11726920.
      View in: PubMed   Mentions: 1313     Fields:    
    157. 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. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. PMID: 11606746; PMCID: PMC60098.
      View in: PubMed   Mentions: 259     Fields:    Translation:Animals
    158. Ceramic capillaries for use in microarray fabrication. Genome Res. 2001 Oct; 11(10):1780-3. George RA, Woolley JP, Spellman PT. PMID: 11591655; PMCID: PMC311114.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    159. The Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 01; 29(1):152-5. 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. PMID: 11125075; PMCID: PMC29818.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansAnimals
    160. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000 Dec; 11(12):4241-57. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. PMID: 11102521; PMCID: PMC15070.
      View in: PubMed   Mentions: 1986     Fields:    Translation:Animals
    161. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 2000 Jul 06; 406(6791):90-4. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. PMID: 10894548.
      View in: PubMed   Mentions: 181     Fields:    Translation:AnimalsCells
    162. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000 Mar; 24(3):227-35. 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. PMID: 10700174.
      View in: PubMed   Mentions: 612     Fields:    Translation:HumansCells
    163. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 08; 95(25):14863-8. Eisen MB, Spellman PT, Brown PO, Botstein D. PMID: 9843981; PMCID: PMC24541.
      View in: PubMed   Mentions: 5543     Fields:    Translation:HumansAnimals
    164. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998 Dec; 9(12):3273-97. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. PMID: 9843569; PMCID: PMC25624.
      View in: PubMed   Mentions: 1415     Fields:    Translation:AnimalsCells
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