Paul Thomas Spellman

Professor, Medicine, University of California Los Angeles

Professor, Human Genetics, University of California Los Angeles

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.

Interests

Cancer, Genetics, Genomics, Precision Medicine, Computational Biology

Education and Training

UC Berkeley12/2003Gene Regulation/Genomics
Stanford University SoMPhD04/2000Genetics
MITSB02/1995Biology

Publications

  1. 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 discovery, 2024.
  2. 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.
  3. 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.
  4. 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 reports, 2024.
  5. 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.
  6. 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.. The Journal of clinical investigation, 2024.
  7. 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.. Journal of clinical and translational science, 2024.
  8. 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.. American journal of human genetics, 2023.
  9. 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.
  10. Goldman EA, Spellman PT, Agarwal A. Defining clonal hematopoiesis of indeterminate potential: evolutionary dynamics and detection under aging and inflammation.. Cold Spring Harbor molecular case studies, 2023.
  11. 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 : the preprint server for biology, 2023.
  12. Boniface CT, Spellman PT. Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response.. Pathology oncology research : POR, 2023.
  13. 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.. Research square, 2023.
  14. 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.
  15. 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.. Nature communications, 2022.
  16. Boniface CT, Spellman PT. Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response.. Pathology oncology research : POR, 2022.
  17. 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 precision oncology, 2022.
  18. 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 reports. Medicine, 2022.
  19. 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.. Nature communications, 2021.
  20. 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.. Nature biotechnology, 2021.
  21. Heskett MB, Spellman PT, Thayer MJ. Differential Allelic Expression among Long Non-Coding RNAs.. Non-coding RNA, 2021.
  22. 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 precision oncology, 2021.
  23. 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.
  24. 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 precision oncology, 2021.
  25. 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 systems, 2021.
  26. 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.
  27. 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 (New York, N.Y.), 2021.
  28. 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.
  29. Matsumoto T, Wakefield L, Peters A, Peto M, Spellman P, Grompe M. Proliferative polyploid cells give rise to tumors via ploidy reduction.. Nature communications, 2021.
  30. 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, Switzerland), 2021.
  31. 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.. Nature communications, 2020.
  32. 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.
  33. 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.. Scientific reports, 2020.
  34. 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.
  35. Heskett MB, Smith LG, Spellman P, Thayer MJ. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.. RNA (New York, N.Y.), 2020.
  36. 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.
  37. 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.. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 2020.
  38. 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 Harbor molecular case studies, 2019.
  39. 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.
  40. 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.
  41. Slansky JE, Spellman PT. Alternative Splicing in Tumors - A Path to Immunogenicity?. The New England journal of medicine, 2019.
  42. 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?. Nature genetics, 2018.
  43. 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.. Nature communications, 2018.
  44. 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 reports, 2018.
  45. 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.. Radiation research, 2018.
  46. 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.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2018.
  47. 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 reports, 2018.
  48. 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.. Molecular therapy : the journal of the American Society of Gene Therapy, 2018.
  49. 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.
  50. 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.. Journal of proteomics, 2018.
  51. 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.
  52. Guo Q, Minnier J, Burchard J, Chiotti K, Spellman P, Schedin P. Physiologically activated mammary fibroblasts promote postpartum mammary cancer.. JCI insight, 2017.
  53. 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 research : BCR, 2017.
  54. Butler TM, Spellman PT, Gray J. Circulating-tumor DNA as an early detection and diagnostic tool.. Current opinion in genetics & development, 2017.
  55. 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 systems, 2016.
  56. 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.. Biochemical and biophysical research communications, 2016.
  57. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2016.
  58. 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 research : BCR, 2016.
  59. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2016.
  60. 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.. Nature communications, 2016.
  61. 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.. Nature methods, 2016.
  62. 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.
  63. 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 (Georgetown, Tex.), 2015.
  64. 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.
  65. 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.. Nature communications, 2015.
  66. 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.. The New England journal of medicine, 2015.
  67. 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.
  68. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2015.
  69. 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.
  70. 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 oncology, 2015.
  71. 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.. Nature medicine, 2015.
  72. 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.
  73. 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 biology, 2015.
  74. 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.. Nature medicine, 2015.
  75. 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.
  76. Chang H, Zhou Y, Borowsky A, Barner K, Spellman P, Parvin B. Stacked Predictive Sparse Decomposition for Classification of Histology Sections.. International journal of computer vision, 2014.
  77. 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 reports, 2014.
  78. 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 research : BCR, 2014.
  79. Zhou Y, Chang H, Barner K, Spellman P, Parvin B. Classification of Histology Sections via Multispectral Convolutional Sparse Coding.. Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops, 2014.
  80. Spellman PT, Gray JW. Detecting cancer by monitoring circulating tumor DNA.. Nature medicine, 2014.
  81. 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.. Nature genetics, 2014.
  82. 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.. Nature communications, 2014.
  83. 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 medicine, 2013.
  84. 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.
  85. Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P. Methods and challenges in timing chromosomal abnormalities within cancer samples.. Bioinformatics (Oxford, England), 2013.
  86. 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.
  87. 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 research, 2013.
  88. Chang H, Borowsky A, Spellman P, Parvin B. Classification of Tumor Histology via Morphometric Context.. Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2013.
  89. 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.. Molecular cancer, 2013.
  90. Nayak N, Chang H, Borowsky A, Spellman P, Parvin B. CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING.. Proceedings. IEEE International Symposium on Biomedical Imaging, 2013.
  91. 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.. Nature genetics, 2013.
  92. Chang H, Nayak N, Spellman PT, Parvin B. Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching.. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 2013.
  93. 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 biology, 2013.
  94. Chang H, Zhou Y, Spellman P, Parvin B. Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology.. Proceedings. IEEE International Conference on Computer Vision, 2013.
  95. 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.. The Journal of clinical investigation, 2012.
  96. 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.
  97. 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 transactions on medical imaging, 2012.
  98. 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 research and treatment, 2012.
  99. Chang H, Han J, Spellman PT, Parvin B. Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.. IEEE transactions on bio-medical engineering, 2012.
  100. 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 research and treatment, 2012.
  101. 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 (Oxford, England), 2012.
  102. 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 research and treatment, 2012.
  103. 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 discovery, 2012.
  104. 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.
  105. 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.
  106. Corless CL, Spellman PT. Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing.. Cancer discovery, 2012.
  107. 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.
  108. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2011.
  109. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2011.
  110. 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 discovery, 2011.
  111. 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 (Oxford, England), 2011.
  112. 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.. Proceedings. IEEE International Symposium on Biomedical Imaging, 2011.
  113. 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.. Nature medicine, 2011.
  114. Spellman P, Gray J. A new treasure in the breast cancer gene hunt.. Nature medicine, 2011.
  115. 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.. Integrative biology : quantitative biosciences from nano to macro, 2011.
  116. Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP. Unifying gene expression measures from multiple platforms using factor analysis.. PloS one, 2011.
  117. 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.. Molecular cancer research : MCR, 2010.
  118. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
  119. 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.
  120. 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.
  121. 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.
  122. 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 medicine, 2009.
  123. Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.. Nature protocols, 2009.
  124. 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 biology, 2009.
  125. 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 medical genomics, 2009.
  126. 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 (Oxford, England), 2009.
  127. 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 research, 2009.
  128. 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-oncology, 2009.
  129. Durinck S, Bullard J, Spellman PT, Dudoit S. GenomeGraphs: integrated genomic data visualization with R.. BMC bioinformatics, 2009.
  130. 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 (Oxford, England), 2008.
  131. 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.
  132. 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.
  133. 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.. Nature biotechnology, 2007.
  134. 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.. Molecular oncology, 2007.
  135. 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 biology, 2007.
  136. 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.
  137. 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.
  138. 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.
  139. 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 to cells : devoted to molecular & cellular mechanisms, 2006.
  140. 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.
  141. Jones AR, Pizarro A, Spellman P, Miller M, FuGE Working Group. FuGE: Functional Genomics Experiment Object Model.. Omics : a journal of integrative biology, 2006.
  142. Spellman P. A status report on MAGE.. Bioinformatics (Oxford, England), 2005.
  143. 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.. Proceedings of the National Academy of Sciences of the United States of America, 2005.
  144. 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 biology, 2004.
  145. 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.. Environmental health perspectives, 2004.
  146. Spellman PT, Sherlock G. Final words: cell age and cell cycle are unlinked.. Trends in biotechnology, 2004.
  147. Spellman PT, Sherlock G. Reply: whole-culture synchronization - effective tools for cell cycle studies.. Trends in biotechnology, 2004.
  148. Pile LA, Spellman PT, Katzenberger RJ, Wassarman DA. The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolism.. The Journal of biological chemistry, 2003.
  149. 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 (Oxford, England), 2002.
  150. 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 (New York, N.Y.), 2002.
  151. 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 biology, 2002.
  152. Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome.. Journal of biology, 2002.
  153. 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.. The EMBO journal, 2002.
  154. 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.. Nature genetics, 2001.
  155. Spellman PT. The future of publishing microarray data.. Briefings in bioinformatics, 2001.
  156. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays.. Proceedings of the National Academy of Sciences of the United States of America, 2001.
  157. George RA, Woolley JP, Spellman PT. Ceramic capillaries for use in microarray fabrication.. Genome research, 2001.
  158. 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 research, 2001.
  159. 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.. Molecular biology of the cell, 2000.
  160. 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.
  161. 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.. Nature genetics, 2000.
  162. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns.. Proceedings of the National Academy of Sciences of the United States of America, 1998.
  163. 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.. Molecular biology of the cell, 1998.