Paul Thomas Spellman - Publications

Affiliations: 
2000 Stanford University, Palo Alto, CA 

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 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, ... ... Spellman PT, et al. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Reports. Medicine. 3: 100525. PMID 35243422 DOI: 10.1016/j.xcrm.2022.100525  0.781
2021 Heskett MB, Spellman PT, Thayer MJ. Differential Allelic Expression among Long Non-Coding RNAs. Non-Coding Rna. 7. PMID 34698262 DOI: 10.3390/ncrna7040066  0.761
2021 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). 11. PMID 33466369 DOI: 10.3390/diagnostics11010073  0.775
2020 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, et al. Transient commensal clonal interactions can drive tumor metastasis. Nature Communications. 11: 5799. PMID 33199705 DOI: 10.1038/s41467-020-19584-1  0.668
2020 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: 6312480. PMID 32565715 DOI: 10.1155/2020/6312480  0.304
2020 Heskett M, Smith LG, Spellman P, Thayer M. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. Rna (New York, N.Y.). PMID 32144193 DOI: 10.1261/Rna.073114.119  0.758
2020 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, ... ... Spellman PT, et al. The evolutionary history of 2,658 cancers. Nature. 578: 122-128. PMID 32025013 DOI: 10.1038/S41586-019-1907-7  0.568
2020 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. PMID 31911616 DOI: 10.1038/S41379-019-0446-Y  0.777
2020 Boniface C, Baker K, Dieg C, Halsey C, Rahmani R, Deffenbach M, Thomas C, Tormoen G, Nabavizadeh N, Spellman P. Abstract PR05: Radiation-assisted Amplification Sequencing (RAMP-Seq): Evaluating the use of stereotactic body radiation therapy (SBRT) for enriching circulating tumor DNA in liquid biopsies Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Liqbiop20-Pr05  0.378
2020 Luoh S, Peto M, Ramsey B, Halsey C, Butler T, Spellman P. Abstract P1-21-04: Comprehensive genomic analysis of synchronous bilateral breast cancer tumors Cancer Research. DOI: 10.1158/1538-7445.Sabcs19-P1-21-04  0.7
2019 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, et al. Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets. Cancer Cell. PMID 30930117 DOI: 10.1016/J.Ccell.2019.02.009  0.349
2019 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. 14: e0205623. PMID 30908483 DOI: 10.1371/Journal.Pone.0205623  0.307
2019 Butler TM, Boniface CT, Johnson-Camacho KM, Tabatabaei S, Melendez D, Kelley T, Gray JW, Corless CL, Spellman P. Circulating Tumor DNA Dynamics using Patient-Customized Assays are Associated with Outcome in Neoadjuvantly-Treated Breast Cancer. Cold Spring Harbor Molecular Case Studies. PMID 30833418 DOI: 10.1101/mcs.a003772  0.681
2019 Slansky JE, Spellman PT. Alternative Splicing in Tumors - A Path to Immunogenicity? The New England Journal of Medicine. 380: 877-880. PMID 30811916 DOI: 10.1056/Nejmcibr1814237  0.363
2018 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, ... ... Spellman PT, et al. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nature Communications. 9: 3815. PMID 30232459 DOI: 10.1038/S41467-018-05729-W  0.336
2018 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. PMID 29749794 DOI: 10.1667/Rr15053.1  0.342
2018 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, ... ... Spellman PT, et al. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Reports. 23: 313-326.e5. PMID 29617669 DOI: 10.1016/J.Celrep.2018.03.075  0.38
2018 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. PMID 29550076 DOI: 10.1016/J.Ymthe.2018.02.014  0.754
2018 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, ... ... Spellman P, et al. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 33: 244-258.e10. PMID 29438696 DOI: 10.1016/J.Ccell.2018.01.003  0.554
2018 Johnson B, Keck J, Morris M, Siex K, Kolodzie A, Parmar S, Riesterer J, Chin K, Gibbs S, Heiser L, Spellman P, Ellrott K, Babur O, Demir E, Margolin A, et al. Abstract 3296: SMMART: Serial measurements of molecular and architectural responses to therapy Cancer Research. 78: 3296-3296. DOI: 10.1158/1538-7445.Am2018-3296  0.411
2018 Dentro S, Leshchiner I, Haase K, Wintersinger J, Deshwar A, Tarabichi M, Rubanova Y, Yu K, García IV, Macintyre G, Kleinheinz K, Livitz D, Malikic S, Donmez N, Sengupta S, ... ... Spellman P, et al. Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types Cancer Research. 78: 3000-3000. DOI: 10.1158/1538-7445.Am2018-3000  0.377
2018 Jolly C, Gerstung M, Leshchiner I, Dentro SC, Gonzalez S, Mitchell TJ, Rubanova Y, Anur P, Rosebrock D, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vásquez-García I, ... ... Spellman PT, et al. Abstract 218: The evolutionary history of 2,658 cancers Cancer Research. 78: 218-218. DOI: 10.1158/1538-7445.Am2018-218  0.38
2017 Guo Q, Minnier J, Burchard J, Chiotti K, Spellman P, Schedin P. Physiologically activated mammary fibroblasts promote postpartum mammary cancer. Jci Insight. 2: e89206. PMID 28352652 DOI: 10.1172/Jci.Insight.89206  0.345
2017 Butler TM, Spellman PT, Gray J. Circulating-tumor DNA as an early detection and diagnostic tool. Current Opinion in Genetics & Development. 42: 14-21. PMID 28126649 DOI: 10.1016/J.Gde.2016.12.003  0.689
2017 Nabavizadeh N, McLaren PJ, Melendez D, Halsey C, Lopez CD, D'Souza S, Enestvedt B, Dolan JP, Thomas CR, Spellman P. Use of circulating tumor DNA levels to gauge necessity of surgery for patients undergoing trimodality therapy for esophageal cancer. Journal of Clinical Oncology. 35: TPS214-TPS214. DOI: 10.1200/Jco.2017.35.4_Suppl.Tps214  0.365
2016 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. PMID 27939881 DOI: 10.1016/J.Bbrc.2016.12.027  0.362
2016 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, et al. 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. 113: E6600-E6609. PMID 27791031 DOI: 10.1073/Pnas.1612835113  0.333
2016 Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, A Dane M, Esch A, Feiler HS, Wang NJ, ... ... Spellman PT, et al. 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. 18: 70. PMID 27368372 DOI: 10.1186/S13058-016-0728-Y  0.349
2016 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, ... ... Spellman PT, et al. 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. PMID 27307436 DOI: 10.1073/Pnas.1606994113  0.354
2016 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. 7: 11588. PMID 27174753 DOI: 10.1038/Ncomms11588  0.741
2016 Risom T, Langer E, Rantala J, Alvarez M, Johnson-Camacho K, Pelz C, Wang N, Spellman P, Califano A, Gray J, Sears R. Abstract B52: Overcoming phenotypic heterogeneity and plasticity in basal-like breast cancer through targeting adaptive pathway use Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Advbc15-B52  0.354
2016 Wedge D, Spellman P, Loo PV. Genomic evolution and heterogeneity in 2,800 cancers European Journal of Cancer. 61. DOI: 10.1016/S0959-8049(16)61255-8  0.328
2015 Fleyshman D, Cheney P, Strose 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.). 0. PMID 26694952 DOI: 10.1080/15384101.2015.1127478  0.333
2015 Ivanov M, Baranova A, Butler T, Spellman P, Mileyko V. Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. Bmc Genomics. 16: S1. PMID 26693644 DOI: 10.1186/1471-2164-16-S13-S1  0.698
2015 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, ... ... Spellman P, et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications. 6: 10001. PMID 26647970 DOI: 10.1038/Ncomms10001  0.349
2015 Lue HW, Cole B, Rao SA, Podalak 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. PMID 26625308 DOI: 10.18632/Oncotarget.5971  0.333
2015 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. 10: e0136407. PMID 26317216 DOI: 10.1371/Journal.Pone.0136407  0.713
2015 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, et al. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination. Proceedings of the National Academy of Sciences of the United States of America. PMID 26286987 DOI: 10.1073/Pnas.1508074112  0.7
2015 Korkola JE, Collisson EA, Heiser L, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, ... ... Spellman PT, et al. Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. Plos One. 10: e0133219. PMID 26181325 DOI: 10.1371/Journal.Pone.0133219  0.328
2015 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. 1: 486-94. PMID 26181259 DOI: 10.1001/Jamaoncol.2015.1432  0.328
2015 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. 10. DOI: 10.1371/Journal.Pone.0122980  0.338
2015 Albiges L, Murray B, Brooks A, Cherniack A, Berger A, Creighton CJ, Ricketts C, Bottaro DP, Srinivasan R, Schmidt LS, Meyerson M, Spellman P, Linehan WM, Choueiri TK. Distinct MET alterations to induce a common phenotype and to define a MET-driven subset of papillary RCC: Results from the Cancer Genome Atlas (TCGA) Kidney Renal Papillary (KIRP) Working Group. Journal of Clinical Oncology. 33: 4521-4521. DOI: 10.1200/Jco.2015.33.15_Suppl.4521  0.369
2015 Fu X, Jeselsohn R, Hollingsworth EF, Lopez-Terrada D, Creighton CJ, Nardone A, Shea M, Heiser LM, Anur P, Wang N, Grasso C, Spellman P, Gutierrez C, Rimawi MF, Hilsenbeck SG, et al. Abstract PD6-2: FoxA1 gene amplification in ER+ breast cancer mediates endocrine resistance by increasing IL-8 Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-Pd6-2  0.361
2014 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, ... ... Spellman PT, et al. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Reports. 9: 1228-34. PMID 25456125 DOI: 10.1016/J.Celrep.2014.10.031  0.342
2014 Spellman PT, Gray JW. Detecting cancer by monitoring circulating tumor DNA. Nature Medicine. 20: 474-5. PMID 24804754 DOI: 10.1038/Nm.3564  0.352
2014 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, ... ... Spellman PT, et al. Integrated analysis of germline and somatic variants in ovarian cancer. Nature Communications. 5: 3156. PMID 24448499 DOI: 10.1038/Ncomms4156  0.565
2013 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, ... ... Spellman PT, et al. Modeling precision treatment of breast cancer. Genome Biology. 14: R110. PMID 24176112 DOI: 10.1186/Gb-2013-14-10-R110  0.326
2013 Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, ... ... Spellman P, et al. The somatic genomic landscape of glioblastoma. Cell. 155: 462-77. PMID 24120142 DOI: 10.1016/J.Cell.2013.09.034  0.398
2013 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. 2: 386. PMID 24102037 DOI: 10.1186/2193-1801-2-386  0.327
2013 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). 29: 3113-20. PMID 24064421 DOI: 10.1093/Bioinformatics/Btt546  0.321
2013 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. 41: 8464-74. PMID 23887935 DOI: 10.1093/Nar/Gkt643  0.428
2013 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. 12: 32. PMID 23621864 DOI: 10.1186/1476-4598-12-32  0.345
2013 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, ... ... Spellman P, et al. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nature Genetics. 45: 362-70, 370e1-2. PMID 23535730 DOI: 10.1038/Ng.2564  0.313
2013 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, ... ... Spellman PT, et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. The Journal of Clinical Investigation. 123: 517-25. PMID 23257362 DOI: 10.1172/Jci65833  0.552
2013 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. 32: 670-82. PMID 23221815 DOI: 10.1109/Tmi.2012.2231420  0.343
2013 Javle MM, Rashid A, Kar SP, Schalper K, Wang N, Peto M, Vauthey J, Aloia TA, Aretxabala XD, Mills GB, Spellman P, Roa I. Identification of unique somatic mutations with functional relevance through genetic characterization of gallbladder cancer (GB ca). Journal of Clinical Oncology. 31: 214-214. DOI: 10.1200/Jco.2013.31.4_Suppl.214  0.322
2013 Heiser LM, Shaw CA, Wang NJ, Grasso C, Anur P, Ng S, Goldstein T, Spellman PT, Stuart J, Osborne K, Gray J, Schiff R. Abstract 5238: Acquired therapeutic resistance is mediated by deregulation of multiple pathways. Cancer Research. 73: 5238-5238. DOI: 10.1158/1538-7445.Am2013-5238  0.316
2012 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. 7: e51786. PMID 23251624 DOI: 10.1371/Journal.Pone.0051786  0.407
2012 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. 136: 693-703. PMID 23104223 DOI: 10.1007/S10549-012-2290-3  0.385
2012 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. 135: 913-22. PMID 22941572 DOI: 10.1007/S10549-012-2226-Y  0.364
2012 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. 135: 505-17. PMID 22875744 DOI: 10.1007/S10549-012-2188-0  0.41
2012 Corless CL, Spellman PT. Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discovery. 2: 23-4. PMID 22585165 DOI: 10.1158/2159-8290.Cd-11-0319  0.3
2012 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, ... ... Spellman PT, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 2724-9. PMID 22003129 DOI: 10.1073/Pnas.1018854108  0.345
2011 Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B. Morphometic analysis of TCGA glioblastoma multiforme. Bmc Bioinformatics. 12: 484. PMID 22185703 DOI: 10.1186/1471-2105-12-484  0.362
2011 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, ... ... Spellman PT, et al. 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. 108: 17761-6. PMID 22006338 DOI: 10.1073/Pnas.1114669108  0.324
2011 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, ... ... Spellman PT, et al. Temporal dissection of tumorigenesis in primary cancers. Cancer Discovery. 1: 137-43. PMID 21984974 DOI: 10.1158/2159-8290.Cd-11-0028  0.38
2011 Spellman P, Gray J. A new treasure in the breast cancer gene hunt Nature Medicine. 17: 422-423. PMID 21475233 DOI: 10.1038/Nm0411-422  0.356
2011 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, et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nature Medicine. 17: 500-3. PMID 21460848 DOI: 10.1038/Nm.2344  0.376
2011 Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP. Unifying gene expression measures from multiple platforms using factor analysis. Plos One. 6: e17691. PMID 21436879 DOI: 10.1371/Journal.Pone.0017691  0.356
2011 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. 3: 490-6. PMID 21416100 DOI: 10.1039/C0Ib00089B  0.334
2011 Sadanandam A, Collisson EA, Olson P, Gibb WJ, Truitt M, Olshen A, Tempero MA, Spellman PT, Hanahan D, Gray JW. Abstract LB-24: Molecular subtypes of pancreatic adenocarcinoma with different biological characteristics and therapeutical responses Cancer Research. 71. DOI: 10.1158/1538-7445.Am2011-Lb-24  0.397
2011 Korkola J, Bayani N, Cooper B, Heiser LM, Spellman PT, Feiler HS, Wooster R, Gray JW. Abstract 639: Inhibition of HER2 signaling using targeted therapeutics in breast cancer cell lines Cancer Research. 71: 639-639. DOI: 10.1158/1538-7445.Am2011-639  0.325
2011 Ng S, Vaske C, Benz S, Durbin J, Szeto C, Heiser L, Wang N, Korkola J, Bayani N, Spellman P, Gray JW, Haussler D, Stuart J. Abstract 49: Constructing pathway based predictors of cancer clinical outcome Cancer Research. 71: 49-49. DOI: 10.1158/1538-7445.Am2011-49  0.391
2010 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. 107: 12587-92. PMID 20616066 DOI: 10.1073/Pnas.1005173107  0.31
2010 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, ... ... Spellman P, et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Molecular Cancer Research : McR. 8: 961-74. PMID 20605923 DOI: 10.1158/1541-7786.Mcr-09-0528  0.371
2010 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. 11: 305. PMID 20525369 DOI: 10.1186/1471-2105-11-305  0.367
2010 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, ... ... Spellman PT, ... ... Spellman PT, ... ... Spellman PT, ... ... Spellman PT, ... ... Spellman PT, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987  0.553
2010 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, ... ... Spellman PT, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 17: 98-110. PMID 20129251 DOI: 10.1016/J.Ccr.2009.12.020  0.409
2010 Gibb WJ, Collisson E, Korkola J, Heiser L, Sadanandam A, Kuo W, Hu Z, Mao J, Wang N, Bayani N, Billig J, Ziyad S, Lewis S, Feiler H, Jakkula L, ... ... Spellman P, et al. Abstract 1979: Algebraic factorization of gene expression profiles reveals subtype-specific drug sensitivities among 54 breast cancer cell lines Cancer Research. 70: 1979-1979. DOI: 10.1158/1538-7445.Am10-1979  0.343
2010 Spellman P. Abstract ES8-2: Modeling Sensitivity to Therapeutic Agents Cancer Research. 70. DOI: 10.1158/0008-5472.Sabcs10-Es8-2  0.32
2009 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, et al. A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. Bmc Medicine. 7: 77. PMID 20003408 DOI: 10.1186/1741-7015-7-77  0.349
2009 Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols. 4: 1184-91. PMID 19617889 DOI: 10.1038/Nprot.2009.97  0.302
2009 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. 10: R31. PMID 19317917 DOI: 10.1186/Gb-2009-10-3-R31  0.333
2009 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, et al. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. Bmc Medical Genomics. 2: 8. PMID 19228381 DOI: 10.1186/1755-8794-2-8  0.31
2009 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. 11: 477-87. PMID 19139420 DOI: 10.1215/15228517-2008-113  0.41
2009 Durinck S, Bullard J, Spellman PT, Dudoit S. GenomeGraphs: integrated genomic data visualization with R. Bmc Bioinformatics. 10: 2. PMID 19123956 DOI: 10.1186/1471-2105-10-2  0.312
2009 Korkola J, Bayani N, Cooper B, Kuo W, Billig J, Ziyad S, Feiler H, Spellman P, Wooster R, Gray JW. Abstract A179: Synergistic interactions of Lapatinib and an AKT inhibitor in HER2 positive breast cancer cell lines depends on PI3K pathway status Molecular Cancer Therapeutics. 8. DOI: 10.1158/1535-7163.Targ-09-A179  0.343
2008 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. 47: 481-9. PMID 18314909 DOI: 10.1002/Gcc.20549  0.363
2008 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, et al. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. Bmc Cancer. 8: 17. PMID 18208621 DOI: 10.1186/1471-2407-8-17  0.309
2007 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. 1: 84-96. PMID 18516279 DOI: 10.1016/J.Molonc.2007.02.004  0.375
2007 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, ... ... Spellman P, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347  0.346
2006 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, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 10: 529-41. PMID 17157792 DOI: 10.1016/J.Ccr.2006.10.009  0.415
2006 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, et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 10: 515-27. PMID 17157791 DOI: 10.1016/J.Ccr.2006.10.008  0.395
2006 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, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489  0.575
2006 Jones AR, Pizarro A, Spellman P, Miller M. FuGE: Functional Genomics Experiment Object Model Omics a Journal of Integrative Biology. 10: 179-184. PMID 16901224 DOI: 10.1089/Omi.2006.10.179  0.306
2006 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. 11: 397-407. PMID 16611243 DOI: 10.1111/J.1365-2443.2006.00953.X  0.309
2006 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. 440: 24. PMID 16511469 DOI: 10.1038/440024A  0.525
2005 Chin K, Devries S, Fridlyand J, Spellman P, Kuo W, Lapuk A, Neve R, Tokuyasu T, Kingsley C, Dairkee S, Chew K, Jain A, Ljung B, Esserman L, Waldman F, et al. Genomic and transcriptional events associated with poor clinical responses to conventional therapies Breast Cancer Research. 7: 1-1. DOI: 10.1186/Bcr1059  0.375
2004 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, et al. Standards for microarray data: an open letter. Environmental Health Perspectives. 112: A666-7. PMID 15345376 DOI: 10.1289/Ehp.112-1277123  0.779
2004 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, et al. Submission of microarray data to public repositories. Plos Biology. 2: E317. PMID 15340489 DOI: 10.1371/Journal.Pbio.0020317  0.768
2004 Spellman PT, Sherlock G. Final words: cell age and cell cycle are unlinked. Trends in Biotechnology. 22: 277-8. PMID 15158055 DOI: 10.1016/J.Tibtech.2004.04.012  0.56
2004 Spellman PT, Sherlock G. Reply: whole-culture synchronization - effective tools for cell cycle studies. Trends in Biotechnology. 22: 270-3. PMID 15158053 DOI: 10.1016/J.Tibtech.2004.04.010  0.583
2003 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. 278: 37840-8. PMID 12865422 DOI: 10.1074/Jbc.M305996200  0.665
2002 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, et al. The underlying principles of scientific publication. Bioinformatics (Oxford, England). 18: 1409. PMID 12424109 DOI: 10.1093/Bioinformatics/18.11.1409  0.538
2002 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, et al. Standards for microarray data. Science (New York, N.Y.). 298: 539. PMID 12387284 DOI: 10.1126/Science.298.5593.539B  0.598
2002 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, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 3: RESEARCH0046. PMID 12225585 DOI: 10.1186/Gb-2002-3-9-Research0046  0.771
2002 Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome. Journal of Biology. 1: 5. PMID 12144710 DOI: 10.1186/1475-4924-1-5  0.55
2002 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. 21: 2568-79. PMID 12032070 DOI: 10.1093/Emboj/21.11.2568  0.523
2002 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, Jr CJS, Stewart JE, Taylor R, et al. A guide to microarray experiments-an open letter to the scientific journals The Lancet. 360: 1019. DOI: 10.1016/S0140-6736(02)11100-7  0.542
2001 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, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 29: 365-71. PMID 11726920 DOI: 10.1038/Ng1201-365  0.619
2001 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. 98: 12590-5. PMID 11606746 DOI: 10.1073/Pnas.221458698  0.521
2001 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. 29: 152-5. PMID 11125075 DOI: 10.1093/Nar/29.1.152  0.757
2000 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. 11: 4241-57. PMID 11102521 DOI: 10.1091/Mbc.11.12.4241  0.739
2000 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. 406: 90-4. PMID 10894548 DOI: 10.1038/35017581  0.505
2000 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, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics. 24: 227-35. PMID 10700174 DOI: 10.1038/73432  0.745
1999 Spellman P, Gasch A, Eisen M, Kao C, Brown P, Botstein D. Functional clustering of genes using microarray gene expression data Nature Genetics. 23: 75-75. DOI: 10.1038/14406  0.727
1998 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. 95: 14863-8. PMID 9843981 DOI: 10.1073/Pnas.95.25.14863  0.749
1998 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. 9: 3273-97. PMID 9843569 DOI: 10.1091/Mbc.9.12.3273  0.782
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