Paul Thomas Spellman - Publications

Affiliations: 
2000 Stanford University, Palo Alto, CA 

117 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
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  1
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  1
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  1
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: 3698. PMID 29925010 DOI: 10.1016/j.celrep.2018.06.032  1
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  1
2018 Rozanov DV, Rozanov ND, Chiotti K, 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, ... ... Spellman PT, et al. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. Journal of Proteomics. PMID 29331515 DOI: 10.1016/j.jprot.2018.01.004  1
2017 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, ... ... Spellman PT, et al. Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer. Plos One. 12: e0186551. PMID 29020035 DOI: 10.1371/journal.pone.0186551  1
2017 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, ... ... Spellman PT, et al. 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. 19: 17. PMID 28183333 DOI: 10.1186/s13058-017-0809-6  1
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  0.52
2016 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, et al. Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling. Cell Systems. PMID 28017544 DOI: 10.1016/j.cels.2016.11.013  1
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  1
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  1
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  1
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  1
2016 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, ... ... Spellman PT, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/nmeth.3773  1
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  1
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  0.72
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  1
2015 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, et al. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. The New England Journal of Medicine. PMID 26536169 DOI: 10.1056/NEJMoa1505917  1
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  1
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  1
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  1
2015 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. 10: e0129566. PMID 26075913 DOI: 10.1371/journal.pone.0129566  1
2015 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. Erratum to: Modeling precision treatment of breast cancer. Genome Biology. 16: 95. PMID 25962591 DOI: 10.1186/s13059-015-0658-5  1
2015 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, ... ... Spellman PT, et al. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nature Medicine. 21: 555-9. PMID 25939062 DOI: 10.1038/nm.3855  1
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  1
2015 Chang H, Spellman PT, Parvin B. Predictive sparse morphometric context for classification of histology sections Proceedings - International Symposium On Biomedical Imaging. 2015: 1004-1007. DOI: 10.1109/ISBI.2015.7164040  1
2015 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. 113: 3-18. DOI: 10.1007/s11263-014-0790-9  1
2014 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: 3081-3088. PMID 25554749 DOI: 10.1109/CVPR.2014.394  1
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  1
2014 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, ... ... Spellman P, et al. 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. 16: 430. PMID 25212826 DOI: 10.1186/s13058-014-0430-x  1
2014 Spellman PT, Gray JW. Detecting cancer by monitoring circulating tumor DNA. Nature Medicine. 20: 474-5. PMID 24804754 DOI: 10.1038/nm.3564  1
2014 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. 46: 318-9. PMID 24675517 DOI: 10.1038/ng.2932  1
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  1
2014 Spellman PT, Stuart J, Gray JW. Understanding and Using Information about Cancer Genomes The Molecular Basis of Cancer: Fourth Edition. 357-368.e3. DOI: 10.1016/B978-1-4557-4066-6.00024-X  1
2013 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. Ieee International Conference On Computer Vision. 169-176. PMID 24770492 DOI: 10.1109/ICCV.2013.28  1
2013 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. 16: 91-8. PMID 24579128 DOI: 10.1007/978-3-642-40763-5_12  1
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  1
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  1
2013 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. 5: 92. PMID 24112773 DOI: 10.1186/gm496  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Nayak N, Chang H, Borowsky A, Spellman P, Parvin B. Classification of tumor histopathology via sparse feature learning Proceedings - International Symposium On Biomedical Imaging. 410-413. DOI: 10.1109/ISBI.2013.6556499  1
2013 Chang H, Borowsky A, Spellman P, Parvin B. Classification of tumor histology via morphometric context Proceedings of the Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2203-2210. DOI: 10.1109/CVPR.2013.286  1
2013 Chang H, Fontenay GV, Bilgin CC, Borowsky A, Spellman P, Parvin B. Molecular Correlates of Morphometric Subtypes in Glioblastoma Multiforme Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. 423-454. DOI: 10.1016/B978-0-12-405926-9.00018-6  1
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  1
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  1
2012 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. 59: 3460-7. PMID 22987497 DOI: 10.1109/TBME.2012.2218107  1
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  1
2012 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). 28: 2804-10. PMID 22923301 DOI: 10.1093/bioinformatics/bts514  1
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  1
2012 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. 2: 685-93. PMID 22628411 DOI: 10.1158/2159-8290.CD-11-0347  1
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  1
2012 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. 13: 94. PMID 22578440 DOI: 10.1186/1471-2105-13-94  1
2012 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, et al. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. Plos One. 7: e34546. PMID 22479643 DOI: 10.1371/journal.pone.0034546  1
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  1
2012 Han J, Chang H, Fontenay GV, Spellman PT, Borowsky A, Parvin B. Molecular bases of morphometric composition in Glioblastoma multiforme Proceedings - International Symposium On Biomedical Imaging. 1631-1634. DOI: 10.1109/ISBI.2012.6235889  1
2012 Chang H, Loss LA, Spellman PT, Borowsky A, Parvin B. Batch-invariant nuclear segmentation in whole mount histology sections Proceedings - International Symposium On Biomedical Imaging. 856-859. DOI: 10.1109/ISBI.2012.6235683  1
2012 Le QV, Han J, Gray JW, Spellman PT, Borowsky A, Parvin B. Learning invariant features of tumor signatures Proceedings - International Symposium On Biomedical Imaging. 302-305. DOI: 10.1109/ISBI.2012.6235544  1
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  1
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  1
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  1
2011 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). 27: 2038-46. PMID 21666266 DOI: 10.1093/bioinformatics/btr329  1
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  1
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  1
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  1
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  1
2011 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 - International Symposium On Biomedical Imaging. 711-714. DOI: 10.1109/ISBI.2011.5872505  1
2011 Nabavizadeh N, Klifa C, Newitt D, Lu Y, Chen YY, Hsu H, Fisher C, Tokuyasu 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 (2011) 3 (910-921) DOI:10.1039/C1IB00043H) Integrative Biology. 3: 1233. DOI: 10.1039/c1ib90045e  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2009 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. 25: 861-867. PMID 19193730 DOI: 10.1093/bioinformatics/btp074  1
2009 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, et al. Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Research. 69: 565-72. PMID 19147570 DOI: 10.1158/0008-5472.CAN-08-3389  1
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  1
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  1
2009 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). 25: 265-71. PMID 19038985 DOI: 10.1093/bioinformatics/btn611  1
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  1
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  1
2008 Spellman PT, Costello JF, Gray JW. Cancer Genomics The Molecular Basis of Cancer. 267-282. DOI: 10.1016/B978-141603703-3.10020-2  1
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  1
2007 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. 8: R246. PMID 18028543 DOI: 10.1186/gb-2007-8-11-r246  1
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  1
2007 Parvin B, Ghosh N, Heiser L, Knapp M, Talcott C, Laderoute K, Gray J, Spellman P. Spectral decomposition of signaling networks 2007 Ieee Symposium On Computational Intelligence and Bioinformatics and Computational Biology, Cibcb 2007. 76-81.  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 Spellman P. A status report on mage Bioinformatics. 21: 3459-3460. PMID 16116036 DOI: 10.1093/bioinformatics/bti591  1
2005 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. 102: 11414-9. PMID 16061818 DOI: 10.1073/pnas.0502240102  1
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  1
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  1
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  1
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  1
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  1
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  1
2002 Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome. Journal of Biology. 1: 5. PMID 12144710  1
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  1
2001 Spellman PT. The future of publishing microarray data. Briefings in Bioinformatics. 2: 316-8. PMID 11808743  1
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  1
2001 George RA, Woolley JP, Spellman PT. Ceramic capillaries for use in microarray fabrication. Genome Research. 11: 1780-3. PMID 11591655 DOI: 10.1101/gr.190801  1
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  1
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  1
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  1
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  1
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  1
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