Search Results - "Paul Spellman"

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt by Durinck, Steffen, Spellman, Paul T, Birney, Ewan, Huber, Wolfgang

“…Genomic experiments produce multiple views of biological systems, among them are DNA sequence and copy number variation, and mRNA and protein abundance…”
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Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets by Cassetta, Luca, Fragkogianni, Stamatina, Sims, Andrew H., Swierczak, Agnieszka, Forrester, Lesley M., Zhang, Hui, Soong, Daniel Y.H., Cotechini, Tiziana, Anur, Pavana, Lin, Elaine Y., Fidanza, Antonella, Lopez-Yrigoyen, Martha, Millar, Michael R., Urman, Alexandra, Ai, Zhichao, Spellman, Paul T., Hwang, E. Shelley, Dixon, J. Michael, Wiechmann, Lisa, Coussens, Lisa M., Smith, Harriet O., Pollard, Jeffrey W.

“…The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorly understood. Here, we show that monocyte subpopulation…”
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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes by Dentro, Stefan C., Leshchiner, Ignaty, Haase, Kerstin, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G., Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Rosebrock, Daniel, Schumacher, Steven E., Fittall, Matthew, Drews, Ruben M., Yao, Xiaotong, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J., McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C., Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S. Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T., Wang, Wenyi, Wedge, David C., Dentro, Stefan C., Leshchiner, Ignaty, Gerstung, Moritz, Jolly, Clemency, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G., Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D., Cao, Shaolong, Cmero, Marek, Cun, Yupeng, Dawson, Kevin J., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew, Getz, Gad, Ha, Gavin, Imielinski, Marcin, Ji, Yuan, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Livitz, Dimitri G., Malikic, Salem, Markowetz, Florian, Martincorena, Inigo, Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Salcedo, Adriana, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Spiro, Oliver, Vázquez-García, Ignacio, Vembu, Shankar, Wheeler, David A., Yao, Xiaotong, Yuan, Ke, Wang, Wenyi, Morris, Quaid D., Spellman, Paul T., Wedge, David C., Van Loo, Peter

“…Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and…”
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Alternative Splicing in Tumors — A Path to Immunogenicity? by Slansky, Jill E, Spellman, Paul T

“…The ability of cancer cells to elicit an immune response depends on several factors, including their expression of neoantigens. How many antigens do tumor…”
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Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data by Sun, Duanchen, Guan, Xiangnan, Moran, Amy E., Wu, Ling-Yun, Qian, David Z., Schedin, Pepper, Dai, Mu-Shui, Danilov, Alexey V., Alumkal, Joshi J., Adey, Andrew C., Spellman, Paul T., Xia, Zheng

“…Bulk and single cell measurements are integrated to identify phenotype-associated subpopulations of cells. Single-cell RNA sequencing (scRNA-seq) distinguishes…”
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Circulating-tumor DNA as an early detection and diagnostic tool by Butler, Timothy M, Spellman, Paul T, Gray, Joe

“…The development of new circulating-tumor DNA (ctDNA) analysis techniques has led to an explosion of studies demonstrating exciting clinical applications…”
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Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease by Butler, Timothy M, Johnson-Camacho, Katherine, Peto, Myron, Wang, Nicholas J, Macey, Tara A, Korkola, James E, Koppie, Theresa M, Corless, Christopher L, Gray, Joe W, Spellman, Paul T

“…The identification of the molecular drivers of cancer by sequencing is the backbone of precision medicine and the basis of personalized therapy; however,…”
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Proliferative polyploid cells give rise to tumors via ploidy reduction by Matsumoto, Tomonori, Wakefield, Leslie, Peters, Alexander, Peto, Myron, Spellman, Paul, Grompe, Markus

“…Polyploidy is a hallmark of cancer, and closely related to chromosomal instability involved in cancer progression. Importantly, polyploid cells also exist in…”
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Detecting cancer by monitoring circulating tumor DNA by Spellman, Paul T, Gray, Joe W

“…DNA that is shed by dead tumor cells into the blood, termed circulating tumor DNA (ctDNA), is a rich resource that could potentially be used for cancer…”
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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer by Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine, Dobrolecki, Lacey E., Chin, Koei, Aswani, Anil J., Wang, Nicholas J., Califano, Andrea, Lewis, Michael T., Tomlin, Claire J., Spellman, Paul T., Adey, Andrew, Gray, Joe W., Sears, Rosalie C.

“…Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted…”
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Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability by Heskett, Michael B., Vouzas, Athanasios E., Smith, Leslie G., Yates, Phillip A., Boniface, Christopher, Bouhassira, Eric E., Spellman, Paul T., Gilbert, David M., Thayer, Mathew J.

“…ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human…”
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Mutation of SIVA, a candidate metastasis gene identified from clonally related bilateral breast cancers, promotes breast cancer cell spread in vitro and in vivo by Vermehren-Schmaedick, Anke, Peto, Myron, Wagoner, Wendy, Chiotti, Kami E, Ramsey, Elizabeth, Wang, Xiaoyan, Rakshe, Shauna, Minnier, Jessica, Sears, Rosalie, Spellman, Paul, Luoh, Shiuh-Wen

“…Metastasis is the most dreaded outcome after a breast cancer diagnosis, and little is known regarding what triggers or promotes breast cancer to spread…”
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Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy by Collisson, Eric A, Sadanandam, Anguraj, Olson, Peter, Gibb, William J, Truitt, Morgan, Gu, Shenda, Cooc, Janine, Weinkle, Jennifer, Kim, Grace E, Jakkula, Lakshmi, Feiler, Heidi S, Ko, Andrew H, Olshen, Adam B, Danenberg, Kathleen L, Tempero, Margaret A, Spellman, Paul T, Hanahan, Douglas, Gray, Joe W

“…This report describes the identification of three molecularly distinct subtypes of pancreatic ductal adenocarninoma (PDA). The classical, quasimesenchymal and…”
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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 by Verhaak, Roel G.W., Hoadley, Katherine A., Purdom, Elizabeth, Wang, Victoria, Qi, Yuan, Wilkerson, Matthew D., Miller, C. Ryan, Ding, Li, Golub, Todd, Mesirov, Jill P., Alexe, Gabriele, Lawrence, Michael, O'Kelly, Michael, Tamayo, Pablo, Weir, Barbara A., Gabriel, Stacey, Winckler, Wendy, Gupta, Supriya, Jakkula, Lakshmi, Feiler, Heidi S., Hodgson, J. Graeme, James, C. David, Sarkaria, Jann N., Brennan, Cameron, Kahn, Ari, Spellman, Paul T., Wilson, Richard K., Speed, Terence P., Gray, Joe W., Meyerson, Matthew, Getz, Gad, Perou, Charles M., Hayes, D. Neil

“…The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM). We describe a robust gene expression-based…”
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FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer by Fu, Xiaoyong, Jeselsohn, Rinath, Pereira, Resel, Hollingsworth, Emporia F., Creighton, Chad J., Li, Fugen, Shea, Martin, Nardone, Agostina, De Angelis, Carmine, Heiser, Laura M., Anur, Pavana, Wang, Nicholas, Grasso, Catherine S., Spellman, Paul T., Griffith, Obi L., Tsimelzon, Anna, Gutierrez, Carolina, Huang, Shixia, Edwards, Dean P., Trivedi, Meghana V., Rimawi, Mothaffar F., Lopez-Terrada, Dolores, Hilsenbeck, Susan G., Gray, Joe W., Brown, Myles, Osborne, C. Kent, Schiff, Rachel

“…Forkhead box protein A1 (FOXA1) is a pioneer factor of estrogen receptor α (ER)–chromatin binding and function, yet its aberration in endocrine-resistant…”
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Corrigendum: Blood, toil, and taxoteres: Biological determinants of treatment-induced ctDNA dynamics for interpreting tumor response by Boniface, Christopher T, Spellman, Paul T

“…[This corrects the article DOI: 10.3389/pore.2022.1610103.]…”
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Subtype and pathway specific responses to anticancer compounds in breast cancer by Heiser, Laura M, Sadanandam, Anguraj, Kuo, Wen-Lin, Benz, Stephen C, Goldstein, Theodore C, Ng, Sam, Gibb, William J, Wang, Nicholas J, Ziyad, Safiyyah, Tong, Frances, Bayani, Nora, Hu, Zhi, Billig, Jessica I, Dueregger, Andrea, Lewis, Sophia, Jakkula, Lakshmi, Korkola, James E, Durinck, Steffen, Pepin, François, Guan, Yinghui, Purdom, Elizabeth, Neuvial, Pierre, Bengtsson, Henrik, Wood, Kenneth W, Smith, Peter G, Vassilev, Lyubomir T, Hennessy, Bryan T, Greshock, Joel, Bachman, Kurtis E, Hardwicke, Mary Ann, Park, John W, Marton, Laurence J, Wolf, Denise M, Collisson, Eric A, Neve, Richard M, Mills, Gordon B, Speed, Terence P, Feiler, Heidi S, Wooster, Richard F, Haussler, David, Stuart, Joshua M, Gray, Joe W, Spellman, Paul T

“…Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of…”
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Functionally defined therapeutic targets in diffuse intrinsic pontine glioma by Grasso, Catherine S, Tang, Yujie, Truffaux, Nathalene, Berlow, Noah E, Liu, Lining, Debily, Marie-Anne, Quist, Michael J, Davis, Lara E, Huang, Elaine C, Woo, Pamelyn J, Ponnuswami, Anitha, Chen, Spenser, Johung, Tessa B, Sun, Wenchao, Kogiso, Mari, Du, Yuchen, Qi, Lin, Huang, Yulun, Hütt-Cabezas, Marianne, Warren, Katherine E, Le Dret, Ludivine, Meltzer, Paul S, Mao, Hua, Quezado, Martha, van Vuurden, Dannis G, Abraham, Jinu, Fouladi, Maryam, Svalina, Matthew N, Wang, Nicholas, Hawkins, Cynthia, Nazarian, Javad, Alonso, Marta M, Raabe, Eric H, Hulleman, Esther, Spellman, Paul T, Li, Xiao-Nan, Keller, Charles, Pal, Ranadip, Grill, Jacques, Monje, Michelle

“…The study describes the use of integrative approaches to search for candidate therapeutic targets for DIPG, and the identification of an HDAC inhibitor as a…”
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Integrated analysis of germline and somatic variants in ovarian cancer by Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D. M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li

“…We report the first large-scale exome-wide analysis of the combined germline–somatic landscape in ovarian cancer. Here we analyse germline and somatic…”
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Epigenetic loss of heterogeneity from low to high grade localized prostate tumours by Eksi, Sebnem Ece, Chitsazan, Alex, Sayar, Zeynep, Thomas, George V., Fields, Andrew J., Kopp, Ryan P., Spellman, Paul T., Adey, Andrew C.

“…Identifying precise molecular subtypes attributable to specific stages of localized prostate cancer has proven difficult due to high levels of heterogeneity…”
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