Works by Spellman, Paul T.

Results: 41

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line.

Published in:

Bioinformatics, 2012, v. 28, n. 21, p. 2804, doi. 10.1093/bioinformatics/bts514

By:

Hill, Steven M.;
Lu, Yiling;
Molina, Jennifer;
Heiser, Laura M.;
Spellman, Paul T.;
Speed, Terence P.;
Gray, Joe W.;
Mills, Gordon B.;
Mukherjee, Sach

Publication type:

Article

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation.

Published in:

Bioinformatics, 2011, v. 27, n. 15, p. 2038, doi. 10.1093/bioinformatics/btr329

By:

Olshen, Adam B.;
Bengtsson, Henrik;
Neuvial, Pierre;
Spellman, Paul T.;
Olshen, Richard A.;
Seshan, Venkatraman E.

Publication type:

Article

Sparse combinatorial inference with an application in cancer biology.

Published in:

Bioinformatics, 2009, v. 25, n. 2, p. 265, doi. 10.1093/bioinformatics/btn611

By:

Sach Mukherjee;
Steven Pelech;
Richard M. Neve;
Wen-Lin Kuo;
Safiyyah Ziyad;
Paul T. Spellman;
Joe W. Gray;
Terence P. Speed

Publication type:

Article

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.

Published in:

BMC Medical Genomics, 2009, v. 2, p. 1, doi. 10.1186/1755-8794-2-8

By:

Yuker Wang;
Carlton, Victoria E. H.;
Karlin-Neumann, George;
Sapolsky, Ronald;
Li Zhang;
Moorhead, Martin;
Wang, Zhigang C.;
Richardson, Andrea L.;
Warren, Robert;
Walther, Axel;
Bondy, Melissa;
Sahin, Aysegul;
Krahe, Ralf;
Tuna, Musaffe;
Thompson, Patricia A.;
Spellman, Paul T.;
Gray, Joe W.;
Mills, Gordon B.;
Faham, Malek

Publication type:

Article

Detecting cancer by monitoring circulating tumor DNA.

Published in:

Nature Medicine, 2014, v. 20, n. 5, p. 474, doi. 10.1038/nm.3564

By:

Spellman, Paul T;
Gray, Joe W

Publication type:

Article

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy.

Published in:

Nature Medicine, 2011, v. 17, n. 4, p. 500, doi. 10.1038/nm.2344

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.

Publication type:

Article

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Published in:

Nature Genetics, 2014, v. 46, n. 4, p. 318, doi. 10.1038/ng.2932

By:

Boutros, Paul C;
Ewing, Adam D;
Ellrott, Kyle;
Norman, Thea C;
Dang, Kristen K;
Hu, Yin;
Kellen, Michael R;
Suver, Christine;
Bare, J Christopher;
Stein, Lincoln D;
Spellman, Paul T;
Stolovitzky, Gustavo;
Friend, Stephen H;
Margolin, Adam A;
Stuart, Joshua M

Publication type:

Article

Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities.

Published in:

BMC Cancer, 2008, v. 8, p. 1, doi. 10.1186/1471-2407-8-17

By:

Press, Joshua Z.;
De Luca, Alessandro;
Boyd, Niki;
Young, Sean;
Troussard, Armelle;
Ridge, Yolanda;
Kaurah, Pardeep;
Kalloger, Steve E.;
Blood, Katherine A.;
Smith, Margaret;
Spellman, Paul T.;
Yuker Wang;
Miller, Dianne M.;
Horsman, Doug;
Faham, Malek;
Gilks, C. Blake;
Gray, Joe;
Huntsman, David G.

Publication type:

Article

Amplification of 11q13 in ovarian carcinoma.

Published in:

Genes, Chromosomes & Cancer, 2008, v. 47, n. 6, p. 481, doi. 10.1002/gcc.20549

By:

Brown, Lindsay A.;
Kalloger, Steve E.;
Miller, Melinda A.;
Shih, Ie-Ming;
McKinney, Steven E.;
Santos, Jennifer L.;
Swenerton, Ken;
Spellman, Paul T.;
Gray, Joe;
Gilks, C. Blake;
Huntsman, David G.

Publication type:

Article

Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27615-8

By:

Eksi, Sebnem Ece;
Chitsazan, Alex;
Sayar, Zeynep;
Thomas, George V.;
Fields, Andrew J.;
Kopp, Ryan P.;
Spellman, Paul T.;
Adey, Andrew C.

Publication type:

Article

Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease.

Published in:

PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0136407

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.

Publication type:

Article

Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

Published in:

PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0133219

By:

Korkola, James E.;
Collisson, Eric A.;
Heiser, Laura;
Oates, Chris;
Bayani, Nora;
Itani, Sleiman;
Esch, Amanda;
Thompson, Wallace;
Griffith, Obi L.;
Wang, Nicholas J.;
Kuo, Wen-Lin;
Cooper, Brian;
Billig, Jessica;
Ziyad, Safiyyah;
Hung, Jenny L.;
Jakkula, Lakshmi;
Feiler, Heidi;
Lu, Yiling;
Mills, Gordon B.;
Spellman, Paul T.

Publication type:

Article

ATM Suppresses SATB1-Induced Malignant Progression in Breast Epithelial Cells.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0051786

By:

Ordinario, Ellen;
Han, Hye-Jung;
Furuta, Saori;
Heiser, Laura M.;
Jakkula, Lakshmi R.;
Rodier, Francis;
Spellman, Paul T.;
Campisi, Judith;
Gray, Joe W.;
Bissell, Mina J.;
Kohwi, Yoshinori;
Kohwi-Shigematsu, Terumi

Publication type:

Article

Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma.

Published in:

PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0034546

By:

Creighton, Chad J.;
Hernandez-Herrera, Anadulce;
Jacobsen, Anders;
Levine, Douglas A.;
Mankoo, Parminder;
Schultz, Nikolaus;
Ying Du;
Yiqun Zhang;
Larsson, Erik;
Sheridan, Robert;
Xiao, Weimin;
Spellman, Paul T.;
Getz, Gad;
Wheeler, David A.;
Perou, Charles M.;
Gibbs, Richard A.;
Sander, Chris;
Hayes, D. Neil;
Gunaratne, Preethi H.

Publication type:

Article

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis.

Published in:

PLoS ONE, 2011, v. 6, n. 3, p. 1, doi. 10.1371/journal.pone.0017691

By:

Xin Victoria Wang;
Verhaak, Roel G. W.;
Purdom, Elizabeth;
Spellman, Paul T.;
Speed, Terence P.

Publication type:

Article

Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-34099-7

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.

Publication type:

Article

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05729-w

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.

Publication type:

Article

Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

Published in:

2017

By:

Korkola, James E.;
Collisson, Eric A.;
Heiser, Laura M.;
Oates, Chris;
Bayani, Nora;
Itani, Sleiman;
Esch, Amanda;
Thompson, Wallace;
Griffith, Obi L.;
Wang, Nicholas J.;
Kuo, Wen-Lin;
Cooper, Brian;
Billig, Jessica;
Ziyad, Safiyyah;
Hung, Jenny L.;
Jakkula, Lakshmi;
Feiler, Heidi;
Lu, Yiling;
Mills, Gordon B.;
Spellman, Paul T.

Publication type:

Correction Notice

Evidence for large domains of similarly expressed genes in the Drosophila genome.

Published in:

Journal of Biology, 2002, v. 1, n. 1, p. 1, doi. 10.1186/1475-4924-1-5

By:

Spellman, Paul T.;
Rubin, Gerald M.

Publication type:

Article

Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project.

Published in:

Journal of Clinical & Translational Science, 2024, v. 8, n. 1, p. 1, doi. 10.1017/cts.2024.9

By:

Zhenzhen Zhang;
Shafer, Autumn;
Johnson-Camacho, Katie;
Adey, Andrew;
Anur, Pavana;
Brown, Kim A.;
Conrad, Casey;
Crist, Rachel;
Farris, Paige E.;
Harrington, Christina A.;
Marriott, Lisa K.;
Mitchell, Asia;
O'Roak, Brian;
Serrato, Vanessa;
Richards, C. Sue;
Spellman, Paul T.;
Shannon, Jackilen

Publication type:

Article

Editorial: The future of publishing microarray data .

Published in:

2001

By:

Spellman, Paul T.

Publication type:

Editorial

Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-73350-3

By:

Wagner, Josiah T.;
Kim, Hyun Ji;
Johnson-Camacho, Katie C.;
Kelley, Taylor;
Newell, Laura F.;
Spellman, Paul T.;
Ngo, Thuy T. M.

Publication type:

Article

ARTIK-52 induces replication-dependent DNA damage and p53 activation exclusively in cells of prostate and breast cancer origin.

Published in:

Cell Cycle, 2016, v. 15, n. 3, p. 455, doi. 10.1080/15384101.2015.1127478

By:

Fleyshman, Daria;
Cheney, Peter;
Ströse, Anda;
Mudambi, Shaila;
Safina, Alfiya;
Commane, Mairead;
Purmal, Andrei;
Morgan, Kelsey;
Wang, Nicholas J.;
Gray, Joe;
Spellman, Paul T.;
Issaeva, Natalia;
Gurova, Katerina

Publication type:

Article

The Toll and Imd pathways are the major regulators of the immune response in Drosophila.

Published in:

EMBO Journal, 2002, v. 21, n. 11, p. 2568, doi. 10.1093/emboj/21.11.2568

By:

De Gregorio, Ennio;
Spellman, Paul T.;
Tzou, Phoebe;
Rubin, Gerald M.;
Lemaitre, Bruno

Publication type:

Article

The Toll and Imd pathways are the major regulators of the immune response in Drosophila.

Published in:

EMBO Journal, 2002, v. 21, n. 11, p. 2568, doi. 10.1093/emboj/21.11.2568

By:

De Gregorio, Ennio;
Spellman, Paul T.;
Tzou, Phoebe;
Rubin, Gerald M.;
Lemaitre, Bruno

Publication type:

Article

Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth.

Published in:

Nature, 2000, v. 406, n. 6791, p. 90, doi. 10.1038/35017581

By:

Gefeng Zhu;
Spellman, Paul T.;
Volpe, Tom;
Brown, Patrick O.;
Botstein, David;
Davis, Trisha N.;
Futcher, Bruce

Publication type:

Article

Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies.

Published in:

NPJ Precision Oncology, 2022, v. 6, n. 1, p. 1, doi. 10.1038/s41698-022-00270-y

By:

Roskams-Hieter, Breeshey;
Kim, Hyun Ji;
Anur, Pavana;
Wagner, Josiah T.;
Callahan, Rowan;
Spiliotopoulos, Elias;
Kirschbaum, Charles Ward;
Civitci, Fehmi;
Spellman, Paul T.;
Thompson, Reid F.;
Farsad, Khashayar;
Naugler, Willscott E.;
Ngo, Thuy T. M.

Publication type:

Article

Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours.

Published in:

Nature Communications, 2016, v. 7, n. 5, p. 11588, doi. 10.1038/ncomms11588

By:

Fei, Suzanne S.;
Mitchell, Asia D.;
Heskett, Michael B.;
Vocke, Cathy D.;
Ricketts, Christopher J.;
Peto, Myron;
Wang, Nicholas J.;
Sönmez, Kemal;
Linehan, W. Marston;
Spellman, Paul T.

Publication type:

Article

Integrated analysis of germline and somatic variants in ovarian cancer.

Published in:

Nature Communications, 2014, v. 5, n. 1, p. 3156, doi. 10.1038/ncomms4156

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.

Publication type:

Article

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09424-z

By:

Gurun, Burcu;
Horton, Wesley;
Murugan, Dhaarini;
Zhu, Biqing;
Leyshock, Patrick;
Kumar, Sushil;
Byrne, Katelyn T.;
Vonderheide, Robert H.;
Margolin, Adam A.;
Mori, Motomi;
Spellman, Paul T.;
Coussens, Lisa M.;
Speed, Terence P.

Publication type:

Article

Differential Allelic Expression among Long Non-Coding RNAs.

Published in:

Non-Coding RNA, 2021, v. 7, n. 4, p. 66, doi. 10.3390/ncrna7040066

By:

Heskett, Michael B.;
Spellman, Paul T.;
Thayer, Mathew J.

Publication type:

Article

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.

Published in:

Diagnostics (2075-4418), 2021, v. 11, n. 1, p. 73, doi. 10.3390/diagnostics11010073

By:

Boniface, Christopher;
Deig, Christopher;
Halsey, Carol;
Kelley, Taylor;
Heskett, Michael B.;
Thomas Jr., Charles R.;
Spellman, Paul T.;
Nabavizadeh, Nima

Publication type:

Article

The Stanford Microarray Database.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 152, doi. 10.1093/nar/29.1.152

By:

Sherlock, Gavin;
Hernandez-Boussard, Tina;
Kasarskis, Andrew;
Binkley, Gail;
Matese, John C.;
Dwight, Selina S.;
Kaloper, Miroslava;
Weng, Shuai;
Jin, Heng;
Ball, Catherine A.;
Eisen, Michael B.;
Spellman, Paul T.;
Brown, Patrick O.;
Botstein, David;
Cherry, J. Michael

Publication type:

Article

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.

Published in:

BMC Bioinformatics, 2012, v. 13, n. 1, p. 94, doi. 10.1186/1471-2105-13-94

By:

Hill, Steven M.;
Neve, Richard M.;
Bayani, Nora;
Kuo, Wen-Lin;
Ziyad, Safiyyah;
Spellman, Paul T.;
Gray, Joe W.;
Mukherjee, Sach

Publication type:

Article

GenomeGraphs: integrated genomic data visualization with R.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-2

By:

Durinck, Steffen;
Bullard, James;
Spellman, Paul T;
Dudoit, Sandrine

Publication type:

Article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Published in:

BMC Bioinformatics, 2006, v. 7, p. 489, doi. 10.1186/1471-2105-7-489

By:

Rayner, Tim F;
Rocca-Serra, Philippe;
Spellman, Paul T;
Causton, Helen C;
Farne, Anna;
Holloway, Ele;
Irizarry, Rafael A;
Junmin Liu;
Maier, Donald S;
Miller, Michael;
Petersen, Kjell;
Quackenbush, John;
Sherlock, Gavin;
Stoeckert Jr, Christian J;
White, Joseph;
Whetzel, Patricia L;
Wymore, Farrell;
Parkinson, Helen;
Sarkans, Ugis;
Ball, Catherine A

Publication type:

Article

Defining clonal hematopoiesis of indeterminate potential: evolutionary dynamics and detection under aging and inflammation.

Published in:

Cold Spring Harbor Molecular Case Studies, 2023, v. 9, n. 2, p. 1, doi. 10.1101/mcs.a006251

By:

Goldman, Elisabeth A.;
Spellman, Paul T.;
Agarwal, Anupriya

Publication type:

Article

ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.95898

By:

Thayer, Mathew;
Heskett, Michael B.;
Smith, Leslie G.;
Spellman, Paul T.;
Yates, Phillip A.

Publication type:

Article

A robust prognostic signature for hormone-positive node-negative breast cancer.

Published in:

Genome Medicine, 2013, v. 5, n. 10, p. 19, doi. 10.1186/gm496

By:

Griffith, Obi L.;
Pepin, François;
Enache, Oana M.;
Heiser, Laura M.;
Collisson, Eric A.;
Spellman, Paul T.;
Gray, Joe W.

Publication type:

Article

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data.

Published in:

Nature Biotechnology, 2022, v. 40, n. 4, p. 527, doi. 10.1038/s41587-021-01091-3

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

Publication type:

Article

The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression

Published in:

Molecular Oncology, 2007, v. 1, n. 1, p. 84, doi. 10.1016/j.molonc.2007.02.004

By:

Kenny, Paraic A.;
Lee, Genee Y.;
Myers, Connie A.;
Neve, Richard M.;
Semeiks, Jeremy R.;
Spellman, Paul T.;
Lorenz, Katrin;
Lee, Eva H.;
Barcellos-Hoff, Mary Helen;
Petersen, Ole W.;
Gray, Joe W.;
Bissell, Mina J.

Publication type:

Article