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Showing 1 to 11 of 11 entries
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Simplified and Unified Access to Cancer Proteogenomic Data.

Journal of proteome research

Lindgren CM, Adams DW, Kimball B, Boekweg H, Tayler S, Pugh SL, Payne SH.
PMID: 33560848
J Proteome Res. 2021 Apr 02;20(4):1902-1910. doi: 10.1021/acs.jproteome.0c00919. Epub 2021 Feb 09.

Comprehensive cancer data sets recently generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) offer great potential for advancing our understanding of how to combat cancer. These data sets include DNA, RNA, protein, and clinical characterization for tumor and...

The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment.

Cell

Rodriguez H, Zenklusen JC, Staudt LM, Doroshow JH, Lowy DR.
PMID: 33798439
Cell. 2021 Apr 01;184(7):1661-1670. doi: 10.1016/j.cell.2021.02.055.

When it comes to precision oncology, proteogenomics may provide better prospects to the clinical characterization of tumors, help make a more accurate diagnosis of cancer, and improve treatment for patients with cancer. This perspective describes the significant contributions of...

Proteogenomics reveals molecular subtypes.

Nature reviews. Clinical oncology

Sidaway P.
PMID: 32719419
Nat Rev Clin Oncol. 2020 Sep;17(9):519. doi: 10.1038/s41571-020-0419-6.

No abstract available.

ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies.

Proteomics

Calinawan AP, Song X, Ji J, Dhanasekaran SM, Petralia F, Wang P, Reva B.
PMID: 32510176
Proteomics. 2020 Nov;20(21):e1900359. doi: 10.1002/pmic.201900359. Epub 2020 Aug 06.

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive multi-omics data resources of deep proteogenomic profiles for multiple cancer types. To enable the broader community of biological and medical researchers to intuitively query, explore, and download data...

Methods, Tools and Current Perspectives in Proteogenomics.

Molecular & cellular proteomics : MCP

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR.
PMID: 28456751
Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29.

With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics,

Proteogenomics: V international Caparica conference on analytical proteomics. V ICAP-2017.

Journal of proteomics

Capelo JL, Lodeiro C, Santos HM, Igrejas G.
PMID: 30296603
J Proteomics. 2019 Jan 16;191:iii-iv. doi: 10.1016/j.jprot.2018.10.001. Epub 2018 Oct 05.

No abstract available.

A User-Friendly Visualization Tool for Multi-Omics Data.

Proteomics

Huh S, Kim MS.
PMID: 32744797
Proteomics. 2020 Nov;20(21):e2000136. doi: 10.1002/pmic.202000136. Epub 2020 Sep 03.

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated large multi-omic datasets for various cancers. Each dataset consists of common and differential data types, including genomics, epigenomics, transcriptomics, proteomics, and post-translational modifications data. They together make up a...

Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer

Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP.
PMID: 30017829
J Thorac Oncol. 2018 Oct;13(10):1519-1529. doi: 10.1016/j.jtho.2018.06.025. Epub 2018 Jul 11.

INTRODUCTION: Despite apparently complete surgical resection, approximately half of resected early-stage lung cancer patients relapse and die of their disease. Adjuvant chemotherapy reduces this risk by only 5% to 8%. Thus, there is a need for better identifying who...

Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.

Journal of proteome research

Chen W, Liu X.
PMID: 33183009
J Proteome Res. 2021 Jan 01;20(1):261-269. doi: 10.1021/acs.jproteome.0c00369. Epub 2020 Nov 12.

In proteogenomic studies, genomic and transcriptomic variants are incorporated into customized protein databases for the identification of proteoforms, especially proteoforms with sample-specific variants. Most proteogenomic research has been focused on combining genomic or transcriptomic data with bottom-up mass spectrometry...

Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.

Journal of proteome research

Chen W, Liu X.
PMID: 33183009
J Proteome Res. 2021 Jan 01;20(1):261-269. doi: 10.1021/acs.jproteome.0c00369. Epub 2020 Nov 12.

In proteogenomic studies, genomic and transcriptomic variants are incorporated into customized protein databases for the identification of proteoforms, especially proteoforms with sample-specific variants. Most proteogenomic research has been focused on combining genomic or transcriptomic data with bottom-up mass spectrometry...

Across the Globe: Proteogenomic Landscapes of Lung Cancer.

Cell

Yanovich-Arad G, Geiger T.
PMID: 32649881
Cell. 2020 Jul 09;182(1):9-11. doi: 10.1016/j.cell.2020.06.016.

In this issue of Cell, articles by Gillette et al., Chen et al., and Xu, et al. collectively provide a deep and comprehensive proteogenomic analysis of lung adenocarcinoma, addressing differences in patient ethnicity and smoking background. They highlight the...

Showing 1 to 11 of 11 entries