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For: Berglund AE, Welsh EA, Eschrich SA. Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. Int J Genomics 2017;2017:2354564. [PMID: 28265563 DOI: 10.1155/2017/2354564] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/15/2016] [Accepted: 01/04/2017] [Indexed: 11/30/2022]  Open
Number Cited by Other Article(s)
1
Berglund AE, Puskas J, Yoder SJ, Smith AT, Marchion DC, Qin D, Mulé JJ, Torres-Roca JF, Eschrich SA. Evaluating the Radiation Sensitivity Index and 12-Chemokine Gene Expression Signature for Clinical Use in a CLIA Laboratory. CANCER RESEARCH COMMUNICATIONS 2025;5:389-397. [PMID: 39932296 PMCID: PMC11873780 DOI: 10.1158/2767-9764.crc-24-0534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/22/2025] [Accepted: 02/06/2025] [Indexed: 02/19/2025]
2
Ye C, Sun Q, Yan J, Xue D, Xu J, Ma H, Li F. Development of fatty acid metabolism score based on gene signature for predicting prognosis and immunotherapy response in colon cancer. Clin Transl Oncol 2024;26:630-643. [PMID: 37480430 DOI: 10.1007/s12094-023-03282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023]
3
Watts J, Allen E, Mitoubsi A, Khojandi A, Eales J, Papamarkou T. Towards Faster Gene Expression Prediction via Dimensionality Reduction and Feature Selection. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023;2023:1-4. [PMID: 38083578 DOI: 10.1109/embc40787.2023.10340962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
4
Li P, Chen C, Li J, Yang L, Wang Y, Dong Z, Mi J, Zhang Y, Wang J, Wang H, Rodriguez R, Tian J, Wang Z. Homologous Recombination Related Signatures Predict Prognosis and Immunotherapy Response in Metastatic Urothelial Carcinoma. Front Genet 2022;13:875128. [PMID: 35559013 PMCID: PMC9086193 DOI: 10.3389/fgene.2022.875128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022]  Open
5
Fernandez MR, Schaub FX, Yang C, Li W, Yun S, Schaub SK, Dorsey FC, Liu M, Steeves MA, Ballabio A, Tzankov A, Chen Z, Koomen JM, Berglund AE, Cleveland JL. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. Cancer Res 2022;82:1234-1250. [PMID: 35149590 DOI: 10.1158/0008-5472.can-21-1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/07/2021] [Accepted: 02/08/2022] [Indexed: 11/16/2022]
6
Kreis J, Nedić B, Mazur J, Urban M, Schelhorn SE, Grombacher T, Geist F, Brors B, Zühlsdorf M, Staub E. RosettaSX: Reliable gene expression signature scoring of cancer models and patients. Neoplasia 2021;23:1069-1077. [PMID: 34583245 PMCID: PMC8479477 DOI: 10.1016/j.neo.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
7
Chao KH, Hsiao YW, Lee YF, Lee CY, Lai LC, Tsai MH, Lu TP, Chuang EY. RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2023-2031. [PMID: 31796413 DOI: 10.1109/tcbb.2019.2956708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
8
Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. Exp Mol Med 2021;53:761-771. [PMID: 33963293 PMCID: PMC8178403 DOI: 10.1038/s12276-021-00612-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 12/14/2022]  Open
9
Yun S, Vincelette ND, Yu X, Watson GW, Fernandez MR, Yang C, Hitosugi T, Cheng CH, Freischel AR, Zhang L, Li W, Hou H, Schaub FX, Vedder AR, Cen L, McGraw KL, Moon J, Murphy DJ, Ballabio A, Kaufmann SH, Berglund AE, Cleveland JL. TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia. Blood Cancer Discov 2021;2:162-185. [PMID: 33860275 PMCID: PMC8043621 DOI: 10.1158/2643-3230.bcd-20-0029] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022]  Open
10
Doultsinos D, Mills IG. Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges. Cancers (Basel) 2021;13:495. [PMID: 33525365 PMCID: PMC7865812 DOI: 10.3390/cancers13030495] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022]  Open
11
Ohandjo AQ, Liu Z, Dammer EB, Dill CD, Griffen TL, Carey KM, Hinton DE, Meller R, Lillard JW. Transcriptome Network Analysis Identifies CXCL13-CXCR5 Signaling Modules in the Prostate Tumor Immune Microenvironment. Sci Rep 2019;9:14963. [PMID: 31628349 PMCID: PMC6802083 DOI: 10.1038/s41598-019-46491-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022]  Open
12
Wu Q, Berglund AE, Wang D, MacAulay RJ, Mulé JJ, Etame AB. Paradoxical epigenetic regulation of XAF1 mediates plasticity towards adaptive resistance evolution in MGMT-methylated glioblastoma. Sci Rep 2019;9:14072. [PMID: 31575897 PMCID: PMC6773736 DOI: 10.1038/s41598-019-50489-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022]  Open
13
Dhawan A, Barberis A, Cheng WC, Domingo E, West C, Maughan T, Scott JG, Harris AL, Buffa FM. Guidelines for using sigQC for systematic evaluation of gene signatures. Nat Protoc 2019;14:1377-1400. [PMID: 30971781 DOI: 10.1038/s41596-019-0136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/11/2019] [Indexed: 11/09/2022]
14
The JAK-STAT1 transcriptional signature in peripheral immune cells reveals alterations related to illness duration and acuity in psychosis. Brain Behav Immun 2019;77:37-45. [PMID: 30503835 PMCID: PMC8521437 DOI: 10.1016/j.bbi.2018.11.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/18/2018] [Accepted: 11/28/2018] [Indexed: 11/22/2022]  Open
15
Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T. Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget 2019;10:810-824. [PMID: 30783512 PMCID: PMC6368226 DOI: 10.18632/oncotarget.26574] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/29/2018] [Indexed: 12/20/2022]  Open
16
Berglund AE, Rounbehler RJ, Gerke T, Awasthi S, Cheng CH, Takhar M, Davicioni E, Alshalalfa M, Erho N, Klein EA, Freedland SJ, Ross AE, Schaeffer EM, Trock BJ, Den RB, Cleveland JL, Park JY, Dhillon J, Yamoah K. Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer. Prostate Cancer Prostatic Dis 2018;22:292-302. [PMID: 30367117 PMCID: PMC6760558 DOI: 10.1038/s41391-018-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/27/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
17
Shao Z, Wang H, Zhou X, Guo B, Gao X, Xiao Z, Liu M, Sha J, Jiang C, Luo Y, Liu Z, Li S. Spontaneous generation of a novel foetal human retinal pigment epithelium (RPE) cell line available for investigation on phagocytosis and morphogenesis. Cell Prolif 2017;50. [PMID: 28924976 PMCID: PMC6529143 DOI: 10.1111/cpr.12386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022]  Open
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