Searching journal content for articles similar to Levy et al. 22 (11): 2101.

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  1. Perspective: The path to routine use of genomic biomarkers in the cancer clinic
    • Paul C. Boutros
    Genome Res. October 2015 25: 1508-1513; doi:10.1101/gr.191114.115
    ...will improve biomarker accuracy. For example, in the same status of KRAS, it was shown that different prognostic mRNA signatures were optimal in KRAS mutant and KRAS wild-type lung cancers, highlighting the synergy of combining somatic SNV and tumor mRNA abundance information into a composite biomarker...
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  2. Research: The transcriptional landscape and mutational profile of lung adenocarcinoma
    • Jeong-Sun Seo,
    • Young Seok Ju,
    • Won-Chul Lee,
    • Jong-Yeon Shin,
    • June Koo Lee,
    • Thomas Bleazard,
    • Junho Lee,
    • Yoo Jin Jung,
    • Jung-Oh Kim,
    • Jung-Young Shin,
    • Saet-Byeol Yu,
    • Jihye Kim,
    • Eung-Ryoung Lee,
    • Chang-Hyun Kang,
    • In-Kyu Park,
    • Hwanseok Rhee,
    • Se-Hoon Lee,
    • Jong-Il Kim,
    • Jin-Hyoung Kang,
    • and Young Tae Kim
    Genome Res. November 2012 22: 2109-2119; Published in Advance September 13, 2012, doi:10.1101/gr.145144.112
    ...expressions of lung cancer Genome Research 2115 www..org cancer genes, such as somatic mutations, gene fusions, alternative splicing events, and cancer outliers, is most likely due to the strong power and comprehensive nature of whole-transcriptome sequencing. Our approach suggests a paradigm for large...
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  3. PERSPECTIVE: Genomic medicine in Mexico: Initial steps and the road ahead
    • Gerardo Jimenez-Sanchez,
    • Irma Silva-Zolezzi,
    • Alfredo Hidalgo,
    • and Santiago March
    Genome Res. August 2008 18: 1191-1198; doi:10.1101/gr.065359.107
    ..., as well as expression analysis in lung, thyroid, and prostate cancer, and leukemias and sarcomas in both humans and in mouse models. In the area of medical proteomics, INMEGEN is developing biomarker discovery projects in melanoma, lung, and breast cancer by analyzing proteomic profiles in blood, saliva...
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  4. PERSPECTIVE: Embracing the complexity of genomic data for personalized medicine
    • Mike West,
    • Geoffrey S. Ginsburg,
    • Andrew T. Huang,
    • and Joseph R. Nevins
    Genome Res. May 2006 16: 559-566; doi:10.1101/gr.3851306
    ...that other forms of data have the potential to contribute valuable information. As an example, proteomic profiling of tumors has identified patterns of protein peaks from mass spectrometry analyses that have the capacity to accurately predict clinical outcome in lung cancer ( Yanagisawa et al. 2003...
  5. LETTER: The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
    • Ken Inoue,
    • Ken Dewar,
    • Nicholas Katsanis,
    • Lawrence T. Reiter,
    • Eric S. Lander,
    • Keri L. Devon,
    • Dudley W. Wyman,
    • James R. Lupski,
    • and Bruce Birren
    Genome Res. June 1, 2001 11: 1018-1033; doi:10.1101/gr.180401
    ...are indicated at top of each lane ( He ) Heart; ( Br ) brain; ( Pl ) placenta; ( Lu ) lung; ( Li ) liver; ( Mu ) skeletal muscle; ( Ki ) kidney; ( Pa ) pancreas. Marker sizes are 9.5, 7.5, 4.4, 2.4, and 1.35 kb. ( B ) Multiple-tissue RT–PCR analyses. NP008/CGI-148 is expressed in a wide variety of tissues. A 2...
  6. Method: A best-match approach for gene set analyses in embedding spaces
    • Lechuan Li,
    • Ruth Dannenfelser,
    • Charlie Cruz,
    • and Vicky Yao
    Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
    ...disease (PDCO), kidney renal clear cell carcinoma (KIRC), pancreatic adenocarcinoma (PAAD), Alzheimer's disease (ALZ), and acute myeloid leukemia (LAML), with their corresponding tissue-specific networks (lung, kidney, pancreas, brain, and blood, respectively). We find that using the tissue...
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  7. Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
    • Siwei Chen,
    • Yuan Liu,
    • Yingying Zhang,
    • Shayne D. Wierbowski,
    • Steven M. Lipkin,
    • Xiaomu Wei,
    • and Haiyuan Yu
    Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
    ...hepatocellular carcinoma, (LUSC) lung squamous cell carcinoma, (READ) rectum adenocarcinoma, (STAD) stomach adenocarcinoma. Number of hotspots included in each Kaplan–Meier analysis (Nprioritized and Nother, respectively): BRCA = 18, 66; ESCA = 13, 33; HNSC = 10, 52; LIHC = 8, 11; LUSC = 17, 51; READ = 20, 43...
  8. Research: Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells
    • Yi Cai,
    • Hsing-Chen Tsai,
    • Ray-Whay Chiu Yen,
    • Yang W. Zhang,
    • Xiangqian Kong,
    • Wei Wang,
    • Limin Xia,
    • and Stephen B. Baylin
    Genome Res. April 2017 27: 533-544; Published in Advance February 23, 2017, doi:10.1101/gr.208108.116
    ...–12 d, (Fig. 1C, numbers 49 and 51) in HCT116 and other CRC, breast, and lung cancer cells (Fig. 1D; Supplemental Fig. S1B), plus using the same approach to further reduce levels of the truncated DNMT1 protein in HCT116 1KO cells, resulted in a progressive, incremental decline in overall DNA methylation...
  9. Research: Plasma cell-free RNA characteristics in COVID-19 patients
    • Yanqun Wang,
    • Jie Li,
    • Lu Zhang,
    • Hai-Xi Sun,
    • Zhaoyong Zhang,
    • Jinjin Xu,
    • Yonghao Xu,
    • Yu Lin,
    • Airu Zhu,
    • Yuxue Luo,
    • Haibo Zhou,
    • Yan Wu,
    • Shanwen Lin,
    • Yuzhe Sun,
    • Fei Xiao,
    • Ruiying Chen,
    • Liyan Wen,
    • Wei Chen,
    • Fang Li,
    • Rijing Ou,
    • Yanjun Zhang,
    • Tingyou Kuo,
    • Yuming Li,
    • Lingguo Li,
    • Jing Sun,
    • Kun Sun,
    • Zhen Zhuang,
    • Haorong Lu,
    • Zhao Chen,
    • Guoqiang Mai,
    • Jianfen Zhuo,
    • Puyi Qian,
    • Jiayu Chen,
    • Huanming Yang,
    • Jian Wang,
    • Xun Xu,
    • Nanshan Zhong,
    • Jingxian Zhao,
    • Junhua Li,
    • Jincun Zhao,
    • and Xin Jin
    Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
    ...). Consistent with the study, we also identified Toxoplasma gondii (Fig. 4A,E). These codetected microorganisms, especially pathogenic bacteria under SARS-CoV-2 infection, can aggravate the lung injury in COVID-19 patients, and microbial profiles of COVID-19 patients revealed by plasma cfRNAs open a novel angle...
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  10. Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
    • Raunak Shrestha,
    • Ermin Hodzic,
    • Thomas Sauerwald,
    • Phuong Dao,
    • Kendric Wang,
    • Jake Yeung,
    • Shawn Anderson,
    • Fabio Vandin,
    • Gholamreza Haffari,
    • Colin C. Collins,
    • and S. Cenk Sahinalp
    Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
    ...alterations that can lead to changes in gene regulation, protein structure, and function (Stratton et al. 2009). Genomic and transcriptomic data provide unique and complementary information about a particular tumor, but the translation of “big” molecular data into insightful and impactful patient outcomes...
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