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gene_networks_inference [2018/12/14 17:34]
admin [Related work]
gene_networks_inference [2019/01/15 16:54] (current)
admin [Related work]
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   - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://​www.cell.com/​cell/​abstract/​S0092-8674(17)30639-6?​innerTabgraphical_S0092867417306396|Cell]],​ 2017 [{{:​ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}} ​ ]. \\  TCGA's HCC data and subtyping using DNA copy number, DNA methylation,​ mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples.   - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://​www.cell.com/​cell/​abstract/​S0092-8674(17)30639-6?​innerTabgraphical_S0092867417306396|Cell]],​ 2017 [{{:​ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}} ​ ]. \\  TCGA's HCC data and subtyping using DNA copy number, DNA methylation,​ mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples.
   - Guillamot, Maria, Luisa Cimmino, and Iannis Aifantis. "The impact of DNA methylation in hematopoietic malignancies."​ [[http://​www.cell.com/​trends/​cancer/​pdf/​S2405-8033(15)00089-8.pdf|Trends in cancer]] 2.2 (2016): 70-83. \\  Reviews and references DNA methylation studies and datasets on AML. E.g., [[http://​www.sciencedirect.com/​science/​article/​pii/​S1535610809004206|Figueroa]] et al. used DNA methylation for classification of 344 AML cases. [[http://​journals.plos.org/​plosgenetics/​article?​id=10.1371/​journal.pgen.1002781|Akalin]] et al. related DNA methylation patterns with mutations in 5 AML cases. "The methylation status of specific genes can predict the future survival of AML patients, suggesting that DNA methylation is a biomarker for clinical outcome"​ see e.g., Figueroa et al, [[http://​www.bloodjournal.org/​content/​bloodjournal/​113/​6/​1315.full.pdf?​sso-checked=true|Jiang]] 2009 (studied MDS to AML progression in 184 cases), and [[http://​www.bloodjournal.org/​content/​115/​3/​636.long?​sso-checked=true|Bullinger]] 2010 (analyzed 92 genomic regions in 182 patients).   - Guillamot, Maria, Luisa Cimmino, and Iannis Aifantis. "The impact of DNA methylation in hematopoietic malignancies."​ [[http://​www.cell.com/​trends/​cancer/​pdf/​S2405-8033(15)00089-8.pdf|Trends in cancer]] 2.2 (2016): 70-83. \\  Reviews and references DNA methylation studies and datasets on AML. E.g., [[http://​www.sciencedirect.com/​science/​article/​pii/​S1535610809004206|Figueroa]] et al. used DNA methylation for classification of 344 AML cases. [[http://​journals.plos.org/​plosgenetics/​article?​id=10.1371/​journal.pgen.1002781|Akalin]] et al. related DNA methylation patterns with mutations in 5 AML cases. "The methylation status of specific genes can predict the future survival of AML patients, suggesting that DNA methylation is a biomarker for clinical outcome"​ see e.g., Figueroa et al, [[http://​www.bloodjournal.org/​content/​bloodjournal/​113/​6/​1315.full.pdf?​sso-checked=true|Jiang]] 2009 (studied MDS to AML progression in 184 cases), and [[http://​www.bloodjournal.org/​content/​115/​3/​636.long?​sso-checked=true|Bullinger]] 2010 (analyzed 92 genomic regions in 182 patients).
 +  - John [[https://​www.youtube.com/​watch?​v=Vyhq7GZFnes|Quackenbush'​s]] talk entitled: "Using Networks to Understand the Genotype-Phenotype Connection"​ \\
  
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