TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
Colaprico, Antonio, Silva, Tiago C, Olsen, Catharina, Garofano, Luciano, Cava, Claudia, Garolini, Davide, Sabedot, Thais S, Malta, Tathiane M, Pagnotta, Stefano M, Castiglioni, Isabella, Ceccarelli, Michele, Bontempi, Gianluca, Noushmehr, Houtan
Published in Nucleic acids research (05.05.2016)
Published in Nucleic acids research (05.05.2016)
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Journal Article
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena
Published in PLoS computational biology (01.03.2019)
Published in PLoS computational biology (01.03.2019)
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Journal Article
Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes
Lehmann, Brian D., Colaprico, Antonio, Silva, Tiago C., Chen, Jianjiao, An, Hanbing, Ban, Yuguang, Huang, Hanchen, Wang, Lily, James, Jamaal L., Balko, Justin M., Gonzalez-Ericsson, Paula I., Sanders, Melinda E., Zhang, Bing, Pietenpol, Jennifer A., Chen, X. Steven
Published in Nature communications (01.11.2021)
Published in Nature communications (01.11.2021)
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Journal Article
Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications
Malta, Tathiane M, de Souza, Camila F, Sabedot, Thais S, Silva, Tiago C, Mosella, Maritza S, Kalkanis, Steven N, Snyder, James, Castro, Ana Valeria B, Noushmehr, Houtan
Published in Neuro-oncology (Charlottesville, Va.) (09.04.2018)
Published in Neuro-oncology (Charlottesville, Va.) (09.04.2018)
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Journal Article
Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer’s disease
C. Silva, Tiago, Young, Juan I., Zhang, Lanyu, Gomez, Lissette, Schmidt, Michael A., Varma, Achintya, Chen, X. Steven, Martin, Eden R., Wang, Lily
Published in Nature communications (18.08.2022)
Published in Nature communications (18.08.2022)
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ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
Silva, Tiago C, Coetzee, Simon G, Gull, Nicole, Yao, Lijing, Hazelett, Dennis J, Noushmehr, Houtan, Lin, De-Chen, Berman, Benjamin P
Published in Bioinformatics (Oxford, England) (01.06.2019)
Published in Bioinformatics (Oxford, England) (01.06.2019)
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Journal Article
Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease
Zhang, Lanyu, Silva, Tiago C., Young, Juan I., Gomez, Lissette, Schmidt, Michael A., Hamilton-Nelson, Kara L., Kunkle, Brian W., Chen, Xi, Martin, Eden R., Wang, Lily
Published in Nature communications (30.11.2020)
Published in Nature communications (30.11.2020)
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Interpreting pathways to discover cancer driver genes with Moonlight
Colaprico, Antonio, Olsen, Catharina, Bailey, Matthew H., Odom, Gabriel J., Terkelsen, Thilde, Silva, Tiago C., Olsen, André V., Cantini, Laura, Zinovyev, Andrei, Barillot, Emmanuel, Noushmehr, Houtan, Bertoli, Gloria, Castiglioni, Isabella, Cava, Claudia, Bontempi, Gianluca, Chen, Xi Steven, Papaleo, Elena
Published in Nature communications (03.01.2020)
Published in Nature communications (03.01.2020)
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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]
Silva, Tiago C, Colaprico, Antonio, Olsen, Catharina, D'Angelo, Fulvio, Bontempi, Gianluca, Ceccarelli, Michele, Noushmehr, Houtan
Published in F1000 research (2016)
Published in F1000 research (2016)
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Journal Article
Distinct sex-specific DNA methylation differences in Alzheimer's disease
C Silva, Tiago, Zhang, Wei, Young, Juan I, Gomez, Lissette, Schmidt, Michael A, Varma, Achintya, Chen, X Steven, Martin, Eden R, Wang, Lily
Published in Alzheimer's research & therapy (15.09.2022)
Published in Alzheimer's research & therapy (15.09.2022)
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Journal Article
Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma
Huang, Yongsheng, Yang, Qian, Zheng, Yueyuan, Lin, Lehang, Xu, Xin, Xu, Xiu-E, Silva, Tiago C, Hazawa, Masaharu, Peng, Li, Cao, Haotian, Ding, Yanbing, Lu, Daning, Berman, Benjamin P, Xu, Li-Yan, Li, En-Min, Yin, Dong
Published in Nucleic acids research (20.09.2021)
Published in Nucleic acids research (20.09.2021)
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Journal Article
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes
Zheng, Yueyuan, Huang, Guowei, Silva, Tiago C., Yang, Qian, Jiang, Yan-Yi, Koeffler, H. Phillip, Lin, De-Chen, Berman, Benjamin P.
Published in Nature communications (30.04.2021)
Published in Nature communications (30.04.2021)
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Journal Article
Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas
Pan, Jian, Silva, Tiago C, Gull, Nicole, Yang, Qian, Plummer, Jasmine T, Chen, Stephanie, Daigo, Kenji, Hamakubo, Takao, Gery, Sigal, Ding, Ling-Wen, Jiang, Yan-Yi, Hu, Shaoyan, Xu, Li-Yan, Li, En-Min, Ding, Yanbing, Klempner, Samuel J, Gayther, Simon A, Berman, Benjamin P, Koeffler, H Phillip, Lin, De-Chen
Published in Cancer research (Chicago, Ill.) (01.07.2020)
Published in Cancer research (Chicago, Ill.) (01.07.2020)
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Journal Article
GENAVi: a shiny web application for gene expression normalization, analysis and visualization
Reyes, Alberto Luiz P, Silva, Tiago C, Coetzee, Simon G, Plummer, Jasmine T, Davis, Brian D, Chen, Stephanie, Hazelett, Dennis J, Lawrenson, Kate, Berman, Benjamin P, Gayther, Simon A, Jones, Michelle R
Published in BMC genomics (16.10.2019)
Published in BMC genomics (16.10.2019)
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RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling
Loh, Xin-Yi, Sun, Qiao-Yang, Ding, Ling-Wen, Mayakonda, Anand, Venkatachalam, Nachiyappan, Yeo, Mei-Shi, Silva, Tiago C, Xiao, Jin-Fen, Doan, Ngan B, Said, Jonathan W, Ran, Xue-Bin, Zhou, Si-Qin, Dakle, Pushkar, Shyamsunder, Pavithra, Koh, Angele Pei-Fern, Huang, Ruby Yun-Ju, Berman, Benjamin P, Tan, Soo-Yong, Yang, Henry, Lin, De-Chen, Koeffler, H Phillip
Published in Cancer research (Chicago, Ill.) (15.01.2020)
Published in Cancer research (Chicago, Ill.) (15.01.2020)
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Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes
Zheng, Yueyuan, Huang, Guowei, Silva, Tiago C., Yang, Qian, Jiang, Yan-Yi, Koeffler, H. Phillip, Lin, De-Chen, Berman, Benjamin P.
Published in Nature communications (28.06.2021)
Published in Nature communications (28.06.2021)
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Journal Article
Sex-specific DNA methylation differences in Alzheimer's disease pathology
Zhang, Lanyu, Young, Juan I, Gomez, Lissette, Silva, Tiago C, Schmidt, Michael A, Cai, Jesse, Chen, Xi, Martin, Eden R, Wang, Lily
Published in Acta neuropathologica communications (26.04.2021)
Published in Acta neuropathologica communications (26.04.2021)
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Journal Article
LR Hunting: A Random Forest Based Cell–Cell Interaction Discovery Method for Single-Cell Gene Expression Data
Lu, Min, Sha, Yifan, Silva, Tiago C., Colaprico, Antonio, Sun, Xiaodian, Ban, Yuguang, Wang, Lily, Lehmann, Brian D., Chen, X. Steven
Published in Frontiers in genetics (20.08.2021)
Published in Frontiers in genetics (20.08.2021)
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Journal Article
Effect of a high crude protein content diet during energy restriction and re-alimentation on animal performance, skeletal growth and metabolism of bone tissue in two genotypes of cattle
Silva, Tiago A C C, Quigley, Simon P, Kidd, Lisa J, Anderson, Stephen T, McLennan, Stuart R, Poppi, Dennis P
Published in PloS one (25.02.2021)
Published in PloS one (25.02.2021)
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