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Tiago Chedraoui Silva
Tiago Chedraoui Silva
Endpoint Health
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TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
A Colaprico, TC Silva, C Olsen, L Garofano, C Cava, D Garolini, ...
Nucleic acids research 44 (8), e71-e71, 2016
26912016
Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma
M Ceccarelli, FP Barthel, TM Malta, TS Sabedot, SR Salama, BA Murray, ...
Cell 164 (3), 550-563, 2016
19632016
The chromatin accessibility landscape of primary human cancers
MR Corces, JM Granja, S Shams, BH Louie, JA Seoane, W Zhou, ...
Science 362 (6413), eaav1898, 2018
9272018
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
M Mounir, M Lucchetta, TC Silva, C Olsen, G Bontempi, X Chen, ...
PLoS computational biology 15 (3), e1006701, 2019
3472019
Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications
TM Malta, CF de Souza, TS Sabedot, TC Silva, MS Mosella, SN Kalkanis, ...
Neuro-oncology 20 (5), 608-620, 2018
2472018
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
TC Silva, A Colaprico, C Olsen, F D'Angelo, G Bontempi, M Ceccarelli, ...
F1000Research 5, 2016
2242016
Before and after: comparison of legacy and harmonized TCGA genomic data commons¡¯ data
GF Gao, JS Parker, SM Reynolds, TC Silva, LB Wang, W Zhou, R Akbani, ...
Cell systems 9 (1), 24-34. e10, 2019
1332019
Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes
BD Lehmann, A Colaprico, TC Silva, J Chen, H An, Y Ban, H Huang, ...
Nature communications 12 (1), 6276, 2021
1102021
ELMER v. 2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
TC Silva, SG Coetzee, N Gull, L Yao, DJ Hazelett, H Noushmehr, DC Lin, ...
Bioinformatics 35 (11), 1974-1977, 2019
992019
Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas
DC Lin, HQ Dinh, JJ Xie, A Mayakonda, TC Silva, YY Jiang, LW Ding, ...
Gut 67 (10), 1769-1779, 2018
992018
Interpreting pathways to discover cancer driver genes with Moonlight
A Colaprico, C Olsen, MH Bailey, GJ Odom, T Terkelsen, TC Silva, ...
Nature communications 11 (1), 69, 2020
772020
Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma
L Chen, M Huang, J Plummer, J Pan, YY Jiang, Q Yang, TC Silva, N Gull, ...
Gut 69 (4), 630-640, 2020
672020
Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer¡¯s disease
L Zhang, TC Silva, JI Young, L Gomez, MA Schmidt, KL Hamilton-Nelson, ...
Nature communications 11 (1), 6114, 2020
642020
SpidermiR: an R/bioconductor package for integrative analysis with miRNA data
C Cava, A Colaprico, G Bertoli, A Graudenzi, TC Silva, C Olsen, ...
International journal of molecular sciences 18 (2), 274, 2017
522017
RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling
XY Loh, QY Sun, LW Ding, A Mayakonda, N Venkatachalam, MS Yeo, ...
Cancer research 80 (2), 219-233, 2020
432020
GENAVi: a shiny web application for gene expression normalization, analysis and visualization
ALP Reyes, TC Silva, SG Coetzee, JT Plummer, BD Davis, S Chen, ...
BMC genomics 20, 1-9, 2019
432019
Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas
J Pan, TC Silva, N Gull, Q Yang, JT Plummer, S Chen, K Daigo, ...
Cancer research 80 (13), 2722-2736, 2020
402020
Sex-specific DNA methylation differences in Alzheimer¡¯s disease pathology
L Zhang, JI Young, L Gomez, TC Silva, MA Schmidt, J Cai, X Chen, ...
Acta neuropathologica communications 9 (1), 77, 2021
282021
Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway
J Carrot-Zhang, X Yao, S Devarakonda, A Deshpande, JS Damrauer, ...
Cell reports 34 (5), 2021
262021
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes
Y Zheng, G Huang, TC Silva, Q Yang, YY Jiang, HP Koeffler, DC Lin, ...
Nature communications 12 (1), 2485, 2021
242021
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