White paper on high‐throughput process development for integrated continuous biomanufacturing

por São Pedro, Mariana N., Silva, Tiago C., Patil, Rohan, Ottens, Marcel
Publicado 2021

PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples

por Odom, Gabriel J., Colaprico, Antonio, Silva, Tiago C., Chen, X. Steven, Wang, Lily
Publicado 2021

MethReg: estimating the regulatory potential of DNA methylation in gene transcription

por Silva, Tiago C, Young, Juan I, Martin, Eden R, Chen, X Steven, Wang, Lily
Publicado 2022

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

por Silva, Tiago C., Colaprico, Antonio, Olsen, Catharina, D'Angelo, Fulvio, Bontempi, Gianluca, Ceccarelli, Michele, Noushmehr, Houtan
Publicado 2016

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

por Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C., Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena
Publicado 2019

SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data

por Cava, Claudia, Colaprico, Antonio, Bertoli, Gloria, Graudenzi, Alex, Silva, Tiago C., Olsen, Catharina, Noushmehr, Houtan, Bontempi, Gianluca, Mauri, Giancarlo, Castiglioni, Isabella
Publicado 2017

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

por Silva, Tiago C, Coetzee, Simon G, Gull, Nicole, Yao, Lijing, Hazelett, Dennis J, Noushmehr, Houtan, Lin, De-Chen, Berman, Benjamin P
Publicado 2019

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

por Zheng, Yueyuan, Huang, Guowei, Silva, Tiago C., Yang, Qian, Jiang, Yan-Yi, Koeffler, H. Phillip, Lin, De-Chen, Berman, Benjamin P.
Publicado 2021

Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

por Zheng, Yueyuan, Huang, Guowei, Silva, Tiago C., Yang, Qian, Jiang, Yan-Yi, Koeffler, H. Phillip, Lin, De-Chen, Berman, Benjamin P.
Publicado 2021

LR Hunting: A Random Forest Based Cell–Cell Interaction Discovery Method for Single-Cell Gene Expression Data

por Lu, Min, Sha, Yifan, Silva, Tiago C., Colaprico, Antonio, Sun, Xiaodian, Ban, Yuguang, Wang, Lily, Lehmann, Brian D., Chen, X. Steven
Publicado 2021

Sex-specific DNA methylation differences in Alzheimer’s disease pathology

por Zhang, Lanyu, Young, Juan I., Gomez, Lissette, Silva, Tiago C., Schmidt, Michael A., Cai, Jesse, Chen, Xi, Martin, Eden R., Wang, Lily
Publicado 2021

Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease

por 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
Publicado 2020

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

por 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
Publicado 2016

GENAVi: a shiny web application for gene expression normalization, analysis and visualization

por 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.
Publicado 2019

Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma

por 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
Publicado 2021

Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes

por 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
Publicado 2021

Interpreting pathways to discover cancer driver genes with Moonlight

por 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
Publicado 2020

Lamina Propria Phagocyte Profiling Reveals Targetable Signaling Pathways in Refractory Inflammatory Bowel Disease

por Jacobsen, Gillian E., Fernández, Irina, Quintero, Maria A., Santander, Ana M., Pignac-Kobinger, Judith, Damas, Oriana M., Deshpande, Amar R., Kerman, David H., Ban, Yuguang, Gao, Zhen, Silva, Tiago C., Wang, Lily, Beecham, Ashley H., McCauley, Jacob L., Burgueño, Juan F., Abreu, Maria T.
Publicado 2022

DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers

por Gull, Nicole, Jones, Michelle R., Peng, Pei-Chen, Coetzee, Simon G., Silva, Tiago C., Plummer, Jasmine T., Reyes, Alberto Luiz P., Davis, Brian D., Chen, Stephanie S., Lawrenson, Kate, Lester, Jenny, Walsh, Christine, Rimel, Bobbie J., Li, Andrew J., Cass, Ilana, Berg, Yonatan, Govindavari, John-Paul B., Rutgers, Joanna K. L., Berman, Benjamin P., Karlan, Beth Y., Gayther, Simon A.
Publicado 2022