Yueyuan Zheng and Guowei Huang and Tiago C. Silva and Qian Yang and Yan-Yi Jiang and H. Phillip Koeffler and De-Chen Lin and Benjamin P. Berman(2021). A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes . Nature Communications. 12. (1). Springer Science and Business Media {LLC}

Lanyu Zhang and Juan I. Young and Lissette Gomez and Tiago C. Silva and Michael A. Schmidt and Jesse Cai and Xi Chen and Eden R. Martin and Lily Wang(2021). Sex-specific DNA methylation differences in Alzheimer’s disease pathology . Acta Neuropathologica Communications. 9. (1). Springer Science and Business Media {LLC}

Min Lu and Yifan Sha and Tiago C. Silva and Antonio Colaprico and Xiaodian Sun and Yuguang Ban and Lily Wang and Brian D. Lehmann and X. Steven Chen(2021). LR Hunting: A Random Forest Based Cell–Cell Interaction Discovery Method for Single-Cell Gene Expression Data . Frontiers in Genetics. 12. Frontiers Media {SA}

Maritza S Mosella and Thais S Sabedot and Tiago C Silva and Tathiane M Malta and Felipe Segato Dezem and Karam P Asmaro and Michael Wells and Abir Mukherjee and Laila M Poisson and James Snyder and Ana C deCarvalho and Tobias Walbert and Todd Aho and Steven Kalkanis and Paula C Elias and Sonir R Antonini and Jack Rock and Houtan Noushmehr and Margaret Castro and Ana Valeria Castro(2021). DNA methylation-based signatures classify sporadic pituitary tumors according to clinicopathological features . Neuro-Oncology. 23. (8). p. 1292--1303. Oxford University Press ({OUP})

Jian Carrot-Zhang and Xiaotong Yao and Siddhartha Devarakonda and Aditya Deshpande and Jeffrey S. Damrauer and Tiago Chedraoui Silva and Christopher K. Wong and Hyo Young Choi and Ina Felau and A. Gordon Robertson and Mauro A.A. Castro and Lisui Bao and Esther Rheinbay and Eric Minwei Liu and Tuan Trieu and David Haan and Christina Yau and Toshinori Hinoue and Yuexin Liu and Ofer Shapira and Kiran Kumar and Karen L. Mungall and Hailei Zhang and Jake June-Koo Lee and Ashton Berger and Galen F. Gao and Binyamin Zhitomirsky and Wen-Wei Liang and Meng Zhou and Sitapriya Moorthi and Alice H. Berger and Eric A. Collisson and Michael C. Zody and Li Ding and Andrew D. Cherniack and Gad Getz and Olivier Elemento and Christopher C. Benz and Josh Stuart and J.C. Zenklusen and Rameen Beroukhim and Jason C. Chang and Joshua D. Campbell and D. Neil Hayes and Lixing Yang and Peter W. Laird and John N. Weinstein and David J. Kwiatkowski and Ming S. Tsao and William D. Travis and Ekta Khurana and Benjamin P. Berman and Katherine A. Hoadley and Nicolas Robine and Matthew Meyerson and Ramaswamy Govindan and Marcin Imielinski and Kanika Arora and Minita Shah and Jennifer Shelton and Reanne Bowlby and Verena Friedl and Mary Goldman and Brian Craft and David I. Heiman and Iman Hajirasouliha and Camir Ricketts and Pavana Anur and Kami E. Chiotti and Samantha J. Caesar-Johnson and John A. Demchok and Martin L. Ferguson and Anab Kemal and Roy Tarnuzzer and Zhining Wang and Liming Yang and Paul T. Spellman and Benjamin Raphael and Rehan Akbani and Jingchun Zhu and Steven J.M. Jones and Hui Shen(2021). Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway . Cell Reports. 34. (5). p. 108707. Elsevier {BV}

Jian Carrot-Zhang and Xiaotong Yao and Siddhartha Devarakonda and Aditya Deshpande and Jeffrey S. Damrauer and Tiago Chedraoui Silva and Christopher K. Wong and Hyo Young Choi and Ina Felau and A. Gordon Robertson and Mauro A.A. Castro and Lisui Bao and Esther Rheinbay and Eric Minwei Liu and Tuan Trieu and David Haan and Christina Yau and Toshinori Hinoue and Yuexin Liu and Ofer Shapira and Kiran Kumar and Karen L. Mungall and Hailei Zhang and Jake June-Koo Lee and Ashton Berger and Galen F. Gao and Binyamin Zhitomirsky and Wen-Wei Liang and Meng Zhou and Sitapriya Moorthi and Alice H. Berger and Eric A. Collisson and Michael C. Zody and Li Ding and Andrew D. Cherniack and Gad Getz and Olivier Elemento and Christopher C. Benz and Josh Stuart and J.C. Zenklusen and Rameen Beroukhim and Jason C. Chang and Joshua D. Campbell and D. Neil Hayes and Lixing Yang and Peter W. Laird and John N. Weinstein and David J. Kwiatkowski and Ming S. Tsao and William D. Travis and Ekta Khurana and Benjamin P. Berman and Katherine A. Hoadley and Nicolas Robine and Matthew Meyerson and Ramaswamy Govindan and Marcin Imielinski(2021). Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway . Cell Reports. 34. (8). p. 108784. Elsevier {BV}

Antonio Colaprico and Catharina Olsen and Matthew H. Bailey and Gabriel J. Odom and Thilde Terkelsen and Tiago C. Silva and Andr{\'{e}} V. Olsen and Laura Cantini and Andrei Zinovyev and Emmanuel Barillot and Houtan Noushmehr and Gloria Bertoli and Isabella Castiglioni and Claudia Cava and Gianluca Bontempi and Xi Steven Chen and Elena Papaleo(2020). Interpreting pathways to discover cancer driver genes with Moonlight . Nature Communications. 11. (1). Springer Science and Business Media {LLC}

Lanyu Zhang and Tiago C. Silva and Juan I. Young and Lissette Gomez and Michael A. Schmidt and Kara L. Hamilton-Nelson and Brian W. Kunkle and Xi Chen and Eden R. Martin and Lily Wang(2020). Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease . Nature Communications. 11. (1). Springer Science and Business Media {LLC}

(2020). Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease . Nature communications.

Gabriel J. Odom and Yuguang Ban and Antonio Colaprico and Lizhong Liu and Tiago Chedraoui Silva and Xiaodian Sun and Alexander R. Pico and Bing Zhang and Lily Wang and Xi Chen(2020). PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi‐Omics Data . PROTEOMICS. 20. (21-22). p. 1900409. Wiley

(2020). Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas . Cancer Research.

Jian Pan and Tiago C. Silva and Nicole Gull and Qian Yang and Jasmine T. Plummer and Stephanie Chen and Kenji Daigo and Takao Hamakubo and Sigal Gery and Ling-Wen Ding and Yan-Yi Jiang and Shaoyan Hu and Li-Yan Xu and En-Min Li and Yanbing Ding and Samuel J. Klempner and Simon A. Gayther and Benjamin P. Berman and H. Phillip Koeffler and De-Chen Lin(2020). Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas . Cancer Research. 80. (13). p. 2722--2736. American Association for Cancer Research ({AACR})

Li Chen and Moli Huang and Jasmine Plummer and Jian Pan and Yan Yi Jiang and Qian Yang and Tiago Chedraoui Silva and Nicole Gull and Stephanie Chen and Ling Wen Ding and Omer An and Henry Yang and Yulan Cheng and Jonathan W Said and Ngan Doan and Winand NM Dinjens and Kevin M Waters and Richard Tuli and Simon A Gayther and Samuel J Klempner and Benjamin P Berman and Stephen J Meltzer and De-Chen Lin and H Phillip Koeffler(2020). Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma . Gut. 69. (4). p. 630--640. {BMJ}

(2019). GENAVi: a shiny web application for gene expression normalization, analysis and visualization . BMC Genomics.

Alberto Luiz P. Reyes and Tiago C. Silva and Simon G. Coetzee and Jasmine T. Plummer and Brian D. Davis and Stephanie Chen and Dennis J. Hazelett and Kate Lawrenson and Benjamin P. Berman and Simon A. Gayther and Michelle R. Jones(2019). GENAVi: a shiny web application for gene expression normalization, analysis and visualization . BMC Genomics. 20. (1). Springer Science and Business Media {LLC}

(2019). Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma . Gut.

(2019). Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data . Cell Systems.

Mohamed Mounir and Marta Lucchetta and Tiago C. Silva and Catharina Olsen and Gianluca Bontempi and Xi Chen and Houtan Noushmehr and Antonio Colaprico and Elena Papaleo(2019). New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx . PLOS Computational Biology. 15. (3). p. e1006701. Public Library of Science ({PLoS})

Silva, Tiago C and Coetzee, Simon G and Gull, Nicole and Yao, Lijing and Hazelett, Dennis J and Noushmehr, Houtan and Lin, De-Chen and Berman, Benjamin P(2018). ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles . Bioinformatics. p. bty902.

Corces, M. Ryan and Granja, Jeffrey M. and Shams, Shadi and Louie, Bryan H. and Seoane, Jose A. and Zhou, Wanding and Silva, Tiago C. and Groeneveld, Clarice and Wong, Christopher K. and Cho, Seung Woo and Satpathy, Ansuman T. and Mumbach, Maxwell R. and Hoadley, Katherine A. and Robertson, A. Gordon and Sheffield, Nathan C. and Felau, Ina and Castro, Mauro A. A. and Berman, Benjamin P. and Staudt, Louis M. and Zenklusen, Jean C. and Laird, Peter W. and Curtis, Christina and , and Greenleaf, William J. and Chang, Howard Y.(2018). The chromatin accessibility landscape of primary human cancers . Science. 362. (6413). American Association for the Advancement of Science

(2017). SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data . International Journal of Molecular Sciences.

Malta, Tathiane M., de Souza, Camila F., Sabedot, Thais S., Silva, Tiago C., Mosella, Maritza Q. S., Kalkanis, Steven N., Snyder, James, Castro, Ana Valeria B., Noushmehr, Houtan(2017). Glioma CpG Island Methylator Phenotype (G-CIMP): Biological and Clinical Implications. Neuro-Oncology. p. nox183.

Lin, De-Chen, Dinh, Huy Q., Xie, Jian-Jun, Mayakonda, Anand, Silva, Tiago Chedraoui, Jiang, Yan-Yi, Ding, Ling-Wen, He, Jian-Zhong, Xu, Xiu- E., Hao, Jia-Jie(2017). Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut. p. gutjnl-2017.

Cava, Claudia, Colaprico, Antonio, Bertoli, Gloria, Graudenzi, Alex, Silva, Tiago C., Olsen, Catharina, Noushmehr, Houtan, Bontempi, Gianluca, Mauri, Giancarlo, Castiglioni, Isabella(2017). SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data. International journal of molecular sciences. 18. (2). p. 274.

Silva, Tiago C., Colaprico, Antonio, Olsen, Catharina, Bontempi, Gianluca, Ceccarelli, Michele, Berman, Benjamin P., Noushmehr, Houtan(2017). TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data. bioRxiv. p. 147496.

Silva TC, Colaprico A, Olsen C et al. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; referees: 1 approved, 1 approved with reservations] F1000Research 2016, 5:1542 (doi: 10.12688/f1000research.8923.2) .

Silva, Tiago C., Colaprico, Antonio, Olsen, Catharina, D'Angelo, Fulvio, Bontempi, Gianluca, Ceccarelli, Michele, Noushmehr, Houtan(2016). TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Research. 5.

Colaprico, Antonio, Silva, Tiago C., Olsen, Catharina, Garofano, Luciano, Cava, Claudia, Garolini, Davide, Sabedot, Thais S., Malta, Tathiane M., Pagnotta, Stefano M., Castiglioni, Isabella(2016). TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic acids research. 44. (8). p. e71.

Ceccarelli, Michele, Barthel, Floris P., Malta, Tathiane M., Sabedot, Thais S., Salama, Sofie R., Murray, Bradley A., Morozova, Olena, Newton, Yulia, Radenbaugh, Amie, Pagnotta, Stefano M.(2016). Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma . Cell. 164. (3). p. 550-563.

Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Michele Ceccarelli, Benjamin Berman, Houtan Noushmehr (2017). TCGAbiolinksGUI: a graphical user interface to analyze cancer genomics and epigenomics data .