Tiago Chedraoui Silva

Formação complementar

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Participação em eventos

Produções bibliográficas

• SILVA, TIAGO C ; YOUNG, JUAN I ; MARTIN, EDEN R ; CHEN, X STEVEN ; WANG, LILY . MethReg: estimating the regulatory potential of DNA methylation in gene transcription. NUCLEIC ACIDS RESEARCH , v. 1, p. 1, 2022.

• EDWARDS, JASMINE S. ; DELABAT, STEPHANIE A. ; BADILLA, ALEJANDRO D. ; DICAPRIO, ROBERT C. ; HYUN, JINHEE ; BURGESS, ROBERT A. ; SILVA, TIAGO ; DYKXHOORN, DEREK M. ; CHEN, STEVEN XI ; WANG, LILY ; ISHIDA, YUJI ; SAITO, TAKESHI ; THOMAS, EMMANUEL . Downregulation of SOCS1 increases interferon-induced ISGylation during differentiation of induced-pluripotent stem cells to hepatocytes. Jhep Reports , v. 4, p. 100592, 2022.

• C. Silva, Tiago ; ZHANG, WEI ; YOUNG, JUAN I. ; GOMEZ, LISSETTE ; SCHMIDT, MICHAEL A. ; VARMA, ACHINTYA ; CHEN, X. STEVEN ; MARTIN, EDEN R. ; WANG, LILY . Distinct sex-specific DNA methylation differences in Alzheimer?s disease. Alzheimers Research & Therapy , v. 14, p. 133, 2022.

• C. Silva, Tiago ; YOUNG, JUAN I. ; ZHANG, LANYU ; GOMEZ, LISSETTE ; SCHMIDT, MICHAEL A. ; VARMA, ACHINTYA ; CHEN, X. STEVEN ; MARTIN, EDEN R. ; WANG, LILY . Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer?s disease. Nature Communications , v. 13, p. 4852, 2022.

• 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. ; et.al . DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH , v. 41, p. 232, 2022.

• CARROT-ZHANG, JIAN ; YAO, XIAOTONG ; DEVARAKONDA, SIDDHARTHA ; DESHPANDE, ADITYA ; DAMRAUER, JEFFREY S. ; SILVA, TIAGO CHEDRAOUI ; WONG, CHRISTOPHER K. ; CHOI, HYO YOUNG ; FELAU, INA ; ROBERTSON, A. GORDON ; CASTRO, MAURO A.A. ; BAO, LISUI ; RHEINBAY, ESTHER ; LIU, ERIC MINWEI ; TRIEU, TUAN ; HAAN, DAVID ; YAU, CHRISTINA ; HINOUE, TOSHINORI ; LIU, YUEXIN ; SHAPIRA, OFER ; et.al . Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Reports , v. 34, p. 108707, 2021.

• ZHANG, LANYU ; YOUNG, JUAN I. ; GOMEZ, LISSETTE ; SILVA, TIAGO C. ; SCHMIDT, MICHAEL A. ; CAI, JESSE ; CHEN, XI ; MARTIN, EDEN R. ; WANG, LILY . Sex-specific DNA methylation differences in Alzheimer?s disease pathology. ACTA NEUROPATHOLOGICA COMMUNICATIONS , v. 9, p. 77, 2021.

• JACOBSEN, GILLIAN ; FERNANDEZ, IRINA ; CUSGUEN, MARIA ALEJANDRA QUINTERO ; SANTANDER, ANA ; PIGNAC-KOBINGER, JUDITH ; DAMAS, ORIANA ; DESHPANDE, AMAR ; KERMAN, DAVID ; BAN, YUGUANG ; GAO, ZHEN ; SILVA, TIAGO ; WANG, LILY ; BURGUENO, JUAN ; ABREU, MARIA . UNIQUE GENE EXPRESSION IN GUT-DERIVED PHAGOCYTIC IMMUNE CELLS FROM IBD PATIENTS. INFLAMMATORY BOWEL DISEASES , v. 27, p. S31-S32, 2021.

• ZHENG, YUEYUAN ; HUANG, GUOWEI ; SILVA, TIAGO C. ; YANG, QIAN ; JIANG, YAN-YI ; KOEFFLER, H. PHILLIP ; LIN, DE-CHEN ; BERMAN, BENJAMIN P. . A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. Nature Communications , v. 12, p. 2485, 2021.

• 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 . Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nature Communications , v. 12, p. 6276, 2021.

• 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 ; et.al . Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas. CANCER RESEARCH , v. 1, p. canres.0390.2020, 2020.

• 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 . Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer?s disease. Nature Communications , v. 11, p. 6114, 2020.

• GAO, GALEN F. ; PARKER, JOEL S. ; REYNOLDS, SHEILA M. ; SILVA, TIAGO C. ; WANG, LIANG-BO ; ZHOU, WANDING ; AKBANI, REHAN ; BAILEY, MATTHEW ; BALU, SAIANAND ; BERMAN, BENJAMIN P. ; BROOKS, DENISE ; CHEN, HU ; CHERNIACK, ANDREW D. ; DEMCHOK, JOHN A. ; DING, LI ; FELAU, INA ; GAHEEN, SHARON ; GERHARD, DANIELA S. ; HEIMAN, DAVID I. ; HERNANDEZ, KYLE M. ; et.al . Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons? Data. Cell Systems , v. 9, p. 24-34.e10, 2019.

• 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. . GENAVi: a shiny web application for gene expression normalization, analysis and visualization. BMC GENOMICS , v. 20, p. 745, 2019.

• SILVA, TIAGO CHEDRAOUI ; COLAPRICO, ANTONIO ; OLSEN, CATHARINA ; MALTA, TATHIANE M ; BONTEMPI, GIANLUCA ; CECCARELLI, MICHELE ; BERMAN, BENJAMIN P ; NOUSHMEHR, HOUTAN . TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. F1000RESEARCH , v. 7, p. 439, 2018.

• SILVA, TIAGO C ; COETZEE, SIMON G ; GULL, NICOLE ; YAO, LIJING ; HAZELETT, DENNIS J ; NOUSHMEHR, HOUTAN ; LIN, DE-CHEN ; BERMAN, BENJAMIN P . ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. BIOINFORMATICS , v. 19, p. 439, 2018.

• CORCES, M. RYAN ; GRANJA, JEFFREY M. ; SHAMS, SHADI ; LOUIE, BRYAN H. ; SEOANE, JOSE A. ; ZHOU, WANDING ; SILVA, TIAGO C. ; GROENEVELD, CLARICE ; WONG, CHRISTOPHER K. ; CHO, SEUNG WOO ; SATPATHY, ANSUMAN T. ; MUMBACH, MAXWELL R. ; HOADLEY, KATHERINE A. ; ROBERTSON, A. GORDON ; SHEFFIELD, NATHAN C. ; FELAU, INA ; CASTRO, MAURO A. A. ; BERMAN, BENJAMIN P. ; STAUDT, LOUIS M. ; ZENKLUSEN, JEAN C. ; et.al . The chromatin accessibility landscape of primary human cancers. SCIENCE (NEW YORK, N.Y.: ONLINE) , v. 362, p. eaav1898, 2018.

• CAVA, CLAUDIA ; COLAPRICO, ANTONIO ; BERTOLI, GLORIA ; GRAUDENZI, ALEX ; SILVA, TIAGO ; OLSEN, CATHARINA ; NOUSHMEHR, HOUTAN ; BONTEMPI, GIANLUCA ; MAURI, GIANCARLO ; CASTIGLIONI, ISABELLA . SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , v. 18, p. 274, 2017.

• 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 ; WANG, MING-RONG ; LI, CHUNQUAN ; XU, LI-YAN ; LI, EN-MIN ; BERMAN, BENJAMIN P ; PHILLIP KOEFFLER, H . Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. GUT , v. 1, p. gutjnl-2017-31, 2017.

• MALTA, TATHIANE M ; DE SOUZA, CAMILA F ; SABEDOT, THAIS S ; SILVA, TIAGO C ; MOSELLA, MARITZA QS ; KALKANIS, STEVEN N ; SNYDER, JAMES ; CASTRO, ANA VALERIA B ; NOUSHMEHR, HOUTAN . Glioma CpG Island Methylator Phenotype (G-CIMP): Biological and Clinical Implications. NEURO-ONCOLOGY , v. 1, p. 1, 2017.

• MOSELLA, MARITZA ; SARRAF, THAIS ; MALTA, TATHIANE ; CHEDRAOUI, TIAGO ; NOUSHMEHR, HOUTAN ; CASTRO, ANA VALÉRIA . GENE-52. EPIGENOMIC GLIOMA SUBTYPE EVALUATION ACROSS 31 TUMOR TYPES. NEURO-ONCOLOGY , v. 19, p. vi103-vi104, 2017.

• CECCARELLI, MICHELE ; BARTHEL, F. P. ; MALTA, TATHIANE M. ; SABEDOT, THAIS S. ; SALAMA, S. R. ; MURRAY, B. A. ; MOROZOVA, O. ; NEWTON, Y. ; RADENBAUGH, A. ; PAGNOTTA, STEFANO M. ; ANJUM, S. ; WANG, J. ; MANYAM, G. ; ZOPPOLI, P. ; LING, S. ; RAO, A. A. ; GRIFFORD, M. ; CHERNIACK, A. D. ; ZHANG, H. ; SILVA, T. C. ; et.al . Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. CELL , v. 164, p. 1, 2016.

• SILVA, TIAGO C. ; COLAPRICO, ANTONIO ; OLSEN, CATHARINA ; D'ANGELO, FULVIO ; BONTEMPI, GIANLUCA ; CECCARELLI, MICHELE ; NOUSHMEHR, HOUTAN . TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000RESEARCH , v. 5, p. 1542, 2016.

• 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 . TCGAbiolinks : an R/Bioconductor package for integrative analysis of TCGA data. NUCLEIC ACIDS RESEARCH , v. 44, p. gkv1507, 2015.

• SILVA, TIAGO CHEDRAOUI ; YEAGER, N. ; COETZEE, S. G. ; YAO, L. ; HAZELETT, D. J. ; NOUSHMEHR, HOUTAN ; LIN, DE-CHEN ; BERMAN, B. P. . ELMER 2.0: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. 2018. (Apresentação de Trabalho/Congresso).

• SILVA, TIAGO C ; YEAGER, N. ; LIN, DE-CHEN ; BERMAN, B. P. . ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profile. 2018. (Apresentação de Trabalho/Congresso).

• SILVA, TIAGO CHEDRAOUI ; COLAPRICO, ANTONIO ; OLSEN, CATHARINA ; BONTEMPI, GIANLUCA ; CECCARELLI, MICHELE ; BERMAN, BENJAMIN P ; NOUSHMEHR, HOUTAN . TCGAbiolinksGUI: A Graphical User Interface to analyze cancer genomics and epigenomics data.. 2017. (Apresentação de Trabalho/Congresso).

• SILVA, TIAGO CHEDRAOUI ; COETZEE, S. G. ; YEAGER, N. ; YAO, L. ; HAZELETT, D. J. ; NOUSHMEHR, HOUTAN ; LIN, DE-CHEN ; BERMAN, B. P. . Enhancer Linking by Methylation/Expression Relationships with the R package (ELMER) version 2.. 2017. (Apresentação de Trabalho/Simpósio).

• SILVA, TIAGO CHEDRAOUI ; COETZEE, S. G. ; NOUSHMEHR, HOUTAN ; HAZELETT, D. J. ; BERMAN, B. P. . Integrative analysis workshop with TCGAbiolinks and ELMER.. 2017. (Apresentação de Trabalho/Conferência ou palestra).

• SILVA, T. C. ; NOUSHMEHR, HOUTAN . EPIGENOMIC AND TRANSCRIPTOMIC ANALYSIS OF ADULT GLIOMA REVEALS CANDIDATE DRIVER TRANSCRIPTION FACTORS INVOLVED IN GLIOMA PROGRESSION. 2016. (Apresentação de Trabalho/Congresso).

Outras produções

Projetos de pesquisa

• 2015 - 2018

  Bioinformatic tool to integrate and understand aberrant epigenomic and genomic changes associated with cancer, Descrição: Cancer, which is one of the major causes of mortality worldwide, is a complex disease orchestrated by aberrant genomic and epigenomic changes that can modify gene regulatory circuits and cellular identity. Emerging evidence obtained through high-throughput genomic data deposited within the public TCGA international consortium suggests that one in ten cancer patients would be more accurately classified by molecular taxonomy versus histology. Therefore, we have hypothesized that the establishment of genome-wide maps of the de novo DNA binding motifs localization coupled with differentially methylated regions and gene expression changes might help to characterize and exploit cancer phenotypes at the molecular level. Technological advances and public databases like The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (roadmap) have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high resolution. Markedly however, biological information is stored in different formats and there is no current tool to integrate the data, highlighting an urgent need to develop bioinformatic tools and/or computational softwares to overcome this challenge. In this context, the main purpose of this study is to implement the development of biOMICs, a package coded in the GNU GPL (General Public License) R programming language that will be submitted to the larger open-source Bioconductor community project. Our expectation is that biOMICs can effectively automate search, retrieve, and analyze the vast (epi)genomic data currently available from TCGA, ENCODE, and Roadmap, and integrate genomics and epigenomics features with researchers own high-throughput data. Furthermore, we will also navigate through these data manually in order to validate the capacity of biOMICs in discovering epigenomic signatures able to redefine subtypes of cancer. Finally, we will use biOMICs to investigate the molecular differences between two subgroups of gliomas, one of the most aggressive primary brain cancer, recently discovered by our laboratory. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Doutorado: (1) . , Integrantes: Tiago Chedraoui Silva - Integrante / NOUSHMEHR, HOUTAN - Coordenador / Camila Souza - Integrante / MALTA, TATHIANE - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa., Número de produções C, T & A: 1

• 2010 - 2011

  IMPLEMENTAÇÃO DE UM ALGORITMO DE ADAPTAÇÃO DA TAXA DE TRANSMISSÃO EM UM SISTEMA GNU/LINUX PARA ROTEADORES WI-FI, Descrição: O OpenWrt é um firmware livre baseado no sistema operacional GNU/Linux e voltado exclusi- vamente para uso em roteadores sem fio residenciais. Além das responsabilidades básicas que um software como este tem em relação ao funcionamento dos roteadores, ele também inclui algoritmos de adaptação da taxa de transmissão. Estes algoritmos não são especificados pelo padrão IEEE 802.11, e por isso possibilita a existência de diversas soluções. Implementou-se no OpenWrt um algoritmo cognitivo para adaptação da taxa de transmissão desenvolvido na UNICAMP, denominado CORA, a partir do qual desenvolveram-se experimentos para comparar os resultados obtidos acerca do algoritmo através do uso de simuladores. Além disso, comparou-se o CORA com o algoritmo existente no OpenWrt. Verificou-se a satisfatori- edade do algoritmo apesar de apresentar um desempenho inferior ao indicado pelos testes prévios de simulação.. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (1) / Mestrado acadêmico: (1) . , Integrantes: Tiago Chedraoui Silva - Integrante / Islene Calciolari Garcia - Coordenador / Luciano Jerez Chaves - Integrante.

Prêmios