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1

Statistical Inference and Reverse Engineering of Gene Regulatory Networks from Observational Expression Data

Emmert-Streib, Frank, Glazko, Galina V., Altay, Gökmen, de Matos Simoes, Ricardo

Journal:

Frontiers in Genetics

Année:

2012

Langue:

english

Fichier:

PDF, 851 KB

english, 2012

2

Repercussions of melatonin on the risk of breast cancer: a systematic review and meta-analysis

Veiga, Eduardo Carvalho de Arruda, Simões, Ricardo, Valenti, Vitor E, Cipolla-Neto, Jose, Abreu, Luiz Carlos, Barros, Ernane Pedro Matos, Sorpreso, Isabel Cristina Esposito, Baracat, Maria Candido P.,

Journal:

Revista da Associação Médica Brasileira

Année:

2019

Langue:

english

Fichier:

PDF, 296 KB

english, 2019

3

A Mek1–Mek2 heterodimer determines the strength and duration of the Erk signal

Catalanotti, Federica, Reyes, Gloria, Jesenberger, Veronika, Galabova-Kovacs, Gergana, de Matos Simoes, Ricardo, Carugo, Oliviero, Baccarini, Manuela

Journal:

Nature Structural and Molecular Biology

Année:

2009

Langue:

english

Fichier:

PDF, 906 KB

english, 2009

4

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

Frank Emmert-Streib, Shailesh Tripathi, Ricardo de Matos Simoes

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 524 KB

english, 2012

5

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Ricardo de Matos Simoes, Shailesh Tripathi, Frank Emmert-Streib

Journal:

BMC Systems Biology

Année:

2012

Langue:

english

Fichier:

PDF, 2.07 MB

english, 2012

6

Interfacing cellular networks ofS. cerevisiaeandE. coli: Connecting dynamic and genetic information

Ricardo de Matos Simoes, Matthias Dehmer, Frank Emmert-Streib

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2013

7

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Frank Emmert-Streib, Funso Abogunrin, Ricardo de Matos Simoes, Brian Duggan…

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 535 KB

english, 2013

8

Functional and genetic analysis of the colon cancer network

Emmert-Streib, Frank, de Matos Simoes, Ricardo, Glazko, Galina, McDade, Simon, Haibe-Kains, Benjamin, Holzinger, Andreas, Dehmer, Matthias, Campbell, Frederick

Journal:

BMC Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2014

9

Antiherpetic Mechanism of a Sulfated Derivative of Agaricus brasiliensis Fruiting Bodies Polysaccharide

Cardozo, Francielle T.G.S., Camelini, Carla Maísa, Leal, Paulo César, Kratz, Jadel Müller, Nunes, Ricardo José, Mendonça, Margarida Matos de, Simões, Cláudia Maria Oliveira

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2014

10

The human disease network

Emmert-Streib, Frank, Tripathi, Shailesh, Simoes, Ricardo de Matos, Hawwa, Ahmed F, Dehmer, Matthias

Journal:

Systems Biomedicine

Année:

2013

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2013

11

Anatomical Description of Guanandi Wood, from Pure Plantation, and its Use as Building Material

Barreiros, Ricardo Marques, Amaral, Simone Simões, de Matos, Carlos Alberto Oliveira, Costa, Alex Siqueira

Journal:

Advanced Materials Research

Année:

2015

Langue:

english

Fichier:

PDF, 339 KB

english, 2015

12

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

Matos Simoes, Ricardo de, Dalleau, Sabine, Williamson, Kate E, Emmert-Streib, Frank

Journal:

BMC Systems Biology

Année:

2015

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2015

13

[IEEE 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Washington, DC, USA (2015.11.9-2015.11.12)] 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer

de Matos Simoes, Ricardo, Mitsiades, Constantine, Williamson, Kate E, Emmert-Streib, Frank

Année:

2015

Langue:

english

Fichier:

PDF, 952 KB

english, 2015

14

samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files

Stupnikov, Alexey, Tripathi, Shailesh, de Matos Simoes, Ricardo, McArt, Darragh, Salto-Tellez, Manuel, Glazko, Galina, Dehmer, Matthias, Emmert-Streib, Frank

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 853 KB

english, 2016

15

NF-κB dysregulation in multiple myeloma

Matthews, Geoffrey M., de Matos Simoes, Ricardo, Dhimolea, Eugen, Sheffer, Michal, Gandolfi, Sara, Dashevsky, Olga, Sorrell, Jeffrey D., Mitsiades, Constantine S.

Journal:

Seminars in Cancer Biology

Année:

2016

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2016

16

intestinal pathogenic bacterial infection

Cronin, Shane J F, Nehme, Nadine T, Limmer, Stefanie, Liegeois, Samuel, Andrew, J, Schramek, Daniel, Leibbrandt, Andreas, Simoes, Ricardo De Matos, Puc, Urszula, Ebersberger, Ingo, Zoranovic, Tamara,

Année:

2010

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2010

17

A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data

Emmert-Streib, Frank, de Matos Simoes, Ricardo, Tripathi, Shailesh, Glazko, Galina V., Dehmer, Matthias

Journal:

Scientific Reports

Année:

2012

Langue:

english

Fichier:

PDF, 736 KB

english, 2012

18

Biomarker classifiers for detection of bladder cancer in patients with haematuria are confounded by smoking and increased age

Simoes, Ricardo de Matos, Emmert-Streib, F., Ruddock, Mark W., O’Rourke, Declan, Duggan, Brian, O’Kane, Hugh F., Abogunrin, Funso, Reid, Cherith N., Williamson, Kate E.

Journal:

Urologic Oncology: Seminars and Original Investigations

Année:

2017

Langue:

english

Fichier:

PDF, 44 KB

english, 2017

19

Bagging Statistical Network Inference from Large-Scale Gene Expression Data

de Matos Simoes, Ricardo, Emmert-Streib, Frank, Pellegrini, Matteo

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 691 KB

english, 2012

20

B-cell lymphoma gene regulatory networks: biological consistency among inference methods

de Matos Simoes, Ricardo, Dehmer, Matthias, Emmert-Streib, Frank

Journal:

Frontiers in Genetics

Année:

2013

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2013

21

The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks

Emmert-Streib, Frank, de Matos Simoes, Ricardo, Mullan, Paul, Haibe-Kains, Benjamin, Dehmer, Matthias

Journal:

Frontiers in Genetics

Année:

2014

Langue:

english

Fichier:

PDF, 1017 KB

english, 2014

22

ESTUDO QUANTITATIVO DA VARIAÇÃO ESTRUTURAL MORFOLÓGICA NA MADEIRA DE Calophyllum brasiliense

Barreiros, Ricardo Marques, Amaral, Simone Simões, Matos, Carlos Alberto Oliveira de, Costa, Alex Siqueira

Journal:

Année:

2016

Fichier:

PDF, 1.79 MB

2016

23

A genome-wide Drosophila epithelial tumorigenesis screen identifies Tetraspanin 29Fb as an evolutionarily conserved suppressor of Ras-driven cancer

Zoranovic, Tamara, Manent, Jan, Willoughby, Lee, Matos de Simoes, Ricardo, La Marca, John E., Golenkina, Sofya, Cuiping, Xia, Gruber, Susanne, Angjeli, Belinda, Kanitz, Elisabeth Eva, Cronin, Shane J.

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 19.94 MB

english, 2018

24

Respostas hormonais agudas a diferentes intensidades de exercícios resistidos em mulheres idosas

Oliveira, Ricardo Jacó de, Lima, Ricardo Moreno, Gentil, Paulo, Simões, Herbert Gustavo, Ávila, Waldney Roberto de Matos e, Silva, Rogério Wagner da, Silva, Francisco Martins da

Journal:

Revista Brasileira de Medicina do Esporte

Année:

2008

Fichier:

PDF, 157 KB

2008

25

Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data

Moore, Daniel, de Matos Simoes, Ricardo, Dehmer, Matthias, Emmert-Streib, Frank

Journal:

Current Genomics

Année:

2018

Fichier:

PDF, 3.42 MB

2018

26

The Brazilian Society of Rheumatology recommendations on investigation and diagnosis of systemic autoimmune myopathies

de Souza, Fernando Henrique Carlos, de Araújo, Daniel Brito, Vilela, Verônica Silva, Simões, Ricardo Santos, Bernardo, Wanderley Marques, Frank, Thais Amanda, da Cunha, Bernardo Matos, Shinjo, Samuel

Journal:

Advances in Rheumatology

Année:

2019

Langue:

english

Fichier:

PDF, 716 KB

english, 2019

27

Molecular markers of MM cell sensitivity and resistance to Natural Killer cells: implications for anti-MM immunotherapy

Gandolfi, Sara, Sheffer, Michal, Lowry, Emily, Dashevsky, Olga, Shirasaki, Ryosuke, de Matos Simoes, Ricardo, Romee, Rizwan, Roth, Jennifer, Mitsiades, Constantine

Journal:

Clinical Lymphoma Myeloma and Leukemia

Année:

2019

Langue:

english

Fichier:

PDF, 76 KB

english, 2019

28

CRISPR studies identify genes preferentially essential for myeloma cells vs. other neoplasias: implications for future therapies selective against MM

Shirasaki, Ryosuke, de Matos Simoes, Ricardo, Downey-Kopyscinski, Sondra, Matthews, Geoffrey, Hu, Yiguo, Sheffer, Michal, Dhimolea, Eugen, Dashevsky, Olga, Gandolfi, Sara, Hengeveld, Paul, Dempster, J

Journal:

Clinical Lymphoma Myeloma and Leukemia

Année:

2019

Fichier:

PDF, 83 KB

2019

29

Combinatorial CRISPR-knockout identifies interactions between key genes and regulatory pathways in myeloma

Downey-Kopyscinski, Sondra, de Matos Simoes, Ricardo, Shirasaki, Ryosuke, Dashevsky, Olga, Gandolfi, Sara, Glassner, Brian J., Bariteau, Megan, Borah, Minasri, Groen, Richard, Doench, John, Mitsiades,

Journal:

Clinical Lymphoma Myeloma and Leukemia

Année:

2019

Fichier:

PDF, 88 KB

2019

30

Gain-of-function studies with CRISPR-based transcriptional activation at endogenous genomic loci reveals genes with critical roles for myeloma cells

Tang, Huihui, Shirasaki, Ryosuke, Gandolfi, Sara, de Matos Simoes, Ricardo, Dashevsky, Olga, Glassner, Brian J., Downey-Kopyscinski, Sondra, Sheffer, Michal, Bariteau, Megan, Doench, John, Mitsiades,

Journal:

Clinical Lymphoma Myeloma and Leukemia

Année:

2019

Fichier:

PDF, 59 KB

2019

31

CRISPR-based functional genomics landscape of genes recurrently mutated in MM

de Matos Simoes, Ricardo, Shirasaki, Ryosuke, Tang, Huihui, Sheffer, Michal, Dashevsky, Olga, Downey-Kopyscinski, Sondra, Dhimolea, Eugen, Bariteau, Megan, Licht, Jonathan, Glassner, Brian J., Levy, J

Journal:

Clinical Lymphoma Myeloma and Leukemia

Année:

2019

Fichier:

PDF, 81 KB

2019

32

Pleiotropic mechanisms drive endocrine resistance in the three-dimensional bone microenvironment

Dhimolea, Eugen, de Matos Simoes, Ricardo, Kansara, Dhvanir, Weng, Xiang, Sharma, Shruti, Awate, Pallavi, Liu, Zhiyi, Gao, Dong, Mitsiades, Nicholas, Schwab, Joseph H., Chen, Yu, Jeselsohn, Rinath, Cu

Journal:

Cancer Research

Année:

2020

Fichier:

PDF, 18.40 MB

2020