Harvard Catalyst Profiles

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Ricardo De Matos Simoes, Dr.Rer.Nat


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Humbert PO, Pryjda TZ, Pranjic B, Farrell A, Fujikura K, de Matos Simoes R, Karim R, Kozieradzki I, Cronin SJF, Neely GG, Meyer TF, Hagelkruys A, Richardson HE, Penninger JM. Correction: TSPAN6 is a suppressor of Ras-driven cancer. Oncogene. 2022 Apr; 41(14):2138. PMID: 35292775; PMCID: PMC8975738.
    Citations:    Fields:    
  2. Humbert PO, Pryjda TZ, Pranjic B, Farrell A, Fujikura K, de Matos Simoes R, Karim R, Kozieradzki I, Cronin SJF, Neely GG, Meyer TF, Hagelkruys A, Richardson HE, Penninger JM. TSPAN6 is a suppressor of Ras-driven cancer. Oncogene. 2022 04; 41(14):2095-2105. PMID: 35184157; PMCID: PMC8975741.
    Citations:    Fields:    Translation:HumansAnimalsCells
  3. Dhimolea E, de Matos Simoes R, Kansara D, Al'Khafaji A, Bouyssou J, Weng X, Sharma S, Raja J, Awate P, Shirasaki R, Tang H, Glassner BJ, Liu Z, Gao D, Bryan J, Bender S, Roth J, Scheffer M, Jeselsohn R, Gray NS, Georgakoudi I, Vazquez F, Tsherniak A, Chen Y, Welm A, Duy C, Melnick A, Bartholdy B, Brown M, Culhane AC, Mitsiades CS. An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. Cancer Cell. 2021 02 08; 39(2):240-256.e11. PMID: 33417832; PMCID: PMC8670073.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  4. Shirasaki R, Matthews GM, Gandolfi S, de Matos Simoes R, Buckley DL, Raja Vora J, Sievers QL, Brüggenthies JB, Dashevsky O, Poarch H, Tang H, Bariteau MA, Sheffer M, Hu Y, Downey-Kopyscinski SL, Hengeveld PJ, Glassner BJ, Dhimolea E, Ott CJ, Zhang T, Kwiatkowski NP, Laubach JP, Schlossman RL, Richardson PG, Culhane AC, Groen RWJ, Fischer ES, Vazquez F, Tsherniak A, Hahn WC, Levy J, Auclair D, Licht JD, Keats JJ, Boise LH, Ebert BL, Bradner JE, Gray NS, Mitsiades CS. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Rep. 2021 01 05; 34(1):108532. PMID: 33406420.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  5. Dhimolea E, de Matos Simoes R, Kansara D, Weng X, Sharma S, Awate P, Liu Z, Gao D, Mitsiades N, Schwab JH, Chen Y, Jeselsohn R, Culhane AC, Brown M, Georgakoudi I, Mitsiades CS. Pleiotropic Mechanisms Drive Endocrine Resistance in the Three-Dimensional Bone Microenvironment. Cancer Res. 2021 01 15; 81(2):371-383. PMID: 32859606.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  6. Manent J, Banerjee S, de Matos Simoes R, Zoranovic T, Mitsiades C, Penninger JM, Simpson KJ, Humbert PO, Richardson HE. Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species. Oncogene. 2017 10 05; 36(40):5658-5660. PMID: 28980625.
    Citations: 5     Fields:    
  7. Manent J, Banerjee S, de Matos Simoes R, Zoranovic T, Mitsiades C, Penninger JM, Simpson KJ, Humbert PO, Richardson HE. Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species. Oncogene. 2017 10 05; 36(40):5576-5592. PMID: 28581519; PMCID: PMC5633656.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  8. Kawalia SB, Raschka T, Naz M, de Matos Simoes R, Senger P, Hofmann-Apitius M. Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. J Alzheimers Dis. 2017; 59(4):1237-1254. PMID: 28800327; PMCID: PMC5611835.
    Citations: 8     Fields:    Translation:Humans
  9. Matthews GM, de Matos Simoes R, Dhimolea E, Sheffer M, Gandolfi S, Dashevsky O, Sorrell JD, Mitsiades CS. NF-?B dysregulation in multiple myeloma. Semin Cancer Biol. 2016 08; 39:68-76. PMID: 27544796.
    Citations: 20     Fields:    Translation:HumansCells
  10. Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016 11 01; 32(21):3345-3347. PMID: 27402900.
    Citations: 6     Fields:    
  11. Buckley NE, Haddock P, De Matos Simoes R, Parkes E, Irwin G, Emmert-Streib F, McQuaid S, Kennedy R, Mullan P. A BRCA1 deficient, NF?B driven immune signal predicts good outcome in triple negative breast cancer. Oncotarget. 2016 Apr 12; 7(15):19884-96. PMID: 26943587.
    Citations: 16     Fields:    Translation:HumansCells
  12. de Matos Simoes R, Dalleau S, Williamson KE, Emmert-Streib F. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC Syst Biol. 2015 May 14; 9:21. PMID: 25971253.
    Citations: 4     Fields:    Translation:HumansCells
  13. Emmert-Streib F, de Matos Simoes R, Glazko G, McDade S, Haibe-Kains B, Holzinger A, Dehmer M, Campbell F. Functional and genetic analysis of the colon cancer network. BMC Bioinformatics. 2014; 15 Suppl 6:S6. PMID: 25079297.
    Citations: 12     Fields:    Translation:Humans
  14. Emmert-Streib F, de Matos Simoes R, Mullan P, Haibe-Kains B, Dehmer M. The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks. Front Genet. 2014; 5:15. PMID: 24550935.
    Citations: 27     
  15. de Matos Simoes R, Dehmer M, Emmert-Streib F. B-cell lymphoma gene regulatory networks: biological consistency among inference methods. Front Genet. 2013; 4:281. PMID: 24379827.
    Citations: 12     
  16. de Matos Simoes R, Dehmer M, Emmert-Streib F. Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. BMC Genomics. 2013 May 11; 14:324. PMID: 23663484.
    Citations: 16     Fields:    Translation:AnimalsCells
  17. Emmert-Streib F, Abogunrin F, de Matos Simoes R, Duggan B, Ruddock MW, Reid CN, Roddy O, White L, O'Kane HF, O'Rourke D, Anderson NH, Nambirajan T, Williamson KE. Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data. BMC Med. 2013 Jan 17; 11:12. PMID: 23327460.
    Citations: 5     Fields:    Translation:Humans
  18. Emmert-Streib F, Tripathi S, de Matos Simoes R. Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct. 2012 Dec 10; 7:44. PMID: 23227854.
    Citations: 10     Fields:    Translation:Humans
  19. Emmert-Streib F, de Matos Simoes R, Tripathi S, Glazko GV, Dehmer M. A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data. Sci Rep. 2012; 2:513. PMID: 22822426.
    Citations:    Fields:    Translation:Humans
  20. de Matos Simoes R, Tripathi S, Emmert-Streib F. Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. BMC Syst Biol. 2012 May 14; 6:38. PMID: 22583750.
    Citations: 11     Fields:    Translation:HumansCells
  21. de Matos Simoes R, Emmert-Streib F. Bagging statistical network inference from large-scale gene expression data. PLoS One. 2012; 7(3):e33624. PMID: 22479422.
    Citations: 50     Fields:    Translation:Animals
  22. Emmert-Streib F, Glazko GV, Altay G, de Matos Simoes R. Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front Genet. 2012; 3:8. PMID: 22408642.
    Citations: 49     
  23. de Matos Simoes R, Emmert-Streib F. Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks. PLoS One. 2011; 6(12):e29279. PMID: 22242113.
    Citations: 12     Fields:    Translation:Humans
  24. Ebersberger I, de Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A. A consistent phylogenetic backbone for the fungi. Mol Biol Evol. 2012 May; 29(5):1319-34. PMID: 22114356.
    Citations: 49     Fields:    Translation:Animals
  25. Cronin SJ, Nehme NT, Limmer S, Liegeois S, Pospisilik JA, Schramek D, Leibbrandt A, Simoes Rde M, Gruber S, Puc U, Ebersberger I, Zoranovic T, Neely GG, von Haeseler A, Ferrandon D, Penninger JM. Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Science. 2009 Jul 17; 325(5938):340-3. PMID: 19520911.
    Citations: 151     Fields:    Translation:AnimalsCells
  26. Catalanotti F, Reyes G, Jesenberger V, Galabova-Kovacs G, de Matos Simoes R, Carugo O, Baccarini M. A Mek1-Mek2 heterodimer determines the strength and duration of the Erk signal. Nat Struct Mol Biol. 2009 Mar; 16(3):294-303. PMID: 19219045.
    Citations: 68     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.