Search Results - "Simoes, Ricardo de Matos"

Genome-Wide RNAi Screen Identifies Genes Involved in Intestinal Pathogenic Bacterial Infection by Cronin, Shane J.F, Nehme, Nadine T, Limmer, Stefanie, Liegeois, Samuel, Pospisilik, J. Andrew, Schramek, Daniel, Leibbrandt, Andreas, Simoes, Ricardo de Matos, Gruber, Susanne, Puc, Urszula, Ebersberger, Ingo, Zoranovic, Tamara, Neely, G. Gregory, von Haeseler, Arndt, Ferrandon, Dominique, Penninger, Josef M

“…Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved…”
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Bagging statistical network inference from large-scale gene expression data by de Matos Simoes, Ricardo, Emmert-Streib, Frank

“…Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from…”
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NF-κB dysregulation in multiple myeloma by Matthews, Geoffrey M., Ph.D, de Matos Simoes, Ricardo, Ph.D, Dhimolea, Eugen, Ph.D, Sheffer, Michal, Ph.D, Gandolfi, Sara, M.D, Dashevsky, Olga, Ph.D, Sorrell, Jeffrey D., B.A, Mitsiades, Constantine S., M.D., Ph.D

“…Abstract The nuclear factor-κB (NF-κB) transcription factor family plays critical roles in the pathophysiology of hematologic neoplasias, including multiple…”
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Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information by de Matos Simoes, Ricardo, Dehmer, Matthias, Emmert-Streib, Frank

“…In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote…”
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Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data by Moore, Daniel, Simoes, Ricardo de Matos, Dehmer, Matthias, Emmert-Streib, Frank

“…Background: Cancer is a complex disease with a lucid etiology and in understanding the causation, we need to appreciate this complexity. Objective: Here we are…”
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Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks by de Matos Simoes, Ricardo, Emmert-Streib, Frank

“…The inference of gene regulatory networks from gene expression data is a difficult problem because the performance of the inference algorithms depends on a…”
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Statistical inference and reverse engineering of gene regulatory networks from observational expression data by Emmert-Streib, Frank, Glazko, Galina V, Altay, Gökmen, de Matos Simoes, Ricardo

“…In this paper, we present a systematic and conceptual overview of methods for inferring gene regulatory networks from observational gene expression data…”
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A genome-wide Drosophila epithelial tumorigenesis screen identifies Tetraspanin 29Fb as an evolutionarily conserved suppressor of Ras-driven cancer by 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 F, Neely, G Gregory, Wernitznig, Andreas, Humbert, Patrick O, Simpson, Kaylene J, Mitsiades, Constantine S, Richardson, Helena E, Penninger, Josef M

“…Oncogenic mutations in the small GTPase Ras contribute to ~30% of human cancers. However, Ras mutations alone are insufficient for tumorigenesis, therefore it…”
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The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks by Emmert-Streib, Frank, de Matos Simoes, Ricardo, Mullan, Paul, Haibe-Kains, Benjamin, Dehmer, Matthias

“…In this study, we infer the breast cancer gene regulatory network from gene expression data. This network is obtained from the application of the BC3Net…”
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Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data by de Matos Simoes, Ricardo, Dalleau, Sabine, Williamson, Kate E, Emmert-Streib, Frank

“…Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and…”
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Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods by Emmert-Streib, Frank, Tripathi, Shailesh, de Matos Simoes, Ricardo

“…High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect…”
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An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence by Dhimolea, Eugen, de Matos Simoes, Ricardo, Kansara, Dhvanir, Al’Khafaji, Aziz, Bouyssou, Juliette, Weng, Xiang, Sharma, Shruti, Raja, Joseline, Awate, Pallavi, Shirasaki, Ryosuke, Tang, Huihui, Glassner, Brian J., Liu, Zhiyi, Gao, Dong, Bryan, Jordan, Bender, Samantha, Roth, Jennifer, Scheffer, Michal, Jeselsohn, Rinath, Gray, Nathanael S., Georgakoudi, Irene, Vazquez, Francisca, Tsherniak, Aviad, Chen, Yu, Welm, Alana, Duy, Cihangir, Melnick, Ari, Bartholdy, Boris, Brown, Myles, Culhane, Aedin C., Mitsiades, Constantine S.

“…Treatment-persistent residual tumors impede curative cancer therapy. To understand this cancer cell state we generated models of treatment persistence that…”
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A consistent phylogenetic backbone for the fungi by Ebersberger, Ingo, de Matos Simoes, Ricardo, Kupczok, Anne, Gube, Matthias, Kothe, Erika, Voigt, Kerstin, von Haeseler, Arndt

“…The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic…”
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Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data by Emmert-Streib, Frank, Abogunrin, Funso, de Matos Simoes, Ricardo, Duggan, Brian, Ruddock, Mark W, Reid, Cherith N, Roddy, Owen, White, Lisa, O'Kane, Hugh F, O'Rourke, Declan, Anderson, Neil H, Nambirajan, Thiagarajan, Williamson, Kate E

“…Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical,…”
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Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins by Shirasaki, Ryosuke, Matthews, Geoffrey M., Gandolfi, Sara, de Matos Simoes, Ricardo, Buckley, Dennis L., Raja Vora, Joseline, Sievers, Quinlan L., Brüggenthies, Johanna B., Dashevsky, Olga, Poarch, Haley, Tang, Huihui, Bariteau, Megan A., Sheffer, Michal, Hu, Yiguo, Downey-Kopyscinski, Sondra L., Hengeveld, Paul J., Glassner, Brian J., Dhimolea, Eugen, Ott, Christopher J., Zhang, Tinghu, Kwiatkowski, Nicholas P., Laubach, Jacob P., Schlossman, Robert L., Richardson, Paul G., Culhane, Aedin C., Groen, Richard W.J., Fischer, Eric S., Vazquez, Francisca, Tsherniak, Aviad, Hahn, William C., Levy, Joan, Auclair, Daniel, Licht, Jonathan D., Keats, Jonathan J., Boise, Lawrence H., Ebert, Benjamin L., Bradner, James E., Gray, Nathanael S., Mitsiades, Constantine S.

“…Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent…”
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TSPAN6 is a suppressor of Ras-driven cancer by Humbert, Patrick O., Pryjda, Tamara Zoranovic, Pranjic, Blanka, Farrell, Andrew, Fujikura, Kohei, de Matos Simoes, Ricardo, Karim, Rezaul, Kozieradzki, Ivona, Cronin, Shane J. F., Neely, G. Gregory, Meyer, Thomas F., Hagelkruys, Astrid, Richardson, Helena E., Penninger, Josef M.

“…Oncogenic mutations in the small GTPase RAS contribute to ~30% of human cancers. In a Drosophila genetic screen, we identified novel and evolutionary conserved…”
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Pleiotropic Mechanisms Drive Endocrine Resistance in the Three-Dimensional Bone Microenvironment by 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, Culhane, Aedín C, Brown, Myles, Georgakoudi, Irene, Mitsiades, Constantine S

“…Although hormonal therapy (HT) inhibits the growth of hormone receptor-positive (HR ) breast and prostate cancers, HT resistance frequently develops within the…”
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Functional and genetic analysis of the colon cancer network by Emmert-Streib, Frank, de Matos Simoes, Ricardo, Glazko, Galina, McDade, Simon, Haibe-Kains, Benjamin, Holzinger, Andreas, Dehmer, Matthias, Campbell, Frederick

“…Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take…”
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samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files by Stupnikov, Alexey, Tripathi, Shailesh, de Matos Simoes, Ricardo, McArt, Darragh, Salto-Tellez, Manuel, Glazko, Galina, Dehmer, Matthias, Emmert-Streib, Frank

“…Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However,…”
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Correction: TSPAN6 is a suppressor of Ras-driven cancer by Humbert, Patrick O., Pryjda, Tamara Zoranovic, Pranjic, Blanka, Farrell, Andrew, Fujikura, Kohei, de Matos Simoes, Ricardo, Karim, Rezaul, Kozieradzki, Ivona, Cronin, Shane J. F., Neely, G. Gregory, Meyer, Thomas F., Hagelkruys, Astrid, Richardson, Helena E., Penninger, Josef M.

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