bg.upf.edu
New IntOGen web to explore driver genes across cancer types » Computational Oncogenomics
http://bg.upf.edu/blog/2015/03/new-intogen-web-to-explore-driver-genes-across-cancer-types
The biomedical genomics blog. New IntOGen web to explore driver genes across cancer types. Coinciding with the publication of our latest paper, on Monday (9 March 2015) ( See blog post. We have crafted a new IntOGen interface which presents the results of the analysis of somatic mutations across almost 7000 cancer samples from 28 different cancer types to identify driver genes. The analysis identified 459. On each page for a gene, cancer type or a project you will find multiple reports, such as a cancers...
bg.upf.edu
In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities » Computational Oncogenomics
http://bg.upf.edu/blog/2015/03/in-silico-prescription-of-anticancer-drugs-to-cohorts-of-28-tumor-types-reveals-novel-targeting-opportunities
The biomedical genomics blog. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. We are pleased to announce the publication of our paper. Describing the landscape of anti-cancer targeted therapeutic opportunities across a cohort of patients of twenty eight of the most prevalent cancers. Prescription approach to obtain the landscape of targeted drugs against cancer driver alterations, composed of three main steps. 1) Discover the actionable.
bg.upf.edu
OncodriveROLE predicts activating and loss of function cancer driver genes » Computational Oncogenomics
http://bg.upf.edu/blog/2014/08/oncodriverole-predicts-activating-and-loss-of-function-cancer-driver-genes
The biomedical genomics blog. OncodriveROLE predicts activating and loss of function cancer driver genes. We are pleased to announce that the Oncodrive methods family has a new member: OncodriveROLE. An approach to classify cancer drivers into loss of function and activating roles. OncodriveROLE joins and complements the previously developed methods that identify cancer driver genes from the list of somatic mutations in cohort of tumors (OncodriveCLUST and OncodriveFM). And freely available online. I...
bg.upf.edu
Biomedical Genomics Group
http://bg.upf.edu/group/tools.php
In our group we have developed several methods and tools for the analysis and visualization of cancer genomics data. Below is a description of the main tools and methods:. A discovery tool for cancer researchers. To identify cancer drivers: OncodriveFM. And classify them according to their role OncodriveROLE. Methods to assess the functional impact of mutations: Condel. Sample Level Enrichment Analysis: SLEA. Integrative OncoGenomics (IntOGen: http:/ www.intogen.org. The IntOGen Mutation Analysis Pipeline.
mpschr.com
mpschr.com - Another no purpose web site. Michael P Schroeder
http://www.mpschr.com/projects
I work am doing my PhD as a bioinformatician at the Biomedical Genomics Group. In Barcelona and am involved in various projects. Some of which, listed below. A framework for analysis and visualization of multidimensional genomic data using interactive heat-maps. So far I have been able to contribute to the scientific literature. And also blog entries at the Biomedical Genomics group. But I also keep myself busy during my "free" time:. Go, Teachers, Go! Is a content managing system to bet on football.
bg.upf.edu
Biomedical Genomics Group
http://bg.upf.edu/group/courses/big.php
Course on Bioinformatics for Integrative Genomics. Exploring and making sense of multidimensional data sets that result from merging heterogeneous genomic data resources. Which of the genes affected by those mutations are already known to be involved in cancer or other diseases? Which pathways or biological processes are affected by the transcriptomic alterations detected in my experiment? To achieve these objectives we will use three tools developed in our lab:. Http:/ www.gitools.org. Christian Perez-L...
bg.upf.edu
Biomedical Genomics Group
http://bg.upf.edu/group/papers.php
Radhakrishnan Sabarinathan, Loris Mularoni, Jordi Deu-Pons, Abel Gonzalez-Perez, Nuria Lopez-Bigas. Nucleotide excision repair is impaired by binding of transcription factors to DNA. Nature 2016, 532, 264-267 (14 April 2016) doi:10.1038/nature17661. Nature News and Views. Ross-Macdonald P, Esteller M, Gray N, Haber DA, Stratton MR, Benes CH, Wessels LFA , Saez-Rodriguez J , McDermott U , Garnett MJ. A landscape of pharmacogenomic interactions in cancer. Cell 166, 1-15, 2016. Iturbide A, Lopez-Bigas N.
bg.upf.edu
How to generate mutation distribution and frequency plots? » Computational Oncogenomics
http://bg.upf.edu/blog/2014/12/how-to-generate-mutation-distribution-and-frequency-plots-2
The biomedical genomics blog. How to generate mutation distribution and frequency plots? Let’s plot some mutations! For our next iteration of the IntOGen database, we wanted to add figures that represent the mutation distribution across the protein sequence. And we found ourselves, just as others. In the situation, that we know that there are solutions, but none is available for us to incorporate in the web portal. Mutation Needle Plot (muts-needle-plot). Select the region and you’ll know. Http:/ registr...
bg.upf.edu
Computational Oncogenomics
http://bg.upf.edu/blog
The biomedical genomics blog. Our paper demonstrating that proteins bound to DNA impair Nucleotide Excision Repair published in Nature. I am very happy to announce that our manuscript describing the increased mutation rate in Transcription Factor Binding Sites (TFBS) in melanomas and lung tumors has been published in today’s issue of Nature. In the manuscript we demonstrate that this accumulation is due to the impairment of Nucleotide Excision Repair (NER) activity by proteins bound to DNA. Where all dat...
genelab-data.ndc.nasa.gov
GeneLab
https://genelab-data.ndc.nasa.gov/genelab/static_pages/dataminingtools
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. GenePattern is a powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. Center f...
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