Tag: GBM

The demand for artificial intelligence software (AI) has increased significantly in recent years, and organizations of all sizes are adopting artificial intelligence to stay competitive. The top AI software and services detailed in this article use artificial intelligence techniques such as generative AI, machine learning, natural language processing, computer vision,…

nuttapong punna/iStock via Getty Images NovoCure Limited (NASDAQ:NVCR) is a good speculative biotech play to look into. That’s because I believe there is an enormous buy opportunity, which was created on the back of a selloff. I believe this selloff occurred as a result of misunderstood phase 3 lung cancer…

Get instant alerts when news breaks on your stocks. Claim your 1-week free trial to StreetInsider Premium here. TransCode Therapeutics, Inc. (NASDAQ: RNAZ) today announced acceptance for publication by Frontiers in Molecular Biosciences of a preclinical study using TransCode’s lead therapeutic candidate, TTX-MC138, in glioblastoma multiforme (GBM). The findings of…

Sweden – Hansa Biopharma (‘Hansa‘), a pioneer in enzyme technology for rare immunological conditions, today announced the first patient has been dosed with imlifidase in the GOOD-IDES-02 trial, a global pivotal phase 3 trial in anti-glomerular basement membrane (anti-GBM) disease. Soren Tulstrup, President and CEO, Hansa Biopharma said, ‘This is…

LUND, Sweden, May 30, 2023 /PRNewswire/ — Hansa Biopharma (“Hansa”), a pioneer in enzyme technology for rare immunological conditions, today announced the first patient has been dosed with imlifidase in the GOOD-IDES-02 trial, a global pivotal phase 3 trial in anti-glomerular basement membrane (anti-GBM) disease. Søren Tulstrup, President and CEO,…

Rznomics Inc., a South Korea based biopharmaceutical company specializing in the development of RNA-based gene therapeutics, has received phase 1/2a IND approval from the U.S. FDA for its glioblastoma multiforme (GBM) treatment. RZ-001 initially obtained IND approval for hepatocellular carcinoma (HCC), but Rznomics also found pre-clinical efficacy in GBM models…

Hello, I want to compare (with a PCA) gene expression against copy number variation at gene level in a TCGA project.When I retrieve the gene expression every value is mapped by sample and gene. But for the copy number variation, I get only chromosomal locations.To do the PCA, I want…

Data collection for HRD prediction model training and validation For the development of the HRD prediction model, 1854 samples (WGS data) from the pan-cancer analysis of whole genomes9 (PCAWG) and 560 breast cancer samples (SNP array data)16 are collected. To obtain a high-confidence training dataset of HRD, samples with BRCA1/2…

PRESS RELEASE Published May 12, 2023 (New York, USA) DelveInsight’s “Diffuse Large B-cell Lymphoma (DLBCL) Market Insights, Epidemiology, and Market Forecast-2032” report delivers an in-depth understanding of Diffuse Large B-cell Lymphoma (DLBCL), historical and forecasted epidemiology as well as the Diffuse Large B-cell Lymphoma (DLBCL) market trends in the United…

Research Alert Newswise — Glioblastoma (GBM) is the most aggressive glioma. Recently, immunotherapy using immune-checkpoint blockage (ICB) has provided therapeutic efficacy to various tumors. Despite an attractive ICB therapy, there have not been beneficial outcomes about GBM patients due to the characteristic of immunosuppressive environment. Thus, it is essential to…

Username or Email Password Forgot your password? Sign In Cancel by RStudio Sign in Register project = “TCGA-GBM”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”, by Ali Reza Rahimi Last updated about 4 hours ago Hide Comments (–) Share Hide Toolbars × Post on: Twitter Facebook Google+ Or…

illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion 0 I have downloaded a miRNA expression dataset from NCBI GEO (GSE25631) to study differential gene expression and perform other analyses. As mentioned in GEO, this profiling was performed on GPL8179 Illumina Human v2 MicroRNA expression beadchip. Accordingly,…

This question was also asked on Biostars I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample…

Activation of the polyamine-hypusine circuit is a hallmark of human cancer and of MYC-driven lymphoma. A, Copy number alterations (CNA) of EIF5A and EIFA2 (left), and of DHPS and DOHH (right) across different cancer types. Abbreviations for the indicated TCGA datasets are: prostate = PRAD; Liver Hepatocellular = LIHC; Diffuse…

I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample IDs with their phenotype) and the non-normalized…

Genome-scale CRISPR screen to identify regulators that maintain mESC pluripotency To establish a function-based PGRN, we first performed a CRISPR-Cas9 mediated genome-wide screen to detect genes essential for self-renewal. mESCs were cultured under Leukaemia inhibitory factors (LIF)/serum condition (L/S), which was commonly used in similar tasks and confer a naïve…

Expression of IGFL2 in cancer According to the TIMER2.0 database results, the difference in IGFL2 expression between cancer and normal tissues was significant in most cancers, including BLCA, BRCA, CHOL, COAD, ESCA, GBM, HNSC, KIRC, KIRP, LIHC, LUAD, LUSC, SKCM, HNSC, STAD THCA, and UCEC, while IGFL2 expression was higher…

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

Differential expression of DDR1 between tumor and normal tissue samples To better understand DDR1 expression levels in various cancer types, we first performed a pan-cancer analysis of 33 cancers in the TCGA database. Excluding cancers without corresponding normal samples, significant differences in DDR1 expression were found between tumor and normal…

Aim: Immunotherapy for glioblastoma multiforme (GBM) is limited because of a strongly immunosuppressive tumor microenvironment (TME). Remodeling the immune TME is an effective strategy to eliminate GBM immunotherapy resistance. Glioma stem cells (GSCs) are inherently resistant to chemotherapy and radiotherapy and involved in immune evasion mechanism. This study aimed to…

CANbridge Pharmaceuticals Inc. has announced that its therapy for glioblastoma has shown a 67% survival rate, three years after the clinical trials ended. Four out of nine of the patients with newly diagnosed glioblastoma multiforme (GBM) who were part of the clinical study were reported to be alive three years…

Newswise — SAN DIEGO, March 6, 2023 /PRNewswire/ — Denovo Biopharma LLC (“Denovo”), a pioneer in applying precision medicine to the development of innovative therapies, set up a gene registry web portal and invites people who suffer from treatment-resistant depression (TRD) to visit www.iMatchDepression.com to help identify whether they or someone they know may…

Presented here is a protocol to engineer a personalized organ-on-a-chip system that recapitulates the structure and function of the kidney glomerular filtration barrier by integrating genetically matched epithelial and vascular endothelial cells differentiated from human induced pluripotent stem cells. This bioengineered system can advance kidney precision medicine and related applications….

We aimed to assess the extent to which it was possible to effectively normalize and combine microarray and RNA-seq data with existing methods for use as a training set for machine learning applications. We assessed performance on holdout sets composed entirely of microarray data and entirely of RNA-seq data. To…

Introduction Melanoma is the deadliest type of skin cancer, with a rising yearly incidence.1,2 Despite the rapid development of checkpoint immunotherapy and targeted therapies, the main melanoma treatment methods include surgical resection and chemotherapy.3,4 Recent immunosuppressive agents increase the one-year survival rate of melanoma patients to more than 50%. However,…

AJIVE integration captures biologically joint-acting and cohort-specific variation AJIVE is an extension of JIVE that employs the use of thresholded Singular Value Decomposition (SVD) to create low-dimension approximations of input data matrices (Fig. 1). Then, through utilizing Principal Angle Analysis, identifies low-dimension subspace bases that either share variation structure (Joint) or…

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces such as R, Python, Scala, Java, JSON and Flow notebook/web interfaces, and works seamlessly with big data technologies such as Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models…

Introduction Gliomas are defined as human malignant tumors derived from glial cells. Gliomas account for almost 80% of all malignant brain tumors.1 To date, gliomas have beendivided into four subgroups from I to IV according to the pathologic grading system.2 The prognosis was associated with the subgroup. For the gliomas, lower…

Nluepke/Pixabay Innovative technologies such as the gene-editing tool CRISPR-Cas9 enable pioneering scientists to develop novel treatments for diseases such as cancer. A new study published in Science Translational Medicine funded by the National Institutes of Health unveils an innovative cancer vaccine developed with CRISPR-Cas9 that both terminates and prevents tumors…

Glioblastoma Multiforme (GBM) is the most aggressive form of primary brain cancer affecting adults. It is a devastating disease with an extremely poor prognosis, with a median survival of 14 to 16 months after treatment.1 The current standard of care, surgical resection followed by concurrent administration of radiation and temozolomide…

What are some alternatives? When comparing miceforest and scikit-learn you can also consider the following projects: Keras – Deep Learning for humans Prophet – Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth. Surprise – A Python scikit for building…

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

A new class of glioma drugs exploits tumors that lack the DNA repair enzyme MGMT; the drugs lead to the generation of cytotoxic DNA and selectively kill tumor cells without the risk of resistance, researchers report. The new approach may lead to new glioma treatments and may represent a new…

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

Name Last modified Size Description Parent Directory   –   TCGA-ACC.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 250K   TCGA-ACC.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 73K   TCGA-ACC.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 37K   TCGA-ACC.2018_02_16.sample_counts.tsv 2018-02-16 01:06 142   TCGA-BLCA.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 1.2M   TCGA-BLCA.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 90K   TCGA-BLCA.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 53K   TCGA-BLCA.2018_02_16.sample_counts.tsv 2018-02-16 01:06 201  …

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see MLInterfaces. Uniform interfaces to R machine learning procedures for data in Bioconductor containers Bioconductor version: 3.3 This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers. Author:…

In this article, we’ll learn about XGBoost, its background, its widely accepted usage in competitions such as Kaggle’s and help you build an intuitive understanding of it by diving into the foundation of this algorithm. XGBoost XGBoost is an algorithm that is highly flexible, portable, and efficient which is based on a decision tree for ensemble learning…

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MethPed. A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes Bioconductor version: 3.4 Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For…

TCGA Agilent level 2 to level 3 0 Hi there, I’m struggling to find documentation about how TCGA aggregated probe level data to gene level data (level 2 to level 3) for the Agilent microarray gene expression datasets (for GBM). I’m asking because the values seem to have been log…