Tag: tcga

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Position Summary Bioinformatics Data Scientist In this age of disruption, organizations need to navigate the future with confidence by tapping into the power of data analytics, robotics, and cognitive technologies such as Artificial Intelligence (AI). Our Strategy & Analytics portfolio helps clients leverage rigorous analytical capabilities and a pragmatic mindset…

Epigenomics, a rapidly advancing field within genomics, delves into the intricate mechanisms that regulate gene expression through chemical modifications to DNA and associated proteins. These epigenetic changes have profound implications for various biological processes and can influence the development of diseases. As the understanding of epigenomics expands, so does the…

Home – Elucidata Bioinformatics Scientist Job For MSc & PhD Bioinformatics, Comp Bio, Biotech Elucidata Bioinformatics Scientist Job For MSc & PhD Bioinformatics, Comp Bio, Biotech Senior Bioinformatics Scientist About the job Your Role: Elucidata is seeking a bioinformatics enthusiast for the role of Senior Bioinformatics Scientist. In this role, you will…

Why sone miRNAs are not present in TCGA data 0 Good Morning, Recently I have tried to perform some analysis using miRNA expression levels from TCGA specimens. I have downloaded data from www.linkedomics.org/login.php. I wonder whether some miRNA are not present in the miRNA expression tables from TCGA? Are those…

Where to get the molecular subtype information of STAD sample in TCGA 0 I want to obtain the molecular subtype information of STAD samples from TCGA, but I downloaded the clinical file from GDC and the phenotype file from UCSC xena, neither of them includes the subtype information. Does anyone…

Bioinformatics Lead Newton, MA (remote ok) Our Client is a Series A, pre-commercial, biotechnology company committed to saving lives through the early detection of cancer. They are looking for a passionate individual to lead Computational Biology for their R&D organization. This individual will play a critical role in the development…

Junior Bioinformatician position in BiNGS   We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core, to lead transcriptomics and epigenetics data analysis projects related but not limited to cancer biology, skin biology, developmental biology, diabetes, and neuron biology.   The mission…

Hi, I want to compare the mRNA expression in cancer patients that have a specific mutation vs. cancer patients that don’t have said mutation, using data from TCGA. I’m trying to combine data from two different tumor types (LUSC and LUAD), which I know is not appropriate to do given…

Alignment of case vs. control from different origin 0 Hi Biostars! I am coming to you with a relatively simple question, but one that i have surprisingly not found and answer to. I am working with a case-cohort of samples that were prepared for RNA-seq as paired reads with a…

RNAseq Data and Pipeline 1 Hello, I am currently trying to do differential gene expression with TCGA data imported with R (GDCquery). I want to utilize DESeq2 as it is widely used and want publication quality results. I am struggling to understand where “raw” counts are found for star –…

Transposable elements (TEs) are typically silenced by DNA methylation and repressive histone modifications in differentiated healthy human tissues. However, TE expression increases in a wide range of cancers and is correlated with global hypomethylation of cancer genomes. We assessed expression and DNA methylation of TEs in fibroblast cells that were…

Job ID: req3395Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USAThe Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The lab addresses some of…

Job Description Job Responsibilities: Lead the development of new bioinformatics algorithms, pipelines, and infrastructure in a cloud-based environment in support of LifeDNA’s discovery platform Apply rigorous standards and processes for code quality, configuration and change management, data provenance, and organization of supporting computational infrastructure to ensure accurate and reproducible analysis…

Microarray-based expression analysis and GEO database analysis The DLBCL-related miRNA expression profiles of GSE29493 and GSE40239 were retrieved from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/). MiR-124’s pan cancer analysis is conducted through online websites (www.picb.ac.cn/dbDEMC/). Bioinformatics predicted NFATc1 as the target of miR-124-3p The miRbase (www.mirbase.org/), miRDB (mirdb.org), and…

Junior Bioinformatics Analyst Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses some…

Why are some WES VCFs larger than others? 2 I’m working with BAMs from TCGA. Some of these exomes are 10x larger than other files: 60GB vs 6GB. I assume that must be depth related. However, the VCFs derived from these larger BAMs have 1.7M entries (300MB+). The exome itself…

How to deal with duplicated gene IDs in TCGA RNA expression data? 0 Hi! I am trying to analyse genes that could be differentially expressed between two groups of patients with breast cancer from the TCGA data, but I noticed that some genes are duplicated (using Gene Entrez IDs), with…

Why are some WES files larger than others? 0 I’m working with BAMs from TCGA. Some of these exomes are 10x larger than other files: 60GB vs 6GB. I assume that must be depth related. However, the VCFs derived from these larger BAMs have 1.7M entries (300MB+). The exome itself…

Home – Elucidata Bioinformatics Job For MSc & PhD Bioinformatics, Comp Bio, Biotech Elucidata Bioinformatics Job For MSc & PhD Bioinformatics, Comp Bio, Biotech Hey there, if you are looking for some assistance with the possible interview questions and answers for the role of Bioinformatics Scientist II at Elucidata, then…

corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database 0 hello everyone.. I have a problem seems to be very easy but I cant find a solution so I need your help. I have downloaded PSI values for CHOL (cholangiocarcinoma) AS events from…

Who You Are: You are an intrepid Bioinformatics Data Analyst passionate about distilling information from biological datasets. You have strong skills in bioinformatics, statistics & statistical learning, data science, data visualization & building data analysis dashboards/reports. You have worked on biological problems involving NGS readouts and understand biological engineering principles….

The Department of Bioinformatics and Computational Biology at MD Anderson Cancer Center, Houston, Texas, USA, is seeking a postdoctoral fellow. The individual will work on cutting edge cancer related research projects at the top ranked cancer hospital in the US. The work involves computational analysis, and no wet lab experience…

The Department of Bioinformatics and Computational Biology at MD Anderson Cancer Center, Houston, Texas, USA, is seeking a postdoctoral fellow. The individual will work on cutting edge cancer related research projects at the top ranked cancer hospital in the US. The work involves computational analysis, and no wet lab experience…

Comment: DoparParam() execution fails when foreach() works by boris • 0 Registration allows me to use ClusterMQ as the backend for foreach/BiocParallel, linking to SLURM and unlocking far larger compute resource… Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170 Have you increased the version so that it builds…

Read the Full Video Transcript Andrea Miyahira: Hi, everyone. I’m Andrea Miyahira and I’m the senior director of global research and scientific communications at PCF. Today I’m joined by Dr. Akash Patnaik, an assistant professor at the University of Chicago Comprehensive Cancer Center. Dr. Patnaik is joining me today to…

Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. Through our partnership with the National Institutes of Health, Kelly Government Solutions offers administrative, IT, engineering, scientific, and healthcare professionals the opportunity to work with the leading medical research center in the…

The Molecular Profiling and Data Science Department is looking for an enthusiastic and motivated Computational Scientist who values independent research in an open and collaborative working environment. You will participate in original studies that span from basic research to translation studies, directly impacting the lives of patients. You will also…

We are hiring a confident Bioinformatics Software Engineer to join our diverse team at TESA Research in Park City, UT.Growing your career as a Full Time Bioinformatics Software Engineer is a fantastic opportunity to develop relevant skills.If you are strong in people management, cooperation and have the right mindset for…

Introduction Pancreatic cancer (PC) is a malignant tumor with a very high mortality rate for which there is no effective treatment other than surgery.1,2 PC is prone to metastasis and invasion in the early stage, and there is no effective means for early detection. Most patients often have cancer metastasis…

RBW Consulting have partnered with a small to mid sized Cambridge base Biotech who are looking to grow their team. There is an opportunity to join a growing Bioinformatics team, report directly into the Director of Bioinformatics and work on multiple projects that are within the clinical trial phase of…

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…

doi: 10.1093/bioinformatics/btad330. Online ahead of print. Affiliations Expand Affiliations 1 Graduate School of Public Health and Health Policy, City University of New York, New York, United States of America. 2 Institute for Implementation Science and Population Health, City University of New York, New York, United States of America. 3 Roswell…

Ruli Gao, PhD, assistant professor of Biochemistry and Molecular Genetics and a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University, was senior author of the study published in the Journal of Clinical Investigation. Northwestern Medicine scientists have shed new light on how the deadliest form of…

Molecular profiling reveals common changes in matched pairs of HNSCC primary tumor and metastasis-derived cell lines Identification of both genetic and functional differences between primary and metastatic variants of HNSCC would be enabled by in vitro models derived independently from these sites from the same patient. Unfortunately, HNSCC tumor cells…

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…

Low-grade gliomas (LGG) are a type of brain tumor that can be lethal, and it is essential to identify genes that are correlated with patient prognosis. In this study, we aimed to use CRISPR-cas9 screening data to identify key signaling pathways and develop a genetic signature associated with high-risk, low-grade…

The tumor microenvironment (TME) dynamically regulates cancer progression and affects clinical outcomes. This study aimed to identify molecular subtypes and construct a prognostic risk model based on TME-related signatures in skin cutaneous melanoma (SKCM) patients. We categorized SKCM patients based on transcriptome data of SKCM from The Cancer Genome Atlas…

Senior Principle Bioinformatics Scientist Permanent £40,000 – £60,000 We have an exciting opportunity for a Senior Bioinformatics Scientist to join our client, a growing biotech company based in Cambridge who are looking to expand their successful team! Our client is actively working on a portfolio of unique DNA projects and…

Cell culture The MDA-MB231 (MB231) human breast cancer cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA) and grown in RPM1-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Waltham, MA) at 37 °C in a humidified atmosphere of 5% CO2 in the air. Cells were…

Abstract Background: Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor, which poses a serious threat to human health. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification involved in regulating a broad range of biological processes and has been considered as potential therapeutic target in types of cancer. However, there…

Background: Metabolites of tryptophan (Trp) metabolism in the tumor microenvironment play crucial immunosuppressive roles in various cancers. However, the role of Trp metabolism in diffuse large B-cell lymphoma (DLBCL) or natural killer/T-cell lymphoma (NK/TCL) remains unelucidated. Methods: We investigated the potential role of Trp metabolism in a cohort of 43…

TCGA CNV data 1p/19q codeletion (whole arm deletion) 2 Hi, you implied that you have already obtained the data. So, please proceed with your analysis. You will have to develop some code that identifies deletion of the entire chromosomal arms. You can create rules that define whether an arm is…

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics…

Identify necroptosis-related lncRNAs in SKCM There are 386 necroptosis-related lncRNAs identified from the data of TCGA and GTEx, as the standard is the coefficients > 0.4 and P < 0.001. After that, flowing the differential expression analysis, 87 necroptosis-related lncRNAs were found to display significantly differential expression with the screen value as |logFC…

Bioinformatics Data Scientist In this age of disruption, organizations need to navigate the future with confidence by tapping into the power of data analytics, robotics, and cognitive technologies such as Artificial Intelligence (AI). Our Strategy & Analytics portfolio helps clients leverage rigorous analytical capabilities and a pragmatic mindset to solve…

Advances in genomic technologies provide researchers with access to more complete molecular datasets than ever before. Next-generation sequencing (NGS) in particular propels both basic and translational research forward, enabling scientists to see the full picture of biology. As a result, researchers now know more about the genetics and pathways underlying…

How to download data for a specific time period in GDC portal? 0 Hello, I am trying to download the data used in a specific paper to benchmark the performance of their model. The paper I am referring to is “Classification of Cancer Types Using Graph Convolutional Neural Networks” (www.frontiersin.org/articles/10.3389/fphy.2020.00203/full)….

Code in google colab: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“TCGAbiolinks”) Error message: Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details. Replacement repositories: CRAN: cran.rstudio.com Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) ‘BiocVersion’, ‘TCGAbiolinks’ Warning…

Bioinformatics Analyst II Job ID: req2894Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

Tumor-infiltrating immune cells 1 Hi, I have a list of genes and samples which got from TCGA in STAR count format and normalize them with edgeR and limma packages, now I want to assess Tumor-infiltrating immune cells, I try TIMER v2, but the input in this site should be TPM-normalized…

Code in google colab: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“TCGAbiolinks”) Error message: Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details. Replacement repositories: CRAN: cran.rstudio.com Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) ‘BiocVersion’, ‘TCGAbiolinks’ Warning…

TCGAbiolinks error 2023 0 Hello! I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got this error: Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) ‘TCGAbiolinks’ Warning message: “package ‘TCGAbiolinks’ is not available for Bioconductor version ‘3.17’ ​What should I do to fix…

How to test DEGs from microarray data on RNA-seq dataset 0 Hi there, I want to create a predictive score of whether a tissue is diseased or healthy with the DEGs that I’ve yielded from a limma analysis (with subsequent refining through stepwise regression methods and currently working on including…

Generation and characterization of rs11706832-variant HEK293T clones A modified version of HEK293T cells where one allele of the entire LRIG1 gene has been deleted15, was used to study the potential effects of the risk SNP rs11706832 on transcriptomics and metabolomics. Sanger sequencing revealed that the single copy of rs11706832 in…

DOI: 10.18129/B9.bioc.OutSplice   This is the development version of OutSplice; to use it, please install the devel version of Bioconductor. Comparison of Splicing Events between Tumor and Normal Samples Bioconductor version: Development (3.17) An easy to use tool that can compare splicing events in tumor and normal tissue samples using…

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…

Slides from this training: qiagen.showpad.com/share/TgxuabZORvDS3uLGCJRGN You asked for it, and we’re here to deliver. We are hosting a comprehensive training on effectively using sample-level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and others through QIAGEN Ingenuity Pathway Analysis (IPA) and the IPA Analysis Match…

Skin cutaneous melanoma (SKCM) has a low early detection rate and a high mortality rate. There are many problems such as side effects and drug resistance in existing therapeutic drugs. Current studies have confirmed that SKCM pathogenesis-related genes promote the invasion and metastasis of cutaneous melanoma, but their roles in…

GDC API: Obtain the Objective Power (or Magnification) of a WSI file 0 I’ve been trying to find out a way to retrieve the Objective Power (or Magnification) of a Whole Slide Image file without downloading it first, using the GDC API. I’ve seen that some WSI’s Objective power might…

WGCNA problem 0 Hello. I have problem to choose soft power for WGCNA. please guide me!! I have 501 sample (cancer=481 , normal=39) that download from TCGA database. Then, normalization and filtration was carried out using TCGA package. With this data I started using WGCNA for co-expression network analysis. For…

     Seq2science ChIP-seq hub ChIP-seqhidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 updated Fix Patcheshidedensesquishpackfull p14 updated Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow Problematic Regionshidedensesquishpackfull new Recomb…

Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…

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…

In a recent interview, Shilpa Gupta, MD, a genitourinary oncologist from Case Comprehensive Cancer Center, discussed findings from the phase 2 BLASST-1 trial (NCT03294304)1 in muscle-invasive bladder cancer (MIBC) she presented at the 2023 ASCO Genitourinary (GU) Cancers Symposium. She also highlighted the latest developments and ongoing challenges in the…

Struggling with protein context of Annovar output 0 Hi, Im having some troubles extracting the protein sequences of missense mutations from annovar output files. I would like to create all of the possible neopeptides arising from missense mutations of TCGA tumor samples. For this I used Annovar to get the…

Multi-omics analyses of the ICC samples Following multiregional sampling of primary ICC cases, we performed multi-omics analyses, including genome, transcriptome, proteome, and metabolome analysis. We used 10 (67 samples), 11 (88 samples), 10 (49 samples) and 10 (49 samples) ICC cases for WES, whole-transcriptome sequencing, proteomic analysis, and metabolomic analysis,…

Unable to create pd file for ChAMP analysis 0 I have downloaded TCGA-BRCA DNA methylation (of data type: Methylation Beta Value) of 895 samples (txt files, not idat files) from GDC portal. That csv file contains CpG probe Ids as rownames and TCGA Ids as column names. I wanted to…

Background: FBXW7 is recognized as a critical tumor suppressor gene and a component of the ubiquitin-proteasome system, mediating the degradation of multiple oncogenic proteins, including c-MYC, Cyclin E, c-Jun, Notch, p53. Around 16% of colorectal cancer (CRC) patients carried FBXW7 somatic mutations, while a comprehensive characterization of FBXW7 somatic mutations…

How can I make a similar mutated gene expression figure with TCGA data 1 Student just starting out in a cancer genomics lab. I have a paper in which I am interested in replicating the first figure to get a grasp on the techniques used, but unsure what steps I…

HhS activation is a marker of poor prognosis in BLCA patients First, HhS scores were calculated and its expression characteristics were analyzed for patients in the TGCA-BLCA cohort. The results showed that HhS was overactivated in patients with higher stage and older age (Fig. 2A, B). And there is no significant…

Hey guys. Good afternoon. I would like to separate the TCGA-STAD data into two groups, one with high expression for gene x, and one with low expression for gene x. I would like to separate these groups according to quartiles, taking the upper and lower quartiles. Then, I would perform…

Ethics statement All experiments were conducted in accordance with the Declaration of Helsinki and the study was approved by the University of Chicago Institutional Review Board, IRB 22-0707. For model training, patients were included from the TCGA breast cancer cohort (BRCA)26. For validation, anonymized archival tissue samples were retrieved from…

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…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

I am trying to download the TCGA-DLBC sequencing data from GDC using Bioconductor’s TCGAbiolinks library. I ran the following code query_TCGA <- GDCquery(project=”TCGA-DLBC”, data.category = ‘Sequencing Reads’, experimental.strategy = ‘RNA-Seq’, data.type=”Aligned Reads”, data.format=”bam”, workflow.type=”STAR 2-Pass Transcriptome”, barcode = c(‘TCGA-GR-7351-01A-11R-2213-07’) ) getResults(query_TCGA) which worked, however when I ran GDCdownload(query_TCGA) it returned:…

Wilmington, Delaware, United States, April 12, 2023 (GLOBE NEWSWIRE) — The global next-generation sequencing data analysis market was valued at USD 610.6 Mn in 2021 and is projected to reach USD 5.4 Bn by 2032 growing at a CAGR of 16.6%. Integration of genome medicine into clinical practice is expected…

Introduction Cervical cancer (CC) is one of the most widespread gynaecological cancers that threatens women’s health in developing countries.Citation1 CC progresses through a long stage of precancerous lesions, called cervical intraepithelial neoplasia (CIN), which is classified into three grades: CIN 1, CIN 2 and CIN 3.Citation2 Human papillomaviruses (HPVs) have…

Introduction Breast cancer is the second most common cancer and is the leading cause of cancer-related death among females worldwide with over 2 million newly diagnosed cases and more than 60 thousand deaths every year.Citation1 Despite advances in treatment, the mortality rate of breast cancer remains high, mainly due to…

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…

Anyone familiar with ICGC’s DCC data releases? 0 Hi all, As part of my project, I wanted to find recurrent somatic mutations in cancer, but not only coding regions, I want to assess the whole genome for noncoding somatic mutations -> Thus I need WGS data. My supervisor directed me…

Job Description: GDIT’s Military Health team is seeking a Data Manager – Bioinformatics Analyst in support of the Naval Health Research Center (NHRC) Infectious Disease Field Surveillance and Laboratory Research Services. As the Navy hub for the Armed Forces Health Surveillance Center the NHRC Operational Infectious Diseases Directorate conducts on-going,…

Bioinformatics Analyst II Job ID: req2894Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The…

Background: The tumor microenvironment plays a crucial role in the oncogenesis and treatment of diffuse large B-cell lymphoma (DLBCL). The H3K9me3-specific histone methyltransferase Suppressor of variegation 3-9 homolog 1 (SUV39H1) is a significant gene that promotes the progression of various malignancies. However, the specific expression of SUV39H1 in DLBCL remains…

Whole-exome genome sequencing on tumor specimens revealed genetic molecular subtypes in advanced bladder cancer that correlated with patient response to immune checkpoint blockade, suggesting that this strategy may aid treatment decision making in this patient population, according to findings from a study published in Journal of Clinical Oncology. “Our study…

Best way to find co-regulated transcripts in TCGA data set 0 I am interested in the possibility of using PCA or other such segmentation approaches to examine whether functionally related components of large multiprotein complexes or signaling pathways are coregulated in cancers. So for example are there specific sub-complexes of…

Designation: Research Scientist – Bioinformatics Identify new targets and potential pipeline molecules for Immuno-oncology by working closely with Artificial Intelligence and drug discovery scientists Provide informatics support to build pipeline for the organization with Chemists, biologists, and pharma R D experts in the area of cancer Build predictive models using…

Position Summary: As a Bioinformatics Specialist you will be responsible for providing solutions to the customer for overcoming the technical difficulties encountered in the analysis pipeline. It is expected of you to have good analytical thinking to understand the error and provide solution and possible explanations for the same. As…

Non-zero expression counts from deleted genes 0 Hi all, I’ve been looking at the RNA-seq data (STAR counts) for homozygously deleted genes (ASCAT copy number = 0) in TCGA and don’t understand what I’m seeing. I expected these genes to have zero or negligible TPMs, but actually the vast majority…

Hi guys, I’m relatively new to any type of analytics work and Rstudio. However, when inputting my TCGA data and doing all of the basic steps, my volcano plot and log2foldchange values seem to all be the opposite of what was expected. I understand perhaps this could just be the…

Certis Oncology Solutions (“Certis”), a precision oncology and translational science company focused on combining functional assays and artificial intelligence to advance personalized medicine, today announced that three abstracts have been accepted for presentation at the upcoming American Association for Cancer Research (AACR) Annual Meeting, to be held in Orlando, Fla….

Regression coefficient for downstream analysis from lasso regression for survival analysis 0 I have one dataset which I have used to build and generate a model for survival prediction. Here I get like 40 genes as my predictor which I have tested both in my test and train dataset so…

Cell line expression of tumor-specific TE-chimeric transcripts. a, Box plots with overlaid dot plots of the number of candidates expressed in each cancer cell line profiled across various tumor types. The ‘N=’ lists the number of cell lines in each boxplot. Box plot format: center line, median; box limits, upper…

Therapy response for multiple cancer types 0 I need help with accessing some kind of analysis. I will appreciate any comment, advice or recommendation about it. I need to learn how expression levels of some genes are associated with therapy (chemo and immunotherapy) response (binary or survival time) for a…

Review . 2023 Mar 14;13:1147239. doi: 10.3389/fonc.2023.1147239. eCollection 2023. Affiliations Expand Affiliations 1 Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China. 2 Qingdao Cancer Institute, Qingdao, China. 3 School of Basic Medicine, Qingdao University, Qingdao, China. 4 Department of Pharmacology, School of Pharmacy, Qingdao University,…

Figure 1. Identification and validation of hsa_circ_0008234 in colon cancer Notes: (A): The highest five increased and decreased circRNAs between the normal and colon cancer tissue obtained from the GSE172229. (B): Volcano plot of the differentially expressed circRNAs with the threshold of |logFC| > 1 and p < 0.05. (C):…

TCGA-BRCA tissue and RNAseq problem 0 I’m trying to analyze RNAseq data from the TCGA-BRCA project. I’ve downloaded the STAR count tsv files as well as the clinical and sample manifests/metadata. The problem is that there is no column entry in the “clinical.tsv” which indicates tissue sample type so as…

NEW YORK ­­­­­­­­­­­­– Transposable element (TE) promoters that get reactivated in cancer cells can lead to chimeric transcripts involving parts of protein-coding genes, resulting in cancer-specific cell surface antigens, a new study has found. The findings point to potential new treatment strategies, including immunotherapy and a pan-cancer vaccine. TEs, also…