Tag: gtex
Talentify.io hiring 100% Remote- Bioinformatics Analyst ($50.00 – $55.00 / hour) in United States
Talentify helps candidates around the world to discover and stay focused on the jobs they want until they can complete a full application in the hiring company career page/ATS. Seeking a Bioinformatics Analyst 100% Remote Description Support of computational research priorities associated with oncology discovery programs. This variably entails querying…
SPECTRAFORCE hiring Bioinformatics Analyst III in North Chicago, Illinois, United States
Title: Bioinformatics Analyst III Duration: 12 Months Location/Site: 100% Remote Pay Rate: $51/hr. – $56/hr. on w2 Job Description Services Overview: Services include support of computational research priorities associated with oncology discovery programs. This variably entails querying public cancer genomics resources for mutation/expression distributions, assessing normal expression, interpreting germline associations…
Job Opening – Bioinformatics Analyst III – North Chicago, IL
job summary: As the largest staffing and recruitment agency in the world, we can commit to finding you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network of…
Deloitte Consulting hiring BioInformatics Data Scientist in Atlanta, Georgia, United States
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…
Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine
Study design and participants The GCKD study is an ongoing prospective observational study that enrolled 5,217 adult persons with CKD between 2010 and 2012. Patients regularly seen by nephrologists with eGFR between 30 and 60 ml min−1 per 1.73 m2 or eGFR >60 ml min−1 per 1.73 m2 with UACR > 300 mg per g (or urinary protein/creatinine ratio > 500 mg…
calculate p value and associated z score for snp-gene pair
calculate p value and associated z score for snp-gene pair 0 Hello everyone, I have genotype file and gene expression file. I want to see whether three of my rsid in genotype file is associated with gene expression. I used matrixeqtl R package to generate p value and see whether…
Bioinformatics Lead job with Delson Talent Consulting
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…
Bioinformatics in Next Generation Sequencing (BiNGS) – Icahn School of Medicine hiring Junior Bioinformatician in New York, New York, United States
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…
Multi-ethnic genome study unlocks new genetic links to health conditions
Human health status can be determined based on the circulating metabolite levels. Although it is important to understand the genetic architecture of these metabolites, to date, they are not well understood. Considering this research gap, a recent Nature Communications study focused on performing whole-genome sequencing analysis of circulating human metabolites in a…
Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation
Vogel, B. et al. The Lancet women and cardiovascular disease Commission: reducing the global burden by 2030. Lancet 397, 2385–2438 (2021). Article PubMed Google Scholar Adlam, D., Alfonso, F., Maas, A., Vrints, C. & Writing Committee. European Society of Cardiology, acute cardiovascular care association, SCAD study group: a position paper…
A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology
Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…
Job: Senior Data Engineer (Bioinformatics) | WFH
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…
An adaptive and robust method for multi-trait analysis of genome-wide association studies using summary statistics
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461:747–53. Article CAS PubMed PubMed Central Google Scholar Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW. Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet….
Creyon Bio hiring Bioinformatics Analyst in San Diego Metropolitan Area
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….
Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture
We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…
Screening/validation of pivotal pancreatic cancer gene DPYD
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…
Multi-ancestry meta-analysis and fine-mapping in Alzheimer’s disease
Tanzi RE, Bertram L. New frontiers in Alzheimer’s disease genetics. Neuron. 2001;32:181–4. Article CAS PubMed Google Scholar Holland D, Frei O, Desikan R, Fan C-C, Shadrin AA, Smeland OB, et al. The genetic architecture of human complex phenotypes is modulated by linkage disequilibrium and heterozygosity. Genetics. 2021;217:iyaa046. Article PubMed PubMed…
Scientist I, Bioinformatics – Virtual based – North Chicago
The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…
Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn’s disease: a multi-omics Mendelian randomization study | BMC Medicine
Baumgart DC, Sandborn WJ. Crohn’s disease. Lancet. 2012;380(9853):1590–605. Article PubMed Google Scholar Bernstein CN. Treatment of IBD: where we are and where we are going. Am J Gastroenterol. 2015;110(1):114–26. Article PubMed Google Scholar Sies H. Oxidative stress: a concept in redox biology and medicine. Redox Biol. 2015;4:180–3. Article CAS PubMed …
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk
Development and benchmarking of MEGAnE Accurate variant genotyping is required for statistical genetics. To enable both discovery and accurate MEV genotyping from genomes studied using short reads, we developed a new bioinformatic tool, mobile element genotype analysis environment (MEGAnE; Supplementary Note). Compared to SVs resolved by long reads, MEGAnE discovers…
Senior Bioinformatics Scientist @ Natera
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…
Comprehensive prediction of immune microenvironment and hot and cold tumor differentiation in cutaneous melanoma based on necroptosis-related lncRNA
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…
Deloitte Jobs – BioInformatics Data Scientist in Atlanta, Georgia, United States
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…
Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing
There are over 20,000 protein-coding genes in the human genome, but only a proportion of them are expressed in each tissue8. In addition to expression, pervasive variations in RNA splicing, including switch-like alternatively spliced exons, have also been observed across different human tissues9. To address this limitation, Wagner et al….
A Better Telescope Gazing at the Transcriptome
Jason Underwood, PhDPacBio In the middle of 2022, the world saw the first image from the Webb Space Telescope, a new cutting-edge instrument certain to unlock new secrets about the universe. That first infrared image showed a tiny sliver of a universe with thousands of galaxies with brightness and clarity…
Alternative CDC20 translational isoforms tune mitotic arrest duration
Musacchio, A. The molecular biology of spindle assembly checkpoint signaling dynamics. Curr. Biol. 25, R1002–R1018 (2015). Article CAS PubMed Google Scholar Lara-Gonzalez, P., Pines, J. & Desai, A. Spindle assembly checkpoint activation and silencing at kinetochores. Semin. Cell Dev. Biol. 117, 86–98 (2021). Article CAS PubMed PubMed Central Google Scholar …
Annotating and prioritizing human non-coding variants with RegulomeDB v.2
Nearly 90% of the disease risk-associated variants identified by genome-wide association studies are in non-coding regions of the genome. The annotations obtained by analyzing functional genomics assays can provide additional information to pinpoint causal variants, which are often not the lead variants identified from association studies. However, the lack of…
Make discoveries from public data (GEO, SRA and more) using QIAGEN Ingenuity Pathway Analysis
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…
Human hg38 chr10:21,513,475-21,525,682 UCSC Genome Browser v446
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…
Scientist, Bioinformatics job with Amplifybio, LLC
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…
Mean read length from bam file
Mean read length from bam file 3 Hi biostars, I have a question about calculating the median read length from a bam file. samtools view GTEX-1192X-0011-R10a-SM-DO941.bam | awk ‘{print length($10)}’ | head -1000 | sort -u Instead of the above command line, is it possible to get a median read…
Scientist I, Bioinformatics – Virtual based job with AbbVie
The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…
Scientists Create Largest Atlas of Post-Zygotic Human Gene Mutations
Researchers headed by a team at Oregon Health & Science University (OHSU) have created what they claim to be the largest atlas of post-zygotic mutations (PZMs) in healthy human tissue. They generated the atlas using 54 tissue and cell types compiled after death from 948 individuals who donated their bodies…
Pan-cancer analysis reveals IGFL2 as a potential target for cancer prognosis and immunotherapy
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…
A pan-cancer analysis of DDR1 in prognostic signature and tumor immunity, drug resistance
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…
Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry
Identification of ancestry-dependent and independent non-HLA SLE-associated variants and downstream target genes Despite the success achieved by GWAS in mapping polygenic disease risk loci in SLE, the biological implications of the majority of identified variants has remained unknown. To gain a broader view of how inherited genetic variation impacts disease…
New Resource Combines Functional Genomics, Diploid Genomes for Variant Annotation
NEW YORK – An international team has characterized the function of genetic variants across more than two dozen tissue types in four individuals of European ancestry who were also assessed by high-quality, long-read sequencing. “This catalog potentially enables us to bootstrap the determination of allelic variants in other, new individuals…
How many parameters should be included in the model design for deseq2?
How many parameters should be included in the model design for deseq2? 0 @912d91f3 Last seen 4 hours ago United States Hi Michael, I am using deseq2 to perform DE analysis over ~100 human postmortem brain tissues, our major interest is finding DEGs between AD and ctrl, meanwhile we also…
Reactivated Promoters in Transposable Elements Help Form Unique Tumor Antigens
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…
Ras interacting protein 1 facilitated proliferation and invasion of diffuse large B-cell lymphoma cells
Introduction Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma, accounting for 30% of non-Hodgkin’s lymphoma. Approximately 150,000 new cases are diagnosed annually worldwideCitation1. DLBCL is characterized by heterogeneity, aggressiveness, and frequent relapse or resistance to chemotherapyCitation2. Due to the heterogeneity of DLBCL, the immunological, pathological, molecular, and genetic…
Genetic Risk of Substance Use Disorders Untangled in Large-Scale GWAS Meta-Analysis
NEW YORK – An international research consortium led by scientists at Washington University in St. Louis has uncovered genetic risk loci associated with many forms of addiction, including to alcohol, tobacco, opioids, and cannabis. The results, from a large-scale genome-wide association study meta-analysis that comprised more than 1.1 million individuals,…
Something wrong with my code concerning bsseq visualization
Here is my code: #### library(bsseq) library(bsseqData) ## —-showData—————————————————————– data(BS.cancer.ex) BS.cancer.ex <- updateObject(BS.cancer.ex) BS.cancer.ex pData(BS.cancer.ex) ## —-smooth,eval=FALSE——————————————————– # BS.cancer.ex.fit <- BSmooth( # BSseq = BS.cancer.ex, # BPPARAM = MulticoreParam(workers = 1), # verbose = TRUE) ## —-showDataFit————————————————————– data(BS.cancer.ex.fit) BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit) BS.cancer.ex.fit ## —-cpgNumbers————————————————————— ## The average coverage of CpGs…
How to find association between a gene-rsid and AD
How to find association between a gene-rsid and AD 0 Hello everyone, I know rs6656401 is AD loci. I did LD analysis in spleen gtex data and found LD snp pair for this rsid. I want to see if the rsid present in spleen for a gene that has LD…
Genome- and transcriptome-wide splicing associations with alcohol use disorder
Samples RNA-seq We used the same publicly available data source of human post-mortem brain samples as Van Booven et al.7, which were collected from the New South Wales Brain Tissue Resource Center. Van Booven et al.7 also performed differential splicing, but they used different methods, included individuals from disparate ancestral…
Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson’s disease
Case selection In this prospective case‒control study, we enrolled PD patients and healthy controls at Asan Medical Center (AMC), Seoul, South Korea, between 2018 and 2020. PD diagnosis was based on the UK PD Society Brain Bank criteria15. Batch 1 (n = 210) and 2 (n = 100) PD cohorts were recruited from January…
ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation
ANKLE1 is the causal gene for breast and ovarian cancer risk in the chr19p13.1 region Expression quantitative trait loci (eQTL) data have revolutionized how geneticists identify candidate causal genes from genome-wide association study (GWAS) loci. We integrated the most recent meta-analysis of breast cancer GWAS10 and Genotype-Tissue Expression (GTEx) project…
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases
Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…
Easy way to split VCF file by chromosome
Easy way to split VCF file by chromosome 2 Hi, Im trying to submit a job on the TOPMED/Michigan imputation server, but it returns an error saying that I need to split my VCF by chromosome Is there an easy way to do this? Will bcftools help? sequence TOPMED chromosome…
Female-Specific Fat Distribution Gene, Regulatory Variant Emerge from Gene Expression Study
NEW YORK – A team led by researchers at the University of Chicago has tracked down a sex-specific genetic variant with ties to fat tissue distribution, particularly the presence of abdominal fat, as well as higher-than-usual blood cholesterol and triglyceride levels. “Our data expand the knowledge on how the genome…
Genetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots
Samples This study was based on the Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) sample37, a population-based case-cohort design to study the genetic and environmental factors associated with severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005 (N = 1,472,762). In total,…
Single-Nuclei Multi-omics Spots Wonky Gene Regulation
10 Feb 2023 Many GWAS variants that raise Alzheimer’s disease risk lie in noncoding stretches of DNA. Do they influence transcription? The answer to this question has been hard to come by, but a new approach might help. Scientists led by Nicholas Cochran, Richard Myers, and Lindsay Rizzardi at HudsonAlpha…
SLC7A11 is a prognostic biomarker in UCEC
Introduction Endometrial cancer (EC) is one of the most frequently diagnosed types of gynecological cancers, second only to cervical cancer in incidence.1 More than 50,000 women die from EC worldwide each year.2 Despite the development of diagnostic techniques and treatment means, the prognosis of advanced EC remains unsatisfactory.3,4 The therapeutic…
Principal/Associate Director Pre-clinical Bioinformatics – Repare Therapeutics
Repare Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal,…
Scientist II, Bioinformatics Job Opening in South Plainfield, NJ at PTC Therapeutics, Inc.
Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…
Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing
Method overview For all presentations, we call the genetic effects on GWAS phenotypes ‘phenotypic effects’ and the effect of gene expression the ‘eQTL effect’. TWAS was originally developed to integrate eQTL and GWAS datasets derived from matched ancestries5. Specifically, it first builds gene expression prediction models using eQTL datasets that…
Drugs to Treat Smoking Addiction Suggested by Multi-Ancestry Transcriptome-Wide Association Study
NEW YORK — Researchers have developed a new approach for transcriptome-wide association analyses that incorporates multi-ancestry data, which they applied to uncover additional genes associated with smoking-related behaviors and suggest new drugs to treat smoking addiction. Transcriptome-wide association studies (TWAS) generally rely on genome-wide association studies and expression quantitative trait…
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
dc.description.abstract © 2020, The Author(s). The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from…
Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442
Custom Tracks 1806hidedensefull 468hidedensefull BT20hidedensefull BT474hidedensefull MCF7hidedensefull T47Dhidedensefull Mapping and Sequencing Base Positionhidedensefull p13 Fix Patcheshidedensesquishpackfull p13 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 RefSeq Acchidedensesquishpackfull…
FinnGen provides genetic insights from a well-phenotyped isolated population
To benchmark our register-based phenotyping and to explore the value of the isolated setting of Finland, we selected 15 diseases with more than 1,000 cases in FinnGen and for which well-powered GWAS data have been published. We evaluated the accuracy of our phenotyping by comparing the genetic correlations and effect…
In Silico Validation Of NcRNA-ncRNA Interaction Sites With NcRNAs Represented By K-mers Features
A recent catalogue of human transcriptome, namely CHESS database, assembled from RNA sequencing experiments as a part of the Genotype-Tissue Expression (GTEx) Project reported more non-coding RNA genes (21,856) than protein-coding (21,306), revealing an unexpectedly vast amount of transcriptional noise (Pertea et al, 2018). In this study, we introduce…
Identification of genetic variants associated with diabetic kidney disease in multiple Korean cohorts via a genome-wide association study mega-analysis | BMC Medicine
Tuttle KR, Bakris GL, Bilous RW, Chiang JL, de Boer IH, Goldstein-Fuchs J, et al. Diabetic kidney disease: a report from an ADA Consensus Conference. Diabetes Care. 2014;37(10):2864–83. Article Google Scholar Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B, et al. Chronic kidney disease: global dimension…
How to download eQTLS data for the Long Read RNASeq data (Glinos et. al., bioRxiv, 2021).
How to download eQTLS data for the Long Read RNASeq data (Glinos et. al., bioRxiv, 2021). 0 0 Entering edit mode 21 hours ago tulika • 0 Hi all, I have downloaded the TPM data for brain tissue from GTeX portal (www.gtexportal.org/home/datasets). I want the corresponding eQTLS data. Do anyone…
Sr. Scientist, Bioinformatics jobs | Hydrogen Group
Summary The ideal candidate will collaborate with biologists and software engineers to develop and improve bioinformatics algorithms for characterizing solid tumors, immuno-oncological targets, and tumor targeting therapies for cancer. This position will report into the Director, Bioinformatics. Responsibilities Design, develop, and apply computational and statistical methods to model complex biological…
Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma
The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…
UCSC Genome Browser | Encyclopedia MDPI
1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS PubMed PubMed Central Article Google Scholar Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….
Population-level variation in enhancer expression identifies disease mechanisms in the human brain
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central Article CAS Google Scholar Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central …
Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435
Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes. Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…
Index of /gbdb/hg38/gtex/cov
Name Last modified Size Description Parent Directory – GTEX-1C475-0726-SM-73KVL.Esophagus_Muscularis.RNAseq.bw 2019-12-16 09:16 160M GTEX-1C475-1826-SM-73KWA.Skin_Sun_Exposed_Lower_leg.RNAseq.bw 2019-12-16 09:16 194M GTEX-1GMR3-0626-SM-9WYT3.Artery_Coronary.RNAseq.bw 2019-12-16 09:16 177M GTEX-1H1E6-0826-SM-9WG83.Pancreas.RNAseq.bw 2019-12-16 09:16 122M GTEX-1HFI6-0011-R7b-SM-CM2SS.Brain_Putamen_basal_ganglia.RNAseq.bw 2019-12-16 09:16 172M GTEX-1HGF4-0011-R5b-SM-CM2ST.Brain_Caudate_basal_ganglia.RNAseq.bw 2019-12-16 09:17 178M GTEX-1HSGN-0726-SM-A9G2F.Thyroid.RNAseq.bw 2019-12-16 09:17 194M GTEX-1HSKV-0011-R1b-SM-CMKH7.Brain_Hippocampus.RNAseq.bw 2019-12-16 09:17 149M GTEX-1I1GU-1226-SM-A9SKT.Esophagus_Gastroesophageal_Junction.RNAseq.bw 2019-12-16 09:17 186M GTEX-1IDJC-1326-SM-CL53H.Colon_Transverse.RNAseq.bw 2019-12-16 09:17 217M GTEX-1IDJU-1026-SM-AHZ2U.Vagina.RNAseq.bw 2019-12-16…
New ‘Ramp Atlas’ Aims to Improve Understanding of Gene Expression
CHICAGO – A first-of-its-kind atlas of “ramp sequences” near the 5′ end of highly expressed genes promises to help researchers better understand gene expression and disease development. Bioinformaticians and computational biologists at the University of Kentucky and Brigham Young University recently released the Ramp Atlas, a compendium of 18,388 tissue-…
Genome-wide association study of musical beat synchronization demonstrates high polygenicity
Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS PubMed PubMed Central Article Google Scholar Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…
Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer
Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article Google Scholar Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central Google Scholar Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…
Impact of sweet, umami, and bitter taste receptor (TAS1R and TAS2R) genomic and expression alterations in solid tumors on survival
Despite being best known for their role in taste sensing1, T2Rs and T1Rs have been identified in various extra-oral tissues where they serve diverse chemosensory roles17,18,19,20,21,22,48. Emerging data on the role of taste receptors in malignancy led us to explore the genetic and expression alterations for solid tumors and implications…
Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights
NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News
Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar Maurano, M. T. et al. Systematic localization of…
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer
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),…
Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma
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…
A genome-scale screen for synthetic drivers of T cell proliferation
Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…
eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects
Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP,…
Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases
Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed PubMed Central Google Scholar El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…
Enrichment of eQTLs in functional categories using the eQTL results from 28 GTEx tissues.
In panel (a)-(c) and (e)-(f), a dot indicates point estimate, and a line indicates 95% confidence interval. (a) Enrichment evaluated using all the SNPs by torus [17] based on the eQTL results from MatrixEQTL, TReC or TReCASE. (b) Enrichment of the top eQTL per gene for the eGenes identified by…
split gtex genotype data by chromosomes.
Hello, I used and edited the command line to use –vcf to import vcf file. I used these commands: for chr in $(seq 1 22); do plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz –chr $chr –recode –out…
Validation of hub genes in acute pancreatitis
Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…
Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits
1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS PubMed PubMed Central Google Scholar 2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…
KINNEY_DNMT1_METHYLATION_TARGETS
Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…
Postdoctoral Fellow job with Cleveland Clinic – Genomic Medicine Institute
We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…
Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus
Researchers at the University of Illinois at Chicago and Washington University describe an online database called OncoDB, designed for analyzing large cancer datasets to detect gene expression shifts and viral infections with potential ties to cancer, such as human papillomavirus. The current version of the resource contains data for more…
Most useful public genomic/genetic databases/tools/applications
Forum:Most useful public genomic/genetic databases/tools/applications 1 Hi guys, I am looking for suggestions/recommendations from the research community regarding public databases that are most commonly used by researchers in their analysis. These could be the open access data or controlled access. Also, what are some of the applications used most commonly…
error while running predictdb tutorial
error while running predictdb tutorial 0 Hello, I am trying to use predictdb tutorial. The link is: github.com/hakyimlab/PredictDB-Tutorial When I run gtex_tiss_chrom.R script, it throws an error Error in file(file, “rt”) : cannot open the connection Calls: main …get_filtered_snp_annot -> %>% -> distinct -> filter -> read.table -> file In…
Multiple stages of evolutionary change in anthrax toxin receptor expression in humans
Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…
(Senior) Bioinformatician job with AL2S3 LTD
(Senior) Bioinformatician AL Solutions are searching for a Bioinformatician or Senior Bioinformatician to work within the Data Science team of an innovative start-up Biotechnology company in Cambridge. This company are developing innovative medicines within the Oncology & Immunology space. Your position will be to drive the development of computational tools…
What exactly is RNA-seq probe?
What exactly is RNA-seq probe? 0 Hi all, I’m a long time lurker, but this is my first post here, so I’m sorry if I do something wrong or post something that is against the rule, I’m new to RNA-seq analysis. But I’ve downloaded a huge dataset with matched RNA-seq…
how to upload more than one rsIDs to get gene expression or eQTL information
GTEX – how to upload more than one rsIDs to get gene expression or eQTL information 1 Hi everyone, I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically. I looked on GTEx but I only found the…
GTEX eQTLs’ extraction
GTEX eQTLs’ extraction 0 Hello everyone, I am a still a student and I am new to this forum, but I would need help regarding GTEX and how to work with it. I was given a task, which includes finding and extracting eQTLs for specific genes from the GTEX portal…
Bioconductor – Bioconductor 3.14 Released
Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…
LncRNA MIAT services as a noninvasive biomarker
Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…
H/ACA snoRNP gene family as diagnostic/prognostic biomarkers
Introduction Primary liver cancer, including hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma, is the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related deaths worldwide.1 High metastasis and recurrence rates, as well as limited treatment options, lead to the poor prognosis of advanced HCC.2 Among patients diagnosed with…
Counting the number of SNPs (VCF) for each genomic coordinates (BED)
Counting the number of SNPs (VCF) for each genomic coordinates (BED) 1 I want to count the number of recorded variations for each genomic coordinates of a .bed file from the corresponding .vcf file. I guess it should be solved by vcftools, but I could not find any suitable option…
Bioinformatics Scientist job with Hyper Recruitment Solutions (HRS)
We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…