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Tag: gtex
Bioconductor Code: yarn
[![Travis-CI Build Status](https://travis-ci.org/jnpaulson/yarn.svg?branch=master)](https://travis-ci.org/QuackenbushLab/yarn) # YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization The goal of yarn is to expedite large RNA-seq analyses using a combination of previously developed tools. Yarn is meant to make it easier for the user to perform accurate comparison of conditions by leveraging many Bioconductor tools and…
Amplifybio, LLC Sr./Scientist, Bioinformatics in South San Francisco, CA | 892968472
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…
Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry
To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…
TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes
Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article CAS PubMed PubMed Central Google Scholar De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article Google Scholar El-Halawany, N….
Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution
Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…
Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer
Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…
Bioinformatics Software Engineer Consultant Job at ProCogia
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
Phenotypic profiling of solute carriers characterizes serine transport in cancer
Cell culture All cell lines used in this study were cultured at 37 °C in 5% CO2 in a humidified incubator. Human cell lines were authenticated by STR profiling using Promega GenePrint 10 and tested for Mycoplasma using Mycoalert (Lonza). Other than HCT116 p21−/− (a gift of B. Vogelstein60) all cell…
Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457
Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes
Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article CAS PubMed Google Scholar International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….
Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes
Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article PubMed PubMed Central Google Scholar Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…
Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes
Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
Solved The following questions are based on the following
The following questions are based on the following paper: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun. 2018; 9:1512. (PMID: 29666371) (i) How is a cis-expression quantitative trait locus (cis-eQTL) defined? (ii) What experimental technique for detecting chromosomal interactions was applied…
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nat. Methods 18, 1196–1203 (2021). Article CAS PubMed PubMed Central Google Scholar Avsec, Ž. et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat. Genet. 53, 354–366 (2021). Article CAS PubMed PubMed Central Google…
ProCogia hiring Bioinformatics Software Engineer Consultant in Vancouver, British Columbia, Canada
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease
We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…
Computational and bioinformatics tools for life sciences
In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…
Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value
Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…
Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals
Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…
Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA
Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…
Discovery from public data (GEO, SRA and more) using Ingenuity Pathway Analysis
Per user feedback, we are hosting a comprehensive training on how to effectively use sample level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources through Ingenuity Pathway Analysis (IPA) and IPA Analysis Match Explorer feature. The trainer will walk through usecases in…
COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma | BMC Gastroenterology
Bioinformatics analysis The GEO database (www.ncbi.nlm.nih.gov/geo/) provided detailed gene expression information for the GSE62165 microarray. Differentially expressed genes were identified using the online tool Morpheus (software.broadinstitute.org/morpheus/) (fold change = normal pancreatic tissue gene expression/PDAC tissue gene expression, P value < 0.05 and |log2(fold change)|>1). The downstream analysis was based on the genes with the…
Primate-specific ZNF808 is essential for pancreatic development in humans
Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…
Advisor/Sr. Advisor – Bioinformatics – Relocation Assistance job with Lilly
At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…
Lilly Advisor/Sr. Advisor – Bioinformatics in New York, NY | 883515845
At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…
St. Jude Children’s Research Hospital hiring Senior Bioinformatics Analyst/Bioinformatics Analyst in Memphis, Tennessee, United States
St. Jude Children’s Research Hospital is looking for a highly motivated Senior Bioinformatics Analyst/Bioinformatic Analyst to contribute to genetic research projects in the Department of Epidemiology and Cancer Control. Our research leverages comprehensive biomedical data from childhood cancer survivors participating in two world-leading cohort studies, CCSS (ccss.stjude.org/ ) and SJLIFE…
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article PubMed Google Scholar Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….
TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons
Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article CAS PubMed PubMed Central Google Scholar Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…
Insights into expression patterns and immunotherapy response prediction
[1] D. Schadendorf, D. E. Fisher, C. Garbe, J. E. Gershenwald, J. Grob, A. Halpern, et al., Melanoma, Nat. Rev. Dis. Primers, 1 (2015), 15003. doi.org/10.1038/nrdp.2015.3 doi: 10.1038/nrdp.2015.3 [2] A. M. M. Eggermont, A. Spatz, C….
Quickly calculating adjusted Fold Change with DESeq2
Hello! I’m working on comparing tumor and healthy samples with DESeq2. My analysis only cares about the adjusted Fold Change values that DESeq2 computes. The input data encompasses a huge number of samples (I’m working with TCGA and GTEX data), and I need to run the calculation a bunch of…
T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome
Hedrick, S. M., Cohen, D. I., Nielsen, E. A. & Davis, M. M. Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature 308, 149–153 (1984). Article CAS PubMed Google Scholar Yanagi, Y. et al. A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains….
Identification of hub genes associated with gastric cancer
Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…
Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients
Background: More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are…
HOXC-AS3 as an Oncological Biomarker and Therapeutic Target
1Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, People’s Republic of China; 2Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, 332007, People’s Republic of China; 3Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330038, People’s Republic of China Correspondence: Hongliang Luo,…
Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis | Molecular Neurodegeneration
van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic Lateral Sclerosis. Lancet (London England). 2017;390:2084–98. Article PubMed Google Scholar Liu MS, Cui LY, Fan DS. Age at onset of Amyotrophic Lateral Sclerosis in China. Acta Neurol Scand. 2014;129:163–7. Article CAS PubMed …
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
A computational protocol, CaseOLAP LIFT, and a use case are presented for investigating mitochondrial proteins and their associations with cardiovascular disease as described in biomedical reports. This protocol can be easily adapted to study user-selected cellular components and diseases. This computational protocol is significant because it allows a work to…
Systematic differences in discovery of genetic effects on gene expression and complex traits
Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article CAS PubMed PubMed Central Google Scholar Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article CAS PubMed PubMed Central Google Scholar Gusev, A. et…
The eQTL analysis to discover unique eGFR-related SNPs for the Taiwanese population
Chen YC, Wong HS, Wu MY, Chou WH, Kao CC, Chao CH, Chang WC, Wu MS (2022) Genome-wide association study for eGFR in a Taiwanese population. Clin J Am Soc Nephrol 17(11):1598–1608. doi.org/10.2215/CJN.02180222 Article CAS PubMed Google Scholar Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmuller G (2015) SNiPA:…
BioSpace hiring Advisor/Sr. Advisor – Bioinformatics in Cambridge, MA
At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…
Comparing feature selection and machine learning approaches for predicting CYP2D6 methylation from genetic variation
1National University of Singapore, Singapore 2Singapore Institute for Clinical Sciences (A*STAR), Singapore 3KK Women’s and Children’s Hospital, Singapore 4Duke-NUS Medical School, Singapore 5National University Hospital, Singapore 6Yale-NUS College, Singapore 7National Healthcare Group, Singapore 8Institute…
PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer
PHF5A expression analysis Figure 1A demonstrated that PHF5A expression level was compared between tumor and corresponding normal tissues using TIMER2 tool. As compared to normal tissues, PHF5A expression was considerably elevated in Bladder urothelial carcinoma (BLCA), Breast invasive carcinoma (BRCA), Cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), Esophageal carcinoma (ESCA), Head and neck…
Simulation of undiagnosed patients with novel genetic conditions
Simulated patient initialization We simulate patients for each of the 2134 diseases in Orphanet20 (orphadata.org, accessed October 29, 2019) that do not correspond to a group of clinically heterogeneous disorders (i.e., Orphanet’s “Category” classification31), have at least one associated phenotype, and have at least one causal gene. For Orphanet diseases…
Amplifybio, LLC Sr./Scientist, Bioinformatics in South San Francisco, CA | 876106342
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…
Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin
Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…
Expression of “DNA damage response” pathway genes in diffuse large B-cell lymphoma: The potential for exploiting synthetic lethality
Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are two of the most prevalent non-Hodgkin’s lymphoma subtypes. Despite advances, treatment resistance and patient relapse remain challenging issues. Our study aimed to scrutinize gene expression distinctions between DLBCL and FL, employing a cohort of 53 DLBCL and 104 FL samples…
Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses
doi: 10.1093/g3journal/jkad229. Online ahead of print. Affiliations Expand Affiliation 1 Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, 84112, USA. Item in Clipboard Nikki D Russell et al. G3 (Bethesda). 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/g3journal/jkad229. Online ahead of print….
The status of the human gene catalogue
Understanding our Genetic Inheritance: The US Human Genome Project, The First Five Years 1991-1995 (US Department of Health and Human Services, US Department of Energy, 1990). Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). Describes the first complete gap-free assembly and annotation of…
Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes
Li QS, Shabalin AA, DiBlasi E, Gopal S, Canuso CM, FinnGen ISGC, et al. Genome-wide association study meta-analysis of suicide death and suicidal behavior. Mol. Psychiatry 2023;28:891–900. McGuffin P, Marusic A, Farmer A. What can psychiatric genetics offer suicidology? Crisis. 2001;22:61–65. Article CAS PubMed Google Scholar Pedersen NL, Fiske A….
Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease
Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…
Whole exome sequencing and transcriptome analysis in two unrelated patients with novel SET mutations
Moeschler JB, Shevell M, Committee on G. Comprehensive evaluation of the child with intellectual disability or global developmental delays. Pediatrics. 2014;134:e903–18. PubMed Google Scholar Patel DR, Cabral MD, Ho A, Merrick J. A clinical primer on intellectual disability. Transl Pediatr. 2020;9:S23–35. PubMed PubMed Central Google Scholar Baker K, Devine RT,…
Fibroblast Growth Factor Receptor 2 (FGFR2), a New Gene Involved in the Genesis of Autism Spectrum Disorder
The ASD patient described here showed a mutation in the FGFR2 gene, located in the chromosomal band 10q26 (Fig. 1a) and encoding the fibroblast growth factor receptor type 2. It belongs to the family of tyrosine kinase receptors (including FGFR1, FGFR3, and FGFR4) that regulate several biological processes, including bone development,…
Bioinformaticist (Scott) – (Job Number: 3258449) at Mass General Brigham in Mei Mass Eye And Ear Main Building Boston, Boston 1070276
!*! A talented bioinformaticist with experience in genomics is sought to join the Massachusetts Eye and Ear Bioinformatics Center (MBC) of the Ocular Genomics Institute (OGI) at Mass Eye and Ear (MEE) and Harvard Medical School. The mission of the OGI is to improve our understanding of the genetic causes…
Genome-wide analysis identifies novel loci influencing plasma apolipoprotein E concentration and Alzheimer’s disease risk
The details of study participants, plasma ApoE measurement, genotyping and imputation, statistical analyses, and functional annotations are given in Online Methods. Association of plasma ApoE concentration with incident dementia and cognition function Whole plasma ApoE concentration at baseline was determined in 3031 participants, of which 2893 were European Americans (EAs),…
Transcriptome-wide association studies: recent advances in methods, applications and available databases
TWAS conducts association tests for each gene-trait pair leveraging analysis from eQTL effects and GWAS associations. Based on the idea of TWAS, the basic workflow can be divided into three steps, as illustrated in Fig. 1. It is noted that different models are contained in various stages and should be distinguished…
Bioinformatics Analyst III job with Frederick National Laboratory for Cancer Research
Bioinformatics Analyst III Job ID: req3697Employee Type: exempt full-timeDivision: Cancer Research Technology ProgramFacility: Rockville: Gaither RdLocation: 2099 Gaither Rd, Rockville, MD 20850 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….
Bioinformatics Analyst III Job in Maryland (MD), $vacancy_industry Career, Full Time Jobs in Frederick National Laboratory for Cancer Research
Bioinformatics Analyst III Job ID: req3697Employee Type: exempt full-timeDivision: Cancer Research Technology ProgramFacility: Rockville: Gaither RdLocation: 2099 Gaither Rd, Rockville, MD 20850 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,…
High G9a Expression in DLBCL and Its Inhibition by Niclosamide to Induce Autophagy as a Therapeutic Approach
Background: Diffuse large B-cell lymphoma (DLBCL) is a malignant lymphoid tumor disease that is characterized by heterogeneity, but current treatment does not benefit all patients, which highlights the need to identify oncogenic genes and appropriate drugs. G9a is a histone methyltransferase that catalyzes histone H3 lysine 9 (H3K9) methylation to…
Cancers | Free Full-Text | High G9a Expression in DLBCL and Its Inhibition by Niclosamide to Induce Autophagy as a Therapeutic Approach
1. Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive malignant lymphoid neoplasm, which accounts for 40% of all malignant lymphoid neoplasms and includes morphologically and molecularly heterogeneous disease subtypes [1,2]. According to gene expression profiling, different forms of DLBCL are subdivided into germinal center B-cell-like (GCB-DLBCL) and activated B-cell-like…
Nuclear genetic control of mtDNA copy number and heteroplasmy in humans
Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…
Advisor/Sr. Advisor – Bioinformatics job in Cambridge at Lilly Company
At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…
Modeling tissue co-regulation estimates tissue-specific contributions to disease
Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020). Article CAS PubMed Google Scholar Ongen, H. et al. Estimating the causal tissues for complex traits and diseases. Nat. Genet. 49, 1676–1683 (2017). Article CAS PubMed Google Scholar …
Bioinformatics analysis of hedgehog interacting protein in colorectal cancer: a study based on GEO data and TCGA data | BMC Gastroenterology
HHIP was lowly expressed in CRC tissues and HHIP expression was associated with cancer patient prognosis We acquired the RNA-sequencing data of CRC from TCGA public database. To pursue possible roles of HHIP in carcinostasis, we first analyzed HHIP expression in 33 types of human cancers. As shown in Fig. 1A,…
Deloitte hiring Bioinformatics Consultant – Python | NextFlow – Federal Health Sector in Atlanta, Georgia, United States
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 the most complex…
Jointly analyzing DEGs – my RNA-seq and GTEx
Jointly analyzing DEGs – my RNA-seq and GTEx – How to do it properly? 0 I have some standard polyA RNA-seq data from whole human tissue that I generated. I want to compare the relative abundance of genes in my tissue dataset with all the other tissues of the body….
Dissecting human population variation in single-cell responses to SARS-CoV-2
Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…
Gene expression changes in sickle cell reticulocytes and their clinical associations
Pauling, L. et al. Sickle cell anemia a molecular disease. Science (New York) 110, 543–8 (1949). Article ADS CAS Google Scholar Connes, P. et al. The role of blood rheology in sickle cell disease. Blood Rev. 30, 111–118 (2016). Article PubMed Google Scholar Browning, J. A. et al. The effect…
eQTL Study Uncovers New Candidate Genes for Adipose Tissue Biology
Researchers have identified new candidate genes involved in adipose tissue biology through an expression quantitative trait loci study of a Greek population. As they report in BMC Genomics, a team from the Biomedical Sciences Research Center Alexander Fleming in Athens and elsewhere conducted eQTL mapping in subcutaneous and visceral adipose…
Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics
Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health and disease. Nat Rev Cardiol. 2019;16(2):83–99. Article PubMed Google Scholar Sakers A, De Siqueira MK, Seale P, Villanueva CJ. Adipose-tissue plasticity in health and disease. Cell. 2022;185(3):419–46. Article CAS PubMed Google Scholar Sun W, von Meyenn F, Peleg-Raibstein…
Neoantigen discovery sheds light on cancer immunogenicity
In a recent article published in Nature Communications, researchers reported a proteogenomic approach to investigate fresh solid melanoma tumor material. The approach combines liquid chromatography-tandem mass spectrometry (LC-MS/MS) of immuno-precipitated human leukocyte antigen class I (pHLA-I) peptides with whole exome sequencing (WES) for the discovery and validation of neoantigen candidates at the…
ClearanceJobs hiring Bioinformatics Engineer with Security Clearance in Atlanta, Georgia, United States
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 the most complex…
Transcriptomic risk scores for attention deficit/hyperactivity disorder
Song P, Zha M, Yang Q, Zhang Y, Li X, Rudan I. The prevalence of adult attention-deficit hyperactivity disorder: A global systematic review and meta-analysis. J Glob Health. 2021;11:1–9. Article Google Scholar Faraone SV, Asherson P, Banaschewski T, Biederman J, Buitelaar JK, Ramos-Quiroga JA, et al. Attention-deficit/hyperactivity disorder. Nat Rev…
Investigating open reading frames in known and novel transcripts using ORFanage
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar Pertea,…
Bioinformatics Consultant with Security Clearance Atlanta, GA – Jobs in USA – jobs –
Job Description 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…
Diabetes drug could promote healthy aging
A research team from the School of Public Health, LKS Faculty of Medicine of the University of Hong Kong (HKUMed), has provided genetic evidence that metformin might promote healthy aging using a cohort study of more than 300,000 participants of European descent (UK Biobank). The proof-of-concept work supports further clinical…
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Luo, Y. et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 48, D882–D889 (2020). Article CAS PubMed Google Scholar Korkmaz, G. et al. Functional genetic screens for enhancer elements in the human genome using CRISPR–Cas9. Nat. Biotechnol. 34, 192–198 (2016). Article CAS PubMed …
Senior Bioinformatics Scientist – Enhanc3D Genomics
VACANCY – Senior Bioinformatics Scientist About Enhanc3D Genomics Enhanc3D Genomics is a functional genomics spinout company from the Babraham Institute (Cambridge, UK) leveraging a disruptive technology to profile interactions of gene promotors with distal DNA regulatory elements that allow unbiased allocation of enhancers to their target genes across the genome….
A systems biology approach to pathogenesis of gastric cancer: gene network modeling and pathway analysis | BMC Gastroenterology
In recent years, different investigations in the area of multi-center genomics research from gene to systems level and next-generation sequencing, clarified the various mechanisms specifically involved in the tumor progression [29]. This study used bioinformatics analysis to further investigate the genes involved in GC pathogenesis. In addition, the current study…
Senior Bioinformatics Engineer in Manila Philippines – Career Connect
This is a remote position. We’re looking for someone with years of experience in machine learning and data science for a Hawaii-based health care company. Lead the development of new bioinformatics algorithms, pipelines, and infrastructure in a cloud-based environment in support of the Company’s discovery platform Apply rigorous standards and…
Predicting gene expression may speed discovery: study | VUMC Reporter
by Bill Snyder In recent years, a virtual tidal wave of studies linking the expression of certain genes to complex diseases as varied as cancer and diabetes has raised hopes for major advances in medical treatment and drug discovery. Yet gene expression datasets from different cell types and tissues…
A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth | BMC Medicine
Martin JA, Hamilton BE, Osterman MJK, Driscoll AK. Births: Final Data for 2018. Natl Vital Stat Rep. 2019;68:1–47. PubMed Google Scholar Liu L, Oza S, Hogan D, Chu Y, Perin J, Zhu J, et al. Global, regional, and national causes of under-5 mortality in 2000–15: an updated systematic analysis with…
Principal Bioinformatics Engineer Job Opening in Waltham, MA at BIO-TECHNE
Job Details Level: Experienced Job Location: Waltham MA – Waltham, MA Position Type: Full Time Education Level: Graduate Degree Salary Range: Undisclosed Travel Percentage: Up to 10% Job Shift: Day Job Category: Research Description Principal Bioinformatics Engineer The Opportunity Exosome Diagnostics, a Bio-Techne brand (NASDAQ: TECH), is a global…
Startup Early Diagnostics Using Tissue-Specific Methylation Atlas to Develop cfDNA Assays
NEW YORK – A new DNA methylation atlas that may be the most comprehensive to date in terms of characterizing methylation by tissue type aims to improve our ability to decipher the tissue of origin of cell-free DNA (cfDNA), helping researchers and physicians detect disease and monitor treatment response. In…
why are databases like gnomad useful in population studies
99, 12451260 (2016). Genet. eCollection 2023. 36, 29362937 (2020). Genet. These assays include massively parallel regulatory assays134, which test synthetic regulatory sequences by screening variants in thousands of untranscribed or untranslated sequences for functional effects in a single experiment, and CRISPR techniques that allow for the introduction of mutations into…
Deloitte hiring Bioinformatics Senior Consultant in Atlanta, Georgia, United States
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 the most complex…
Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power
Abstract A core problem in genetics is eQTL mapping, in which genetic variants associated with changes in expression of genes are identified. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between…
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells
Stewart, J. B. & Chinnery, P. F. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat. Rev. Genet. 22, 106–118 (2021). Article CAS PubMed Google Scholar Stewart, J. B. & Chinnery, P. F. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat. Rev. Genet….
Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy
Walhovd, K. B. et al. Neurodevelopmental origins of lifespan changes in brain and cognition. Proc. Natl Acad. Sci. USA 113, 9357–9362 (2016). Article CAS PubMed PubMed Central Google Scholar Damian, R. I., Spengler, M., Sutu, A. & Roberts, B. W. Sixteen going on sixty-six: a longitudinal study of personality stability…
how to calculate predicted expression using weights from model file
how to calculate predicted expression using weights from model file 0 Hello, I am using prediXcan method to generate model based on gtex data for brain frontal tissue. I am able to train the model file and using Predict.py script to generate predicted expression. I want to ask how does…
Integrated bioinformatics and wet-lab analysis revealed cell adhesion prominent genes CDC42, TAGLN and GSN as prognostic biomarkers in colonic-polyp lesions
Clinicopathological characteristics of patients with pre-cancerous lesions Clinicopathological features of the 20 included patients with colon polyps were extracted from their files and presented at the beginning of the survey. All resected samples were categorized into high-risk and low-risk polyps based on reported pathological feature of the samples. The mean…
Comorbidity genetic risk and pathways impact SARS-CoV-2 infection outcomes
Kousathanas, A. et al. Whole genome sequencing reveals host factors underlying critical Covid-19. Nature. doi.org/10.1038/s41586-022-04576-6 (2022). Article PubMed PubMed Central Google Scholar COVID-19 HGI. & Ganna, A. Mapping the human genetic architecture of COVID-19: an update. medRxiv. doi.org/10.1101/2021.11.08.21265944 (2022). Horowitz, J. E. et al. Genome-wide analysis provides genetic evidence that…
Senior Bioinformatics Scientist – Monoceros Biosystems, LLC
Senior Bioinformatics Scientist position available at Monoceros Biosystems Who We AreMonoceros Biosystems is a rapidly growing bioinformatics service provider to small and established drug discovery companies, as well as biotechnology investment firms. To support our explosive growth, we are looking for strong bioinformatics/computational biology programmers and scientists to join our…
BioSpace hiring Scientist I, Bioinformatics in North Chicago, Illinois, United States
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…
How do I correctly format my limma/eBayes code?
How do I correctly format my limma/eBayes code? 0 Here is part of my data table, which I will call “df”: Subject.ID Sex V1 V2 V3 V4 V5 1 GTEX-1117F female 4.24944534 0.18307358 1.99276843 0.21785110 0.74777407 2 GTEX-1128S male 3.286585483 0.165944088 1.843983844 0.444455046 0.307311939 3 GTEX-11EMC female 3.31947343 0.27846061 1.46519089…
Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program
Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…
Mapping interindividual dynamics of innate immune response at single-cell resolution
Ethical compliance This project was approved by the Wellcome Sanger Institute Animal Welfare and Ethical Review Body and complied with all relevant ethical regulations regarding animal research and human studies. Human cells were obtained from HipSci24, where they were collected from volunteers recruited from the National Institute for Health and…
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…