Tag: NIH

Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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Why is mtDNA maternal only? : explainlikeimfive

Mitochondria are kind of like an in-between of cell-organelles and bacteria that live in your cells. They are not made by your cells, but they replicate on their own (by splitting in two). For this, they use their own DNA (the mtDNA), not the DNA of your cells. When an…

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RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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A Dark Genome Link to Schizophrenia and Bipolar Disorder

Source: Mahmoud-Ahmed/Pixabay A new study published in Molecular Psychiatry by researchers at the University of Cambridge reported areas located in the dark genome that appear to be associated with schizophrenia and bipolar disorder. These proteins may serve as potential drug targets in addition to biological indicators for distinguishing between the…

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NIH researchers develop first stem cell model of albinism to study related eye conditions

News Release Tuesday, January 11, 2022 Use of patient-derived stem cells will enable high-throughput drug screening for potential therapeutics. Researchers at the National Eye Institute (NEI) have developed the first patient-derived stem cell model for studying eye conditions related to oculocutaneous albinism (OCA). The model’s development is described in…

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GenBank Archives – U.S. Right to Know

EcoHealth Alliance President Peter Daszak opposed the public release of Covid-19-related virus sequence data gathered from China as part of the U.S. Agency for International Development’s (USAID) PREDICT program, according to emails obtained by U.S. Right to Know. The conversation in late April 2020 involved employees of EcoHealth Alliance, a…

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Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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NIH Study Shows Using CareDx’s AlloSure Lung for Transplant Surveillance is More Effective than Diagnostic Bronchoscopy at Identifying Rejection

SOUTH SAN FRANCISCO, Calif., Jan. 07, 2022 (GLOBE NEWSWIRE) — CareDx, Inc.,  (Nasdaq: CDNA) – The Transplant Company™ focused on the discovery, development, and commercialization of clinically differentiated, high-value healthcare solutions for transplant patients and caregivers – today announced the results of a study led by the National Institutes of…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Researchers identify new bacteria and viruses on human skin

Data representing the diverse range of microbes found in the human skin microbiome. Credit: Karen Arnott/EMBL Researchers at EMBL’s European Bioinformatics Institute (EMBL-EBI), the National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI), the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases, and colleagues have identified…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Researchers identify new bacteria and viruses in human skin

Data representing a variety of microorganisms found in the human skin microflora. Credits: Karen Arnott / EMBL Researchers and colleagues at EMBL’s European Bioinformatics Institute (EMBL-EBI), National Institutes of Health (NIH) National Institute for Human Genome (NHGRI), NIH National Institute for Arthritis, Musculoskeletal and Skin Diseases are new bacteria and…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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SAMD9

cite web | title = Entrez Gene: SAMD9 sterile alpha motif domain containing 9| url = www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=54809| accessdate = ] PBB_Summarysection_title = summary_text = References Further reading PBB_Further_reading citations = *cite journal | author=Maruyama K, Sugano S |title=Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with…

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Haplogroup M (mtDNA)

In human genetics, Haplogroup M is a human mitochondrial DNA (mtDNA) haplogroup. An enormous haplogroup spanning many continents, the macro-haplogroup M is a branch of the haplogroup L3. M is believed to have originated in Asia [Gonzalez et al., [www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1945034 Mitochondrial lineage M1 traces an early human backflow to Africa]…

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UMass Chan Medical School hiring Research Lab Tech I – Neurogenerative Disease (CRISPR-Cas gene editing) in Worcester, Massachusetts, United States

OverviewGENERAL SUMMARY OF POSITION: We are seeking a Research Technician to work collaboratively on CRISPR-Cas gene editing of the Huntington’s Disease (HD) gene. HD is a devasting neurodegenerative disease that currently has no effective treatment. Our goal is to develop gene editing methods to inactivate or correct the disease-causing version…

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Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome

Significance Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that…

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makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version of BLAST (Version 2.11.0+) and downloaded the refseq_protein database from NCBI using the following code wget ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz The database gets downloaded…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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hg38 Import custom reference upload error

Our version of TS is 5.12.2 When trying to upload new custom reference fasta (downloaded from ncbi ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz, gunzipped and renamed to hg38.fasta) through “Import custom reference” in interface an error occures: “uploaded file size is incorrect” (to be honest the error was not shown in logs, because of TypeError…

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NIH-SOAR-NCI-Bioinformatics Scientist in Rockville, MD

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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some signatures that have been suppressed by RefSeq/GenBank are not in wort

For example, the following accessions have been “suppressed” in RefSeq and GenBank, and do no appear in wort (/group/ctbrowngrp/irber/data/wort-data/wort-genomes/sigs/<accession>.sig). I checked newer version numbers and still did not find these accessions (e.g. GCA_900474135*sig). Looking on GenBank, I see the record has been suppressed/removed: www.ncbi.nlm.nih.gov/assembly/GCF_900474135.2/ GCA_900474135.2 GCA_002798115.1 GCA_001308105.1 I couldn’t find…

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Postdoctoral Position in Structural Bioinformatics job with National Institute of Allergy and Infectious Diseases (NIAID)

  Postdoctoral Position in Structural Bioinformatics Department of Health and Human Services National Institutes of Health National Institute of Allergy and Infectious Diseases The Structural Bioinformatics Core Section (SBIS) at the National Institute of Allergy and Infectious Diseases (NIAID), Vaccine Research Center (VRC), located on the main National Institutes of…

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CMT2 Research Projects Launched by CMTA Seed Money Win NIH Funds

Two research projects focused on developing gene-editing therapies for Charcot-Marie-Tooth disease type 2 (CMT2) — both launched with seed monies from the Charcot-Marie-Tooth Association-Strategy to Accelerate Research (CMTA-STAR) program — have now been awarded additional funding from the National Institutes of Health (NIH). According to a CMTA press release, these NIH…

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RefSeq-announce Info Page

RefSeq-announce — Public RefSeq Release announcements   About RefSeq-announce This mail list is used to announce changes or updates to the NCBI RefSeq collection. Announcements will be made for full RefSeq Releases to the FTP site. Additional mail may be sent when large genomes are added to the collection, or…

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Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine – University of Calgary – job portal

University of Calgary Home Prospective Students Current Students Alumni Community Faculty & Staff Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Share this Job: Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine Job ID: 24643 Updated:…

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computeMatrix in deeptool is Running with no result

computeMatrix in deeptool is Running with no result 0 Hi All, I wonder if someone can help me in explaining what to input on the -R <bed file> argument of the code below? computeMatrix scale-regions -S <bigwig file(s)> -R <bed file> -b 1000 what I did for example, I download…

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Dec 10 | CS Colloquium Series: “Multi-scale Data Integration and Causal Inference for Biological and Medical …

Event listing from University of Pittsburgh: Friday, December 10 from 2:00 PM to 3:00 PM Abstract: The advancement of technologies for high-throughput collection of personal data, including environmental, lifestyle, clinical and biomedical data, has inadvertently transformed biology and medicine. Integrating and co-analyzing these different data streams has become the research…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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Kraken2

Kraken2 0 I wanted to make a kraken database but i got this error while running the command.I am using Kraken2 $ kraken2-build –standard –threads 24 –db kraken2database/ Downloading nucleotide gb accession to taxon map… done.Downloading nucleotide wgs accession to taxon map… done.Downloaded accession to taxon map(s)Downloading taxonomy tree data……

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The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…

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Research Support Officer job with EMBL

EMBL’s European Bioinformatics Institute (EMBL-EBI) is seeking a Research Support Officer to assist the Service Team Leaders leading EMBL-EBI’s resources with overall scientific management. The Research Support Officer role will provide an exciting opportunity to develop your skills in a wide range of areas. The nature of the role is…

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BioSpace hiring Bioinformatics Python Developer in Rockville, Maryland, United States

We are currently searching for a Bioinformatics Python Developer to provide support to the National Institutes of Health (NIH). This opportunity is a permanent, full-time position with MSC, and it is on-site in Rockville, MD. Duties & Responsibilities The role will be responsible for developing and extending software solutions for…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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What is the single nucleotide polymorphism database ( dbsnp )?

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…

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Biology Career Job Links

Web Resources Virtualab Home AgricultureBioinformaticsBiophysicsCancerCareerCellBiologyDevelopmentEcologyEducationFunGeneticsGenomicsHealthLabMicrobiologyMolecularMoleculeNeurosciencesPaleontologyPlantPolicySociety Instructionsupplierprotocol… Career Links AACC Onlin – American Association of Clinical Chemistry career center. Academia : Job listings in academia, major US universities, and positions in Australia, Canada, and Europe. Academic Employment Network: US academic positions. Academic network : Jobs in higher education. Academic, Physician…

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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…

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In some lymphomas, ibrutinib yields “almost unheard-of” survival rates

Younger patients with two genetic subtypes of diffuse large B cell lymphoma (DLBCL) – specifically MCD and N1 – show substantial improvements in survival with the addition of ibrutinib to standard R-CHOP chemotherapy, compared with R-CHOP alone, new research shows. The findings, published Nov. 4, 2021, in Cancer Cell, come…

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Cardiac impact of high-frequency irreversible electroporation using an asymmetrical waveform on liver in vivo

Animals All animal experimental protocols were approved by the Institutional Animal Care and Use Committee of The General Hospital of People’s Liberation Army (License Number: 2019-D15-07). The study was conformed to the National Institutes of Health Guide for Animal Care and Use of Laboratory Animals (NIH Publication No. 85-23, revised…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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What does it mean BLASTx in de novo RNAseq analysis?

What does it mean BLASTx in de novo RNAseq analysis? 1 Hi, all. I try to get an assembly stat. According to some articles, it tends to have information that can be obtained by BLAST. For example, “Top BLASTx-hit species” and “Percent of gene with at least one BLASTx hit…

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Bioinformatics Scientist in Gaithersburg, MD

We are currently searching for a Bioinformatics Scientist to provide support to the National Institutes of Health (NIH). This opportunity is a full-time position with MSC, and it is on-site in Gaithersburg, MD. Duties & Responsibilities Work independently and collaboratively to develop or optimize procedures that improve the throughput of…

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Why do non-smokers develop lung cancer? Healing practice

Why do people who have never smoked get lung cancer? In recent research, three subtypes of lung cancer were classified by non-smokers. (Photo: utah51/stock.adobe.com) Analysis: Lung cancer in non-smokers Even if smoking is the main risk factor for developing lung cancer, it is not uncommon for people who have never…

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Precomputed secondary structure prediction from sequence

Precomputed secondary structure prediction from sequence 2 Hi, Most services that predict secondary structure from sequence, such as psipred, have an online webserver or a program you’d have to run locally (which would take quite a bit for a whole proteome). e.g. bioinf.cs.ucl.ac.uk/psipred/result/0fc9a438-c3d8-11e3-a745-00163e110593 I was wondering if anyone knew a…

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GenBank Biologist – Bethesda, MD

Job Description Interested in an exciting and rewarding alternative career in the biosciences? Tired of bench work? Enjoy puzzles and problem solving? Incredibly detail oriented? If you answered yes to these questions, consider joining our team of highly skilled and dedicated scientists working on site at the National Center for…

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deepmind alphafold github

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

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The 13 health care leaders on the list

Time this week released its “100 Most Influential People” list, which includes a number of individuals who have made major contributions to health care. The 10 ‘most influential’ health care companies, according to TIME The list This year, TIME recognized several health care providers, scientists, public health officials, and advocates for their…

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Bioinformatician I/II/III – Job posted on PostdocJobs.com

Job Description Farmington, Connecticut Apply Summary The Robinson lab is seeking a Bioinformaticician to join our team that focuses on the development of software and ontologies for biomedical research. Our team of expert biological curators, bioinformaticians, and computer scientists maintain and enhance a knowledge extraction and refinement process that delivers…

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Penn Medicine Awarded $6 Million to Advance Understanding of Human Genome Function in Health and Disease

Hao Wu, PhD, an assistant professor of Genetics in the Perelman School of Medicine at the University of Pennsylvania PHILADELPHIA— The National Institutes of Health (NIH) has selected Penn Medicine as one of 25 award recipients across 30 sites in the United States to serve as Impact of Genomic Variation…

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Whole genome sequencing and RNA sequencing data analysis for a bacterial strain

Whole genome sequencing and RNA sequencing data analysis for a bacterial strain 1 Hello, I am new RNA sequencing work. I have raw fastq files (from extracted RNA and DNA both) for bacteria “Paucibacter toxinivorans strain IM4”. I am not able to find whole reference genome for the same bacteria….

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How can I get PHRED score?

How can I get PHRED score? 1 Hi, all. I am trying to get the assembly stat(Table S1.) according to the following paper about de novo assembly. [www.ncbi.nlm.nih.gov/pmc/articles/PMC7266049/%5D%5B1] In the table, there is an item “Mean read PHRED score after filtering and trimming”. How can I get this? Is there…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Jennifer Doudna’s CRISPR startup Mammoth Biosciences goes unicorn

The gene-editing tool CRISPR is moving toward the market, promising better tests, disease cures — and maybe even a woolly mammoth. The big picture: CRISPR is already a historic scientific achievement, but we’re just now entering the moment when it will begin to impact patients and possibly the planet. Driving…

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Liftover nonmodel VCF

Liftover nonmodel VCF 1 Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I’ve found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can…

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Whole genome sequencing for a bacterial strain for RNA sequencing

Whole genome sequencing for a bacterial strain for RNA sequencing 0 Hello, I am new RNA sequencing work. I have raw fastq files (from extracted RNA and DNA both) for bacteria “Paucibacter toxinivorans strain IM4”. I am not able to find whole reference genome for the same bacteria. But, there…

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Dr. J. Curtis Nickel Urinary Microbiome Study Using MicroGenDX NGS Indicates Microbial Diversity Varies by Age and Gender | News

ORLANDO, Fla., Sept. 14, 2021 /PRNewswire-PRWeb/ — A study to help understand the implications of Next-Generation DNA Sequencing (NGS) in the diagnosis and treatment of Urinary Tract Infections (UTIs) and other inflammatory urological conditions has been completed, and results were presented at the September, 2021 AUA Conference. The study, a collaboration…

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Dr. J. Curtis Nickel Urinary Microbiome Study Using MicroGenDX NGS Indicates Microbial Diversity Varies by Age and Gender

MicroGenDX Logo The study, a collaboration between Dr. J. Curtis Nickel and MicroGen Diagnostics, identified some 643 microbial species among 211 healthy subjects (106 female and 105 male) using NGS, with significant differences in microbial diversity based on gender, age, and previous antibiotic use. ORLANDO, Fla. (PRWEB) September 14,…

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Bioinformatics Manager I Job Opening in Frederick, MD at Frederick National Laboratory

Bioinformatics Manager I Job ID: req2120Employee Type: exempt full-timeFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 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…

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‘Can’t connect to eutils.ncbi.nlm.nih.gov:443’

‘Can’t connect to eutils.ncbi.nlm.nih.gov:443′ 0 Using an AWS AMI to predict small RNA targets. Getting following error. =========Prepping RefSeq Files==================== [Wed Sep 8 08:34:12 UTC 2021] 500 Can’t connect to eutils.ncbi.nlm.nih.gov:443 No do_post output returned from ‘https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP039025&rettype=native&retmode=text&edirect=6.00&tool=edirect&email=ubuntu@ip-172-31-26-35.ec2.internal‘ Result of do_post http request is $VAR1 = bless( { ‘_msg’ => ‘Can’t…

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R Bioconductor Courses

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

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the institutions that shaped Black researchers’ careers

Students at the historically Black Hampton University in Virginia cheer their graduation after an address by former US president Barack Obama.Credit: Jahi Chikwendiu/The Washington Post/Getty More than 100 historically Black colleges and universities (HBCUs) operate across the United States, most dating to the late 1800s, when they were founded in…

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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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NHGRI selects Dr. Charles Rotimi as scientific director

The National Human Genome Research Institute (NHGRI) has selected Charles Rotimi, Ph.D., as the next scientific director. In this role, he will lead the institute’s Intramural Research Program, which conducts basic and clinical research to enable a greater understanding of human disease and to develop better methods to detect, prevent…

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Postdoctoral Research Associate / Bioinformatics Analyst Job Opening in North Chicago, IL at Rosalind Franklin University of Medicine & Science

Position Summary Dr. Monika Waszczuk (Department of Psychology, Rosalind Franklin University of Medicine and Science) is seeking to appoint a Postdoctoral Research Fellow / Bioinformatics Analyst to work on a variety of ongoing research projects that explore the role of genetic vulnerability in PTSD, depression, and other mental health problems….

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tabix for ID column

tabix for ID column 4 Hello, I’m looking for something similar to tabix. But instead of looking for informations within a given region, I would like to use the values in the ID column for quickly lookup. So for example I would like to take the compressed dbSNP file, index…

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Annotate Structural variants with population specific allele frequency values

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

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CRISPR Convenience: Cas7-11 Redefines RNA Editing

Scientists, typically, are on their own after their post-doc ends. Sometimes, albeit rarely, they team up, blending their ideas, money, and people. Connie Cepko, PhD, and Cliff Tabin, PhD, pioneered the idea of a lab partnership, spending the last few decades working together in their shared lab at Harvard Medical…

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Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

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UC San Diego researchers receive $6 million NIH grant to study insulin-producing cells

Sequencing the human genome -; a feat accomplished in 2003 -; provided the list of ingredients that make up a human being, but not the instructions that explain how those ingredients are used by each cell type to create complex “meals.” In other words, just because we know the sequence…

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$6M NIH Grant Launches UC San Diego Consortium to Study Insulin-Producing Cells

Sequencing the human genome — a feat accomplished in 2003 — provided the list of ingredients that make up a human being, but not the instructions that explain how those ingredients are used by each cell type to create complex “meals.” In other words, just because we know the sequence…

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NIH unraveling cause behind never smokers’ lung cancers

Researchers identified three subtypes of lung cancer among never smokers with the disease, who comprise about 10-20% of the lung cancer patient population, according to the National Institutes of Health. Nonsmokers’ tumors were found to stem from mutations driven by natural bodily processes, the agency announced. Lung cancer is blamed…

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Breakout “CRISPR platform” company Mammoth Biosciences is officially a unicorn

The CRISPR-based biotech startup Mammoth Biosciences is officially a unicorn, the company says. The billion dollar valuation comes on the back of a $150 million series D round led by Redmile Group, with participation from Foresite Capital, Senator Investment Group, Sixth Street, Greenspring Associates, Mayfield, Decheng Capital, Plum Alley and…

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UCSC knownCanonical hg19 vs. hg38

Hello, We have an FAQ page that covers this topic (genome.ucsc.edu/FAQ/FAQgenes.html#singledownload). As posted by ATpoint, it boils down to different datasets and different approaches. hg19 knownCanonical was last updated in 2013 and built primarily from RefSeq and GenBank sequences and a few other sources. One isoform was identified from each…

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Connect with CARD to explore frontiers of Alzheimer’s and related dementias science

Andrew SINGLETON, Director,Center for Alzheimer’s and Related Dementias (CARD). While some of you may already know me as a long-time investigator in NIA’s intramural research program, I’m excited to further connect with the extramural research community in my new role as director of the Center for Alzheimer’s and Related Dementias…

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NCBI NR protein db nr.gz FASTA inflate error?

NCBI NR protein db nr.gz FASTA inflate error? 0 Hello all, I’m trying to download and makedb for the nr.gz FASTA file from NCBI. I originally used wget ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz to download the nr.gz file. It worked (seemingly). But when I try to run $diamond makedb –in nr.gz -d nr I…

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Get rsID for a list of SNPs in an entire GWAS sumstats file

Here is a fairly efficient way to do this; assuming hg38 and BEDOPS and standard Unix tools installed. $ bedmap –echo –echo-map-id –delim ‘t’ <(awk ‘{n=split($0,a,/[:_]/); print “chr”a[1]”t”a[2]”t”a[2]+1″t”a[3]”https://www.biostars.org/”a[4];}’ sumstats.txt | sort-bed -) <(wget -qO- hgdownload.cse.ucsc.edu/goldenPath/hg38/database/snp150.txt.gz | gunzip -c | cut -f2-5 | sort-bed -) > answer.bed This gets around making…

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Has anyone here used the MAC tool for merging assemblies?

Has anyone here used the MAC tool for merging assemblies? 0 I’m relatively new to whole genome work and have been exploring various tools for assembling/mapping genomes. I’ve read that not all assembly tools/programs are created equal and often times it is valuable to assess assemblies from multiple tools for…

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PROVEAN not working

PROVEAN not working 2 Hello All, I’m having troubles making PROVEAN work. I’m getting this error while trying to run PROVEAN /gpfs01/home/x/NCBI-BLAST/blastdb/ftp.ncbi.nih.gov/blast/db/nr [17:44:08] searching related sequences… [18:45:32] clustering subject sequences… ./provean.sh: line 187: 41879 Segmentation fault $COMMAND Any idea what I’m doing wrong? provean • 652 views • link updated…

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Bioinformatics Scientist | Washington, DC

Bioinformatics Scientist | Washington, DC | Kelly Services Location: Start New Search: bioinformatics scientistfluidicsbiodefensemicrobiomedna sequencingngsrnabioinformaticsnihsurgeglobal healthvaccineinfectious diseasecomputationalallergymicrobiologymachine learningclinical researchbethesdahiv aids Kelly ServicesWashington, DC Full-time Perform a wide variety of complex procedures and techniques in support of RTB including Affymetrix fluidics and hybridization protocols; high-throughput TaqMan processing; microarray data analysis; high-throughput…

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Human Genome Project: How This Most-Hyped Breakthrough Could Directly, Indirectly Affect Lives

Since the Human Genome Project began a few decades ago, genomics has grown increasingly ingrained in science, medicine, and, increasingly, everyday life. Genomics has evolved from a niche subject linked with a moonshot project to a scientific field critical in fields as diverse as microbiology and cancer. What’s ahead for…

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NIH-SOAR NIEHS- Bioinformatics Scientist in Rockville, MD

Overview:Bioinformatics ScientistOverall summary:The position will independently provide support services to satisfy the overall operational objectives of the National Institute on Environmental Health Sciences.Deliverables:Work products and documents related to designing experiments; analyze and interpret the biological data; prepare and present the results based on the scientific objectives; collaborate with and support…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Significance The collection of large amounts of whole-genome sequencing data allowed for identification of mutational signatures, which are characteristic combinations of substitutions in the context of neighboring bases. The clinical significance of these mutational signatures is still largely unknown. In neuroblastoma, we showed that high levels of cytosine > adenine…

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NIH collaborates on test predictive of peripheral nerve sheath tumor occurrence

The U.S. National Institutes of Health had its hands full with the Rapid Acceleration of Diagnostics (RADx) program as the COVID-19 pandemic unwound, but the agency’s other work on diagnostics is bearing fruit. NIH said Aug. 31 that its collaboration with an academic research institute has led to development of…

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Bioinformatics Scientist (Open Level) – Bild Laboratory job with City of Hope

Thank you for your interest. Please note, the purpose of this posting is to recruit for on-going and future positions. About City of HopeCity of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening…

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Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Lantern Pharma Expands Management Team with Appointment of Two Leading Industry Executives to Support Clinical and Manufacturing Initiatives

DALLAS, Sept. 2, 2021 /PRNewswire/ — Lantern Pharma (NASDAQ: LTRN), a clinical stage biopharmaceutical company using its proprietary RADR® artificial intelligence (“A.I.”) platform to transform the cost, pace, and timeline of oncology drug discovery and development, today announced the addition of two senior industry executives to support the Company’s clinical…

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NIH blood test spots cancerous tumors in people with NF1, most common cancer predisposition syndrome: study

An estimated one in every 3,000 people around the globe has neurofibromatosis type 1, or NF1, a condition caused by a mutation in the NF1 gene that carries with it an increased risk of developing cancerous tumors, making it the most common cancer predisposition syndrome in the world. About half…

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Industrializing CRISPR

Sponsored content brought to you by Kevin Holden, PhD Kevin Holden, PhD, Head of Science at Synthego, discusses the importance of industrializing CRISPR as the technology matures and makes inroads in the clinic. GEN: What’s new and interesting to you in the world of CRISPR? HOLDEN: Some of the most…

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In mouse study, rewired cells automatically release biologic drug in response to inflammation — ScienceDaily

With a goal of developing rheumatoid arthritis therapies with minimal side effects, researchers at Washington University School of Medicine in St. Louis have genetically engineered cells that, when implanted in mice, will deliver a biologic drug in response to inflammation. The engineered cells reduced inflammation and prevented a type of…

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Antibiotic Resistance Genes | IDR

Witawat Tunyong,1 Weewan Arsheewa,2 Sirijan Santajit,3,4 Thida Kong-ngoen,1 Pornpan Pumirat,1 Nitat Sookrung,5,6 Wanpen Chaicumpa,6 Nitaya Indrawattana1 1Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; 2Department of Microbiology, Phrapokklao Hospital, Chanthaburi, 22000, Thailand; 3School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, 80161, Thailand;…

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Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

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Rebecca Kneale Gould: In matters of life and death, reading the sources is critical

This commentary is by Rebecca Kneale Gould of Monkton, associate professor of environmental studies at Middlebury College. Two recent commentaries in VTDigger attempt to raise suspicions about vaccination, the No. 1 priority for our leaders managing the Covid crisis in Vermont.  Such commentaries demand further scrutiny, particularly because their authors…

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Postdoctoral Fellow in Bioinformatics Job in North Carolina (NC), Higher-Ed/Education Career, Jobs in University of North Carolina at Charlotte

Postdoctoral Fellow in BioinformaticsUNC Charlotte – Charlotte, NC The Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte seeks a post-doctoral fellow to work under the supervision of Dr. Anthony Fodor. The successful applicant will work on NIH supported projects that investigate the role of…

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