Tag: genomic

Development and clinical evaluation of a CRISPR/Cas13a-based diagnostic test to detect Mycobacterium tuberculosis in clinical specimens

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB) complex, remains one of the leading infectious causes of death worldwide, with an estimated 1.6 million TB deaths in 2021 (World Health Organization, 2022). Rapid and accurate TB diagnosis is critical to ensure timely initiation of anti-TB therapy (Walzl et al., 2018)….

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Whole Genome Sequencing Market Size [2023-2028]|Country Wise

Report Overview: Whole genome sequencing is the process of determining the complete DNA sequence of an organism’s genome, including all of its genes and other DNA elements. It provides a comprehensive view of an organism’s genetic makeup, which can be used for a variety of purposes, such as disease diagnosis…

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Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis

Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380(9859), 2095–2128 (2012). Google Scholar  Blachier, M., Leleu, H., Peck-Radosavljevic, M., Valla, D. C. & Roudot-Thoraval, F….

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Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

Isolation of pure populations of MuSCs and niche cells by fluorescence-activated cell sorting (FACS) Hindlimb muscles were dissected from young (4–6 weeks old) or aged (22–26 months old) C57BL/6J (Jackson Laboratory, 000664) mice and minced until no visible tissue chunks were visible. Muscle was then digested in a 15 ml Falcon…

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Organellar DNA continues to provide a rich source of information in the genomics era

doi: 10.1111/mec.16872. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, USA. 2 Biology PhD Program, CUNY Graduate Center, 365 5th Ave, New York, NY, USA. Item in Clipboard Christopher…

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Job Application for Data Scientist, Bioinformatics at Tome Bio

Tome Biosciences is the programmable gene insertion company. Using CRISPR, our technologies allow us to insert any genetic sequence of any size at any location into any genome. We are writing the final chapter in genomic medicines, delivering cures to patients through cell and genome engineering. Data Scientist, Bioinformatics  …

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Eye DNA Synthesis Advances in Active Biotech ETF ARKG

It’s hard to imagine it now, but at the turn of the millennium, the big advancement in technology was not the latest phone app, it was the Human Genome Project. Since then, genetics advancements are now powering health and biotech industries, with the latest upgrades coming in DNA synthesis. A…

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Postdoc in Bioinformatics/Data Science at Department of Drug Design and Pharmacology – University of Copenhagen – job portal

Job Portal Postdoc in Bioinformatics/Data Science at Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen We are looking for a highly motivated and dynamic postdoc for an ambitious bioinformatician / data scientist for a two-year Postdoc with possibilities for extension commencing 1 May…

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Bioinformatics Analyst I Job in Maryland (MD), Other Career, Full Time Jobs in Frederick National Laboratory for Cancer Research

Bioinformatics Analyst I Job ID: req3323Employee Type: exempt full-timeDivision: Cancer Research Technology ProgramFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

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Bioconductor – TSRchitect

DOI: 10.18129/B9.bioc.TSRchitect     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TSRchitect. Promoter identification from large-scale TSS profiling data Bioconductor version: 3.14 In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in…

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Bioinformatics Analyst III (Remote) Position In North Chicago, IL

Job Description Evaluate, develop, and implement computational methods, pipelines and tools for data analysis and visualization. Interpret results and contribute to hypothesis generation. Implement our existing analytical workflows and establish new workflows as needed for analysis of new techniques with NGS or feature readouts Work closely with scientific teams to…

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Principal Bioinformatics Software Engineer, NGS Data Pipeline – Roche

The Position Roche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools, and software/systems infrastructures so researchers and clinicians can make better health decisions faster. The path to curing cancer…

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Researchers Go Beyond Gene Variant Analysis With Nascent Pangenome-Based Methods

NEW YORK – Graph-based genomes, such as the one being built by the Human Pangenome Reference Consortium (HPRC), are already being used to do more than just genetic variant analysis. Last week, researchers from the University of California, Santa Cruz published a paper in Nature Methods showing how a graph…

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Bioinformatics Analysis of Viral Metagenomic Sequencing

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly…

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How To Install r-bioc-annotationhub on Kali Linux

In this tutorial we learn how to install r-bioc-annotationhub on Kali Linux. r-bioc-annotationhub is GNU R client to access AnnotationHub resources Introduction In this tutorial we learn how to install r-bioc-annotationhub on Kali Linux. What is r-bioc-annotationhub This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub…

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Dicentric Recombinant Chromosome 18 due to Maternal Paracentric Inversion Analyzed by Array CGH – Abstract – Molecular Syndromology

Log in to MyKarger to check if you already have access to this content. Buy FullText & PDF Unlimited re-access via MyKarger Unrestricted printing, no saving restrictions for personal use read more CHF 38.00 * EUR 35.00 * USD 39.00 * …

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Could Africa be the future for genomics research?

Scientists at the African Centre of Excellence for Genomics of Infectious Diseases in Ede, Nigeria, prepare samples for DNA sequencing.Credit: ACEGID In 2020, an analysis of 426 African genomes, involving researchers from 15 African countries, uncovered 3 million new variants in the human genome1. The discovery contributed to the development…

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Study demonstrates intrahost MPXV variation within a single lesion

In a recent study published in Emerging Infectious Diseases, researchers reported on the clinical and molecular characteristics of monkeypox (MPX) virus (MPXV) infections in Finland. Study: Intrahost Monkeypox Virus Genome Variation in Patient with Early Infection, Finland, 2022. Image Credit: ART-ur/Shutterstock Background Ever since 2022, an unprecedented MPXV outbreak has…

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Eurojobs.com: Software Engineer – Bioinformatics

One of the world’s leading corporations in the Diagnostics and Life Science Research Sector is looking for a Software Engineer to work for one of their fasted developing subsidiaries in the spatial biology field. They are looking for someone with a strong biology background to use their industry and technical…

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Senior Data Scientist, Translational Bioinformatics Job

Job Description Who we are: Calico (Calico Life Sciences LLC) is an Alphabet-founded research and development company whose mission is to harness advanced technologies and model systems to increase our understanding of the biology that controls human aging. Calico will use that knowledge to devise interventions that enable people to…

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Dr. Fran Supek receives an ERC Consolidator g

image: Dr. Fran Supek view more  Credit: IRB Barcelona The project to be carried out at IRB Barcelona has been awarded €2M to address an understudied mutation type known as structural variants. Using machine learning approaches, as well as innovative sequencing techniques, the laboratory will study the role of these mutations…

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Trem2 H157Y increases soluble TREM2 production and reduces amyloid pathology | Molecular Neurodegeneration

Generation, genotyping, and off-target analysis of Trem2 H157Y knock-in mice Trem2 H157Y knock-in mice were generated via CRISPR/Cas9 by the Hope Center Transgenic Vectors Core of the Washington University [25]. CRISPR gRNAs for in vitro testing were identified using CRISPOR (crispor.tefor.net/) and synthesized as gBlocks (Integrated DNA Technologies, IDT) with…

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Bioinformatics Analyst Jobs in Mettawa IL \ Data Sciences Job Recruiters

The Genomic Research Center Computational Oncology group (GRC-CO) at  is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of cancer.  GRC is a center of excellence for bioinformatics, functional genomics, human genetics, and genomic…

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Clinical Diagnostic Application Segment Anticipated to be the Most Attractive During 2023- 2033

Request For Free Sample Report of “Metagenomics Market”@ www.persistencemarketresearch.com/samples/25099 Metagenomics plays an important role in bioremediation as microorganisms are the main agents of bioremediation. Microorganisms are responsible for degradation of environmental pollutants. The metagenome of a contaminated environment includes all the DNA involved in that environment. Genetic information is used to…

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ADAMTS4 is involved in the production of the Alzheimer disease amyloid biomarker APP669-711

APP669-711 is proteolytically generated from various cells under physiological conditions Although γ-secretase-mediated C-terminal variations of Aβ have been extensively analyzed, the N-terminal variations of secreted Aβ have not been investigated to date. Importantly, several analyses of cell-based models and genetically modified animals harboring the APP mutant carrying the Swedish mutation…

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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform | BMC Bioinformatics

Comparison of read level and improving the mapping efficiency according to trimming Since the generation of high-quality WGBS data ultimately impacts the quantification and interpretation of Cs methylation levels, it is indispensable to monitor the raw data quality and interrogate the appropriate pre-processing step to cleanse data [1]. To avoid…

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Seqlengths of x contains NA values!

Hello, I would like to use ORFik to determine the coverage of the different ORFs across the maize genome. I have ribo-seq data, the latest annotation file (a GFF3), and the v5 genome fasta file for B73. After running my code, three Large CompressedGRangesLists are created and none of them…

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Visualize variants and percentage of variants from one sample of Amplicon Seq data?

Visualize variants and percentage of variants from one sample of Amplicon Seq data? 0 Hello, We are analyzing viral evolution by analyzing mutations present in a specific genomic location and how it evolves over time. We are performing amplicon sequencing of a specific region that is 222-228 bp at intervals….

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Cost-effective and accurate genomics analysis with Sentieon on AWS

This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…

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gff file from NCBI RefSeq GCF dataset has an invalid format

Thank you for noticing this. It is indeed an issue in the GFF3 file. The root of the problem is it’s a gene that is impossible to correctly represent in GFF3 because it incorporates sequence from both strands via trans_splicing. The complexity of this gene can be seen on the…

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Issue with VCF format while using Pharmcat

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

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Bioinformatics Analyst Position In North Chicago, IL

Job Description Job Title: Bioinformatic Analyst III The Genomic Research Center Computational Oncology group (GRC-CO) at Company is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of cancer. Company’s GRC is a center of…

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Rapid clonal identification of biallelic CRISPR/Cas9 knock-ins using SNEAK PEEC

Here we provide a tool that directly selects biallelically edited knock-ins using cell-surface displays, thereby eliminating the need for extensive clonal verification. By doing so SNEAK PEEC greatly reduces the considerable effort currently expended to obtain biallelically edited clones. The ability to generate a clonal population with multiple edits is…

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Research Fellow, Bioinformatician (Cancer Science Institute of Singapore) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) — with an emphasis on computational cancer genomics — is immediately available at The Cancer Science Institute of Singapore (a part of The National University of Singapore). The postholder will work with the laboratories of Prof. Ashok Venkitaraman, on a project studying the…

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The $100 genome: What breaking this accessibility barrier means for the future of genetic testing

Cheaper sequencing will also aid researchers working on diseases which have traditionally been underfunded. Bamshad cites cystic fibrosis, a condition which affects around 40,000 children and adults in the U.S., as one particularly pertinent example. “Funds for gene discovery for rare diseases are very limited,” he says. “We’re one of…

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MGI Makes its Mark in Dubai with Latest Platforms at MEDLAB Middle East and Arab Health

DUBAI, UAE, Jan. 30, 2023 /PRNewswire/ —  MGI Tech Co., Ltd. (“MGI”), a company committed to building core tools and technology to lead life science, will introduce many of its latest gene sequencing platforms and sample preparation system at MEDLAB Middle East 2023, taking place 6-9 February in Dubai. Ahead of…

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Screening of lymphoma radiotherapy-resistant genes

Introduction Lymphoma, a cancer characterized by a malignant tumor of the immune system that originates in the lymph nodes or lymphoid tissue, is one of the most common cancers worldwide. According to GLOBOCAN, the incidence of non-Hodgkin lymphoma (NHL) in both males and females ranked top ten among all cancers…

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Research associate (f/m/d) PostDoc Biology, Bioinformatics

Located in Brunswick, Germany. The Thünen Institute of Forest Genetics, one of the 15 Federal Research Institutes for Rural Areas, Forestry and Fisheries in Germany, is offering a 1,5-year position (100 %) starting as soon as possible for a research associate (f/m/d) (PostDoc Biology, Bioinformatics) to study genomic patterns of…

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Global Metagenomics Market 2023: Clinical Diagnostic

The Metagenomics Market is an emerging segment of the healthcare industry. Metagenomics is a “bottom-up” approach to studying the entire gene makeup of microbial communities without having to culture them in a lab setting. This allows for greater insight into how microbes interact with each other and their environment, as…

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Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients

doi: 10.1038/s41397-023-00299-7. Online ahead of print. Affiliations Expand Affiliations 1 Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. 2 Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA. 3 Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. amye@unc.edu….

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Bioinformatics Lead Scientist – Acutis Diagnostics Inc

The Bioinformatics Lead Scientist will report directly to the Chief Scientific Officer to develop/implement and validate bioinformatics/data processing pipelines to accurately interpret, analyze, and report results of DNA and RNA next generation sequencing in oncology, performs data management, data analysis, and LIMS implementation to generate annotated final lab report. In…

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Bioinformatics Analyst (Remote) – Rangam Consultants Inc.

Job Title: Bioinformatics Analyst Length of the assignment: 6 mo – 12 months This is a remote position. PhD or Masters preferred. The client is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of…

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Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish

Isolation, phenotypic identification, pathogenicity and antibiogram profiling Enterococcus faecalis strains BFF1B1, BFFF11 and BFPS6 were cultured in Streptococcus selective agar media (Himedia, India). The culture characteristics such as colony, morphological, physiological and biochemical characteristics of these strains BFF1B1, BFFF11 and BFPS6 were summarized in the Supplementary Table S1. All of…

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Definition of sequencing in Microbiology, Biology.

Examples of sequencing in the following topics: Sequences A sequence is an ordered list of objects (or events). Also, the sequence $(1, 1, 2, 3, 5, 8)$, which contains the number $1$ at two different positions, is a valid sequence. Sequences can be finite, as in this example, or infinite,…

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Research Assistant Bioinformatics – Florida Atlantic University

The job is open as long as you see this. See updates here: dllab.org/positions/bioinformaticians.pdf The College of Medicine is seeking a Bioinformatics Research Assistant who can assist in development of bioinformatics pipelines and analyze genomics data for a Bioinformatics and Computational Genomics laboratory which focuses on high-throughput genomic sequencing data…

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Sharing GWAS summary statistics results in more citations

Analyses The GWAS Catalog10 is an established and high-quality repository of curated human GWAS results, providing easy access to summary statistics made public by authors (via curator inclusion or author submission). Its large coverage (400,000+ associations from 5690 publications as of May 2022) and its easy-to-access statistics make it an…

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Bioinformatics Services Market is expected to grow from USD 2.8 billion in 2022 to USD 8.7 billion by 2030 : GreyViews

Pune India, Jan. 28, 2023 (GLOBE NEWSWIRE) — The market has been studied for the below mentioned-segmentation and regional analysis for North America, Europe, Asia, South America, and the Middle East and Africa. These are the key regions where the bioinformatics services market is operating and is predicted to expand…

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Quantitative dose-response analysis untangles host bottlenecks to enteric infection

A small number of C. rodentium founders initiates enteric infection To enable monitoring of the pathogen population’s diversity during infection, we introduced short, random, ~20 nucleotide DNA tags (barcodes) at a neutral location in the C. rodentium genome. As previously described5, monitoring barcode diversity using high-throughput DNA sequencing and the…

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Molecular epidemiology of CRKP | IDR

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

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Bioinformatics Software Engineer II/III – Frederick National Laboratory for Cancer Research

Bioinformatics Software Engineer II/III Job ID: req2614Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses…

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Bioinformatics Analyst – Virology – J. Craig Venter Institute

JCVI – La Jolla, CA Job Responsibilities: The Bioinformatics Analyst – Virology will work as a member of the Scheuermann bioinformatics research team on analysis of viral genomic, immune epitope, protein structure, and related data for the purpose of vaccine development for newly emerging viral pathogens as part of a…

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Principal/Associate Director Pre-clinical Bioinformatics – Repare Therapeutics

Repare Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal,…

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Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation

RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods may influence gene expression estimates. We examined the influence of multiple technical variables on estimated gene…

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A chromosome-level genome assembly of Plantago ovata

Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…

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Rapid emergence of extensively drug-resistant Shigella sonnei in France

Antimicrobial susceptibility data of S. sonnei in France Our review of S. sonnei antimicrobial susceptibility data obtained between 2005 and 2021 (based on 7121 isolates received and confirmed at the French National Reference Center for E. coli, Shigella and Salmonella, FNRC-ESS, Institut Pasteur) revealed a sharp increase in the percentage…

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counting reads in a fastq file using a refrence fasta file

counting reads in a fastq file using a refrence fasta file 1 Hi I have a reference fasta file containing 130,000 unique sequences (barcodes), each 30nts long. These sequences were synthesized with random incorporation of nucleotides in each position, so they have very large hamming distance. I had a pool…

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Variants studied for intestinal disease due to fat malabsorption

If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells. pathogenic likely pathogenic uncertain significance likely benign benign not provided total 59…

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Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

Scott M, Dobson A. The role of parasites in regulating host abundance. Parasitol Today. 1989;5:176–83. CAS  Google Scholar  Tompkins D, Dobson A, Arneberg P, Begon M, Cattadori I, Greenman J, et al. Parasites and host population dynamics. The ecology of wildlife diseases. 2002; 45–62. Thomas F, Poulin R, Brodeur J….

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Does Ancient Egyptian mummies not have any DNA left? –

Scientists have come up with reliable ways to sequence and check DNA, and used Egyptian mummies to do the first successful genomic tests. The problem, it was thought, is that Egyptian mummy DNA couldn’t be sequenced. But a group of international researchers, using unique methods, have overcome the barriers to…

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CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA. 2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA. 3 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 4 Curriculum in…

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Research Associate in Stem Cell Neurobiology job with KINGS COLLEGE LONDON

  Job description We are looking for a skilled research associate with a molecular biological background to join a vibrant group investigating amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD). You will be using CRISPR to gene edit human stem cells to introduce unpublished disease-linked mutations. This work will entail the use of…

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CRISPR Therapeutics AG (NASDAQ:CRSP) Receives Consensus Recommendation of “Hold” from Brokerages

Shares of CRISPR Therapeutics AG (NASDAQ:CRSP – Get Rating) have been given an average rating of “Moderate Buy” by the twenty analysts that are covering the firm, Marketbeat Ratings reports. Two analysts have rated the stock with a sell rating, three have given a hold rating and ten have assigned…

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Research Fellow, Bioinformatician, Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) in computational cancer genomics is immediately available at The Cancer Science Institute of Singapore (The National University of Singapore). This PDF will lead a newly funded project in the laboratory of Dr. Jason Pitt that will explore how germline genetics and cell-of-origin…

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The Global Bioinformatics Market size is expected to reach $19.9 billion by 2028, rising at a market growth of 12.5% CAGR during the forecast period

ReportLinker In order to serve several fields of scientific study, including biomedicine, bioinformatics—a mix of biology and information technology—links biological data with methods for information storage, dissemination, and analysis. New York, Jan. 27, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Global Bioinformatics Market Size, Share &…

Continue Reading The Global Bioinformatics Market size is expected to reach $19.9 billion by 2028, rising at a market growth of 12.5% CAGR during the forecast period

DekaBank Deutsche Girozentrale reduces its holdings in CRISPR Therapeutics AG (NASDAQ:CRSP)

The most recent report that DekaBank Deutsche Girozentrale submitted to the Securities and Exchange Commission (SEC) indicates that during the third quarter, the financial institution’s holdings in CRISPR Therapeutics AG (NASDAQ: CRSP) were reduced by 56.2%. The institutional investor was left with 20,000 shares after selling 25,660 shares over the…

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Remote Visualization of Local Genome Alignments Aids Pathogenic Variant Evaluation for Rare Disease

CHICAGO – A group at Spain’s National Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG) in Barcelona has harnessed a protocol for accessing sequencing and variant data to help assess potentially pathogenic genetic variants within the context of a European Union-funded program to improve diagnosis of rare diseases. The CNAG-CRG…

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Multiomics Approach Improves Diagnosis of Rare Disease, Methylmalonic Aciduria

Genomic methods, specifically whole exome and whole genome sequencing, have been at the center of diagnosing rare, genetic diseases. For example, diagnosing the inborn errors of metabolism (IEM) disease, Methylmalonic aciduria (MMA), has relied largely on the detection of genomic mutations. However, the current approach is limiting. MMA can be…

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New Products Posted to GenomeWeb: Qiagen, Thermo Fisher, Bionano Genomics, BillionToOne, More

Qiagen CLC Genomics Workbench Premium Qiagen Digital Insights has released an update to its Qiagen CLC Genomics Workbench Premium, incorporating a software accelerator called LightSpeed for faster analysis of next-generation sequencing data. The company said that this technology will allow laboratories to process a genome sequenced at 34X depth in 25 minutes for…

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Whole Genome DNA Illumina sequencing – Infravec2

Description Material provided: dataUnit definition: Whole Genome SequencingLibrary Preparation: Illumina DNA Prep or TruSeq Nano Sample Prep Kit400 million reads for 2×150 Paired End Length equivalent to ca 30X sequence depth for 1 sample of Aedes spp (estimated genome size: 1.38 Gb) or to ca 100X sequence depth for 1…

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Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep | BMC Genomics

Zhao E, Yu Q, Zhang N, Kong D, Zhao Y. Mitochondrial DNA diversity and the origin of Chinese indigenous sheep. Trop Anim Health Prod. 2013;45(8):1715-22. Liu J, Ding X, Zeng Y, Yue Y, Guo X, Guo T, et al. Genetic diversity and phylogenetic evolution of Tibetan sheep based on mtDNA D-loop…

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Discovering unique microbes made easy with DO

Article Highlight | 27-Jan-2023 New article describes how to extract and analyze genomes from microbiomes using the Department of Energy Systems Biology Knowledgebase DOE/US Department of Energy image: Overview of Metagenome-Assembled Genome Extraction data and analysis workflow using KBase apps. view more  Credit: Image courtesy of Chivian, D. et al. Metagenome-assembled…

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Time-dependent microbial shifts during crayfish decomposition in freshwater and sediment under different environmental conditions

Seilacher, A. Arbeitskonzept zur konstruktions-morphologie. Lethaia 3, 393–396 (1970). Google Scholar  Seilacher, B. A., Reif, W.-E. & Westphal, F. Sedimentological, ecological and temporal patterns of fossil Lagerstätten. Philos. Trans. R. Soc. Lond. B 311, 5–23 (1985). ADS  Google Scholar  Gibbons, N. E. & Reed, G. B. The effect of autolysis…

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Software Finds Common Biomarkers for PAH, Metabolic Syndrome

Genes associated with both pulmonary arterial hypertension (PAH) and metabolic syndrome have been identified using computer software tools, a study reports. Metabolic syndrome, thought to promote PAH, is a cluster of conditions marked by high blood pressure, elevated blood sugar, excess body fat around the waist, and abnormal cholesterol or…

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Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

Charlesworth, B. & Charlesworth, D. Population genetics from 1966 to 2016. Heredity 118, 2–9 (2017). CAS  Google Scholar  Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J. & Meester, L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol….

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Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains

Faraone, S. V. et al. Attention-deficit/hyperactivity disorder. Nat. Rev. Dis. Prim. 1, 15020 (2015). Article  Google Scholar  Franke, B. et al. The genetics of attention deficit/hyperactivity disorder in adults, a review. Mol. Psychiatry 17, 960–987 (2012). Article  CAS  Google Scholar  Dalsgaard, S., Leckman, J. F., Mortensen, P. B., Nielsen, H….

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Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing

Method overview For all presentations, we call the genetic effects on GWAS phenotypes ‘phenotypic effects’ and the effect of gene expression the ‘eQTL effect’. TWAS was originally developed to integrate eQTL and GWAS datasets derived from matched ancestries5. Specifically, it first builds gene expression prediction models using eQTL datasets that…

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Cellinfinity Bio Announces Publication and Licensing of Key Technology for Directed Evolution of Cells That Allows for More Effective Adoptive Cell Therapy

WEST HAVEN, Conn. & SAN FRANCISCO–(BUSINESS WIRE)–Cellinfinity Bio, a privately held pioneer biotechnology company developing first/best-in-class cell therapy products against solid tumors and other diseases, today announced the publication of CLASH (CRISPR-based Library-scale AAV perturbation with Simultaneous HDR knock-in), a platform that for the first time enables massively parallel genomic…

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Acq-GAs in Advanced Colorectal Cancer Patients Receiving Cetuximab-Based First-Line Chemotherapy

The following is a summary of “Acquired Genomic Alterations on First-Line Chemotherapy With Cetuximab in Advanced Colorectal Cancer: Circulating Tumor DNA Analysis of the CALGB/SWOG-80405 Trial (Alliance),” published in the January 2023 issue of Oncology by Raghav, et al. In metastatic colorectal cancer (mCRC), acquired genomic alterations (Acq-GAs), including RAS,…

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Bioinformatics Analyst III

× Job Title:  Bioinformatics Analyst III # of Openings:  1 Contract Length: 6 mos Key Responsibilities• Evaluate, develop, and implement computational methods, pipelines and tools for data analysis and visualization. Interpret results and contribute to hypothesis generation.• Implement our existing analytical workflows and establish new workflows as needed for analysis…

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Pharmacogenomics Market to Exceed USD 14,107.80 Mn by 2028 Says, The Insight Partners

According to our latest study on “Pharmacogenoics Market Forecast to 2028 – COVID-19 Impact and Global Analysis – by Technology, Application, and End User,” the market is projected to reach US$ 14,107.80 million by 2028 from US$ 7,087.81 million in 2021; it is expected to grow at a CAGR of 10.3%…

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Cambridge father of DNA sequencing excited by potential of Chem-map to understand how drugs interact with human genome

One of the fathers of modern DNA sequencing has led research into a powerful new method of understanding how many drugs interact with the human genome. Professor Sir Shankar Balasubramanian, of the University of Cambridge, says Chem-map will make it easier to develop new therapies. Dr Shankar Balasubramanian. Picture: Nathan…

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The Promise of Large Language Models in Genomics

Contributed Commentary by Vanessa Braunstein, NVIDIA  January 27, 2023 | Elucidating information directly from DNA to understand RNA’s and human proteins’ downstream structure and function is the holy grail of nearly a century of molecular biology research. The central dogma of the field—that DNA is transcribed into RNA before translation…

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Research Associate, Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A research associate position is available immediately in Prof Daniel Tenen’s lab for a highly motivated Master or Ph.D. graduate with background in molecular or cellular biology, and bioinformatics to develop a novel, fully automated analysis pipeline for the newly emerging ChIP sequencing methods: “Cut and Run” and…

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Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga

Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014). Article  CAS  Google Scholar  Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and…

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Senior Bioinformatics Java Engineer, cBioPortal for Cancer Genomics at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

The Knowledge Systems Group (KSG) at DFCI is currently seeking a Senior Bioinformatics Java Engineer to contribute to the open source cBioPortal for Cancer Genomics. The cBioPortal for Cancer Genomics is the leading visualization and analysis tool for cancer genomics.  It is an open-source software platform that enables interactive, exploratory…

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Bioinformatics Research Scientist – University of Minnesota

REQUIRED SKILLS AND EXPERIENCE 1. Fluency in one programming and one scripting languages is required (Python, R/Matlab/Splus, Perl, Java) 2. Experience in developing algorithms for analysis of biological data. Experience in algorithm development for analysis of massively parallel sequencing data (NGS seq, RNA-seq/scRNAseq etc..) is highly desirable. 3. A track…

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Magnetic Bead Purification Kits Market Intelligence Report Offers Key Futuristic Top Trends, Research Methodology and Competitive Landscape By 2028

“ The business intelligence report on the Magnetic Bead Purification Kits Market denotes the key growth drivers, hurdles, and other expansion opportunities that are formulating the industry’s growth direction throughout the forecast timeframe. Request Sample Copy of this Report @ www.marketstudyreport.com/request-a-sample/5649741 Global Magnetic Bead Purification Kits Market Size was estimated…

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Novel papillomaviruses identified in Malayan and Chinese pangolins

Papillomaviruses are non-enveloped, double-stranded DNA (dsDNA) viruses with a circular genome. Infection with these viruses can lead to several clinical symptoms ranging from subclinical, cutaneous, and mucosal warts to cancerous lesions in vertebrate hosts.  A new study published in the journal Biology Letters identifies two novel lineages of papillomaviruses by mining…

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Postdoctoral Research Fellow – Epigenomics/Bioinformatics in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Details Posted: 26-Jan-23 Location: Cincinnati, Ohio Salary: Open Categories: Academic / Research Description A computational postdoctoral position in bioinformatics and epigenomics (computational/experimental) is available in Dr. Yaping Liu’s lab in the Division of Human Genetics. One of the research directions in Dr. Liu’s group is to study single-cell multi-omics data…

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Principal Bioinformatics Software Engineer, Java Development at Roche in Santa Clara, CA 202201-103435

The Position This position may be based out of Santa Clara, California, USA, with remote work locations possible in The United States. Impact Healthcare Roche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics…

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Bioinformatics Analyst III (W2 Only) – SPECTRAFORCE TECHNOLOGIES Inc. – Remote

Job Title: Bioinformatics Analyst III Location: Remote Duration: 6 Months Pay Range : $52 – $57/hr on W2   Description: Key Responsibilities Evaluate, develop, and implement computational methods, pipelines and tools for data analysis and visualization. Interpret results and contribute to hypothesis generation. Implement our existing analytical workflows and establish…

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“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks

“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks 0 Hi! I’m working with various genomic data and while trying to use gffread, stringtie and cufflinks I went through the same error: Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ?…

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Researchers report on a genome-wide reconstruction of human microbes to develop personalized therapies

In a recent study published in Nature Biotechnology, researchers reported on AGORA2, an expansion of their previously published resource, AGORA, both resources of genomewide metabolic reconstructions of human intestinal microbes. Study: Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Image Credit: nobeastsofierce/Shutterstock Human intestinal microbes synthesize biological metabolites,…

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error making Txdb from GTF and fasta files

Hello, I would like to use ORFik to map Ribo-reads to different ORFs in the maize genome. The latest version of the genome is Zm-B73-REFERENCE-NAM-5.0.fa. The annotation file is a GFF3. I have the genome fasta file, the fasta fai file, and the GFF3 file. The ORFik package uses GTF…

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Elderly patients with DLBCL see improved survival with at least six treatments

January 26, 2023 2 min read Source/Disclosures Published by: Source: Ananth S, et al. Poster 2276. Presented at: ASH Annual Meeting and Exposition; Dec. 10-13, 2022; New Orleans. Disclosures: Ananth reports no relevant financial disclosures. Please see abstract for all other researchers’ relevant financial disclosures. …

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NY Genome Center Team Harnesses Ultima Genomics Platform for High-Sensitivity ctDNA Sequencing

BALTIMORE – Researchers from the New York Genome Center and Weill Cornell Medicine and their collaborators have demonstrated the utility of Ultima Genomics’ sequencing platform for sensitive blood-based cancer monitoring, using whole-genome error-corrected sequencing of circulating cell-free DNA (ccfDNA) at high coverage. In a preprint posted on BioRxiv last year, the…

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Author Correction: Genomic basis for RNA alterations in cancer

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK Claudia Calabrese, Nuno A. Fonseca, Lara Urban, Claudia Calabrese, Nuno A. Fonseca, Lara Urban, Liliana Greger, Nuno A. Fonseca, Lara Urban, Claudia Calabrese, Liliana Greger, Roland F. Schwarz, Oliver Stegle, Alvis Brazma, Alvis Brazma, Roland F. Schwarz & Oliver Stegle ETH Zurich, Zurich, Switzerland Natalie R. Davidson, André Kahles, Kjong-Van Lehmann, Natalie R. Davidson, André Kahles, Kjong-Van Lehmann, Stefan G. Stark, André Kahles, Kjong-Van Lehmann, Natalie R….

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Amgen, Illumina, and Nashville Biosciences Announce Genome Sequencing Agreement

deCODE genetics, a subsidiary of Amgen, will whole-genome sequence 35,000 African-American samples provided by Illumina and Nashville Biosciences. Illumina, a DNA sequencing and array-based technologies provider, and Nashville Biosciences, a subsidiary of Vanderbilt University Medical Center (VUMC), have teamed up with Amgen to provide whole-genome sequencing of approximately 35,000 DNA…

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Best Database Of Transcription Factor Binding Sites

Best Database Of Transcription Factor Binding Sites 8 (a) Which is the best database for transcription factor binding site, TRANSFAC or JASPAR? Why? (b) Is it still valid to assume, “transcription factor binding sites are only present in 5’UTR and in promoter region”? Note: kindly put references in your answer….

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