Tag: qPCR

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32.,PLOS Neglected Tropical Diseases

Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32. PLOS Neglected Tropical Diseases ( IF 4.411 ) Pub Date : 2022-01-06 , DOI: 10.1371/journal.pntd.0010112 Sirawit Jirawannaporn,Umaporn…

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Effects of Cellulolytic Bacteria on Nitrogen-Fixing Bacteria, 16S rRNA, nifH Gene Abundance, and Chemical Properties of Water Hyacinth Compost

Effects of Cellulolytic Bacteria on Nitrogen-Fixing Bacteria, 16S rRNA, nifH Gene Abundance, and Chemical Properties of Water Hyacinth Compost ประเภทเอกสาร บทความในวารสาร 10.1007/s42729-020-00399-4 ชื่อวารสาร Journal of Soil Science and Plant Nutrition ฉบับที่/หน้า ปีที่ 21 ฉบับที่ 1 หน้า 768-779 วารสารออนไลน์: ดรรชนี-อังกฤษ Cellulolytic bacteria;nifH gene abundance;Nitrogen-fixing bacteria;Water…

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Investigating changes in the proteostasis capabilities of iPSC-neurons during development and in FTD using iPSC-neurons with MAPT mutations

This article was originally published here Alzheimers Dement. 2021 Dec;17 Suppl 2:e058308. doi: 10.1002/alz.058308. ABSTRACT BACKGROUND: Mutations in microtubule-associated protein tau (MAPT) gene are causative of Frontotemporal Dementia (FTD). Many of the features associated with the development of tau pathology, e.g high levels of tau phosphorylation, are also present in…

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Sr. Manager of Manufacturing – Resumetojobs.com

NuProbe USA is seeking an experienced Sr. Manager, In-Vitro Diagnostics Operations who will be responsible for all aspects of manufacturing, including design transfer of newly developed products from research & development. The successful candidate will control production planning, scheduling and forecasting. The candidate will lead continuous improvements in manufacturing as…

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China Paper Sharing | SEU/TJU: circRNA is a gene therapy target for RCC Manufacturer and Supplier

  Basic information Title: ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma   Journal: Molecular Cancer     Impact factor: 27.401   Vazyme products:   HiScript® III 1st Strand cDNA Synthesis Kit (+gDNA wiper)(number: Vazyme #R312, for 1st Strand cDNA Synthesis) AceQ® qPCR SYBR Green Master Mix (High ROX Premixed)(number: Vazyme…

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New bioinformatics method to analyze viral sgRNA

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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Bioinformatician – qPCR and annotation directions Jobs at Nalagenetics, Jakarta

We are hiring a bioinformatics specialist interested in developing a clinical decision support for implementation of genetics in clinical settings. The person will be responsible of building analytical pipelines forpatients’ genomic, demographic, and individual data, as well as working with our senior software engineer tointegrate our knowledge base with existing…

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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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Sr Scientist – IVD Development – Houston

NuProbe USA Inc . is looking for a Staff/Senior Scientist to lead the IVD project development program at NuProbe to support both research and in vitro diagnostic (IVD) assays for use in medical research, clinical trials, regulatory submissions, and clinical diagnostic use.  NuProbe USA is a rapidly growing company and…

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bioinformatics vacancy

On the one hand, I really liked the diversity of the bioinformatics program, and, with a degree in bioinformatics, there are many possible career paths. Updated on 2 December 2021. Exact wages will depend on experience and the industry an individual works in. Working experience with structural antigen analyses and…

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Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

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Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off

Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR….

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eli5 RNA Spike-ins : explainlikeimfive

I’m a data scientist trying to branch out into more bioinformatics/genetics. My tutorial is counting spike-ins, but his explanation was over my head: 1 – AnnData and Preprocessing spike-ins | Kaggle ” Because this is smartseq2 data, we may have spike-ins. An RNA spike-in is an RNA transcript of known…

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Research Fellow, Precision Medicine job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The NUS Resilience & Growth Research Fellow (NUS R&G-RF) will be responsible to work closely with the Principal Investigator and study team members to ensure the successful completion of industry-linked non-coding RNA (ncRNA) biomarker discovery research projects and subsequent functional validation of the identified ncRNA biomarkers in a…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Boston, Massachusetts, United States

IDT is the leading manufacturer of custom oligonucleotides and proprietary technologies for genomics applications. Our work is complex and cutting-edge, and our team members are curious, creative thinkers who understand that good data drives smart decisions. At IDT, we realize that although science may be uniform, people are unique. We…

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Bioinformatics Scientist – Houston | Mendeley Careers

NuProbe USA is hiring two NGS Bioinformatics Scientists for its Houston (TX) location. NuProbe is the US-based R&D subsidiary of NuProbe Global, a company devoted to the development of novel non-invasive DNA and RNA diagnostic assays. Currently, NuProbe has several products based on NGS, qPCR, and sanger technologies. The Innovation…

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dbCAN-PUL

dbCAN-PUL PULID Characterization Method(s) Substrate Organism Publication Publish Date Type Num Genes Num CAZymes CazyFamily PUL0046 NMR, sequence homology analysis O-antigen Escherichia coli 29738687 O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104. Biochemistry (Mosc). 2018 May;83(5):534-541. doi: 10.1134/S0006297918050061….

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Bioconductor – HTqPCR

Automated analysis of qPCR data Bioconductor version: 2.5 Analysis of Ct values from quantitative real-time PCR (qPCR) assays. Data can be analyzed in high throughput across multiple conditions or replicates, and in spatially-defined formats such ABI TaqMan Low Density Arrays and conventional 96- or 384-well plates. HTqPCR handles data loading,…

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New bioinformatics method for viral sgRNA analysis

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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26S rRNA gene is not useful for identifying Saccharomycodes ludwigii by qPCR

Through intensive research and development, quantitative polymerase chain reaction (qPCR) has emerged as a dominant tool for precision clinical detection of many pathogenic microbial species in difficult-to-analyse sample matrixes. The method requires precise and specific targeting of unique species-identifying regions of particular gene in a microbe. To do this, species-specific…

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Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes

This article was originally published here Arthritis Res Ther. 2021 Nov 30;23(1):290. doi: 10.1186/s13075-021-02660-2. ABSTRACT BACKGROUND: We performed expression quantitative trait locus (eQTL) analysis in single classical (CL) and non-classical (NCL) monocytes from patients with systemic lupus erythematosus (SLE) to quantify the impact of well-established genetic risk alleles on transcription…

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DNA Script Receives CE Mark for Syntax Enzymatic DNA Synthesis Platform

NEW YORK – DNA Script said on Tuesday that it has received CE marking for its Syntax enzymatic DNA synthesis platform, clearing the way for the benchtop DNA printer’s commercial sales in Europe. The CE marking covers the benchtop instrument, reagents, and consumables, the firm said. The Syntax platform can…

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Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes | Arthritis Research & Therapy

Patients and samples Whole blood samples from 15 Female SLE patients fulfilling the American College of Rheumatology criteria for the diagnosis of SLE [11, 12] and five age-sex matched healthy controls were procured from the Mayo Clinic, Rochester, MN. Exclusion criteria included pregnancy, active acute infection, chronic infection (e.g., hepatitis…

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A CRISPR/Cas12a-based DNAzyme visualization system for rapid, non-electrically dependent detection of Bacillus anthracis

Introduction Anthrax, a serious zoonotic disease, is caused by Bacillus anthracis. Because B. anthracis spores can be used as biological warfare and terrorism agents, the development of sensitive, efficient detection methods for this pathogen is important and urgently needed. Currently, B. anthracis is detected by identifying its vegetative cells and…

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Will Kallisto show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene?

Will Kallisto show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene? 0 Hello, I was wondering if Kallisto will show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene?…

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Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

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Pulmonary Infection Revealed by Metagenomic NGS

1Department of Biomedical Engineering, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People’s Republic of China; 2Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People’s Republic of China Background: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by…

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TANK prevents IFN-dependent fatal diffuse alveolar hemorrhage by suppressing DNA-cGAS aggregation

Abstract Diffuse alveolar hemorrhage (DAH) is one of the serious complications associated with systemic lupus erythematosus, an autoimmune disease whose pathogenesis involves type I IFNs and cytokines. Here, we show that TANK, a negative regulator of the NF-κB signaling via suppression of TRAF6 ubiquitination, is critical for the amelioration of…

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Serial dilutions on qPCR should be compulsory ? What if I do have data without serial dilution? Objectively compute CT values.

Dear community, Let me put in context my question: I am working with qPCR to detect the absence/presence of a certain mutation in a given gene. However, the laboratorians that give me the data do not make serial dilutions on the input DNA samples, nor on the internal control. So…

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Data scientist bioinformatics, Singapore – Job Dispatch

Data Scientist (Bioinformatics) Our client is an emerging Biotech company that specialises in oncology diagnostics products. Responsibilities: In-depth data analysis with machine learning and statistical methods Identify novel DNA/RNA/ncRNA biomarkers Develop models for multi-marker diagnostic test Facilitate the design and execution of the experiment, the process set up and quality…

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Zhang Jin’s group reported that rRNA biogenesis regulates the fate transition of mouse ES-2C-like cells

On November 9, 2021, the Stem Cell and Regenerative Medicine Center of the Department of Basic Medicine, Zhejiang University School of Medicine/The First Affiliated Hospital of Zhejiang University School of Medicine/Zhejiang Liangzhu Laboratory Zhang Jin’s research group published a titled ” rRNA Biogenesis ” in Nature Communications . Regulates Mouse…

Continue Reading Zhang Jin’s group reported that rRNA biogenesis regulates the fate transition of mouse ES-2C-like cells

Dura cells in the etiopathogenesis of Crouzon syndrome: the effects of FGFR2 mutations in the dura cells on the proliferation of osteoblasts through the hippo/YAP mediated transcriptional regulation pathway

Background: FGFR2 (fibroblast growth factor receptor 2) mutations are implicated in the etiopathogenesis of syndromic craniosynostosis, and C278F- or C342Y-FGFR2 mutations can lead to Crouzon syndrome. The dura mater exerts crucial effects in the regulation of cranial suture development. However, the underlying mechanisms of these biological processes are rarely studied….

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Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA

Significance Extrachromosomal circular DNA (eccDNA) plays a role in human diseases such as cancer, but little is known about the impact of eccDNA in healthy human biology. Since eccDNA is a tiny fraction of nuclear DNA, artificial amplification has been employed to increase eccDNA amounts, resulting in the loss of…

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Transcriptome Sequencing Explores the Mechanism of Baicalin on Bone Ca

Introduction With the continuous improvement of cancer treatment technology, the 3-year and 5-year survival rates of cancer patients have been greatly improved. However, cancer still cause pain to the patients, which seriously affects their quality of life. This is because in many common cancers, tumors can easily metastase to the…

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Bioinformatics NGS Data Analyst position in Andover, Massachusetts

Job Description: Position Summary: The qualified candidate will join the Analytical Research and Development Microbiology and Strategy Testing organization in Andover, MA, a QC (GMP) laboratory that supports biotherapeutic clinical manufacturing. Candidate will report directly to Microbiology Group Leader (Principal Scientist, Ph.D.). We are recruiting an expert…

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RNA-Seq and qPCR

RNA-Seq and qPCR 0 Greetings! For a rice gene LOC_Os06g51060 Relative (to control group) Log2FC values obtained by qPCR and RNA-Seq are as follows: See here: There is a difference in values as well a TREND. I have quite a few other such genes and this problem has effected them…

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Blackhawk Genomics Announces Launch of HerediSeq and PanSeq Genomic Analysis Kits

SAN FRANCISCO (PRWEB) November 16, 2021 Blackhawk Genomics LLC, a molecular diagnostics technology company, today announced the launch of the HerediSeq and PanSeq genomic analysis kits designed to detect structural variants and elucidate difficult-to-characterize genomic regions using long-read sequencing. HerediSeq chemistry resolves deletions and duplications, repetitive regions and pseudogenes,…

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Canine Somatic Cell Reprogramming and Its Facilitation through Inhibition of Endogenous p53

Numerous efforts have been made to establish bona fide iPSCs from companion animals such dogs and cats. Generation of iPSCs from companion animals would provide useful unrestricted cell resources with a vast scientific potential. To name a few applications, they can be exploited as new models for regenerative medicine and as therapeutic…

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Research Associate, Cell Engineering – Philadelphia

Position Title: Research Associate, Cell Engineering Position Level: Research Associate/Sr. Research Associate Reports to: Shelby Keating, Scientific Associate Company Background: Century Therapeutics is developing novel allogeneic living cell products for oncology that overcome the limitations of current cell therapies. Century’s genetically-engineered, universal iPSC-derived immune effector cell products are designed to…

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Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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Hairpin structure facilitates high-fidelity DNA amplification reactions in both qPCR and high-throughput sequencing

Abstract Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation…

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In Brief This Week: Caris Life Sciences, Psomagen, Tempus, CareDx, HTG Molecular, Epigenomics, More

NEW YORK – Caris Life Sciences said this week that the Georgia Cancer Center at Augusta University has joined its Precision Oncology Alliance, a collaborative network of 55 leading cancer centers and academic institutions seeking to advance comprehensive cancer profiling and establish standards of care for molecular testing in oncology….

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Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

doi: 10.3389/fgene.2021.769690. eCollection 2021. Affiliations Expand Affiliations 1 Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang, China. 2 Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China. 3 Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang,…

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CRISPR-Cas9 Mediated Exonic Disruption for HIV-1 Elimination

Abstract Background A barrier to HIV-1 cure rests in the persistence of proviral DNA in infected CD4+ leukocytes. The high HIV-1 mutation rate leads to viral diversity, immune evasion, and consequent antiretroviral drug resistance. While CRISPR-spCas9 can eliminate latent proviral DNA, its efficacy is limited by HIV strain diversity and…

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MBE presentaties transformation/electroporation, PCR, AKTA, IC/50 –

Presentaties in het engels voor de onderwerpen transformation/electroporation, PCR/qPCR, A…Bekijk meer Geüpload doorBob Wildema Academisch jaar 2021/2022 Nuttig?10 Delen Reacties Log in of registreer om reacties te kunnen plaatsen. Studenten bekeken ook LABJOURNAAL MBE MBE PT1B – Dit zijn de voorbereidende PT’s Pt 3 mbe – Dit zijn de voorbereidende…

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DNA Script on Track for Release of Enzymatic DNA Synthesis Platform in 2022

NEW YORK – DNA Script is expanding its operations and is on track to commercially launch its Syntax enzymatic DNA synthesis platform early next year after gathering feedback from early-access users at the Broad Institute and elsewhere. Last month, the French company, which has locations in Paris and South San…

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The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits

Significance In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the…

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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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Transcription factor binding sites and variants around cis-regulaory elements

Hello, I need your help regarding transcription factors and their gene targets (association with protein coding genes). What do I have? List of several protein coding genes and experimentally confirmed variants located in their cis-regulatory elements (CREs), up to 3kbp from TSS in cancer cell lines. What do I want…

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Technical officer in Bioinformatics (m/f) at LNS

TECHNICAL OFFICER IN BIOINFORMATICS (M/F) Type of contract: Full-time and determined duration contract (CDD) The Laboratoire national de santé (Luxembourg public institution) is recruiting a Technical officer in Bioinformatics (m/f) for the Department of Microbiology in a full time position (40h/week) with a fixed-term contract of 12 months (ending 30 september 2022). About the Laboratoire…

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Researchers Develop CRISPR-based Rapid Diagnostic Tool for SARS-CoV-2

Study lead author Dan Brogan (left) and coauthor Calvin Lin review results from a SENSR reaction using a light cycler qPCR machine. Photo by Michelle Fredricks, UC San Diego Physical Sciences Blending experts from molecular genetics, chemistry and health sciences, researchers at the University of California San Diego have created a…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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Phosphorus hiring DNA Sequencing Laboratory Technician in Secaucus, New Jersey, United States

Company OverviewAt Phosphorus, our mission is to extend and improve lives by making genomics a foundational part of everyone’s health and wellness journey. We have built a verticalized genetic testing platform, from wet lab chemistry to software and bioinformatics, allowing us to provide the most comprehensive, medical-grade genetic tests at…

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Recruitment of Research Associate/Senior Research Associate at IDEAYA Biosciences, San Francisco

About IDEAYA Biosciences: Biotechnology company IDEAYA Biosciences (NASDAQ: IDYA) develops synthetic lethality-focused precision medicine for cancer patients using DNA sequencing and other molecular diagnostics. The company is publicly traded. Small molecule drug discovery is integrated with biomarker identification and validation to identify patient populations most likely to benefit from the…

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New Products Posted to GenomeWeb: Roche, Jumpcode Genetics, Mikrogen, More

Roche Avenio Tumor Tissue Comprehensive Genomic Profiling Kit Roche has launched its Avenio Tumor Tissue Comprehensive Genomic Profiling (CGP) Kit for research use. The jointly developed project from Roche and Foundation Medicine delivers information about complex genomic signatures, including tumor mutational burden, microsatellite instability, and loss of heterozygosity, in addition…

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normalization – What statistics can I use on qPCR data composed of several runs if all normality tests fail on the dataset?

I have >100 qPCR experiments that I’d like to analyze together, each containing the same set of genes (10 genes of interest and 2 reference genes). I have four different samples (untreated & 3 treatments) from the same cell culture. Our setup allows two of them to be run at…

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Intergenerational Effects of Maternal Obesity on Offspring Mitochondrial Reactive Oxygen Species Production and DNA Damage

Abstract: Epidemiological studies have shown that offspring from pregnancies complicated by maternal obesity have a 4-fold greater risk for developing childhood obesity and symptoms of metabolic syndrome. The developmental origins of health and disease (DOHaD) hypothesis states that certain environmental exposures during critical windows of development may have consequences for…

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HTqPCR – Multiple plates for multiple samples: How made a correct pData?

I have a set of seven files from runs on 48 low-throughput qpcr system. So, our runs have 48 max samples. In fact, we have 30 reactions per run. Our file is like this: File1.csv 1 10-A1-C C9 1 IDH Endogenous Control 12.6929092407226 2 10-A1-C C10 1 IDH Endogenous Control…

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Single-cell Analysis of Genome Engineering | Learning Center

ENGINEERED CELLS & SINGLE-CELL ANALYSIS Many of today’s cutting-edge research methods and therapies rely on the engineering of cells. By precisely altering DNA, genome engineering makes it possible to probe the relationship between a gene and its function, repair dysfunctional genes, or add functionality to cells. Changing the genome often involves…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

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qPCR primer design for multiple transcript variants

qPCR primer design for multiple transcript variants 0 Hello, I am a little new to NCBI tools and can’t quite wrap my head around primer design on the website. I am trying to design primers to run single-step qPCR for one gene’s expression. There are 3 transcript variants, all of…

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Danaher Jobs – Bioinformatics Specialist in Shanghai, China

Three years of prior sales experience required; preferably in life science reagents/consumables. Proven track record of meeting or exceeding sales targets for at least 2 years required. Residing in the assigned region and extensive familiarity with existing academic, corporate, and government accounts in the region required. Applications experience within NGS,…

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very different outputs from rMATS vs altanalyze

alternative splicing: very different outputs from rMATS vs altanalyze 0 We are comparing two RNA-seq datasets (read length = 150nt, depth = 50M reads, 2 conditions, n = 4 per condition) for alternative splicing. I used rMATS and altanalyze to find alternative splicing events. However, there is very little overlap…

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Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing

Author Correction: Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment “ρ(-)”. Consequently, Figure 2(g) legend has been modified accordingly,. “MirCs were generated from mitochondrial disease patient-derived (7S) fibroblasts. (a) mtDNA CN during the procedure of MirC generation. Fibroblasts that received gene transfer, designated as 7S_ρ(-) were cultivated with…

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Senior Director / VP of Bioinformatics

A successful candidate will manage a team of bioinformaticians and ultimately be responsible for providing technical guidance on data generation and analysis for gene expression, genotyping, microarray, sanger sequencing, Next-Generation Sequencing, and other genomic platform data. Additional activities include designing and developing new assays and protocols for genomic applications. These…

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randomreads.sh adding abundances for metagenomic like distribution

randomreads.sh adding abundances for metagenomic like distribution 0 Hi, I have 9 genomes, I would like to produce a metagenome like distribution using randomreads.sh. I concatenated genome fasta files in one reference file. Then, ran as below. ../bbmap/randomreads.sh ref=simplified_catgenome.fasta out1=20M.read1.fastq out2=20M.read2.fastq length=125 paired=t metagenome=t genome=9 reads=20000000 However, I would like…

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Labcorp Employment – Senior Bioinformatics Scientist

jobitlyem Saturday, 9th Oct 2021 Job Description: Labcorp is recruiting a Sr Bioinformatics Scientist for a dynamic team in either Westborough, MA, Raleigh, NC or Atlanta, GA. This position can also be Remote based. She/He will improve understanding of biological measurements and assay performance, to design, develop and extend algorithms…

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Research Bioinformatician I – Applied Genomics Job Opening in Los Angeles, CA at Cedars-Sinai

JOB SUMMARY:Under close supervision, the Research Bioinformatician I performs general bioinformatics analysis and software support for projects involving in omics. The RBI will manage omic data including loading and querying data from database system and public repositories, and transform and merge multilevel omic data into user-friendly formats, assist in development,…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Coralville, Iowa, United States

IDT is the leading manufacturer of custom oligonucleotides and proprietary technologies for genomics applications. Our work is complex and cutting-edge, and our team members are curious, creative thinkers who understand that good data drives smart decisions. At IDT, we realize that although science may be uniform, people are unique. We…

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Tumor Biology Lab Research Associate Job at UC San Diego Health

– Advertisement – Tumour Biology Lab Research Associate Job at UC San Diego Health Filing Deadline: Mon 10/18/2021 For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus before they…

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Frontiers | Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices

Introduction The advent of modern culture-independent bacterial DNA sequencing technologies allows to achieve an in-depth characterization of the microbial communities inhabiting the human and animal bodies as well as the microbial consortia residing in other environments (Browne et al., 2016; Milani et al., 2017). These innovative metagenomics approaches, such as…

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Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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40th Anniversary Recollections & Predictions

To help celebrate GEN’s 40th Anniversary with this special October issue, we asked scientists and business professionals in academia and industry to give us their reflections, impressions, and insights on the biotechnology industry and the life sciences. We also queried them on what they believe the future might look like…

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CRISPR Gene Therapies: Assessing the Success of Gene Edits Using ddPCR

β-thalassemia is one of the most common autosomal recessive diseases in the world and researchers are seeking to produce a gene therapy to treat the condition. Scientists are applying a variety of strategies and techniques to correct the underlying genetic imbalance that causes β-thalassemia, including using CRISPR to correct the…

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Director for the Experimental Bioinformatics Laboratory (ref. PD/21/21) – Institute for Research in Biomedicine Barcelona – job portal

A) RESEARCH LABORATORIES · Barcelona Created in 2005 by the Generalitat de Catalunya (Government of Catalonia) and the University of Barcelona, IRB Barcelona is a Severo Ochoa Centre of Excellence–a seal that was awarded in 2011. The institute is devoted to conducting research of excellence in biomedicine and to transferring…

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Network plot from expression data in R using igraph

[last update: January 27, 2020] igraph allows you to generate a graph object and search for communities (clusters or modules) of related nodes / vertices. igraph is utilised in the R implementation of the popular Phenograph cluster and community detection algorithm (used in scRNA-seq and mass cytometry), and also in…

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bioinformatics data scientist

A light-hearted and analogy-filled companion to the authors’ acclaimed online course (coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. * Proposes own bioinformatics projects that can improve our business * Acts as a bioinformatics leader in the projects in charge and provides appropriate and effective supports….

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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia

Study design and data collection We performed a cross-sectional, multisite study in 11 districts along Ethiopia’s borders with Eritrea, Sudan and South Sudan, located within three of its nine administrative regions. On average, ten health facilities were selected from each district, including four districts of Amhara Region (northwest Ethiopia), six…

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Quercetin inhibits the proliferation of multiple myeloma cells by upregulating PTPRR expression

This article was originally published here Acta Biochim Biophys Sin (Shanghai). 2021 Sep 24:gmab128. doi: 10.1093/abbs/gmab128. Online ahead of print. ABSTRACT Multiple myeloma (MM) is an incurable disease characterized by malignant plasma cell clonal expansion in the bone marrow; therefore, inhibiting the proliferation of plasma cells is an important approach…

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Functional succinate dehydrogenase deficiency is a common adverse feature of clear cell renal cancer

Clear cell renal cell carcinoma (ccRCC) is by far the most common type of kidney cancer, accounting for ∼80% of all kidney cancers (1). Despite recent advances, metastatic ccRCC is a generally incurable malignancy, with a 5-y survival rate <20%, highlighting the need for further biologic and therapeutic insights in…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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Epistasis shapes the fitness landscape of an allosteric specificity switch

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

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Persistent Systems hiring Bioinformatics Data Scientist – South SFO, CA in Santa Clara, California, United States

About PersistentWe are a trusted Digital Engineering and Enterprise Modernization partner, combining deep technical expertise and industry experience to help our clients anticipate what’s next. Our offerings and proven solutions create unique competitive advantage for our clients by giving them the power to see beyond and rise above. We are…

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MYO10 drives genomic instability and inflammation in cancer

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

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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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Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Resequencing of soybean accessions from low latitudes To investigate the genomic basis for the natural variation in soybean adaptation to low latitudes, we conducted whole-genome resequencing of a panel of 329 soybean accessions collected from 15 countries and covering all soybean subgroups in which 165 accessions are from in low-latitude…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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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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Advanced Enzymes to facilitate SARS-CoV-2 Research

Research focused on SARS-CoV-2 has become a primary focus in genomic and molecular biology fields. The availability of accurate, efficient, and consistent analytical tools, including new methods for screening and studying virus-host interactions, is critical. In this webinar we will discuss the latest advancements in thermostable DNA polymerases enabling sensitive…

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Startup BugSeq Bioinformatics Achieves High SARS-CoV-2 Detection Rate With Nanopore Sequencing

CHICAGO – Canadian startup BugSeq Bioinformatics has devised a method of detecting pathogens via metagenomic nanopore sequencing that the company says is more accurate and sensitive than PCR and microbial cultures. Notably, the technology does not need to target specific pathogens like PCR and microbial culture tests must. The firm…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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qPCR data analysis

qPCR data analysis 1 Hi All, We are currently using the Applied biosciences StepOne qPCR system. The software does not give us the SD, SEM, P-value for the expression profile. Is there any package in R, which can do data analysis with all the statistics involved? Please do let me…

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RT-qPCR really high fold change

RT-qPCR really high fold change 0 Hello everyone, I am getting really high gene fold change values for one of the gene of interest i.e. ~70000 folds. I am using SYBR green as a polymerase. Is this normal ? If something is wrong, how can I improve my experiment and…

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Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

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