Tag: DNA-seq

University OverviewThe University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that provide opportunities for…

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

Opportunity with an esteemed client company of Sanskruti Solutions (Bio-IT Firm): Position: Bioinformatics Software Developer No. of Positions: 01 Job Location: Wakad (Pune) / Powai (Mumbai) Open For: Both Male / Female Candidates possessing requisite skills and experience as desired by us. Job Summary: We are seeking a highly motivated and skilled Bioinformatics Software…

Produced in Partnership with SPT LabtechMay 30 2023Reviewed by Aimee Molineux Next-generation sequencing (NGS) has transformed the medical and biological sciences, delivering enhanced throughput and improved affordability. The fundamentals of NGS library preparation remain mostly unchanged, despite a substantial drop in the time required (now taking less than half a…

View the Job Description of Bioinformatics Analyst Summary: Under the general supervisionof the Bioinformatics Scientist Department Manager Laboratory Directors andPathologists and in accordance with established policies and procedures theBioinformatics Analyst performs independently in the Department of Pathology. TheBioinformatics Analyst will be responsible for analyzing clinical NextGeneration Sequencing data contributing to…

APPLICATION CLOSING DATE: July 3rd, 2023 Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centers: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health Data Science….

SUMMARY The Genetics Department is a basic science department located in the George and Cynthia Mitchell Basic Sciences Research Building at the world-renowned University of Texas MD Anderson Cancer Center in the heart of the Texas Medical Center. The focus is on advancing knowledge of the molecular genetic mechanisms that…

Posted by hagansa2 on Wednesday, May 17, 2023 in Job Opportunities . Bioinformatics Scientist will be responsible for assisting research and development team in a collaborative and multi-disciplinary effort in developing and validating OmniSeq’s molecular diagnostic and next generation sequencing based bioinformatics analysis pipelines, along with playing an important role…

Animal rearing and samples collection Our experiment was designed to compare eight female Laiwu pigs (LW) with eight female Lulai pigs (LU) which crossbred between LW and Yorkshire breeds. All pigs were born and raised for approximately two years (715 ± 33 days, Table 1) under uniform housing and feeding conditions at Jing-Qi-Shen…

How is it different from typing the same into ChatGPT? And it does not take 2-3 minutes … Can you give me two variant callers? Sure, variant callers are bioinformatics software tools used to identify variants (like SNPs and indels) from sequence data. Here are two commonly used variant callers:…

WES variant calling with DNBSEQ-T7 – technical quality assessment 0 Hi everyone! I recently received whole exome sequencing samples that were sequenced on an MGI sequencing instrument, DNBSEQ-T7. I am interested in somatic variant-calling on the paired tumor-normal samples. As this isn’t the canonical Illumina sequencer, an issue that I…

News:7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin) 0 7th Berlin Summer School in NGS Data Analysis When? September 4-8, 2023 Where? Berlin, Germany Link? Website The purpose of this intense one week summer course is to get a deep understanding in Next-Generation Sequencing (NGS) with…

Introduction Hyperuricemia is a disease caused by irregular purine metabolism, which is always accompanied by excessive production or abnormal excretion of uric acid (UA).1 Most notably, the overall incidence of hyperuricemia in China has been increasing over the past decade with the westernization of eating habits.2,3 However, there are blind…

DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article  PubMed  Google Scholar  Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…

Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes 1 Hi All, I would like to download the promoter enhancer, exon, intron, 3’prime, 5’prime positions of all genes from the human genome hg38 version. I have seen a couple of information in the…

Ahsan, D. A., Naser, M. N., Bhaumik, U., Hazra, S. & Bhattacharya, S. B. Migration, Spawning Patterns and Conservation of Hilsa Shad (Tenualosa ilisha) in Bangladesh and India. Publ. by Acad. Found. India, New Delhi Int. Union Conserv. Nat. Nat. Resour. 95 (2014). De, D. et al. Nutritional profiling of…

Bioinformatician position available at NIH (Bethesda, MD) We seek a bioinformatician/data scientist with a strong record of collaborative interactions with biologists. The successful candidate must have a M.S or Ph.D. degree in bioinformatics, computational biology, computer science, or a related field and have the ability to work independently or as…

We are looking for an enthusiastic Postdoctoral researcher who is eager to work on the computational reconstruction of dynamic blood-cancer interactomes from longitudinal multiomics data. Organization: University of Innsbruck Country: Austria Department(s): Institute of Molecular Biology and Digital Science Center (DiSC) Research Field: Bioinformatics Researcher Profile: Postdoctoral researcher Type of…

News:Next-Generation Sequencing Data Analysis: A Practical Introduction (May 3-5, 2023 in Munich, Germany) 0 📣Attention all biologists! 🧬 Are you interested in expanding your knowledge in Next-Generation Sequencing (NGS) and bioinformatics? 🧐 Look no further! We are excited to announce our upcoming hands-on workshop on NGS Data Analysis from May…

Onsite role   Scientific Associate – Bioinformatics   We are seeking a highly motivated bioinformatics scientist to perform quality control and analysis of next-generation sequencing data (e.g., RNA-sequencing and cell-free DNA-sequencing) from clinical trial samples. The successful candidate will work collaboratively with computational biologists, drive quality control of sequencing data,…

Bad quality fastq files for analysis 0 I am working on a project that requires me to identify multiple fastq files with low quality. What can be a possible starting point for this sort of data search? quality bad DNA-seq fastq alignment • 113 views Login before adding your answer….

Bioinformatics is an interdisciplinary field that analyzes and interprets biological data by combining biology, computer science, and statistics. There are various tools and techniques available for data analysis and interpretation. The software tools used in bioinformatics range from simple command-line utilities to more complex graphical programs and standalone web-services made…

Job Description The Bioinformatics Platform at the Immunology Translational Research Program NUS,  utilizes state-of-the-art methods in pipelines and workflow to analyze data to gain biological insights. The platform works with a number of medium to high throughput technologies like microbiome metagenomics, single-cell omics, next generation sequencing (RNA-seq, DNA-seq, etc), Luminex…

Genetic Variation studies often involve analyzing samples from a previously studied species. For instance, it is of interest to examine genomes of various cultivars, strains, or populations of the same species. In such cases, it may be necessary to perform de novo DNA-Seq assembly to obtain the genome of the…

The Bioinformatics Platform at the Immunology Translational Research Program NUS, utilizes state-of-the-art methods in pipelines and workflow to analyze data to gain biological insights. The platform works with a number of medium to high throughput technologies like microbiome metagenomics, single-cell omics, next generation sequencing (RNA-seq, DNA-seq, etc), Luminex multiplex assays, Microarrays,…

Opportunity with an esteemed client company of Sanskruti Solutions: Position: Bioinformatician Job Location: Wakad (Pune) / Powai (Mumbai) Open For: Both Male / Female Candidates possessing requisite skills and experience as desired by us. Job Summary: We are seeking a highly motivated and skilled Bioinformatician to join our team. The successful candidate will have…

We are looking for an intelligent, hard-working, and dynamic individual to join Bioinformatics and Molecular Data group, a subdivision of the Dana-Farber Cancer Institute (DFCI) Informatics and Analytics Department. The group encompasses expertise in bioinformatics, machine learning, and computational biology and works with some of the most prominent research and…

Principal Bioinformatics Engineer Form Bio is working with Colossal Biosciences to build the future of genome engineering, and that requires new tools, and we’re looking for someone who is interested in breaking ground on projects across our species teams. The Principal Bioinformatics Engineer needs to have strong programming skills, a…

RNA Editing data from RNA-seq 1 Does anyone help me to generate RNA editing data from raw RNA-seq data of FUNGALmodel system which has reference genome at JGI? Also would like to explain the protocol of RNA editing. NOTE Most of the RNA editing tool I found is for human…

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

Biochemical Sciences Location: Guildford Salary: £42,149 to £48,836 per annum Fixed Term for 4 years Post Type: Full Time Closing Date: 23.59 hours BST on Sunday 31 July 2022 Reference: 072121-R-R-R We are excited to invite applications for a four-year Dean’s Research Fellowship in the School of Biosciences (Faculty of Health and Medical Sciences)…

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

RPKM, how to normalize for library size 1 Hi everybody! I’m working on several metagenomes (so not trascriptomes), and I mapped high quality reads to a database made of nucleotide sequences through bowtie2. I want to convert raw mapping counts of each gene in RPKM. I know this method might…

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Internal Number: 2022-26921 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to…

Job Description: Bioinformatics Specialist (Pathology and Laboratory Medicine) University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey….

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

7 1 4 genbank,MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from…

Bioinformatics postdoctoral position There is an immediate opening for a bioinformatics postdoctoral position in Tahlan Laboratory at the Department of Biology (www.mun.ca/faculty/ktahlan/index.php) to study the epidemiology and evolution of mycobacterial pathogenesis using whole genome sequencing (WGS, Illumina) data. Responsibilities: Bioinformatics analysis of WGS DNA-seq data. Writing results for publication. Qualifications:…

Strange speed up in GATK LeftAlignIndels 1 Hi! I noticed a strange thing, I have been running a DNA-seq pipeline like this: reads -> bwa-mem2 -> picard SortSam -> picard MergeSamFiles -> picard MarkDuplicates -> gatk LeftAlignIndels … gatk LeftAlignIndels has always taken around 4 hours to complete with the…

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

6500 – The number of associates in the Novartis Institutes for BioMedical Research (NIBR). This division is the innovation engine of Novartis, focusing on powerful new technologies that have the potential to help produce therapeutic breakthroughs for patients. We are seeking a bioinformatics scientist to coordinate the processing and…

Researchers in the US and France report on a “rapid identification of methylase specificity” sequencing (RIMS-seq) approach for characterizing 5-methylcytosine methylation-related methylase enzyme specificity in concert with DNA sequencing in bacterial genomes. After validating the sequencing strategy, the team used RIMS-seq to assess synthetic and real gut microbial communities or…