Tag: DNAseq

Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

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NGS Data Analysis Workshops 2024

News:NGS Data Analysis Workshops 2024 0 Exciting News: ecSeq Bioinformatics 2024 Workshops Are Here! We’re thrilled to announce our diverse range of bioinformatics workshops for 2024, now open for registration! Whether you’re a beginner or looking to deepen your expertise, our courses are designed to elevate your skills in the…

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Bioconductor – semisup

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

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Bioconductor – maftools

DOI: 10.18129/B9.bioc.maftools     Summarize, Analyze and Visualize MAF Files Bioconductor version: Release (3.6) Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal…

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Staff Scientist, Bioinformatics in San Jose , CA for Takara Bio USA

Details Posted: 01-Nov-23 Location: San Jose , California Type: Full Time Salary: $145k – $155k USD Categories: Academic / Research Research Positions Years of Experience: 5 – 10 Salary Details: Please note this job description may not cover or contain a comprehensive listing of activities, duties or responsibilities that are…

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Bioconductor – regioneR (development version)

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

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NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

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Bioconductor – TitanCNA

DOI: 10.18129/B9.bioc.TitanCNA     Subclonal copy number and LOH prediction from whole genome sequencing of tumours Bioconductor version: Release (3.13) Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome…

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Stanford Health Care hiring Sr. Bioinformatics Staff Scientist – Clinical Genomics Lab – Full Time, Days in Palo Alto, CA

If you’re ready to be part of our legacy of hope and innovation, we encourage you to take the first step and explore our current job openings. Your best is waiting to be discovered. Day – 08 Hour (United States of America) From primary care to complex specialty care, Stanford…

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Online Course – A Practical Introduction to NGS Data Analysis

News:Online Course – A Practical Introduction to NGS Data Analysis – October 23-25, 2023 0 Online Course – A Practical Introduction to NGS Data Analysis Quality Control, Read Mapping, Visualization and DNA Variant Analysis When? October 23-25, 2023, 9 am – 5 pm (CEST UTC+2) Where? Online Link? Website In…

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MeiraGTx hiring Bioinformatics Analyst in New York, New York, United States

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

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Downstream analysis on multi-sample or single-sample VCF files?

Downstream analysis on multi-sample or single-sample VCF files? 0 Hello, I use GATK best practices in my analysis (mainly dnaseq pipeline) and as it is suggested the pipeline calls genotypes on all the samples together and at the end creates an “allSamples.vcf.gz” file. At this stage one approach would be…

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Targeted DNA Sequencing Market Forecast from 2023 – 2030 Growing at a CAGR of 9% with Key Players and Market Analysis

The “Targeted DNA Sequencing Market” report draws on various inferences to analyze the challenges within the industry. The final draught highlights the industry’s typical problems as well as the businesses facing them. This report is of 143 pages. The Targeted DNA Sequencing market is expected to grow annually by 9%…

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Takara Bio USA, Inc. hiring Staff Scientist, Bioinformatics in San Jose, CA

Job Title: Staff Scientist, BioinformaticsReports to: R&D Group Leader, BioinformaticsFLSA Class: ExemptLearn more about our company and how we support you:Takara Bio USA (TBUSA) empowers life science discovery. We bring innovation and inspiration to every scientist – promoting discoveries that improve health and the environment. We hold values that all…

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Stanford University hiring Bioinformatician in Stanford, California, United States

Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated bioinformatician. This position within our bioinformatics core team will support our bioinformatics consulting services for faculty and researchers via the Genetics Bioinformatics Service Center (GBSC). For…

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Add 8-mers before and after of my AA change

Add 8-mers before and after of my AA change 0 Hi All, could anyone please help in this? I have mutational variants (AA change), I would like to add 8 AA before and after to my mutational variants. Is there any way to do this? Actually, I’m trying to run…

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Sunrise Systems, Inc. hiring Bioinformatics Data Scientist in Lawrence, New Jersey, United States

Job Title: Research Scientist (Bioinformatics Scientist) Location: 50% Onsite role in Lawrenceville, NJ (Hybrid) Duration: 12 months (with possible extension) Position Type : Hourly contract Position (W2 only) Pay Rate: $60/hour on W2. Senior Research Scientist, Disease Strategy and Late Stage Hematology, Translational Bioinformatics **5+ years of bioinformatics data analysis experience in the…

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Cancer Immunogenomics Bioinformatics Analyst – BayOne Solutions

Role: Cancer Immunogenomics Bioinformatics AnalystLocation: REMOTE ( need someone who can support in PST hours)Type: 6+ months Rate : $50/Hr. W2 Details: The Cancer Immunogenomics (CIgx) team is seeking a contract bioinformatics analyst with ~2+ years of experience (either in industry or an academic research lab during a degree) to…

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Translational Bioinformatics Research Scientist job with Alpha Consulting

TRANSLATIONAL BIOINFORMATICS RESEARCH SCIENTIST LAWRENCEVILLE, NJ 5+ years of bioinformatics data analysis experience in the Cancer Research setting or Biopharma space 50% onsite/50% remote Required Skills: Ph.D. or M.Sc. with 3+ years of experience- in computational biology, bioinformatics, biostatistics, or another relevant field. Experience in cancer research institutions, biotech or…

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MeiraGTx hiring Bioinformatics Analyst/Scientist I, Molecular and Protein Engineering in New York, New York, United States

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

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What happens when a bioinformatician has his own genome sequenced for $300?

News:What happens when a bioinformatician has his own genome sequenced for $300? 0 Of Course! He goes even deeper by analyzing the analysis itself! Unveil the mysteries of genetics as a bioinformatician explores his own DNA through affordable consumer whole-genome sequencing. With raw data provided by Nebula Genomics, he navigates…

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Integrated Resources, Inc ( IRI ) hiring Computational Biologist/Bioinformatician in Mississauga, Ontario, Canada

This contract position provides the opportunity to implement and deliver bioinformatics tools for a wide range of applications working with proteomics. The candidate will join a team focused on infrastructure developments for proteomics and collaboration with many research groups in Genentech, working with both bioinformatics and bench biology teams. Responsibilities…

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Stanford Health Care hiring Senior Bioinformatics Scientist in Palo Alto, California, United States

This is a Stanford Health Care job. A Brief Overview Senior Staff Scientist will be part of a growing clinical genomics team of bioinformaticians, lab scientists, data curation scientists, clinicians and medical fellows. The Clinical Genomics Program (CGP) is a collaboration between Stanford Hospitals and Stanford School of Medicine to…

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Genomewide paired DNA-RNAseq analyses to discover intronic splice mutation hotspots in neurological disorders

Abstract Paired DNA-RNA sequencing analyses enhance diagnostic yield in rare disorders by revealing pathogenic splice mutations that cannot be identified using DNAseq based methods alone. However, such analyses are typically restricted to known disease gene panels and focus on causal variants close to intron-exon boundaries. Here, we developed SpliPath (Splicing…

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Bioconductor – karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

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Bioinformatics Data Scientist – Sunrise Systems, Inc.

Sunrise System Inc. is currently looking for Bioinformatics Data Scientist in Lawrenceville, NJ with one of our top clients. Job Title: Bioinformatics Data ScientistJob Id: 23-04105Location: Lawrenceville, NJ 08648Duration: 12 monthsPosition Type: Hourly contract Position (W2 only) Note: 50%Onsite Job Description: Senior Research Scientist, Disease Strategy and Late Stage Hematology, Translational Bioinformatics 5+ years of…

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Sunrise Systems, Inc. hiring Bioinformatics Scientist in Lawrence, New Jersey, United States

Sunrise System Inc. is currently looking for Bioinformatics Scientist in Lawrenceville, NJ with one of our top clients. Job Title: Bioinformatics Scientist Job Id: 23-04105 Location: Lawrenceville, NJ 08648 Duration: 12 months Position Type: Hourly contract Position (W2 only) Note: 50%Onsite Job Description: Senior Research Scientist, Disease Strategy and Late…

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Translational Bioinformatics Research Scientist Jobs in Lawrenceville NJ

TRANSLATIONAL BIOINFORMATICS RESEARCH SCIENTIST LAWRENCEVILLE, NJ 5+ years of bioinformatics data analysis experience in the Cancer Research setting or Biopharma space 50% onsite/50% remote Required Skills: Ph.D. Or M.Sc. With 3+ years of experience- in computational biology, bioinformatics, biostatistics, or another relevant field. Experience in cancer research institutions, biotech or…

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Bioconductor – miaSim

DOI: 10.18129/B9.bioc.miaSim   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see miaSim. Microbiome Data Simulation Bioconductor version: 3.16 Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell’s Neutral model is used to determine the abundance matrix. The…

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Bioinformatics Analyst – Astrix

Bioinformatics Analyst Location: South San Francisco, California Type: Contract Job #39364 We are seeking a highly motivated Bioinformatics Analyst to work on the analysis and interpretation of high-throughput genomic and clinical data, to investigate immune cell crosstalk within the tumor microenvironment. This individual will be affiliated primarily with developing software to simulate…

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Bioinformatics Pipeline Development with Nextflow (May 15-17 in Leipzig, Germany)

News:Bioinformatics Pipeline Development with Nextflow (May 15-17 in Leipzig, Germany) 0 Streamline your research through the development of reproducible analysis pipelines In a nutshell Learn the fundamental best-practices of bioinformatic pipeline development Understand how workflow management systems can accelerate your research Use state-of-the-art, open source software to make complex analyses…

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Supported Tools – MultiQC

Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….

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Python 01 in Bioinformatics | Processing Gene Sequences from Scratch

1. Download of sequence data When we start to understand the processing flow of the sequence, we first need to know the sequence download URL. One of the well-known websites is NCBI (National Center for Biotechnology Information) US National Center for Biotechnology Information. 1. Enter NCBI through the following website,…

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Bioconductor – samExploreR

DOI: 10.18129/B9.bioc.samExploreR     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see samExploreR. samExploreR…

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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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Director of Bioinformatics Research Job Opening in Hudson, FL at M2GEN

Director of Bioinformatics Research Location:  Remote Status:  Full-time ExemptReports to:  VP Bioinformatics & BiostatisticsDirect Reports:  Build and lead a team consisting of bioinformatics research scientists that support internal business development client engagements, as well as, external academic partner research projects and biopharma sponsored bioinformatics services Who we are M2GEN is…

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Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

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Bioconductor – Clomial

DOI: 10.18129/B9.bioc.Clomial     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Clomial. Infers clonal composition of a tumor Bioconductor version: 3.12 Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained…

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