BOL: Related items

Postdoctoral Fellowship at Department of Psychiatry, Warneford Hospital, Oxford

Tue, 01 Sep 2015 05:24:49 -0500

Applications are invited for a postdoctoral research assistant to work in the Translational Neuroscience and Dementia Research Group (TNDRG) on a project using informatics approaches to understand and prevent dementia, specifically on the role of the immune system in Alzheimer’s. The post is for a fixed-term duration of 1 year.

Working with other members of the TNDRG you will analyse complex genomic and epidemiological datasets, evaluating which computational tools are most suitable. You will contribute to the generation of innovative tools for linking epidemiological and multilevel omics datasets, ensuring that computer programs are written in a form that other collaborators can use and expand.

You will have or be close to completion of a PhD in either: bioinformatics; neuroscience; machine learning; statistics; epidemiology; neurology; or other relevant field. You will have experience programming on either R, Matlab, Python, C++, Java or any other imperative, object oriented or functional language.

Please direct Informal enquiries to Dr Alejo Nevado-Holgado (alejo.nevado-holgado@psych.ox.ac.uk).

You will be required to upload a supporting statement explaining how you meet the selection criteria for the post, a CV, and details of two referees as part of your online application.

The closing date for applications is 12.00 midday on 2 September 2015. Interviews will be held on Tuesday 15 September 2015.

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118696

Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016

Yeshodari — Fri, 05 Feb 2016 06:43:28 -0600

Live Webinar on Streamlining large scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016

Abstract: Strand NGS includes comprehensive workflows for DNA-Seq, RNA-Seq, Small RNA-Seq, ChIP-Seq, MeDIP-Seq, and Methyl-Seq analysis. Each workflow includes a quality assessment and filter section, followed by a workflow-specific analysis section. The pipeline functionality in Strand NGS allows users to execute a sequence of analysis steps with specific parameters - all without any manual intervention. This simplifies the analysis in large scale sequencing projects where every sample needs to be processed identically.

In this webinar we will discuss the pre-packaged pipelines present in Strand NGS. The packaged pipelines have well-chosen default parameters and are suitable for users analyzing data for the first time in the tool. We will also show how advanced users can customize pipelines and share them with other Strand NGS users. Finally, we will show a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and emails quality reports - all from within Strand NGS.

Speaker: Dr. Vamsi Veeramachaneni, Vice President - Bioinformatics, Strand Life Sciences

Details: Session 1: 2:30 PM IST, Session 2 : 10:30 PM IST
Register here: http://www.strand-ngs.com/webinar_registration

Webinar on Unique Molecular Identifier (UMI)-powered Ultra-sensitive Variant Calling using Strand NGS - Case Study

Strand — Tue, 07 Nov 2017 03:55:52 -0600

Webinar on Unique Molecular Identifier-powered Ultra-sensitive Variant Calling using Strand NGS - Case Study

by Dr. Pandurang Kolekar, Bioinformatics Engineer, Strand Life Sciences

Abstract:

Unique Molecular Identifiers (UMIs) are short random nucleotide sequences that are increasingly being used in high-throughput sequencing experiments. In this webinar, we will highlight the UMI-friendly features of Strand NGS v3.1 including support for handling well known and customised UMI libraries, QC metrics, consensus alignment, UMI-based family size filters for read list, genome browser enabled with UMI-specific features and filters, UMI-aware variant calling parameters, and exporting UMI-tagged aligned samples. These all features together empower users to harness the potential of UMI-tagged NGS data for deeper insights. A case study demonstrating application of these UMI-based features in Strand NGS for low frequency variant calling in cfDNA sample will be presented.

UMI-tagged NGS libraries allow, ultra-sensitive detection of low frequency variants from liquid biopsy samples using DNA-Seq and accurate quantification of transcript-level expression using RNA-Seq. The recent release of Strand NGS v3.1, is equipped with the necessary features to efficiently analyse UMI-tagged NGS data helping researchers and labs involved in rare variant calling like in cfDNA based cancer diagnostics, and accurate transcript quantification with RNA-Seq.

Webinar Details:

Session 1: 13 Dec 2017, 2:30 PM IST
Session 2: 13 Dec 2017, 9:30 PM IST

Register here: http://www.strand-ngs.com/webinar_registration

Webinar on RNA-Seq Data Analysis on 28 Feb 2018

Strand — Thu, 22 Feb 2018 06:38:48 -0600

Strand NGS is a biologist friendly NGS analysis tool that allows biologists to analyze their data using a very intuitive workflow for the analysis and visualization of RNA-Seq data. This webinar will give an overview of the workflow which includes Transcriptome/ Genome alignment, Differential expression analysis, Splicing events and gene fusion detection. Strand NGS also supports novel discovery like identification of novel genes, exons and novel splice junctions.
We will highlight the use of Strand NGS features such as PCA, sample correlation, clustering, Venn diagrams, CVA, UMI support and elastic genome browser used in RNA-Seq workflow that supports large scale RNA-Seq data analysis too. The tool also supports biological contextualization on the set of interesting genes from the data by allowing downstream analysis such as GO and pathway analysis. The product has an option to create pipelines for time consuming jobs which automates analysis and leaves more time for end data interpretation. This webinar will give an overview of the features in the RNA-Seq data analysis workflow in Strand NGS.

Details:
Session 1: 28 Feb 2018, 9 AM CET
Session 2: 28 Feb 2018, 8 AM PST
Register here: http://www.strand-ngs.com/webinar_registration

About Speaker:

Dr. Suman Kapoor, Manager- Application Science at Strand Life Sciences, has over 11 years experience in molecular biology, next-generation sequencing based testing, clinical genomics, and personalized medicine for disease management and prenatal testing. Dr. Suman holds a Ph.D in Molecular and Cell Biology from Indian Institute of Science, Bangalore. Prior to joining Strand NGS team, Suman has worked extensively on protein synthesis in eubacteria and has experience working in CAP and NABL accredited lab validating and interpreting NGS based diagnostic tests.