Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'

Abstract

Whole exome DNA sequencing (WES) or whole genome DNA sequencing (WGS) allows detection of mutations and polymorphisms in all exonic and genomic regions, respectively, while messenger RNA sequencing (RNA-Seq) enables quantitative analysis of gene expression. Mutations in the genome result in diverse transcriptional aberrations that can be missed in a stand-alone WES/WGS analysis. An integration of DNA variant analysis and RNA-Seq analysis enables one to investigate the consequences of genomic changes in the RNA transcripts including germline and somatic changes, imprinting, RNA editing and allele specific expression (ASE). In this webinar, we will demonstrate this integrated approach using Strand NGS to identify high confidence mutations, RNA editing events and ASE in cancer.

Webinar Details

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

About Speaker:

Dr. Veena Hedatale, has a PhD in Plant Genetics from The Radboud University, Netherlands focused on meiosis and recombination. Her prior academic experience at Cornell University was on genetic mapping and gene transformation in Rice. She has worked with Monsanto, and contributed to data mining, database development as well as gene/promoter/pathway discovery for traits related to yield and stress in crop species. At Strand, Veena has worked on Pharmacogenomic analysis of targets and Gene family analysis projects. Currently, she is part of the Strand NGS Application Science team and is involved in the analysis of next generation sequencing data.

Please feel free to contact us 24/5, for availing free online training or if you have any questions.

The project is on bacterial gene gain and loss and emerging pathogenicity, and is described in full here: https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015 . The EMBL-EBI / Cambridge Computational Biomedical Postdoctoral (“EBPOD”)

The closing date for applications is 3 September 2015. Nick Goldman EMBL-European Bioinformatics Institute Nick Goldman

More at https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015

Usage: perl run_rcorrector.pl [OPTIONS]
OPTIONS:
	Required
	-s seq_files: comma separated files for single-end data sets
	-1 seq_files_left: comma separated files for the first mate in the paried-end data sets
	-2 seq_files_right: comma separated files for the second mate in the paired-end data sets
	-i seq_files_interleaved: comma sperated files for interleaved paired-end data sets
	Optional
	-k INT: kmer_length (<=32, default: 23)
	-od STRING: output_file_directory (default: ./)
	-t INT: number of threads to use (default: 1)
	-trim : allow trimming (default: false)
	-maxcorK INT: the maximum number of correction within k-bp window (default: 4)
	-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
	-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
	-stdout: output the corrected reads to stdout (default: not used)
	-verbose: output some correction information to stdout (default: not used)
	-stage INT: start from which stage (default: 0)
		0-start from begining(storing kmers in bloom filter) ;
		1-start from count kmers showed up in bloom filter;
		2-start from dumping kmer counts into a jf_dump file;
		3-start from error correction.

Address of the bookmark: https://github.com/mourisl/Rcorrector/

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

Essential requirements: Experience of using bioinformatics tools.

Experience of working in Linux. Basic knowledge of computer network administration.

Desirable: Knowledge of Linux installation/administration and proficiency in either of the following:

Shell/PERL/Java/Python/VB/Oracle/MySQL/C/CUDA.

Qualification: PhD. or First class M.Sc degree in Bioinformatics or Biotechnology/life science with specialization in Bioinformatics.

Fellowships: Rs 22,000/- with HRA for PhD qualified, Rs 16000/- with HRA for NET/BET/BINC/GATE qualified and 12000/- with HRA for non NET qualified applicants.

Interested candidates may send their complete biodata along with a write-up of their experience and suitability for the position to Dr. Dinesh Gupta by email only to dinesh@icgeb.res.in within 15 days of publication of this advertisement. Kindly mark the email with subject “Application for BIF-RA-2013”

Closing date for applications: 18 October 2013

Only short listed candidates will be invited for an interview at ICGEB.

No TA/DA will be paid for attending the interview.

Advertisement: http://www.icgeb.org/tl_files/Vacancies/BIF-RA-Advt.pdf

Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical approach and Splicing events detection. Strand NGS also supports novel discovery like identification of novel genes, exons and Novel splice junctions, alongside it can also detect gene fusion events. Further downstream analysis such as GO and pathway analysis can be performed on the set of interesting genes. 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 and also highlights on parameters within each feature that can be optimized depending on datasets and analysis needs.

Speaker: Mr. Sugandan Sivamani, Senior Application Scientist, Strand Life Sciences

Date: 9th Nov, Session 1 for SAPK/ APFO: 2:30 PM IST Date: 9th Nov, Session 2 for AFO/ EMEA: 9:00 AM PST

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

Applications on plain paper along with details of CV (relevant photocopies of their
qualifications/experience and reprints of published work to be attached) are invited from qualified candidates for Research Fellowship in CSIR- sponsored research project.

JRF/SRF/RA (one vacancy)

CSIR sponsored “In silico design, identification and in vitro validation of lead molecule inhibitors to Bcr-Abl kinase”

JRF: M.Sc in Chemistry/ Bioinformatics/ Biotechnology with I division and NET or GATE qualified

SRF: M.Sc in chemistry/ Bioinformatics/ Biotechnology with at least two years of post- M.Sc research experience as evidenced from published papers in standard refereed journals in relevant area

RA: PhD in chemistry/ Bioinformatics/ Biotechnology with research experience in
relevant area.

As per CSIR guidelines

Notes:
1) You may visit the University of Hyderabad website www.uohyd.ernet.in to learn more about the University of Hyderabad.
2) Applicants should note that the appointment to be made is purely temporary and there is no right for claiming for any regular appointment in the University.
3) No TA/DA will be paid for attending the interview or at the time of joining the post, if selected.
4) The application should be submitted by post/courier/in-person to the address given below on or before November 1st 2013.

Prof. Lalitha Guruprasad
W-103, Gurbakhsh Singh Building
School of Chemistry
University of Hyderabad
Hyderabad- 500 046
5) Short-listed candidates will be called for interview at a short notice.

Advertisement: http://www.uohyd.ac.in/images/recruitment/chemisry_advt_101013.pdf

Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519

Address of the bookmark: https://pachterlab.github.io/kallisto/about

Available immediately until 30th November 2015, to work on the development of bioinformatics approaches to aid analysis of data derived from the metabolomic profiling of biological matrices. The successful applicant will lead research activities on an FP7 funded EU-wide collaborative project aimed at establishing biomarker-based strategies for high throughput diagnostic screening. Key tasks will involve multivariate analysis of large datasets, bioinformatic-based selection and validation of identified markers, construction of metabolomic spectral profile databases and development of machine learning/database searching approaches amenable to analytical screening techniques. This position will offer the opportunity to travel and undertake work with project collaborators based in the Republic of Ireland and Europe.

Informal enquiries may be directed to Dr Terry McGrath, email: terry.mcgrath@qub.ac.uk.

Anticipated interview date: Thursday 31st October 2013
Salary scale: £30,424 – £39,649 per annum (including contribution points)
Closing date: Monday 21st October 2013

Telephone (028) 90973044 FAX: (028) 90971040 or e-mail on personnel@qub.ac.uk

The University is committed to equality of opportunity and to selection on merit. It therefore welcomes applications from all sections of society and particularly welcomes applications from people with a disability.

Fixed term contract posts are available for the stated period in the first instance but in particular circumstances may be renewed or made permanent subject to availability of funding.

More @ https://hrwebapp.qub.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=5616943npO&WVID=6273090Lgx&LANG=USA