BOL: Related items

RA at ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

Mon, 22 Feb 2016 05:21:34 -0600

ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

HYDERABAD-500030

F.No. 5-42/2016/Rectt.

WALK IN INTERVIEW

Eligible candidates are invited to attend Walk in Interview to fill up the (purely) temporary post of Junior Research Fellow (One) under Extramural Research Project entitled “Transcriptome and proteome analysis for identification of candidate genes responsible for pistillate nature in castor “ to be held on 04.03.2016 at 11.00 AM at ICAR – Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad. The tenure of the project is up to 31.03.2017. The requirement and other terms and conditions for the Junior Research Fellow are as under :-

Junior Research Fellow (One)

Nucleic acid isolations, molecular analysis, bioinformatic analysis

.M.Sc.Biotechnology/Bioinformatics

Post Graduation in Life Sciences.

Candidates having Post Graduate degree in Basic Sciences with 3 years Bachelor’s degree and 2 years Master’s Degree 1,2,3 should have NET qualification.

Experience in Plant Biotechnology and Bioinformatics

Rs.25000/- + 30% HRA per month (At present)

More Info : http://icar-iior.org.in/media/docs/employment/2016/jrf-int.pdf

Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention & Research (ICMR) on Contract basis

Tue, 15 Nov 2016 17:15:48 -0600

National Institute Of Cancer Prevention & Research - ICMR

Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention & Research (ICMR) on Contract basis
Project entitled: “Next generation EGFR inhibitor identification using ligand based QSAR technique”

Essential: M.Sc. in Bioinformatics or related field. Desirable: Experience in QSAR and structure based drug designing.
Age: 28 years
No.of Post: 1

Pay Scale : Rs.27000

Application format is attached and should be sent by post to Dr. Subhash M Agarwal, Scientist D, Division of Bioinformatics, National Institute of Cancer Prevention & Research (ICMR), Plot No. I-7, Sector-39, Noida 201301 (U.P).

More at http://www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf

RA Bioinformatics at NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS, INDIA

Wed, 26 Jul 2017 03:49:52 -0500

NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS
(An Autonomous Institution of the Government of India)
P.O.: N.S.S., Kalyani 741251, West Bengal

Advertisement No. 137/ESTB/NIBMG/17-18

Position available Project Description: Several positions are available for the project titled: “A unified web-portal for analysis, integration and visualization of multi-omics data”. The goal of this project is to develop a user-accessible resource for integrated analysis and visualization of multi-OMICs data sets (including gene expression, genotype, methylation, microRNA, etc.). Data sets generated on various platforms shall be maintained in a stable database, accessed through standard querying mechanisms, and the results shall be displayed via user-friendly interface. The analysis engine shall run on open-source software (such as R/Bioconductor) developed in-house. All positions are contractual.

Appointment will be initially given for a period of one year which is extendable depending upon performance, availability of funds and requirements of the institute.

Project Code: 20275 Position: (No. of positions available)

Research Associate (3)

Position 1: Ph.D. or equivalent in statistics, computer science, mathematics, bioinformatics, or related subject.
Position 1: Those with experience in database management shall be preferred. Experience with UNIX or GNU/Linux operating system.
Position 1: Creation and maintenance of a database for population- and diseaseassociated variation resource. Development of programmatic interface for querying the database, filtering of the results and identification of genes of interest.

Rs. 36000/- + 10% HRA

Please apply online via web link http://apply.nibmg.ac.in/ (no other form of application will be accepted). The last date of application is 14-08-2017. All letters to attend screening test and /or interview will be sent only to the short-listed candidates by Email only. No correspondence will be made with applicants who are not shortlisted /not called for screening test and /or interview. No TA/DA will be paid for attending the screening test and /or interview.
Detail information at http://www.nibmg.ac.in/academic/Advt_20275.pdf

More Info: http://www.nibmg.ac.in/?q=Project%20Linked%20Personnel

Does anyone have Nanopore latest updates?

Poonam Mahapatra — Mon, 12 Aug 2013 12:19:29 -0500

There was a lot of buzz about Oxford Nanopore Technologies® is developing the GridION™ system and miniaturised MinION™ device. These are a new generation of electronic molecular analysis system for use in scientific research, personalised medicine, crop science, security/defence and more. The platform technology uses nanopores to analyse single molecules including DNA/RNA and proteins. With a broad patent portfolio, the Oxford Nanopore pipeline includes biological nanopores and solid-state nanopores.

Is this available, or still under trial mode?

https://www.nanoporetech.com/

https://www.nanoporetech.com/technology/the-minion-device-a-miniaturised-sensing-system/the-minion-device-a-miniaturised-sensing-system

RNA Bioinformatics and High Throughput Analysis Jena

Sat, 09 Nov 2013 20:03:56 -0600

Research Topics:

High Throughput Sequencing Analysis
Comparative Genomics
Identification and Annotation of Non-coding RNAs
Bioinformatic Analysis and System Biology of Viruses
Coevolution of Proteins and RNAs
Algorithmic Bioinformatics
Phylogenetic Analysis

http://www.rna.uni-jena.de/index.php

Bio-Rad Acquires GnuBIO

Rahul Agarwal — Sat, 19 Apr 2014 10:36:36 -0500

http://www.businesswire.com/news/home/20140411005331/en/Bio-Rad-Acquires-GnuBIO-Developer-Droplet-Based-DNA-Sequencing#.U1KXnPm1b8o

Deadly Human Pathogen Cryptococcus Sequenced

Rahul Agarwal — Fri, 25 Apr 2014 11:02:21 -0500

"Now, researchers have sequenced the entire genome and all the RNA products of the most important pathogenic lineage of Cryptococcus neoformans, a strain called H99. The results, which appear in PLOS Genetics, also describe a number of genetic changes that can occur after laboratory handling of H99 that make it more susceptible to stress, hamper its ability to sexually reproduce and render it less virulent."

Source:

http://www.biosciencetechnology.com/news/2014/04/deadly-human-pathogen-cryptococcus-fully-sequenced

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004292

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

Pathway Analysis

Rahul Agarwal — Fri, 03 Oct 2014 08:51:13 -0500

Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose the relationships between these genes. With availability of more genomics, transcriptomics and proteomics data, interactions between genes involve in multiple pathways become more clear and also relationships between the genes, their transcripts, and their gene products. However, existing tools and dbs mainly based on knowledge driven approach in which pathways will be identified by finding the correlation between the information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) and gene expression result for a specific conditions for instance tumor, obesity , cold resistant crops/plants, etc.

Introductory Articles/ppt/sources:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375

http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf

http://gettinggeneticsdone.blogspot.de/2012/03/pathway-analysis-for-high-throughput.html

http://davetang.org/muse/tag/pathway/

https://www.biostars.org/p/42219/

http://bioinformatics.ca//files/public/Pathways_2014_Module4_v2.pdf

http://bioinformatics.ca//files/public/Pathways_2014_Module2.pdf

Impotant Database and Tools:

GeneMANIA, Cytoscape, IPA and Metacore (Commerical ), Pathway Commons, Reactome ,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, Amigo, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go

Popular R based tools:

Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE,GOStat

More:

http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+

cutadapt

Radha Agarkar — Fri, 13 May 2016 04:54:50 -0500

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads.

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

Address of the bookmark: https://cutadapt.readthedocs.io/en/stable/installation.html#quickstart