BOL: Related items

translate2R

Rahul Nayak — Fri, 21 Nov 2014 01:16:06 -0600

After their presentation at the international “user!” conference, data analysis specialist eoda starts the public alpha testing of translate2R. With the start of alpha testing the innovative migration solution by the company hailing from Kassel discards the working title “translateR” and takes on the final product brand name “translate2R”. translate2R is a service for the automated translation of SPSS® syntax to R code, therefore supporting data analysts with a quick and low-risk migration to R.

The manual translation of many, frequently rather complex SPSS scripts often presents itself as a tedious and error-prone task, and represents a rather large obstacle for many analysts and companies to migrate to a modern, open source data management and analysis tool like R. With translate2R this hurdle will be diminished substantially.

Find at https://service.eoda.de/translater/?lang=en

Bioinformatics Workshops - NO CODING REQUIRED

eliabrodsky — Mon, 09 Apr 2018 13:06:01 -0500

Pine Biotech, Inc., a US-based startup working with the Tauber Bioinformatics Research Center is offering a full curriculum online preparing students without any technical background for real-life challenges with large scale biomedical data. Workshops on processing, analysis and biomedical interpretation of Next Generation Sequencing data cover important up-to-date algorithms and machine learning approaches. The most important thing is that there are virtually no pre-requisites such as coding, biostatistics or advanced medical skills. If you know what gene is and how the genes are expressed, you are ready to take the courses or join our workshops. Learn more: https://edu.t-bio.info/workshops/

Junior Research Fellow (JRF) / Project Fellow @ Kalasalingam University

Thu, 19 Dec 2013 13:23:39 -0600

Applications are invited from interested candidates for the post of one Junior Research Fellow / Project Fellow on a purely temporary basis in a time bound research project (3 years) sponsored by Science and Engineering Research Board, Government of India, New Delhi.

Name of the fellowship: Junior Research Fellow (JRF) / Project Fellow

Title of the project: Genome-wide Mapping of Murine Specific Dengue T-cell Epitopes: Computational Prediction, Identification and use as Candidate Vaccines

Duration: 3 years

Fellowship: Rs. 18,000 for first 2 years and Rs. 20,000 for 3rdyear (for M.Tech. candidates)

Rs. 16,000 for first 2 years and Rs. 18,000 for 3rdyear (for M.Sc. candidates with NET qualification)

Rs. 8,000 for first 2 years and Rs. 10,000 for 3rdyear (for M.Sc. candidates without NET qualification)

Qualifications: M.Tech. in Biotechnology / M.Sc. in any branch of Life Sciences

Desirable Experience: Minimum of two years research experience in any of the following areas: Immunology / Microbiology / Gene Manipulation / Bioinformatics

Interested and eligible candidates may apply with their resume along with relevant documents and a passport size photograph to the Principal Investigator by post (or e-mail) on or before December 31, 2013. Only short listed candidates will be called for written test and/or interview. Selected candidate may register for PhD in Kalasalingam University. No TA/DA will be paid for attending interview.

Dr. K. Sundar
Principal Investigator (SERB Project)
Department of Biotechnology
Kalasalingam University
Krishnankoil – 626126, Tamil Nadu
sundarkr@klu.ac.in

Directional dominance on stature and cognition in diverse human populations

Rahul Agarwal — Sat, 11 Jul 2015 12:43:51 -0500

Analysis of the genomes of >350,000 individuals revealed the existence of a small though measureable association between genome-wide homozygosity and some vital complex traits...

Directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

Address of the bookmark: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14618.html

Bioinformatics approach to Boar Taint

Rahul Agarwal — Wed, 17 Jul 2013 15:50:37 -0500

Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and sex steroids share a common pathway which makes removal of boar taint a very challenging task. Castration is a traditional solution to remove boar taint but it also results in bad quality of meat due to low level of steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint compounds can be used as genetic markers in selection of male pigs with reduced boar taint levels. Resequencing of a total of 47 samples belong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of SNPs was prepared after filtering SNPs on the basis of SNP quality, coverage of SNP allele, functional and structural annotation, and repeats, etc. Selected SNPs will be genotyped in sample population for validation and then used for constructing SNPs haplotypes in close linkage disequilibrium with QTLs and fine mapping of QTLs through association mapping of genotyped SNPs.

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

Latest paper on comparison of mapping tools

Rahul Agarwal — Tue, 03 Sep 2013 18:00:38 -0500

A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

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

Genomics and sequencing approach for identification of biomarkers to assess the efficacy of TGF-βRI inhibitors (of liver cancer) in vivo

Rahul Agarwal — Tue, 05 Aug 2014 13:55:32 -0500

Liver cancer is third leading cause of deaths and fourth most frequent occuring cancer worldwide. There are multiple signaling pathways responsible for causing cancer amongst which TGFb is most important cytokine whose signaling pathway promote cancer. However, main problem is to cure this cancer at late stage where we still have no treatment strategy to tackle this deadly cancer. Hence we need to find out new therapeutic target. One way is to look the relationships between mRNA, methylation and miRNA data of patients with different pathological conditions (cancer vs control either with inhibitor/not). MiRNA is small RNA molecules known to inhibit mRNA expression of particular gene by binding improperly to 3'UTR region of a gene and hence block binding of TF /translation of gene. CpG regions is known to located at promoter region of gene (5' UTR) and usually hypomethylated which allow to gene to transcribe and translate however sometime this region become hyper-methylated thats prevent expression of host gene. Thus , integration of these three data reveal new targets and pathways important for causing or preventing cancer and also reveal biomarker thats check the effects of inhibitor on signaling pathway underlying liver cancer.