<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/2882?offset=150 https://bioinformaticsonline.com/opportunity/view/40305/naab-doak-graduate-fellowship-bovine-genomics-course Thu, 28 Nov 2019 21:45:35 -0600 <![CDATA[NAAB Doak Graduate Fellowship bovine genomics course]]> This is a reminder for all that seek a fully funded MSc in bovine genetics, or those that know talented BSc students who want to progress their education.

The deadline for the NAAB Doak Graduate Fellowship is less than a month away.

Applications are accepted until the 1st of December.

Please check the attachment or visit our website for further details:

https://www.naab-css.org/news/-naab-doak-graduate-fellowship

Sophie Eaglen
NAAB

]]> https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links Thu, 13 Feb 2020 00:20:00 -0600 https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links <![CDATA[genomics public data links !]]> List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight Wed, 06 Jan 2021 19:49:21 -0600 https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight <![CDATA[Breeding Insight]]> Breeding Insight at Cornell University will leverage recent improvements in genomics and open source informatics components, and in partnership with small breeding programs, will enable these programs to harness  powerful digital tools to accelerate their genetic gains

Breeding Insight is funded by the U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS) through Cornell University. The USDA ARS delivers scientific solutions to national and global agricultural challenges. As a global leader in agricultural discovery through scientific excellence, ARS is committed to delivering cutting-edge, scientific tools and innovative solutions for American farmers, producers, industry, and communities to support the nourishment and well-being of all people; sustaining our nation’s agroecosystems and natural resources; and ensuring the economic competitiveness and excellence of our agriculture.

Address of the bookmark: https://www.breedinginsight.org/

]]> BioStar https://bioinformaticsonline.com/opportunity/view/43227/project-associate-i-project-associate-ii-senior-project-associate-igib Thu, 05 Aug 2021 16:11:32 -0500 <![CDATA[Project Associate-I | Project Associate-II | Senior Project Associate @ IGIB]]> Experience in Next Generation Sequencing (NGS) application and interest in Genomics/ Clinical / Translational Applications. OR Good computational programming skills and deep interest in working on interface of Genomics and Clinical application.

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen

]]> https://bioinformaticsonline.com/researchlabs/view/44400/pevzner-lab Thu, 02 Nov 2023 05:39:26 -0500 <![CDATA[Pevzner Lab !]]> The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.

https://bioalgorithms.ucsd.edu/research4.html

]]> https://bioinformaticsonline.com/news/view/6302/a-allele-of-slc24a5-gene-is-found-to-be-responsible-for-variation-in-skin-color-of-south-east-asians-and-europeans Tue, 12 Nov 2013 21:02:27 -0600 https://bioinformaticsonline.com/news/view/6302/a-allele-of-slc24a5-gene-is-found-to-be-responsible-for-variation-in-skin-color-of-south-east-asians-and-europeans <![CDATA[A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East Asians and Europeans]]> Key finding:

  1. rs1426654 SNP of SLC24A5 gene is decider of skin pigmentation variation in South Asia
  2. rs1426654-A allele is widely spread throughout the Indian subcontinent 
  3. Skin pigmentation is also account by the combination of processes like selection and demographic history of populations affected by their language and origin
  4. Sign of positive selection in Europeans, Middle East, Pakistan, Central Asia and North India but not in South India
  5. In European , A-allele is almost reached to fixation

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912

]]> Rahul Agarwal https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files Sat, 08 Feb 2020 04:44:55 -0600 https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files <![CDATA[Explore taxdump files !]]> This is an extract of taxdump-readme.txt to be found at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ The content of the archive -------------------------- It may look like this: delnodes.dmp division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp readme.txt The readme.txt file gives a brief description of *.dmp files. These files contain taxonomic information and are briefly described below. Each of the files store one record in the single line that are delimited by "\t|\n" (tab, vertical bar, and newline) characters. Each record consists of one or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters. The brief description of field position and meaning for each file follows. nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxonomy database parent tax_id -- parent node id in GenBank taxonomy database rank -- rank of this node (superkingdom, kingdom, ...) embl code -- locus-name prefix; not unique division id -- see division.dmp file inherited div flag (1 or 0) -- 1 if node inherits division from parent genetic code id -- see gencode.dmp file inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent mitochondrial genetic code id -- see gencode.dmp file inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet comments -- free-text comments and citations names.dmp --------- Taxonomy names file has these fields: tax_id -- the id of node associated with this name name_txt -- name itself unique name -- the unique variant of this name if name not unique name class -- (synonym, common name, ...) division.dmp ------------ Divisions file has these fields: division id -- taxonomy database division id division cde -- GenBank division code (three characters) division name -- e.g. BCT, PLN, VRT, MAM, PRI... comments gencode.dmp ----------- Genetic codes file: genetic code id -- GenBank genetic code id abbreviation -- genetic code name abbreviation name -- genetic code name cde -- translation table for this genetic code starts -- start codons for this genetic code delnodes.dmp ------------ Deleted nodes (nodes that existed but were deleted) file field: tax_id -- deleted node id merged.dmp ---------- Merged nodes file fields: old_tax_id -- id of nodes which has been merged new_tax_id -- id of nodes which is result of merging ]]> Jit https://bioinformaticsonline.com/researchlabs/view/42958/claus-peter-stelzer-lab Mon, 15 Mar 2021 15:24:41 -0500 <![CDATA[Claus-Peter Stelzer Lab]]> Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently.

More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research

]]> https://bioinformaticsonline.com/researchlabs/view/5254/mike-ritchie-lab Wed, 02 Oct 2013 15:25:45 -0500 <![CDATA[Mike Ritchie Lab]]> Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new statistical methods with a focus on the detection of gene-gene interactions associated with human disease.

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/

]]> https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield Sat, 10 May 2014 04:33:28 -0500 https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield <![CDATA[GPS DNA tracking - University of Sheffield]]> University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps]]>