BOL: Related items

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

miRNA database and tools

Rahul Agarwal — Mon, 09 Jun 2014 07:58:40 -0500

Since few years miRNA has shown to play important role in therapeutic related research and also known to play vital role in controlling gene expression specifically at transcriptional and post-transcription levels. Here are some important DBs and tools related with miRNA:

miRNA Sequencing data analysis : http://tools.genxpro.net/omiras/

miRNApath( R based tool) : http://www.bioconductor.org/packages/release/bioc/html/miRNApath.html

miRWalk DB : http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/

TargetScanHuman : http://www.targetscan.org/

RNAhybrid : http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/welcome.html

RNA22 predictor : http://cbcsrv.watson.ibm.com/rna22.html

miRNA predictor : http://www.microrna.org/microrna/home.do

Plant miRNA DB :http://bioinformatics.cau.edu.cn/PMRD/

miRBASE DB: http://www.mirbase.org/

Plant RNA predictor : http://plantgrn.noble.org/psRNATarget/

miRNA Interaction DB : http://starbase.sysu.edu.cn/

Sequencing based miRNA DB : http://mirgator.kobic.re.kr/

predicted A-to-I edited miRNA DB : http://microrna.osumc.edu/mireditar/

Animal, plant and virus miRNA DB : http://lemur.amu.edu.pl/share/php/mirnest/

Atlantic Salmon miRNAs DB : http://www.molgenv.com/ssa_mirnas_db_home.php

miRNA prediction on UTRs : http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html

Idea of analysing miRNA Sequencing data :

http://www.illumina.com/applications/epigenetics/small_rna_analysis.ilmn

More:

http://www.bioconductor.org/help/search/index.html?q=miRNA+target

Post-doctoral position / Scientist (m/f/d) in Bioinformatics

Mon, 15 Mar 2021 11:34:23 -0500

The Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. in Dortmund is looking for a Post-doctoral position / Scientist (m/f/d) in Bioinformatics

More at

https://www.isas.de/files/redaktion/jobs/2021/18.60.1_Postdoc_deNBI_06_21_AS.pdf

https://www.isas.de/en/news/062021-post-doctoral-position-scientist-mfd-in-bioinformatics

Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator

Jit — Wed, 24 May 2017 08:41:41 -0500

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Poonam Mahapatra — Mon, 26 Aug 2019 18:07:33 -0500

Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads.

Address of the bookmark: https://github.com/yjx1217/LRSDAY

Compressive Genomics

Rahul Agarwal — Sun, 11 Aug 2013 11:13:58 -0500

The key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In other words, a single DNA sequence isn't particularly compressible but a set of sequences shares so much in common that the redundancy can be used to store them in a much smaller storage space. (Source:e-article from Alex Armstrong)

http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html

http://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data

http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html

http://bioinformatics.oxfordjournals.org/content/29/13/i283.full

http://groups.csail.mit.edu/cb/cast/

Illuminating next generation sequencing data with Go

Rahul Agarwal — Fri, 23 Aug 2013 07:13:33 -0500

Another good lecture for Illumina sequencing data analysis from

Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

Address of the bookmark: http://talks.biogo.googlecode.com/git/illumination/illumination.pdf

ArrayGen Next Generation Genome Browser Coming Soon !!!

ArrayGen Technologies — Thu, 03 Dec 2015 05:52:09 -0600

The ANG genome browser is a visualization tool, developed by ArrayGen Technologies. This is a fast and an efficient genome browser, built with Javafx and Java swing. ANG genome browser was built for latest next generation sequencing data analysis. It is platform independent and much simpler to use.

The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integrated with other browsers or tools for analysis of genome.

Biggest Human Brain Project (HBP) launched!!!

Rahul Agarwal — Mon, 07 Oct 2013 19:50:55 -0500

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs