Tag Archives: peer bork

NAR database issue (always a treasure trove)

The advance access release of most of the  NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We’ll be writing up additional more extensive blog posts on it and doing some tips of the week over the next couple months, but I thought I’d highlight the issue and some of the reports:

There are a lot of updates to many of the databases we know and love (links to go full text article): UCSC Genome Browser, Ensembl, UniProt, MINT, SMART, WormBase, Gene Ontology,  ENCODE, KEGG, UCSC Archaeal Browser, IMG/M, DBTSS, InterPro and others (we have tutorials on all those listed here).

And, as an indication of the explosion of data available (itself a subject of a database issue article, SRA), there are a lot of new(ish) databases on specific datatypes such as MINAS, a database of metal ions in nucleic acids (nice name :D); doRiNA, a database of RNA interactions in post-transcriptional regulation; BitterDB, a database of bitter compounds and well over 100 more.

And I’ll give a special shout out to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu
Ensembl: http://www.ensembl.org/
UniProt: http://www.uniprot.org/
MINT: http://mint.bio.uniroma2.it/mint/
SMART: http://smart.embl.de/
WormBase: http://www.wormbase.org/
Gene Ontology: http://www.geneontology.org/
ENCODE: http://genome.ucsc.edu/ENCODE/
KEGG: http://www.kegg.jp
UCSC Archaeal Brower: http://archaea.ucsc.edu/
IMG: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
DBTSS: http://dbtss.hgc.jp/
InterPro: http://www.ebi.ac.uk/interpro

 

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Peer Bork wins 2009 award

Royal Society and Académie des sciences Microsoft Award was won by Peer Bork this year. The award is funded by Microsoft (250,000 euro) and is given to

recognise and reward scientists working in Europe who have made a major contribution to the advancement of science through the use of computational methods.

It was awarded to Peer Bork for his work on the human microbiome. Peer definitely deserves it, as does his lab.The science and scientists that come from the Bork group are stellar. Ok, so I have a personal interest in this: I worked in his lab for 4 years, from 1999-2003. It was one of the best experiences (science and personal) of my life. Also, BioByte Solutions, started by a Bork lab researcher, has helped put together our new free database and resource search (which we’ll be introducing next week).

Congratulations Peer! Now, what is he going to do with that 368,000 dollars?!

And let me use this opportunity to point out some of the great tools and databases developed by the Bork group:
STRINGAnalysis of known and predicted protein-protein interactions in all known genomes (OpenHelix Tutorial, by subscription)
STITCHDatabase of known and predicted interactions of chemicals and proteins.
SMARTDomain analysis (OpenHelix Tutorial, by subscription)
iTOLan online tool for the display and manipulation of phylogenetic trees.
XplorMedDataming in MedLine (OpenHelix Tutorial, by subscription)

And a whole lot more

A shout out or two, Bork paper and on the shoulders of giants…

Just thought I’d give a shout out… two in fact:

First, my former Postdoc advisor, Peer Bork, and lab just published an excellent paper in Science entitled “Drug Target Indentification Using Side-Effect Similarity.” It’s an excellent example of the marriage of computational genomics and experimental biology. Fascinating stuff (I’m only slightly biased, but it is). I’ll do a more in depth review later.

Second, Bora at Blog Around the Clock got together with gg of skullsinthestars and created a “The Giant’s Shouldersblog carnival. This grew out of the Classics Challenge  ( “read and research an old, classic scientific paper and write a blog post about it”) at skullinthestarts (which our own Mary had an excellent submission to if I do say so myself). It was so popular they decided to make it a monthly thing. Which is good, because now I can do the one I wanted to do before for August’s carnival. July’s carnival is here at Blog around the Clock.

Metagenomes in Nature

Nature had a nice feature on metagenomics last week and another on the Human microbiome metagenomics. You’ll need to have a subscription to access those :(, but the gist of the latter news feature is the possibilities of Human microbiome research, pros and cons and the projects out there. There are a lot. In order of amount of funding they are:

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New Tutorial Suite on SMART (protein domain analysis)

Comprehensive Tutorial on the SMART Bioinformatics Resource enables researchers to quickly and effectively use invaluable resource.

January 11, 2008 (Seattle WA) OpenHelix today announced the availability of a tutorial suite on the SMART bioinformatics resource (http://smart.embl-heidelberg.de/). SMART, created by the Bork Lab at the European Molecular Biology Laboratory (EMBL), contains information on hundreds of domains, and provides extensive annotations, phylogenetic analyses, and links to relevant resources about the domains.The tutorial suite, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contains a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorial, researchers can quickly learn to effectively use this resource that helps them understand the evolution of function within multi-domain proteins. SMART brings together several functions that a researcher would otherwise have to perform separately.The tutorial will teach users to:

  • perform various text and sequence searches
  • find proteins based on their domain architecture
  • browse for key information about the evolutionary history and relationships of domains of interest to your researchTo find out more about this and other tutorial suites visit www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

Speaking of the Bork lab…

In the previous post I briefly mentioned a paper coming out of the Bork lab at EMBL.

The lab just made public a new tool: STITCH, “a resource to explore known and predicted interactions of chemicals and proteins.” This is a sister project to STRING, a great tool for exploring the interactions of proteins

Metagenomics

Just a short post with some information:

Metagenomics is the new genomics :). NIH Roadmap has a new initiative, the Human Microbiome Project with a bit of funding :) . Meanwhile, other projects and databases are developing such as Integrated Microbial Genomes w/ Microbiome Samples (or IMG/M) and Camera. It’s an exciting and fascinating field (my former colleagues at the Bork lab just published interesting research in this field), though some scientists of course have their doubts.