Freitag, 4. Dezember 2009

Hadoop and Life Sciences - some cool talks from the Hadoop Conference in NY

General talk about life sciences at EC2 using Hadoop
http://vimeo.com/7351342

Protein Alignment in the Cloud
http://vimeo.com/7115816

Nice :)

Sonntag, 29. November 2009

Science review - 2009 week 45, 46 and 47

Gossip
Nature vs. MAD:
http://www.nature.com/nature/journal/v462/n7270/full/462242a.html
Alberts about a better funding and better science
http://www.sciencemag.org/cgi/content/full/326/5957/1163?rss=1
Alberts about PhD students lost in translation- with advice and hints - very cool:
http://www.sciencemag.org/cgi/content/full/326/5955/916?rss=1
A true letter about (IMHO) a huge problem in Science: Management
http://www.sciencemag.org/cgi/content/full/326/5956/1062-a?rss=1
A super cool essay about academia, industry and skills:
http://www.nature.com/nrm/journal/v10/n12/full/nrm2796.html


Next generation sequencing:
Bing - not from Microsoft  - a framework to manage and evaluate data from NGS:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-4XPYXJY-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=1b9b25e7610687136d0ba1e4fc3119bb


Binding promiscuity
An introduction by Nature:
http://www.nature.com/nature/journal/v462/n7270/full/462167a.html
and a cool paper:
http://www.nature.com/nature/journal/v462/n7270/full/462167a.html
and a paper I think is worth mentioning in this case:

Cloud computing in life sciences
Aligning and SNP calling in the cloud
http://genomebiology.com/2009/10/11/R134

Transcription factors and regulation
State of the Art:
http://www.nature.com/msb/journal/v5/n1/full/msb200988.html

RNA structure
TPP riboswitch - ligand free
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4XPYXRM-3&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=646fe1d1ba339fa66c8116362ca853dc

Virus RNA packaging mediated by an RNA switch:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4XPYXRM-5&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=1ec65e5a1a729a33ac8fc39a3f89400f

Ago silencing complex - from the Patel / Tuschl labs:
http://www.nature.com/nature/journal/v461/n7265/full/nature08434.html

Politics
About the Antarctic Treaty - I hope it lasts as ice is melting and states can expand their greed for natural resources easily
http://www.nature.com/nature/journal/v462/n7272/full/462412a.htm


Protein protein docking 
Knapp about selecting the most likely native docking decoy
http://www3.interscience.wiley.com/cgi-bin/fulltext/122617886/HTMLSTART


The future of publication

Article-Level Metrics and the Evolution of Scientific Impact - PLoS Biology:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000242?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosbiology%2FNewArticles+%28PLoS+Biology%3A+New+Articles%29&utm_content=Google+Reader
Public access is cool:
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000237?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosbiology%2FNewArticles+%28PLoS+Biology%3A+New+Articles%29&utm_content=Google+Reader

Drug discovery - book recommendations collected by Derek Lowe

really cool:
http://pipeline.corante.com/archives/2009/11/28/recommended_books_for_medicinal_chemists_part_one.php
thanks Derek and contributors!

Mittwoch, 4. November 2009

It wasn't me!

Must have been somebody else. For instance: The genes in me :)

http://www.nature.com/news/2009/091030/full/news.2009.1050.html

My bet: Berlusconi has some genes for bribing people what means he is not really responsible for his wrongdoings. So this is clearly a preparation for his upcoming trials.

Btw - the Italians have a gene that forces them to vote for incapable presidents. And the germans... well... ok...

Montag, 2. November 2009

Science review - 2009 week 44

Gossip:
Hwang moves on:
http://www.sciencemag.org/cgi/content/full/326/5953/650-a?rss=1

Nanotechnology and Russia:
http://www.nature.com/nature/journal/v461/n7267/full/4611028a.html

Hunting is fun:
http://www.sciencemag.org/cgi/content/full/326/5952/506?rss=1

After the HIV vaccine revolution Nature did not like the hype:
http://www.nature.com/nature/journal/v461/n7268/full/4611174a.html


Sequencing:
A cool review about cance genome sequencing:
http://hmg.oxfordjournals.org/cgi/content/full/18/R2/R163

Sequencing and sorting - that's cool:
http://www.nature.com/nmeth/journal/v6/n10/abs/nmeth.1370.html


Structural Biology:
Fast strctural comparisons based on vectors:
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2843?rss=1

and also:
Algorithms for the optimal superposition of proteins...:
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2751?rss=1

A good starting point provided by the PLoS ONE for the SGC:
http://www.plosone.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pone.c01.i04


Systems Biology:
Kitano on networks and implications for drug design:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000550

Donnerstag, 22. Oktober 2009

Science review - 2009 week 43

Glamour:
Nature about scientists talking journalists fooling them and how to react (and how not):
http://www.nature.com/nature/journal/v461/n7266/full/461848a.html


About the Polymath project, where a mathematic problem was solved using an open approach with wikis and so on - really cool:
http://www.nature.com/nature/journal/v461/n7266/full/461879a.html

and then you could also read an article about Google Wave and it's impact for science (accoring to the author - I am less sure there will be an impact).:
http://www.nature.com/nature/journal/v461/n7266/full/461881a.html

KAUST - the universtiy in the desert (and in a dictatorship like kingdom):
http://www.sciencemag.org/cgi/content/full/326/5951/354?rss=1

PLoS Medicine - refocuses and adopts new interesting concepts - from Twitter to PLoS Currents:
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000167


Methylation:
An interview with one of founders of "methylation": Adrian Bird
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000667

Nice debate about how methylation patterns are generated:
http://www.nature.com/nrg/journal/v10/n11/full/nrg2651.html

RNA:
Three way junctions in RNA - found in many RNA structures:
http://rnajournal.cshlp.org/content/15/11/1949.short?rss=1


Biology and Chemistry:
Nature Chemical Biology about the downsides of an reductionist apporach - Cells are more than the simple sum of it's part (systems biology?)
http://www.nature.com/nchembio/journal/v5/n11/full/nchembio.258.html
http://www.nature.com/nchembio/journal/v5/n11/full/nchembio.241.html

RNA and Chromatin structure control a range of biological processes - an overview:
http://www.nature.com/nrg/journal/v10/n11/full/nrg2692.html

Structual Biology:
Oberving biology in atomic resolution in real time - cool:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCV-4XGTJ7J-1&_user=1676895&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054205&_version=1&_urlVersion=0&_userid=1676895&md5=635a71eaba1f693b8a8e71044c882860

Bioinformatics:
A new twist for determining possible drug targets based on kinetic network models:
http://www.biomedcentral.com/1471-2105/10/344

Know the CPU architecture and make BLAST faster:
http://www.biomedcentral.com/1471-2105/10/329

Riboswitch detection on sequence level:
http://www.biomedcentral.com/1471-2105/10/325

Donnerstag, 15. Oktober 2009

Glad to know that the PSI is advancing

PSI (Protein Structure initiative) is an initiative that aims to shed light on proteins with roughly unknown function.

There is a new videocast available from a recent meeting:
http://videocast.nih.gov/PastEvents.asp?c=4

Want to know more? Here's the FAQ:
http://www.nigms.nih.gov/Initiatives/PSI/psi_biology/psibiology_faqs.htm

And the corresponding press report is at:
http://kb.psi-structuralgenomics.org/update/2009/10/full/nw_psisgkb.2009.47.html