ACS versus LeadScope - a sad summary

How big companies can easily kill smaller companies. There is something wrong in the legal system I guess:

http://depth-first.com/articles/2010/11/04/acs-versus-leadscope-leadscope-tells-its-story-in-court-document/

Cancer and the modern world

Cancer is really the pest of modern times. Often people tend to believe that the amount of cancer cases has increased. And - of course - in former times there was much less cancer.

True.

But only because people died earlier. Subsequently not many cancer types would occur at those ages. Despite that even the old greek described melanoma.

The other interesting thing is: If people become older. Their peers will be more likely die of cancer. That causes imho a huge bias in the perception of cancer.

Derek Lowe writes about it in detail:
http://pipeline.corante.com/archives/2010/10/20/is_cancer_a_disease_of_the_modern_world.php

Statistics and the validity of medical literature

http://pipeline.corante.com/archives/2010/10/19/trusting_the_medical_literature.php

Rebattle of anti blogger argumentation by Egon

http://chem-bla-ics.blogspot.com/2010/10/royce-murray-and-caveat-emptor.html

Mendeley CiteULike and a bit of controversy

Some thoughts about Mendeley and CiteULike:

http://blindscientist.genedrift.org/2010/09/17/a-short-list-of-things-i-dont-like-about-mendeley

http://scienceoftheinvisible.blogspot.com/2010/09/long-list-of-things-i-dont-like-about.html

http://chem-bla-ics.blogspot.com/2010/09/list-of-things-i-miss-in-citeulike.html

Cool papers August 10

My picks:
Nature Reviews drug discovery: Gene and drug matrix for personalized cancer therapy
http://www.nature.com/nrd/journal/v9/n8/full/nrd3181-c1.html

Nature BT: Can HIV be cured by Stem cell therapy?
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-807.html#/ref1


Nature Reviews Cancer: The evolutionary dynamics of cancer prevention:
http://www.nature.com/nrc/journal/v10/n8/full/nrc2892.htm

Colleagues from my grad school in PLoS CB: Alexander Skupin, Helmut Kettenmann, Martin Falcke

about Calcium Signals Driven by Single Channel Noise
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000870

Nature BT:  Microarrays in the clinic:
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-810.html

Interesting papers:
TIBS about a VDAC (Voltage dependent anion channel between mitrochondria and cytosol) and the validity of 3D structures
http://dx.doi.org/10.1016/j.tibs.2010.03.005


Zhiping Weng scores benchmarks again - protein protein docking benchmark version 4.0 in Proteins
http://onlinelibrary.wiley.com/doi/10.1002/prot.22830/abstract

Nice read about enchancing docking by using known templates that match. Especially the evaluation is cool: Proteins: Docking by structural similarity at protein-protein interfaces
http://onlinelibrary.wiley.com/doi/10.1002/prot.22812/pdf

PLoS Medicine tells us that having friends is healthy. I do not like the generalized sentences at the beginning (10% of britains feel lonely and stuff like that) without any references. But the rest is telling.
Social Relationships and Mortality Risk: A Meta-analytic Reviewhttp://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000316

Nature SMB about how they internally fight plagiarism:
http://www.nature.com/nsmb/journal/v17/n8/full/nsmb0810-917.html

Genome Biology wants better genome annotations: Genomic information infrastructure after the delugehttp://genomebiology.com/2010/11/7/402

Nature Biotechnology about a sad success. Gaining 3 months on average.
Industry makes strides in melanoma.
http://www.nature.com/nbt/journal/v28/n8/full/nbt0810-763.html

Nature expresses concerns about a Enzyme activity chip:
http://www.nature.com/news/2010/100728/full/466540b.html

Nature - finally - direct to consumer DNA tests will be regulated: http://www.nature.com/nature/journal/v466/n7308/full/466797a.html

Nature about really cheap shots by republicans on science funds (alhtough it's funny to read):
http://www.nature.com/nature/journal/v466/n7308/full/466797b.html

Nature reviews two book reviews about Leadership:
http://www.nature.com/nature/journal/v466/n7308/full/466819a.html

Nature News: Citizen science: Folding at home becomes gaming and thinking at home:
http://www.nature.com/news/2010/100804/full/466685a.html


Bioinformatics: Over-optimism in bioinformatics. A really cool study how over-optimism biases papers:
http://bioinformatics.oxfordjournals.org/cgi/content/full/26/16/1990

Nature about kill'em all (mosquitos):
http://www.nature.com/news/2010/100721/full/466432a.html

RNA - not waste - again:
http://www.nature.com/nature/journal/v466/n7306/full/nature09190.html

WTF? ACS Chemical information and modeling reviews Word perfect.
http://pubs.acs.org/doi/full/10.1021/ci100291b

ACS CINFM: Comparing ligand binding pockets usind C alphas alone:
http://pubs.acs.org/doi/abs/10.1021/ci100210c

Nature Reviews Cancer: It's nicer with Dicer - miRNA levels are lowered in human caners - but why? http://www.nature.com/nrc/journal/v10/n8/full/nrc2910.html

Science about Do We Have the Energy for the Next Transition?
http://www.sciencemag.org/cgi/content/full/329/5993/780?rss=1

Cool papers July 10

Nature says: Happy birthday human genome :) with this special:
http://www.nature.com/news/specials/humangenome/index.html

PLoS CB tells us about the history of Bioinformatics aka Computational Biology aka Biological Mathematics aka...
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000809

Interesting NGS + RNA Expression profiling setup:
Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencinghttp://nar.oxfordjournals.org/cgi/content/full/38/12/3999

Nature Genetics explores GWAS and the limits of what SNPs can tell:
On beyond GWAS:
http://www.nature.com/ng/journal/v42/n7/full/ng0710-551.html
Common SNPs explain a large proportion of the heritability for human height:
http://www.nature.com/ng/journal/v42/n7/full/ng.608.html


A novel GWAS analysis package based on Random Forrests 
Bioinformatics: On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data:
http://bioinformatics.oxfordjournals.org/cgi/content/full/26/14/1752

Future of publication - no real conclusion from Nature. Interesting: arxiv.org is mentioned, but busted because it is used "only" as preprint server and not as discussion platform.
Nature: When blogs make sense
http://www.nature.com/nature/journal/v466/n7302/full/466008a.html

Nature Reviews Cancer: Envisioning the future of early anticancer drug development:  http://www.nature.com/nrc/journal/v10/n7/full/nrc2870.html

Nature Reviews Genetics: Next-generation genomics: an integrative approach
http://www.nature.com/nrg/journal/v11/n7/full/nrg2795.html

Protein superposition reloaded - this time especially for variation. Hmm. I do not see any comparison with other methods:
BMC Bioinformatics: Robust probabilistic superposition and comparison of protein structures
http://www.biomedcentral.com/1471-2105/11/363

BMC Bioinformatics: Knowledge-based annotation of small molecule binding sites in proteins
http://www.biomedcentral.com/1471-2105/11/365

Nature Reviews Drug Discovery: Integrating molecular diagnostics into anticancer drug discoveryhttp://www.nature.com/nrd/journal/v9/n7/abs/nrd3135.html

Science: Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:
 http://www.sciencemag.org/cgi/content/full/329/5987/75?rss=1

Science Traveler's guide: Summer trips featuring some german places (Martin Gropius Bau in Berlin is really cool):
http://www.sciencemag.org/cgi/content/full/329/5987/34-a?rss=1

Epigenetics takes the centerstage again. Not sure what this means:
http://www.sciencemag.org/cgi/content/full/329/5987/27?rss=1

The Seductive Allure of Behavioral Epigeneticshttp://www.sciencemag.org/cgi/content/full/329/5987/24?rss=1