Posts Tagged ‘afp14’

My “public” notes from ISMB 2014

July 19, 2014

I took lots of notes at ISMB 2014. I saved “public” versions of these as a storified tweet-stream, viz:

https://storify.com/markgerstein/tweet-related-to-ismb-2014-i0imsb14-i0afpsig-ismb

I also tagged lots of sites & papers that I discovered at the meeting, viz:

https://linkstream2.gerstein.info/tag/i0ismb14
https://linkstream2.gerstein.info/tag/i0afpsig

http://www.iscb.org/ismb2014 [Main meeting]

http://biofunctionprediction.org/node/7 [AFP SIG]

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chinese cancer data

July 18, 2014

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759719/

Annotated somatic variants and interactive variant analysis results are available online atwww.ingenuity.com/acrg2012.

Eighty-eight primary HCC tumors and matched adjacent nontumor liver tissues were analyzed by whole-genome DNA sequencing to identify somatic mutations and HBV integration sites. The vast majority (92%,n = 81) of patients in this cohort were HBV carriers (i.e., HBsAg seropositive) suffering from chronic hepatitis B or cirrhosis. None of the patients were hepatitis C virus (HCV) positive

the data:

http://gigadb.org/dataset/100034

The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652

chinese cancer data

July 17, 2014

the data:

http://gigadb.org/dataset/100034

The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652

Ensemble Methods in Machine Learning. Proceedings of the First International Workshop on Multiple Classifier Systems

July 13, 2014

Rich C, Alexandru N-M, Geoff C, Alex K (2004) Ensemble selection from libraries of
models. Proceedings of the twenty-first international conference on Machine learning. Banff, Alberta, Canada: ACM.
http://www.niculescu-mizil.org/papers/shotgun.icml04.revised.rev2.pdf

Thomas GD (2000) Ensemble Methods in Machine Learning. Proceedings of the First International Workshop on Multiple Classifier Systems: Springer-Verlag.
http://www.eecs.wsu.edu/~holder/courses/CptS570/fall07/papers/Dietterich00.pdf http://dl.acm.org/citation.cfm?id=743935

.@deniseOme Good ref is TG Dietterich #Ensemble Methods in
#MachineLearning MCS ’00
http://www.eecs.wsu.edu/~holder/courses/CptS570/fall07/papers/Dietterich00.pdf Not rel. to @ensembl #ismb #afp14

ref 17 & 18

BioCreative – Latest 3 News Items

July 12, 2014

http://www.biocreative.org/

BMC Bioinformatics | Full text | A new measure for functional similarity of gene products based on Gene Ontology

July 12, 2014

BMC Bioinformatics | Full text | A new measure for functional similarity of gene products based on Gene Ontology
http://www.biomedcentral.com/1471-2105/7/302

Related to:
http://papers.gersteinlab.org/papers/funcsim/

Information-theoretic evaluation of predicted ontological annotations

July 12, 2014

http://bioinformatics.oxfordjournals.org/content/29/13/i53.short

Predicting phenotype from patterns of annotation

July 12, 2014

Roth lab paper
http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i183.long

Manual curation is not sufficient for annotation of genomic databases

July 12, 2014

Hunter lab pub

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516305/

PLOS ONE: The Impact of Multifunctional Genes on “Guilt by Association” Analysis

July 12, 2014

Pavlidis mentions: …Multifunctional Genes…
http://www.plosone.org/article/info%253Adoi%252F10.1371%252Fjournal.pone.0017258 … hubbiness predicts these better than more complex methods #ismb #afp14