linkstream2 microblog

Dark side of the..genome
http://www.Nature.com/nature/journal/v538/n7624/full/538275a.html QT: NextGen..has been..the tech engine of #ENCODE..but..hi-res livecell imaging [is coming]

Has figure from Khurana et al. Nat. Rev. Genet. (’16)

QT:{{”
“Next-generation sequencing has been — and still is — the
technological engine of ENCODE. But looking ahead, researchers might be able to roll out high-resolution live-cell imaging on a large scale to watch the state of the genome change in real time using specific markers. This technology could be disruptive. “If we had a better microscope, we wouldn’t be sequencing anymore,” says
Stamatoyannopoulos”
“}}

#Machinelearning applications in…genomics
http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html Nice overview of key distinctions betw generative & discriminative models

In their review, “Machine learning in genetics and genomics”, Libbrecht and Noble overview important aspects of application of machine learning to genomic data. The review presents illustrative classical genomics problems where machine learning techniques have proven useful and describes the differences between supervised, semi-supervised and unsupervised learning as well as generative and discriminative models. The authors discuss considerations that should be made when selecting the right machine learning approach depending on the biological problem and data at hand, provide general practical guidelines and suggest possible solutions to common challenges.

The Race to Clone #BRCA1 http://www.sciencemag.org/content/343/6178/1462.abstract
Lessons on #LOF mutations, synthetic lethality, silly gene names & the 2-hit hypothesis

synthetic lethality (PARP inhibitors), gene names (RING fingers)

Analysis of noncoding somatic mutations &…expression alterations http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html 505 WGS variants w. RNAseq, #TCGA as of Mar ’14

all of what’s in TCGA as of spring ’14

505 TCGA WGS Somatic mutations, Expression Calls, CNA
via
https://www.synapse.org/#!Synapse:syn2882200

Orthogonal to PCAWG-607 (Alexandrov et al + 100 "public" stomach cancers)