linkstream2 microblog

Visualizing virus assembly…inside…bacteria
http://www.nature.com/nature/journal/v502/n7473/full/nature12604.html Phase-contrast #cryoET resolves subcellular structures (eg ribosomes)

Cryo-ET determines diff structural snapshots virus during assembly. One tomogram to work out whole pathway.

Wei Dai,
Caroline Fu,
Desislava Raytcheva,
John Flanagan,
Htet A. Khant,
Xiangan Liu,
Ryan H. Rochat,
Cameron Haase-Pettingell,
Jacqueline Piret,
Steve J. Ludtke,
Kuniaki Nagayama,
Michael F. Schmid,
Jonathan A. King
& Wah Chiu

Nature 502, 707–710 (31 October 2013) doi:10.1038/nature12604

http://bib.oxfordjournals.org/content/16/1/1.abstract

Benchmarking
http://www.htslib.org/benchmarks/CRAM.html

Similarity #network fusion for aggregating data types http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2810.html Combines mRNA, miRNA & gene fusions to classify cancer subtypes
http://compbio.cs.toronto.edu/SNF/SNF

Nice graph of seq. machine output v time

http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00340-8

Identification of #Asthma Phenotypes Using Cluster Analysis
http://www.atsjournals.org/doi/abs/10.1164/rccm.200906-0896OC#.VWk-gFxViko 5 canonical groups based on lung function, meds usage, &c

Canonical clustering of asthmatic patients into different groups

Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma http://www.atsjournals.org/doi/abs/10.1164/rccm.201408-1440OC Consistent blood expression patterns

Noninvasive Analysis of the Sputum Transcriptome Discriminates
Clinical Phenotypes of Asthma (ATS Journals)

Yan, X., Chu, J.-H., Gomez, J., Koenigs, M., Holm, C., He, X., Perez,
M. F., Zhao, H., Mane, S., Martinez, F. D., Ober, C., Nicolae, D. L.,
Barnes, K. C., London, S. J., Gilliland, F., Weiss, S. T., Raby, B.
A., Cohn, L., and Chupp, G. L. “Non-Invasive Analysis of the Sputum
Transcriptome Discriminates Clinical Phenotypes of Asthma” American
Journal of Respiratory and Critical Care Medicine (2015):
doi:10.1164/rccm.201408-1440OC,

QT:{{"
Conclusions: There are common patterns of gene expression in the
sputum and blood of children and adults that are associated with near
fatal, severe and milder asthma.
"}}

ALK Mutations Confer Differential Oncogenic Activation
http://www.cell.com/cancer-cell/abstract/S1535-6108%2814%2900393-6 MD modeling better assessing #SNV impact than stats, ie sift

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma

Scott C. Bresler
Daniel A. Weiser
Peter J. Huwe
…
Ravi Radhakrishnan
Mark A. Lemmon
Yaël P. Mossé

DOI: http://dx.doi.org/10.1016/j.ccell.2014.09.019

“this has got to be a record… imported this into Zotero to find the total author count. It’s 1,014”
http://www.g3journal.org/content/5/5/719.abstract

Banjo Raises $100 Million to Detect World Events in Real Time http://blogs.wsj.com/digits/2015/05/06/banjo-raises-100-million-to-detect-world-events-in-real-time Will their global "crystal ball" notice this tweet?