Benchmarking
http://www.htslib.org/benchmarks/CRAM.html
Posts Tagged ‘from’
CRAM vs BAM
June 10, 2015Similarity network fusion for aggregating data types on a genomic scale : Nature Methods : Nature Publishing Group
June 1, 2015Similarity #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
Found this review
May 31, 2015Nice 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 in the Severe Asthma Research Program (ATS Journals)
May 30, 2015Identification 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
Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma (ATS Journals)
May 30, 2015Analysis 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 and Sensitivity to ALK Inhibition Therapy in Neuroblastoma: Cancer Cell
May 22, 2015ALK 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
Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
May 15, 2015“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
May 9, 2015Banjo 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?
BRAF pseudogene and cancer development
April 17, 2015BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]
http://www.cell.com/cell/abstract/S0092-8674(15)00244-5
Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.
Karreth FA1, Reschke M1, Ruocco A1, Ng C1, Chapuy B2, Léopold V1, Sjoberg M3, Keane TM3, Verma A4, Ala U1, Tay Y1, Wu D5, Seitzer N1, Velasco-Herrera Mdel C3, Bothmer A1, Fung J1, Langellotto F6, Rodig SJ7, Elemento O4, Shipp MA2, Adams DJ3, Chiarle R8, Pandolfi PP9.
Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments
demonstrated that pseudogenes contribute….
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet. 2012
April 12, 2015Changes in [DHS] #regulatory element activity…[over 3 primates] associated w/ altered…expression & pos. selection
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002789
DHS across 3 primates finds species specific sites associated with differential expression & positive selection
Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE*. Extensive evolutionary changes in regulatory element activity during human origins are
associated with altered gene expression and positive selection. PLoS Genet. 2012 Jun; 8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28. PubMed PMID: 22761590; PubMed Central PMCID: PMC3386175
SUMMARY (from csds):
The study is focused on analyzing genotype-phenotype correlation by looking at the evolution of DHS sites across three primate genomes: human, chimp and macaque. By comparing the data they were able to identify common DHS sites across the three species (sites that show similar DHS levels) and also species-specific sites. All the assays were supported by ChiP experiments. The study identified >2000 regulatory elements that were gained/lost since the divergence of
human and chimp. Looking at DNase and RNAseq data the authors show that the enrichment of regulatory elements next to genes with species-specific expression, suggests that the gain or loss of DHS sites impacts transcript abundance. The human DHS sites were enhanced for chromatin marks predictive of enhancers, while common regions were preferentially associated with promoters and insulators. By looking at species specificity, they found that species-specific DHS gains are cell type specific while both species specific DHS gains and losses are subject to positive selection. The common DHS sites are conserved and are suggested to have roles involving transcription and general housekeeping.
