http://bioinformatics.oxfordjournals.org/content/30/21/3004.long
Archive for the 'SciLit' Category
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus
May 14, 2016Cell lineage analysis in human brain using endogenous retroelements. – PubMed – NCBI
May 7, 2016Cell-lineage analysis in human #brain using endogenous retroelements http://www.cell.com/neuron/abstract/S0896-6273(14)01137-4 Tracing L1 insertions w/ #singlecell sequencing
Using single cell WGS of 16 neuronal cells the authors investigated two somatic insertions of L1Hs elements in an adult human brain. Using these results the authors infer that L1 somatic insertions are infrequent and ALUs and SVAs somatic retrotransposition are extremely rare. Assessing two L1Hs insertions in 32 samples across different regions of this same adult brain, they found that while one insertion was spatially restricted (2x1cm region), the other was found across all samples of the adult brain (but not found in other tissues such as Heart, Lung, etc.). The more restricted one (L1Hs#1) is inferred to have happened during the Fetal stage (first trimester) while the broader one happened earlier, approximately 2 weeks
post-fertilization. Overall the paper is clear, concise, and simple. It answers an interesting biological question: Can retrotransposition be used as a marker of cell clonal expansion? It does, although the retrotransposition frequency is very small and SNVs might support better results for the same analysis due to their higher frequency..
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations : Nature Genetics : Nature Publishing Group
May 2, 2016Identification of [872] sig. mutated regions across #cancer types http://www.nature.com/ng/journal/v48/n2/full/ng.3471.html ranges from noncoding annotations to 3D structure
Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences: Cell
April 24, 2016Learning the…Determinants of Alternative #Splicing [in a largely linear model] from Millions of Random Sequences
http://www.cell.com/cell/abstract/S0092-8674(15)01271-4
** Rosenberg et al Cell. 2015
Builds a model of splicing using a library of randomized sequence Also, builds a generalized model for predicting effect of a SNP in the Geuvadis RNAseq
7mer model does well with lots of data
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information – Cheung – 2015 – Journal of Computational Chemistry – Wiley Online Library
April 17, 2016Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24232/full
Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen
First published: 27 October 2015
DOI: 10.1002/jcc.24232
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer | Genome Biology | Full Text
April 17, 2016two papers for journal club:
1. What are super-enhancers? Pott et al., Nature Genetics (2015) http://www.nature.com/ng/journal/v47/n1/full/ng.3167.html
2. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn et al., Genome Biology (2016)
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2
#Epigenomic analysis detects aberrant super-enhancer DNA methylation in human #cancer
https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2 hypo-Me of many large blocks
MicroRNA silencing for cancer therapy targeted to the tumour microenvironment : Nature : Nature Publishing Group
April 8, 2016miRNA silencing for…therapy targeted to the [acidic] tumor microenviron., w/ #pHLIP
http://www.nature.com/nature/journal/v518/n7537/abs/nature13905.html miR-155 moves beyond biomarker
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data | BMC Systems Biology | Full Text
April 8, 2016DREM…reconstruction of…regulatory #networks from time-series expression http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-104 Classic approach using 3-level IO #HMMs
PLOS Computational Biology: Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
April 3, 2016Discovering TFBSs in…Repetitive Regions of #Genomes with Multi-Read
Analysis http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002111 CSEM uses EM to refine site occupancy
Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111
http://www.stat.wisc.edu/~keles/Software/multi-reads/
CSEM
An expanded sequence context model broadly explains variability in polymorphism levels across the human genome : Nature Genetics : Nature Publishing Group
March 26, 2016Expanded seq. context model…explains variability in polymorphism[s] http://www.nature.com/NG/journal/vaop/ncurrent/full/ng.3511.html Reminiscent of GOR sec. structure prediction
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