@markgerstein: Korbel mentions: Criteria for Inference of
Chromothripsis in Cancer Genome
http://t.co/TslcrZsmNv #BTGCG14
http://www.sciencedirect.com/science/article/pii/S0092867413002122
Archive for the 'SciLit' Category
Criteria for Inference of Chromothripsis in Cancer Genomes — ScienceDirect
October 13, 2014Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nature Methods (2010) 7: 248-249.
October 11, 2014Server for predicting damaging missense #mutations
http://www.nature.com/nmeth/journal/v7/n4/full/nmeth0410-248.html Polyphen2 uses both structure & sequence (eg ASA & conservation)
http://www.ncbi.nlm.nih.gov/pubmed/20354512
Polyphen2 includes both structural and sequence features to predict the effect of nonsynonymous substitutions on protein function. Similar to many other methods, Polyphen2 uses evolutionary conservation as one of the features to identify functionally important residues. Integration of 3D-structure, membrane-specific features (PHAT matrix for TM regions) and other features such as protein-domain and active-site are the strengths of Polyphen2 compared to other sequence-based software making it a good tool for prediction.
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study : Nature Biotechnology : Nature Publishing Group
October 10, 2014Multiplatform assessment of #transcriptome profiling [w.] RNAseq http://www.nature.com/nbt/journal/v32/n9/full/nbt.2972.html Nice plots showing great effect of poly-A selection
Signaling hypergraphs: Trends in Biotechnology
October 9, 2014Signaling #hypergraphs
http://www.cell.com/trends/biotechnology/abstract/S0167-7799(14)00071-7 Edges from interactions of 2 sets of nodes. Better representation of assemblies & #complexes.
QT:{{”
each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs)……The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies).
“}}
Signaling hypergraphs. Ritz et al. (2014) TIB
This opinion paper advocates the use of hypergraphs to complement graph-based signaling network and pathway analyses, where each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs). They argue that
hypergraphs is a set-based method that acts like a more general version of a graph. The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies). They propose that hypergraphs can be very useful in situations where the effects of individual proteins might be neglected in graphs but will have a noticeable effect when these proteins are included in protein complexes as hypernodes. They use 3 applications as examples: pathway enrichment, pathway reconstruction, and pathway crosstalk.
Searching for missing heritability: Designing rare variant association studies
October 5, 2014Searching for missing heritability… rare variant association studies http://www.pnas.org/content/111/4/E455.abstract Pessimistic on #RVAS in #noncoding regions
Nice overview of study design. Good journal-club material.
What Big Data means to me — Bourne 21 (2): 194 — Journal of the American Medical Informatics Association
September 30, 2014Bourne mentions “What Big Data means to me”
(http://jamia.bmj.com/content/21/2/194.extract ) in connection with the creation of a digital ecosystem #ydod2014
Analysis of noncoding regulatory mutations in cancer
September 29, 2014http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3101.html
An interesting report of potential non-coding drivers without actually doing any wet lab work.
“These methods identify recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74 and SDHD, as well as previously identified mutations in the TERT promoter”. In the text they mention “Khurana et al. also reported WDR74 promoter mutations in 2 of the 20 prostate cancer genomes analyzed”.
PLOS Computational Biology: Spatial Generalization in Operant Learning: Lessons from Professional Basketball
September 29, 2014Spatial Generalization in… Learning: Lessons from… #Basketball http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003623 How past success changes your tendencies to shoot
Describes constructing a learning matrix for how a player will update his tendency to shoot
from a certain region of the court based on his past successes or failures
The Parable of Google Flu: Traps in Big Data Analysis
September 29, 2014Parable of #Google Flu: Traps in #BigData Analysis http://www.sciencemag.org/content/343/6176/1203.summary Replicating results is hard, w/ an ever-changing search algorithm
Blood transciptome paper
September 28, 2014Splicing changes along the blood lineage, good ex. of the
state-of-the-art in human transcriptomics
http://www.sciencemag.org/content/345/6204/1251033.abstract
Science 26 September 2014:
Vol. 345 no. 6204
DOI: 10.1126/science.1251033
Transcriptional diversity during lineage commitment of human blood progenitors
Chen et al.
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