Posts Tagged ‘splicing’

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences: Cell

April 24, 2016

Learning 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

Machine Intelligence Cracks Genetic Controls | Quanta Magazine

December 28, 2014

https://www.quantamagazine.org/20141218-machine-intelligence-cracks-genetic-controls/

QT:{{”

The splicing code is just one part of the noncoding genome, the area that does not produce proteins. But it’s a very important one. Approximately 90 percent of genes undergo alternative splicing, and scientists estimate that variations in the splicing code make up anywhere between 10 and 50 percent of all disease-linked mutations. “When you have mutations in the regulatory code, things can go very wrong,” Frey said.

“People have historically focused on mutations in the protein-coding regions, to some degree because they have a much better handle on what these mutations do,” said Mark Gerstein, a bioinformatician at Yale University, who was not involved in the study. “As we gain a better understanding of [the DNA sequences] outside of the protein-coding regions, we’ll get a better sense of how important they are in terms of disease.”

Scientists have made some headway into understanding how the cell chooses a particular protein configuration, but much of the code that governs this process has remained an enigma. Frey’s team was able to decipher some of these regulatory regions in a paper published in 2010, identifying a rough code within the mouse genome that regulates splicing. Over the past four years, the quality of genetics data — particularly human data — has improved dramatically, and
machine-learning techniques have become much more sophisticated, enabling Frey and his collaborators to predict how splicing is affected by specific mutations at many sites across the human genome. “Genome-wide data sets are finally able to enable predictions like this,” said Manolis Kellis, a computational biologist at MIT who was not involved in the study.

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AI Teams Up With Genomics To Find Disease Causing Mutations : Science : Design & Trend

December 28, 2014

http://www.designntrend.com/articles/32141/20141223/ai-teams-up-genomics-find-disease-causing-mutations.htm

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

April 27, 2014

Protein… #network of alternatively spliced isoforms from brain…: Half of the interactions from #splicing variants
http://www.nature.com/ncomms/2014/140411/ncomms4650/abs/ncomms4650.html

An RNA map predicting Nova-dependent splicing regulation : Abstract : Nature

December 27, 2012

bioinformatics + expt. reveal particular seq. motif (YCAY) important in splicing in brains
http://www.nature.com/nature/journal/v444/n7119/abs/nature05304.html