Tag Archives: algorithms

RNA-Seq Assembly – Fundamental Limits, Algorithms and Software

rna-seq

David Tse – Stanford University Symposium on Turbo Codes and Iterative Information Processing Bremen, Germany August 20, 2014 Joint work with Sreeram Kannan and Lior Pachter. Research supported by NSF Center for Science of Information

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Empowered by Maverix, Biologist Uses RNA-seq to Understand Autism

rna-seq

In Nathaniel Heintz’s molecular biology lab at Rockefeller University, scientists study brain function and dysfunction under a wide array of conditions, from drug abuse to depression. Marian Mellén, a postdoctoral fellow in the lab, is using RNA-seq and other data ...

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MIRPIPE – quantification of microRNAs in niche model organisms

rna-seq

MicroRNAs represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such ...

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APADB: a database for alternative polyadenylation and microRNA regulation events

Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing ...

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FANSe2: A Robust Tool for Quantitative NGS Applications

rna-seq

Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) ...

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