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Name: Esa Pitkänen
Type: User
Company: University of Helsinki
Bio: Group leader at Institute for Molecular Medicine Finland, University of Helsinki
Location: Helsinki
Name: Esa Pitkänen
Type: User
Company: University of Helsinki
Bio: Group leader at Institute for Molecular Medicine Finland, University of Helsinki
Location: Helsinki
Computational method for Comparative ReConstruction of genome-scale metabolic networks
Joint structural variant analysis of DELLY and BreakDancer calls
Perlin noise library for Python
MSI quantification of PCAWG tumors
Algorithm for finding branching metabolic pathways in large metabolic networks
This repository contains code used in the manuscript entitled “Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival” (https://www.biorxiv.org/content/10.1101/443580v1 ) Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are usually repressed, they become active in several human cancers, in particular those of the gastrointestinal tract. Here we characterize retrotransposon insertions in 202 colorectal tumor whole genomes and investigate their associations with molecular and clinical characteristics. We found highly variable retrotransposon activity among tumors and identified recurrent insertions in 15 known cancer genes. In approximately 1% of the cases we identified insertions in APC, likely to be tumor-initiating events. Insertions were positively associated with the CpG island methylator phenotype and the genomic fraction of allelic imbalance. Clinically, high number of insertions was independently associated with poor disease-specific survival.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
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TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
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China tencent open source team.