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A Genomic Analysis Pipeline and Its Application to Pediatric Cancers
IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Michael Zeller,Christophe N. Magnan,Vishal R. Patel,Paul Rigor,Leonard Sender,Pierre Baldi
Issue Date:September 2014
We present a cancer genomic analysis pipeline which takes as input sequencing reads for both germline and tumor genomes and outputs filtered lists of all genetic mutations in the form of short ranked list of the most affected genes in the tumor, using eith...
Mining Eclipse Developer Contributions via Author-Topic Models
Mining Software Repositories, International Workshop on
By Erik Linstead, Paul Rigor, Sushil Bajracharya, Cristina Lopes, Pierre Baldi
Issue Date:May 2007
We present the results of applying statistical author-topic models to a subset of the Eclipse 3.0 source code consisting of 2,119 source files and 700,000 lines of code from 59 developers. This technique provides an intuitive and automated framework with w...
Sourcerer: a search engine for open source code supporting structure-based search
Found in: Companion to the 21st ACM SIGPLAN conference on Object-oriented programming languages, systems, and applications (OOPSLA '06)
By Cristina Lopes, Erik Linstead, Paul Rigor, Pierre Baldi, Sushil Bajracharya, Trung Ngo, Yimeng Dou
Issue Date:October 2006
We present Sourcerer, a search engine for open-source code. Sourcerer extracts fine-grained structural information from the code and stores it in a relational model. This information is used to implement a basic notion of CodeRank and to enable search form...
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