Sourcerer: a search engine for open source code supporting structure-based search. - Sushil Krishna Bajracharya; Trung Chi Ngo; Erik Linstead; Yimeng Dou; Paul Rigor; Pierre Baldi; Cristina Videira Lopes (OOPSLA Companion, 2006)

Mining concepts from code with probabilistic topic models. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (ASE, 2007)

Mining Eclipse Developer Contributions via Author-Topic Models. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (MSR, 2007)

Mining Internet-Scale Software Repositories. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (NIPS, 2007)

MotifMap: a human genome-wide map of candidate regulatory motif sites. - Xiaohui Xie; Paul Rigor; Pierre Baldi (Bioinform., 2009)

Sourcerer: mining and searching internet-scale software repositories. - Erik Linstead; Sushil Krishna Bajracharya; Trung Chi Ngo; Paul Rigor; Cristina Videira Lopes; Pierre Baldi (Data Min. Knowl. Discov., 2009)

Data structures and compression algorithms for high-throughput sequencing technologies. - Kenny Daily; Paul Rigor; Scott Christley; Xiaohui Xie; Pierre Baldi (BMC Bioinform., 2010)

MotifMap: integrative genome-wide maps of regulatory motif sites for model species. - Kenneth Daily; Vishal R. Patel; Paul Rigor; Xiaohui Xie; Pierre Baldi (BMC Bioinform., 2011)

A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. - Michael Zeller; Christophe N. Magnan; Vishal R. Patel; Paul Rigor; Leonard Sender; Pierre Baldi (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Applications in High-throughput Sequencing Technologies: From Compression Algorithms and Data Warehousing to Understanding Gene Regulation and Diseases at Scale. - Paul Rigor (2015)