Christina Boucher

Recent Lab News

14.02.2015 "Misassembly Detection using Paired-End Sequence Reads and Optical Mapping data" by Martin Muggli, Simon Puglisi, Roy Ronen, and Christina Boucher accepted to ISMB 2015 in first round of acceptance (9% acceptance on first round).

15.01.2015 misSEQuel website released.

15.01.2015 Article about USDA grant.

03.01.2015. "Variable-Order de Bruijn Graphs" by Christina Boucher, Alex Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane accepted to DCC 2015, also, described as "Best of 2014". Full article posted on arXiv here

24.11.2014 "Misassembly Detection using Paired-End Sequence Reads and Optical Mapping data" posted on Homolog.us here.

21.10.2014 "Paradigm Shift: Revolutionizing Our Understanding of Antimicrobial Resistance Ecology through Whole Genome Analysis of Microbial Communities" (PI: Paul Morley, 2.2M) funded by USDA.

08.10.2014"The generating function approach for peptide identification in spectral networks" by Adrian Guthals, Christina Boucher, and Nuno Bandeira to appear in the Journal of Computational Biology.

01.10.2014 TWIN website released.

22.06.2014 "Efficient Indexed Alignment of Contigs to Optical Maps" by Martin Muggli, Simon J. Puglisi and Christina Boucher accepted to WABI 2014.

06.02.2014 "The generating function approach for peptide identification in spectral networks" by Adrian Guthals, Christina Boucher, and Nuno Bandeira accepted to RECOMB 2014 and will be presented at the 2014 ASMS Conference on Mass Spectrometry and Allied Topics.

10.25.2013 The Colorado Clinical and Translational Sciences Institute (CCTSI) awarded $48.4 million from NIH.

09.01.2013 Dr. Boucher (CS) and Dr. Susan VandeWoude (MIP) are recipients of a new Morris Animal Foundation award entitled, "Application of Genomic Technologies for the Detection and Discovery of Feline Viruses".

I am an Assistant Professor at the Department of Computer Science at Colorado State University in Fort Collins, Colorado. Prior to joining the faculty at Colorado State University, I worked as a Post-Doctoral Researcher at the University of California, San Diego in Pavel Pevzner's lab. In November 2010, I received my doctorate degree in Computer Science from the University of Waterloo under the supervision of Ming Li and Prabhakar Ragde.

My research aims to design and implement efficient algorithms that solve computational problems in genomics and transcriptomics. I frequently collaborate with biologists, mathematicians and clinician scientists in the tool development in order to ensure their practical application.

The Boucher lab greatly appreciates the support from the following granting agencies: NIH (CCTSI), Morris Animal Foundation, and Windows Azure for Research.

Currently, hiring GRAs (senior undergrad, MS or PhD) to work on antimicrobial resistence.

Variable-Order de Bruijn Graphs

Christina Boucher, Alex Bowe, Travis Gagie, Simon J. Puglisi and Kunihiko Sadakane. Variable-Order de Bruijn Graphs. To appear in proceedings of DCC 2015

Efficient Indexed Alignment of Contigs to Optical Maps

Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. Efficient Indexed Alignment of Contigs to Optical Maps. In Proceedings of WABI 2014, pages 68-81.

SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers

Christine Lo, Boyko Kakaradov, Daniel Lokshtanov and Christina Boucher. "SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers," Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.11, no.4, pp.648-656, July-Aug. 2014 doi: 10.1109/TCBB.2014.2304294

Genome sequences of ATCC 29281 and a pin and northern red oak isolate of Lonsdalea quercina subsp. quercina

Jorge Ibarra Caballero, Marcelo Zerillo, Jacob Snelling, Whitney Cranshaw, Christina Boucher, and Ned Tisserat. Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina. Genome Announcements 2014 Jun 12;2(3). pii: e00584-14. doi: 10.1128/genomeA.00584-14.

The Generating Function Approach for Peptide Identification in Spectral Networks

Adrian Guthals, Christina Boucher and Nuno Bandeira. The Generating Function Approach for Peptide Identification in Spectral Networks. In Proceedings of RECOMB 2014, pages 85-99.