Portable Nanopore Analytics: Are We There Yet?
Portable Nanopore Analytics: Are We There Yet? Marco Olivia, Kaden King, Kevin Wong, Grace Benson, Christina Boucher, Franco Milicchio, and Mattia Prosperi. To appear in the Journal of Bioinformatics

Succinct Dynamic de Bruijn Graphs.
Succinct Dynamic de Bruijn Graphs. Bahar Alapanahi, Alan Kuhnle, Simon Puglisi, Leena Salmela, Christina Boucher. To appear in the Journal of Bioinformatics.

Matching reads to many genomes with the r-index.
Matching reads to many genomes with the r-index. Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini (Multiple senior authors). Journal of Computational Biology, Volume 227, Issue 4, pages 514 – 518, 2020.

Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems..
Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems. Pablo Rovira, Tim McAllister, Steven M Lakin, Sharon R Cook, Enrique Doster, Noelle R Noyes, Maggie D Weinroth, Xiang Yang, Jennifer K Parker, Christina Boucher, Calvin Booker, Dale R. Woerner, Keith Belk, and Paul Morley. Frontiers in Microbiology, Volume 10, Article 1980, 2019.

A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification..
A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification. Enrique Doster, Pablo Rovira, Noelle R Noyes, Brandy A Burgess, Xiang Yang, Margaret D Weinroth, Lyndsey Linke, Roberta Magnuson, Christina Boucher, Keith E. Belk, and Paul S. Morley. Frontiers in Microbiology, Volume 10, Article 2499, 2020.

Building Large Updatable Colored de Bruijn Graphs via Merging.
Building Large Updatable Colored de Bruijn Graphs via Merging. Martin Muggli, Bahar Alipanahi and Christina Boucher. Presented at International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Basel, Switzerland, 2019. 9 pages. [Accepted rate: 18%]. To appear in Journal of Bioinformatics

Aligning Optical Maps to de Bruijn graphs
Aligning Optical Maps to de Bruijn graphs. Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, and Christina Boucher. Journal of Bioinformatics, Article btz. 069, DOI: 10.1093/bioinformatics/btz069.

Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multi-Drug Resistant Extended-Spectrum β-lactamase producing Escherichia coli.
Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multi-Drug Resistant Extended-Spectrum β-lactamase producing Escherichia coli. Lin Teng, Shinyoung Lee, Amber Ginn, Sarah Markland, Raies Mir, Nicolas DiLorenzo, Christina Boucher, Mattia Prosperi, Judith Johnson, J. Glenn Morris, and Kwang Cheol Jeong. Applied Environmental Microbiology, Article 03030-18, 2019, DOI: 10.1128/AEM.03030-18.

Practical Dynamic de Bruijn Graphs
Practical Dynamic de Bruijn Graphs. Victoria Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, and Travis Gagie. Journal of Bioinformatics, Volume 34, Issue 24, pp 4189-4195, 2018.

Prefix-Free Parsing for Building Big BWTs.
Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. Algorithms for Molecular Biology, 2019, 14:13 https://doi.org/10.1186/s13015-019-0148-5. Conference version in proceedings of WABI 2018.

Error correcting optical mapping data
Error correcting optical mapping data. Kingshuk Mukherjee, Darshan Washimkar, Martin D Muggli, Leena Salmela, and Christina Boucher. GigaScience, Volume 7, Issue 6, 1 June 2018, giy061, https://doi.org/10.1093/gigascience/giy061

Counting motifs in dynamic networks
Counting motifs in dynamic networks. Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher and Tamer Kahveci. BMC Systems Biology. BMC Systems Biology, 2018, 12(Suppl 1):6.

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.
Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period. Enrique Doster, Pablo Rovira, Noelle R. Noyes, Brandy A Burgess, Xiang Yang, Margaret D Weinroth, Steven M LakinG, Christopher J Dean, Lyndsey Linke, Roberta Magnuson, Kenneth I Jones, Christina Boucher, Jamie Ruiz, Keith E Belk, Paul S Morley. Frontiers of Microbiology, Volume 9, Article 1715. 2018.

Succinct Colored de Bruijn Graphs.
Martin D. Muggli, Alex Bowe, Noelle R. Noyes, Paul Morley, Keith Belk, Rob Raymond, Travis Gagie, Simon Puglisi, and Christina Boucher. In press at Journal of Bioinformatics (Impact Factor = 5.766)

MEGARes: an antimicrobial resistance database for high throughput sequencing
MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Research. 2017 Jan 4;45(D1):D574-D580 doi: 10.1093/nar/gkw1009. Epub 2016. Lakin, Steven*; Dean, Chris*; Noyes, Noelle*; Dettenwanger, Adam; Ross, Annie; Doster, Enrique; Rovira, Pablo; Abdo, Zaid; Jones, Kenneth; Ruiz, Jaime; Belk, Keith; Morley, Paul; Boucher, Christina. *: these authors contributed equally to this work

Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain
Xiang Yang, Noelle R. Noyes, Enrique Doster, Jennifer N. Martin, Lyndsey M. Linke, Roberta J. Magnuson, Hua Yang, Ifigenia Geornaras, Dale Woerner, Kenneth L. Jones, Jaime Ruiz, Christina Boucher, Paul S. Morley, and Keith E. Belk. Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain. Appl. Environ. Microbiol. AEM.00078-16; Accepted manuscript posted online 12 February 2016, doi:10.1128/AEM.00078-16

On the Hardness of Counting and Sampling Center Strings.
Christina Boucher and Mohamed Omar. "On the Hardness of Counting and Sampling Center Strings," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, no.6, pp.1843,1846, Nov.-Dec. 2012. Conference version in the proceedings of the 17th Annual Symposium on String Processing and Information Retrieval (SPIRE 2010), pages 128--135.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
5. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Carla Mavian, Sergei Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne-Mieke Vandamme, Simon Dellicour, Samuel V Scarpino, Charlotte Houldcroft, Julian Villabona-Arenas, Taylor K Paisie, Nídia S Trovão, Christina Boucher, Yun Zhang, Richard H Scheuermann, Olivier Gascuel, Tommy Tsan-Yuk Lam, Marc A Suchard, Ana Abecasis, Eduan Wilkinson, Tulio de Oliveira, Ana I Bento, Heiko A Schmidt, Darren Martin, James Hadfield, Nuno Faria, Nathan D Grubaugh, Richard A Neher, Guy Baele, Philippe Lemey, Tanja Stadler, Jan Albert, Keith A Crandall, Thomas Leitner, Alexandros Stamatakis, Mattia Prosperi, Marco Salemi. Proceedings of the National Academy of Sciences, Volume 117, Issue 23, pages 12522-12523, 2020.

Resistome diversity in cattle and the environment decreases during beef production
Noelle R Noyes, Xiang Yang, Lyndsey M. Linke, Roberta J. Magnuson, Adam Dettenwanger, Shaun Cook, Ifigenia Geornaras, Dale R. Woerner , Sheryl P. Gow, Tim A. McAllister, Hua Yang, Jaime Ruiz, Kenneth L. Jones, Christina A. Boucher, Paul S. Morley, Keith E. Belk. 2016. Resistome diversity in cattle and the environment decreases during beef production. eLife 2016;5:e13195

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. Alan KuhnleP, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini (Multiple senior authors). In the proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB) Washington, DC, pp 158-173, 2019. [Accepted rate: 8%].

A Succinct Solution to RMap Alignment
A Succinct Solution to Rmap Alignment. Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. In the proceedings of Workshop on Algorithms in Bioinformatics (WABI), Helsinki, Finland, Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Article 12, pp 1-16, 2018.

Recoloring the Colored de Bruijn Graph.
Recoloring the Colored de Bruijn Graph. Bahar AlipanahiG, Alan KuhnleP, and Christina Boucher. In the proceedings of String Processing and Information Retrieval (SPIRE), Lima, Peru, pp 1-11, 2018.

Identification of co-evolving temporal networks.
Identification of co-evolving temporal networks. Rasha Elhesha, Aisharjya Sarkar, Christina Boucher and Tamer Kahveci. In the proceedings of the International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC), Washington, DC, 2018, 8 pp.

Exploring Non-touchscreen Gestures for Smartwatches
Shaikh Shawon Arefin Shimon, Courtney Lutton, Zichun Xu, Sarah Morrison-Smith, Christina Boucher, and Jaime Ruiz. 2016. Exploring Non-touchscreen Gestures for Smartwatches. In Proceedings of the 2016 CHI Conference on Human Factors in Computing Systems (CHI '16). ACM, New York, NY, USA, 3822-3833. DOI: http://dx.doi.org/10.1145/2858036.2858385

Opportunities for Supporting Large-Scale Collaborative Projects
Morrison-Smith, S., Boucher, C., Wang, I., and Ruiz, J. 2016. Opportunities for Supporting Large-Scale Collaborative Projects. In Proceedings of Computer-Supported Cooperative Work and Social Computing (CSCW '16): Workshop on Large-scale Collaborative Projects to Affect Societal Change.

Consensus Patterns (Probably) Has no EPTAS
Christina Boucher, Christine Lo, and Daniel Lokshtanov. Consensus Patterns (Probably) Has no EPTAS. To appear in the proceedings of the European Symposium on Algorithms (ESA 2015). Awarded best paper at ESA 2015.

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

On Approximating String Selection Problems with Outliers.
Christina Boucher, Gadi Landau, Avivit Levy, David Pritchard, and Oren Weimann. On Approximating String Selection Problems with Outliers. In proceedings of the 23rd Annual Combinatorial Pattern Matching (CPM 2012), pages 427--438.

Smoothed Analysis of the Closest String Problem.
Christina Boucher and Kathleen Wilkie. Smoothed Analysis of the Closest String Problem. In proceedings of the 17th Annual Symposium on String Processing and Information Retrieval (SPIRE 2010), pages 107--118.

On the Structure of Small Motif Recognition Instances
Christina Boucher, Daniel Brown and Stephane Durocher. On the structure of small motif recognition instances. In proceedings of the 15th Annual String Processing and Information Retrieval Symposium (SPIRE 2008), pages 269--281.

A Graphical Game Model of Drug Binding
Christina Boucher and Maja Omanovic. A graphical game model of drug binding. In proceedings of the International Conference on Artificial Intelligence (ICAI 2007), pages 621--627.