Recent Lab News 

01.06.2019 Martin Muggli will present Succinct De Bruijn Graph Construction for Massive Populations Through Space-Efficient Merging at ISMB/ECCB 2019

01.06.2019 Christina gave a talk on how BWT can be used to build and represent the colored de Bruijn graph at the Dagstuhl Seminar called 25 Years of the Burrows-Wheeler Transform.  Thank you to all the organizers.

01.06.2019 Five new journal articles and 3 new conference papers from Boucher lab.  Will be posted soon. 

01.09.2018 StringBio 2018 will be held in Orlando, Florida October 25 -- 27th. We are inviting students to submit abstracts to be considered for 15-20 minute oral presentations.  Registration deadline: October 1, 2018 (NO registration fee)

20.06.2018 Christina and Vikas Bansal will be the PC Chair for RECOMB SEQ 2019.   

20.06.2018 Practical Dynamic de Bruijn Graphs accepted to Journal of Bioinformatics.  Alan and Victoria's code is found on GitHub

11.06.2018 A succinct solution to Rmap alignment accepted to WABI 2018.  Martin's code is found on GitHub.  BioRxiv paper to be posted soon.

11.06.2018 Prefix-Free Parsing for Building Big BWTs accepted to WABI 2018.  BioRxiv has a preliminary version.

01.05.2018 Third Generation Sequencing Data Analytics on Mobile Devices: an Out-of-Core Approach accepted to FNC 2018.

01.05.2018 Correction of Optical Mapping Data published in GigaScience.  Code avaliable on github.

01.05.2018 Alan Kuhnle presented Practical Dynamic de Bruijn graphs at DSB 2018 in Helsinki. 

01.03.2018 Christina is the PC Chair for ACM BCB 2018.  Please contact her if you would like to join the PC. 

01.03.2018 Resistome SNP Calling via Read Colored de Bruijn Graphs accepted to RECOMB SEQ 2018.  Congratulations Bahar!

01.03.2018 Christina is the Poster Chair for RECOMB 2018. Please contact her concerning any matters.

01.03.2018 Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing published at Microbiome.

31.07.2017 Disentangled Long-Read De Bruijn Graphs via Optical Maps accepted to WABI 2017. Congratulations Bahar!

31.07.2017 Succinct Colored de Bruijn Graphs. Published at the Journal of Bioinformatics. Congratulations Martin!

31.07.2017  Targeted enrichment for pathogen detection and characterization in three felid species. Published at the Journal of Clinical Microbiology.

01.01.2017 MEGARes: an antimicrobial resistance database for high throughput sequencing published at Nucleic Acids Research.  

01.08.2016 Christina Boucher is a keynote spearker for the Computational Pan-genomics ECCB 2016 workshop.

06.08.2016 "Colored de Bruijn Graphs" accepted for Late Breaking Research Presentation at ISMB 2016. 

01.08.2016 Christina Boucher is a keynote spearker for RECOMB-seq 2016

06.17.2015 "Consensus Patterns (Probably) Has no EPTAS" accepted to ESA 2015 [26% acceptance rate].

03.01.2015 "The SLOW GROWTH 3 pentatricopeptide repeat protein is required for the splicing of mitochondrial nad7 intron 2 in Arabidopsis" accepted to Plant Physiology. 

02.14.2015 "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).  Described on here.


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I am an Assistant Professor at the Department of Computer and Information Science and Engineering at the University of Florida.  

Check my Google Scholar for all my papers. 

My research lab develops novel analysis methods that use current and upcoming technologie for generating biological data and build resources–such as a misassembly correction method or a resistome surveillance method–that benefit both researchers in bioinformatics and life sciences. Each of our analysis methods incorporate the use of discrete algorithms or data structures.

The Boucher lab greatly appreciates the support from the following granting agencies:

  • NIH R01: Developing Computational Methods for Surveillance of Antimicrobial Resistant Agents (PI: Boucher)
  • NSF III: A Scalable and Efficient Optical Map Assembler (PI: Boucher)
  • USDA NIFA: Paradigm shift: revolutionizing our understanding of antimicrobial resistance ecology through whole genome analysis of microbial communities (Lead PIs: Belk / Morley / Yang)
  • Morris Animal Foundation
  • Windows Azure for Research

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%].

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.

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