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ORCIDChristina Boucher 0001
Christina Anne Boucher
Person information
- affiliation: University of Florida, Department of Computer and Information Science and Engineering, Gainesville, FL, USA
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2020 – today
- 2024
[j37]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Pfp-fm: an accelerated FM-index. Algorithms Mol. Biol. 19(1): 15 (2024)- [j36]Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino
:
r-indexing the eBWT. Inf. Comput. 298: 105155 (2024) - [c46]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola:
Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM 2024: 12:1-12:16 - [c45]Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh:
Another virtue of wavelet forests. DCC 2024: 559 - [c44]Justin Kim, Rahul Varki, Marco Oliva, Christina Boucher:
Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage. ESA 2024: 78:1-78:15 - [c43]Mattia Prosperi, Simone Marini, Christina Boucher:
An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. ICHI 2024: 93-102 - [c42]Michael Aaron G. Sy, Mattia Prosperi, Mohammadali Serajian, Christina Boucher, Panayotis Takis Benos, Simone Marini:
Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. MIE 2024: 212-213 - [c41]Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh:
Another Virtue of Wavelet Forests. SPIRE 2024: 184-191 - [i16]Carson Stillman, Jonathan E. Bravo, Christina Boucher, Sara Rampazzi:
The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices. CoRR abs/2407.12001 (2024) - 2023
- [j35]Christina Boucher:
Special Issue: Algorithms in Bioinformatics. Algorithms 16(1): 21 (2023) - [j34]Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni:
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. 39(9) (2023) - [j33]Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm, Simone Marini, Mattia Prosperi, Noelle R. Noyes, Paul S. Morley, Christina Boucher:
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Nucleic Acids Res. 51(D1): 744-752 (2023) - [c40]Aaron Hong, Massimiliano Rossi, Christina Boucher:
LZ77 via Prefix-Free Parsing. ALENEX 2023: 123-134 - [c39]Marco Oliva, Travis Gagie, Christina Boucher:
Recursive Prefix-Free Parsing for Building Big BWTs. DCC 2023: 62-70 - [c38]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi:
Data Structures for SMEM-Finding in the PBWT. SPIRE 2023: 89-101 - [c37]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Acceleration of FM-Index Queries Through Prefix-Free Parsing. WABI 2023: 13:1-13:16 - [i15]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Acceleration of FM-index Queries Through Prefix-free Parsing. CoRR abs/2305.05893 (2023) - [i14]Christina Boucher, Travis Gagie, Aaron Hong, Yansong Li, Norbert Zeh:
Another virtue of wavelet forests? CoRR abs/2308.07809 (2023) - 2022
- [j32]Mattia Prosperi, Christina Boucher, Jiang Bian, Simone Marini:
Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. Artif. Intell. Medicine 130: 102326 (2022) - [j31]Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia Prosperi:
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. 23(2) (2022) - [j30]Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher:
MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29(2): 169-187 (2022) - [j29]Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher:
Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29(2): 188-194 (2022) - [j28]Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén:
Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. 21(1): 81-108 (2022) - [j27]Kingshuk Mukherjee, Daniel Dole-Muinos, Massimiliano Rossi, Ayomide Ajayi, Mattia Prosperi, Christina Boucher:
Finding Overlapping Rmaps via Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3114-3123 (2022) - [c36]Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher:
CSTs for Terabyte-Sized Data. DCC 2022: 93-102 - [c35]Christina Boucher:
Building scalable indexes that can be efficiently queried. IPDPS Workshops 2022: 142 - [c34]Christina Boucher, Dominik Köppl, Herman Perera, Massimiliano Rossi:
Accessing the Suffix Array via φ -1-Forest. SPIRE 2022: 86-98 - [e3]Christina Boucher, Sven Rahmann:
22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, September 5-7, 2022, Potsdam, Germany. LIPIcs 242, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2022, ISBN 978-3-95977-243-3 [contents] - [i13]Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia Prosperi:
Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus. CoRR abs/2207.07458 (2022) - 2021
- [j26]Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher:
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. Algorithms Mol. Biol. 16(1): 6 (2021) - [j25]Bahar Alipanahi, Martin D. Muggli, Musa Jundi, Noelle R. Noyes, Christina Boucher:
Metagenome SNP calling via read-colored de Bruijn graphs. Bioinform. 36(22-23): 5275-5281 (2021) - [j24]Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher:
Succinct dynamic de Bruijn graphs. Bioinform. 37(14): 1946-1952 (2021) - [j23]Mattia Prosperi, Simone Marini, Christina Boucher:
Fast and exact quantification of motif occurrences in biological sequences. BMC Bioinform. 22(1): 445 (2021) - [c33]Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi:
PFP Compressed Suffix Trees. ALENEX 2021: 60-72 - [c32]Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi:
PHONI: Streamed Matching Statistics with Multi-Genome References. DCC 2021: 193-202 - [c31]Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher:
Efficiently Merging r-indexes. DCC 2021: 203-212 - [c30]Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino:
r-Indexing the eBWT. SPIRE 2021: 3-12 - [c29]Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino:
Computing the Original eBWT Faster, Simpler, and with Less Memory. SPIRE 2021: 129-142 - [i12]Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino:
Computing the original eBWT faster, simpler, and with less memory. CoRR abs/2106.11191 (2021) - [i11]Mattia Prosperi, Simone Marini, Christina Boucher, Jiang Bian:
Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. CoRR abs/2107.03383 (2021) - 2020
- [j22]Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36(3): 682-689 (2020) - [j21]Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36(9): 2974 (2020) - [j20]Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol:
Portable nanopore analytics: are we there yet? Bioinform. 36(16): 4399-4405 (2020) - [j19]Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. J. Comput. Biol. 27(4): 500-513 (2020) - [j18]Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Matching Reads to Many Genomes with the r-Index. J. Comput. Biol. 27(4): 514-518 (2020) - [j17]Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E. Belk, Noelle R. Noyes, Paul S. Morley:
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucleic Acids Res. 48(Database-Issue): D561-D569 (2020) - [c28]Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher:
Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI 2020: 9:1-9:16 - [e2]Christina Boucher, Sharma V. Thankachan:
String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Orlando, FL, USA, October 13-15, 2020, Proceedings. Lecture Notes in Computer Science 12303, Springer 2020, ISBN 978-3-030-59211-0 [contents] - [i10]Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi:
PFP Data Structures. CoRR abs/2006.11687 (2020) - [i9]Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi:
PHONI: Streamed Matching Statistics with Multi-Genome References. CoRR abs/2011.05610 (2020)
2010 – 2019
- 2019
- [j16]Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun:
Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14(1): 13:1-13:15 (2019) - [j15]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. 14(1): 25 (2019) - [j14]Martin D. Muggli, Bahar Alipanahi, Christina Boucher:
Building large updatable colored de Bruijn graphs via merging. Bioinform. 35(14): i51-i60 (2019) - [j13]Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher:
Aligning optical maps to de Bruijn graphs. Bioinform. 35(18): 3250-3256 (2019) - [c27]Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci:
Co-evolving Patterns in Temporal Networks of Varying Evolution. BCB 2019: 494-503 - [c26]Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. RECOMB 2019: 158-173 - [i8]Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Matching reads to many genomes with the r-index. CoRR abs/1908.01263 (2019) - 2018
- [j12]Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie:
Practical dynamic de Bruijn graphs. Bioinform. 34(24): 4189-4195 (2018) - [j11]Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci:
Counting motifs in dynamic networks. BMC Syst. Biol. 12(1): 1-12 (2018) - [c25]Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci:
Identification of Co-evolving Temporal Networks. BCB 2018: 591-592 - [c24]Franco Milicchio, Marco Oliva, Christina Boucher, Mattia Prosperi:
Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept. FNC/MobiSPC 2018: 219-226 - [c23]Bahar Alipanahi, Alan Kuhnle, Christina Boucher:
Recoloring the Colored de Bruijn Graph. SPIRE 2018: 1-11 - [c22]Christina Boucher, Travis Gagie, Alan Kuhnle, Giovanni Manzini:
Prefix-Free Parsing for Building Big BWTs. WABI 2018: 2:1-2:16 - [c21]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
A Succinct Solution to Rmap Alignment. WABI 2018: 12:1-12:16 - [e1]Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop:
Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018. ACM 2018 [contents] - [i7]Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. CoRR abs/1811.06933 (2018) - 2017
- [j10]Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher:
Succinct colored de Bruijn graphs. Bioinform. 33(20): 3181-3187 (2017) - [j9]Steven M. Lakin, Christopher J. Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher:
MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 45(Database-Issue): D574-D580 (2017) - [c20]Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI 2017: 1:1-1:14 - 2016
- [c19]Shaikh Shawon Arefin Shimon, Courtney Lutton, Zichun Xu, Sarah Morrison-Smith, Christina Boucher, Jaime Ruiz:
Exploring Non-touchscreen Gestures for Smartwatches. CHI 2016: 3822-3833 - 2015
- [j8]Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher:
Misassembly detection using paired-end sequence reads and optical mapping data. Bioinform. 31(12): 80-88 (2015) - [j7]Adrian Guthals, Christina Boucher, Nuno Bandeira:
The Generating Function Approach for Peptide Identification in Spectral Networks. J. Comput. Biol. 22(5): 353-366 (2015) - [c18]Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi:
Fast and efficient compression of high-throughput sequencing reads. BCB 2015: 325-334 - [c17]Sarah Morrison-Smith, Christina Boucher, Andrea Bunt, Jaime Ruiz:
Elucidating the role and use of bioinformatics software in life science research. BCS HCI 2015: 230-238 - [c16]Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane:
Variable-Order de Bruijn Graphs. DCC 2015: 383-392 - [c15]Christina Boucher, Christine Lo, Daniel Lokshtanov:
Consensus Patterns (Probably) Has no EPTAS. ESA 2015: 239-250 - [c14]Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén:
Relative Select. SPIRE 2015: 149-155 - [i6]Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén:
Relative Select. CoRR abs/1506.03262 (2015) - 2014
- [j6]Christine Lo, Boyko Kakaradov, Daniel Lokshtanov, Christina Boucher:
SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers. IEEE ACM Trans. Comput. Biol. Bioinform. 11(4): 648-656 (2014) - [c13]Adrian Guthals, Christina Boucher, Nuno Bandeira:
The Generating Function Approach for Peptide Identification in Spectral Networks. RECOMB 2014: 85-99 - [c12]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
Efficient Indexed Alignment of Contigs to Optical Maps. WABI 2014: 68-81 - [i5]Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz, Christina Boucher:
HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly. CoRR abs/1408.5592 (2014) - [i4]Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane:
Variable-Order de Bruijn Graphs. CoRR abs/1411.2718 (2014) - [i3]Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher:
Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data. CoRR abs/1411.5890 (2014) - 2013
- [j5]Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann:
On approximating string selection problems with outliers. Theor. Comput. Sci. 498: 107-114 (2013) - [c11]Mark F. Rogers, Christina Boucher, Asa Ben-Hur:
SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. BCB 2013: 247 - 2012
- [j4]Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner:
SEQuel: improving the accuracy of genome assemblies. Bioinform. 28(12): 188-196 (2012) - [j3]Christina Boucher, Mohamed Omar:
On the Hardness of Counting and Sampling Center Strings. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1843-1846 (2012) - [c10]Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann:
On Approximating String Selection Problems with Outliers. CPM 2012: 427-438 - [i2]Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann:
On Approximating String Selection Problems with Outliers. CoRR abs/1202.2820 (2012) - 2011
- [j2]Christina Boucher, Bin Ma:
Closest string with outliers. BMC Bioinform. 12(S-1): S55 (2011) - [c9]Christina Boucher:
The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity. MFCS 2011: 158-169 - [i1]Christina Boucher, Christine Lo, Daniel Lokshtanov:
Outlier Detection for DNA Fragment Assembly. CoRR abs/1111.0376 (2011) - 2010
- [b1]Christina Anne Boucher:
Combinatorial and Probabilistic Approaches to Motif Recognition. University of Waterloo, Ontario, Canada, 2010 - [j1]Christina Boucher, James King:
Fast motif recognition via application of statistical thresholds. BMC Bioinform. 11(S-1): 11 (2010) - [c8]Christina Boucher, Kathleen P. Wilkie:
Why Large Closest String Instances Are Easy to Solve in Practice. SPIRE 2010: 106-117 - [c7]Christina Boucher, Mohamed Omar:
On the Hardness of Counting and Sampling Center Strings. SPIRE 2010: 127-134
2000 – 2009
- 2009
- [c6]Christina Boucher, Daniel G. Brown:
Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding. BICoB 2009: 139-150 - [c5]Christina Boucher:
Faster Algorithms for Sampling and Counting Biological Sequences. SPIRE 2009: 243-253 - 2008
- [c4]Christina Boucher, Daniel G. Brown, Stephane Durocher:
On the Structure of Small Motif Recognition Instances. SPIRE 2008: 269-281 - 2007
- [c3]Maja Omanovic, Christina Boucher:
An Ant Colony Optimization Heuristic for the Combinatorial Auction Problem. IC-AI 2007: 176-184 - [c2]Christina Boucher, Maja Omanovic:
A Graphical Game Model of Drug Binding. IC-AI 2007: 621-627 - [c1]Christina Boucher, Daniel G. Brown, Paul Church:
A Graph Clustering Approach to Weak Motif Recognition. WABI 2007: 149-160
Coauthor Index
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