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Christina Boucher 0001
Christina Anne Boucher
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- 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
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
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. 39(9) (2023) - [j33]Nathalie Bonin
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
Data Structures for SMEM-Finding in the PBWT. SPIRE 2023: 89-101 - [c37]Aaron Hong, Marco Oliva, Dominik Köppl
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
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. 23(2) (2022) - [j30]Massimiliano Rossi
MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29(2): 169-187 (2022) - [j29]Massimiliano Rossi
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
Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. 21(1): 81-108 (2022) - [j27]Kingshuk Mukherjee
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
Accessing the Suffix Array via φ -1-Forest. SPIRE 2022: 86-98 - [e3]Christina Boucher
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
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
Succinct dynamic de Bruijn graphs. Bioinform. 37(14): 1946-1952 (2021) - [j23]Mattia Prosperi
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
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
r-Indexing the eBWT. SPIRE 2021: 3-12 - [c29]Christina Boucher
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
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
Portable nanopore analytics: are we there yet? Bioinform. 36(16): 4399-4405 (2020) - [j19]Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie
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
Matching Reads to Many Genomes with the r-Index. J. Comput. Biol. 27(4): 514-518 (2020) - [j17]Enrique Doster
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
Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI 2020: 9:1-9:16 - [e2]Christina Boucher
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
Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14(1): 13:1-13:15 (2019) - [j15]Martin D. Muggli, Simon J. Puglisi
Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. 14(1): 25 (2019) - [j14]Martin D. Muggli
Building large updatable colored de Bruijn graphs via merging. Bioinform. 35(14): i51-i60 (2019) - [j13]Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela
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
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
Prefix-Free Parsing for Building Big BWTs. WABI 2018: 2:1-2:16 - [c21]Martin D. Muggli, Simon J. Puglisi
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
Succinct colored de Bruijn graphs. Bioinform. 33(20): 3181-3187 (2017) - [j9]Steven M. Lakin, Christopher J. Dean, Noelle R. Noyes
MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 45(Database-Issue): D574-D580 (2017) - [c20]Bahar Alipanahi, Leena Salmela
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI 2017: 1:1-1:14 - 2016
- [c19]Shaikh Shawon Arefin Shimon
Exploring Non-touchscreen Gestures for Smartwatches. CHI 2016: 3822-3833 - 2015
- [j8]Martin D. Muggli, Simon J. Puglisi
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
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
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
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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last updated on 2024-10-23 20:34 CEST by the dblp team
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