Christina Boucher

115 papers A* 1A 4B 13C 21Misc 2Journal 60Unranked 13

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes". Bioinform. Jarno N. Alanko, Ilya B. Slizovskiy, Daniel Lokshtanov, Travis Gagie, Noelle R. Noyes, Christina Boucher
2025	—	`conf`	Comparative Evaluation of Clinical Large Language Models and Machine Learning to Predict Antimicrobial Resistance in Hospital-Onset Sepsis. AIME (1) Scott A. Cohen, Ziyi Chen, Jiang Bian, Christina Boucher, Yonghui Wu, Mattia Prosperi
2025	B	`conf`	Devider: Long-Read Reconstruction of Many Diverse Haplotypes. RECOMB Jim Shaw, Christina Boucher, Yun William Yu, Noelle R. Noyes, Heng Li
2025	J	`jnl`	Enhancing Data Compression: Recent Innovations in LZ77 Algorithms. J. Comput. Biol. Aaron Hong, Christina Boucher
2025	J	`jnl`	Formal verification of bioinformatics software using model checking and theorem proving. Briefings Bioinform. Hansika Weerasena, Aruna Jayasena, Christina Boucher, Prabhat Mishra
2025	B	`conf`	How Hand Constraints Influence User Defined Gestures in Mixed Reality. Graphics Interface Alexander Barquero, Niriksha Regmi, Oluwatomisin Obajemu, Rohith Venkatakrishnan, Christina Boucher, Lisa Anthony, Jaime Ruiz
2025	J	`jnl`	Leveraging large language models to predict antibiotic resistance in Bioinform. Conrad Testagrose, Sakshi Pandey, Mohammadali Serajian, Simone Marini, Mattia Prosperi, Christina Boucher
2025	—	`conf`	Optimizing the Performance of the FM-Index for Large-Scale Data. The Expanding World of Compressed Data Eddie Ferro, Christina Boucher
2025	—	`conf`	Phasing Data from Genotype Queries via the μ-PBWT. The Expanding World of Compressed Data Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, Yuri Pirola
2025	C	`conf`	Recursive Parsing and Grammar Compression in the Era of Pangenomics (Invited Talk). WABI Christina Boucher
2025	J	`jnl`	SDSL-Mobile: Enabling space-efficient data structures for mobile applications. SoftwareX Alexander Barquero, Anisha Wadhwani, Tyler Pencinger, Aaron Hong, Jaime Ruiz, Mattia Prosperi, Christina Boucher
2024	—	`conf`	An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. ICHI Mattia Prosperi, Simone Marini, Christina Boucher
2024	C	`conf`	Another Virtue of Wavelet Forests. SPIRE Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh
2024	B	`conf`	Another virtue of wavelet forests. DCC Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh
2024	J	`jnl`	Pfp-fm: an accelerated FM-index. Algorithms Mol. Biol. Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
2024	—	`conf`	Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. MIE Michael Aaron G. Sy, Mattia Prosperi, Mohammadali Serajian, Christina Boucher, Panayotis Takis Benos, Simone Marini
2024	A	`conf`	Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage. ESA Justin Kim, Rahul Varki, Marco Oliva, Christina Boucher
2024	J	`jnl`	Scalable Bioinform. Mohammadali Serajian, Simone Marini, Jarno N. Alanko, Noelle R. Noyes, Mattia Prosperi, Christina Boucher
2024	B	`conf`	Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola
2024	J	`jnl`	The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices. CoRR Carson Stillman, Jonathan E. Bravo, Christina Boucher, Sara Rampazzi
2024	J	`jnl`	r-indexing the eBWT. Inf. Comput. Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino
2023	C	`conf`	Acceleration of FM-Index Queries Through Prefix-Free Parsing. WABI Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
2023	J	`jnl`	Acceleration of FM-index Queries Through Prefix-free Parsing. CoRR Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
2023	J	`jnl`	Another virtue of wavelet forests? CoRR Christina Boucher, Travis Gagie, Aaron Hong, Yansong Li, Norbert Zeh
2023	C	`conf`	Data Structures for SMEM-Finding in the PBWT. SPIRE Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi
2023	A	`conf`	LZ77 via Prefix-Free Parsing. ALENEX Aaron Hong, Massimiliano Rossi, Christina Boucher
2023	J	`jnl`	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. 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
2023	B	`conf`	Recursive Prefix-Free Parsing for Building Big BWTs. DCC Marco Oliva, Travis Gagie, Christina Boucher
2023	J	`jnl`	Special Issue: Algorithms in Bioinformatics. Algorithms Christina Boucher
2023	J	`jnl`	μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
2022	C	`ed.`	22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, Potsdam, Germany, September 5-7, 2022 WABI Christina Boucher, Sven Rahmann
2022	C	`conf`	Accessing the Suffix Array via φ SPIRE Christina Boucher, Dominik Köppl, Herman Perera, Massimiliano Rossi
2022	J	`jnl`	Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. Artif. Intell. Medicine Mattia Prosperi, Christina Boucher, Jiang Bian, Simone Marini
2022	—	`conf`	Building scalable indexes that can be efficiently queried. IPDPS Workshops Christina Boucher
2022	B	`conf`	CSTs for Terabyte-Sized Data. DCC Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher
2022	J	`jnl`	Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
2022	J	`jnl`	Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
2022	J	`jnl`	Finding Overlapping Rmaps via Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. Kingshuk Mukherjee, Daniel Dole-Muinos, Massimiliano Rossi, Ayomide Ajayi, Mattia Prosperi, Christina Boucher
2022	J	`jnl`	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 Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia Prosperi
2022	J	`jnl`	MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher
2022	J	`jnl`	Syotti: scalable bait design for DNA enrichment. Bioinform. Jarno N. Alanko, Ilya B. Slizovskiy, Daniel Lokshtanov, Travis Gagie, Noelle R. Noyes, Christina Boucher
2022	J	`jnl`	Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia Prosperi
2021	J	`jnl`	Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. CoRR Mattia Prosperi, Simone Marini, Christina Boucher, Jiang Bian
2021	C	`conf`	Computing the Original eBWT Faster, Simpler, and with Less Memory. SPIRE Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino
2021	J	`jnl`	Computing the original eBWT faster, simpler, and with less memory. CoRR Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino
2021	B	`conf`	Efficiently Merging r-indexes. DCC Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher
2021	J	`jnl`	Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. Algorithms Mol. Biol. Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
2021	J	`jnl`	Fast and exact quantification of motif occurrences in biological sequences. BMC Bioinform. Mattia Prosperi, Simone Marini, Christina Boucher
2021	J	`jnl`	Metagenome SNP calling via read-colored de Bruijn graphs. Bioinform. Bahar Alipanahi, Martin D. Muggli, Musa Jundi, Noelle R. Noyes, Christina Boucher
2021	A	`conf`	PFP Compressed Suffix Trees. ALENEX Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
2021	B	`conf`	PHONI: Streamed Matching Statistics with Multi-Genome References. DCC Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
2021	J	`jnl`	Succinct dynamic de Bruijn graphs. Bioinform. Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher
2021	C	`conf`	r-Indexing the eBWT. SPIRE Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino
2020	J	`jnl`	Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. J. Comput. Biol. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2020	C	`conf`	Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. WABI Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucleic Acids Res. Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E. Belk, Noelle R. Noyes, Paul S. Morley
2020	J	`jnl`	Matching Reads to Many Genomes with the r-Index. J. Comput. Biol. Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2020	J	`jnl`	PFP Data Structures. CoRR Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
2020	J	`jnl`	PHONI: Streamed Matching Statistics with Multi-Genome References. CoRR Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
2020	J	`jnl`	Portable nanopore analytics: are we there yet? Bioinform. Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol
2020	C	`ed.`	String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Orlando, FL, USA, October 13-15, 2020, Proceedings SPIRE Christina Boucher, Sharma V. Thankachan
2019	J	`jnl`	Aligning optical maps to de Bruijn graphs. Bioinform. Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher
2019	J	`jnl`	Building large updatable colored de Bruijn graphs via merging. Bioinform. Martin D. Muggli, Bahar Alipanahi, Christina Boucher
2019	—	`conf`	Co-evolving Patterns in Temporal Networks of Varying Evolution. BCB Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci
2019	B	`conf`	Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. RECOMB Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2019	J	`jnl`	Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2019	J	`jnl`	Matching reads to many genomes with the r-index. CoRR Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2019	J	`jnl`	Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun
2018	C	`conf`	A Succinct Solution to Rmap Alignment. WABI Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2018	J	`jnl`	Counting motifs in dynamic networks. BMC Syst. Biol. Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci
2018	J	`jnl`	Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. CoRR Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2018	—	`conf`	Identification of Co-evolving Temporal Networks. BCB Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci
2018	J	`jnl`	Practical dynamic de Bruijn graphs. Bioinform. Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie
2018	C	`conf`	Prefix-Free Parsing for Building Big BWTs. WABI Christina Boucher, Travis Gagie, Alan Kuhnle, Giovanni Manzini
2018	—	`ed.`	Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018 BCB Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop
2018	C	`conf`	Recoloring the Colored de Bruijn Graph. SPIRE Bahar Alipanahi, Alan Kuhnle, Christina Boucher
2018	—	`conf`	Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept. FNC/MobiSPC Franco Milicchio, Marco Oliva, Christina Boucher, Mattia Prosperi
2017	C	`conf`	Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2017	J	`jnl`	MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 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
2017	J	`jnl`	Succinct colored de Bruijn graphs. Bioinform. Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher
2016	A*	`conf`	Exploring Non-touchscreen Gestures for Smartwatches. CHI Shaikh Shawon Arefin Shimon, Courtney Lutton, Zichun Xu, Sarah Morrison-Smith, Christina Boucher, Jaime Ruiz
2015	A	`conf`	Consensus Patterns (Probably) Has no EPTAS. ESA Christina Boucher, Christine Lo, Daniel Lokshtanov
2015	—	`conf`	Elucidating the role and use of bioinformatics software in life science research. BCS HCI Sarah Morrison-Smith, Christina Boucher, Andrea Bunt, Jaime Ruiz
2015	—	`conf`	Fast and efficient compression of high-throughput sequencing reads. BCB Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi
2015	J	`jnl`	Misassembly detection using paired-end sequence reads and optical mapping data. Bioinform. Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
2015	C	`conf`	Relative Select. SPIRE Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
2015	J	`jnl`	Relative Select. CoRR Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
2015	J	`jnl`	The Generating Function Approach for Peptide Identification in Spectral Networks. J. Comput. Biol. Adrian Guthals, Christina Boucher, Nuno Bandeira
2015	B	`conf`	Variable-Order de Bruijn Graphs. DCC Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane
2014	C	`conf`	Efficient Indexed Alignment of Contigs to Optical Maps. WABI Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2014	J	`jnl`	HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly. CoRR Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz, Christina Boucher
2014	J	`jnl`	Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data. CoRR Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
2014	J	`jnl`	SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers. IEEE ACM Trans. Comput. Biol. Bioinform. Christine Lo, Boyko Kakaradov, Daniel Lokshtanov, Christina Boucher
2014	B	`conf`	The Generating Function Approach for Peptide Identification in Spectral Networks. RECOMB Adrian Guthals, Christina Boucher, Nuno Bandeira
2014	J	`jnl`	Variable-Order de Bruijn Graphs. CoRR Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane
2013	J	`jnl`	On approximating string selection problems with outliers. Theor. Comput. Sci. Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann
2013	—	`conf`	SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. BCB Mark F. Rogers, Christina Boucher, Asa Ben-Hur
2012	J	`jnl`	On Approximating String Selection Problems with Outliers CoRR Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann
2012	B	`conf`	On Approximating String Selection Problems with Outliers. CPM Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann
2012	J	`jnl`	On the Hardness of Counting and Sampling Center Strings. IEEE ACM Trans. Comput. Biol. Bioinform. Christina Boucher, Mohamed Omar
2012	J	`jnl`	SEQuel: improving the accuracy of genome assemblies. Bioinform. Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner
2011	J	`jnl`	Closest string with outliers. BMC Bioinform. Christina Boucher, Bin Ma
2011	J	`jnl`	Outlier Detection for DNA Fragment Assembly CoRR Christina Boucher, Christine Lo, Daniel Lokshtanov
2011	B	`conf`	The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity. MFCS Christina Boucher
2010	J	`jnl`	Fast motif recognition via application of statistical thresholds. BMC Bioinform. Christina Boucher, James King
2010	C	`conf`	On the Hardness of Counting and Sampling Center Strings. SPIRE Christina Boucher, Mohamed Omar
2010	C	`conf`	Why Large Closest String Instances Are Easy to Solve in Practice. SPIRE Christina Boucher, Kathleen P. Wilkie
2009	—	`conf`	Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding. BICoB Christina Boucher, Daniel G. Brown
2009	C	`conf`	Faster Algorithms for Sampling and Counting Biological Sequences. SPIRE Christina Boucher
2008	C	`conf`	On the Structure of Small Motif Recognition Instances. SPIRE Christina Boucher, Daniel G. Brown, Stephane Durocher
2007	C	`conf`	A Graph Clustering Approach to Weak Motif Recognition. WABI Christina Boucher, Daniel G. Brown, Paul Church
2007	Misc	`conf`	A Graphical Game Model of Drug Binding. IC-AI Christina Boucher, Maja Omanovic
2007	Misc	`conf`	An Ant Colony Optimization Heuristic for the Combinatorial Auction Problem. IC-AI Maja Omanovic, Christina Boucher