Christina Boucher

According to our database, Christina Boucher authored at least 81 papers between 2007 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Pfp-fm: an accelerated FM-index.

Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie

Algorithms Mol. Biol., December, 2024

r-indexing the eBWT.

Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino

Inf. Comput., 2024

The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices.

Carson Stillman, Jonathan E. Bravo, Christina Boucher, Sara Rampazzi

CoRR, 2024

Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics.

Michael Aaron G. Sy, Mattia Prosperi, Mohammadali Serajian, Christina Boucher, Panayotis Takis Benos, Simone Marini

Proceedings of the Digital Health and Informatics Innovations for Sustainable Health Care Systems, 2024

An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs.

Mattia Prosperi, Simone Marini, Christina Boucher

Proceedings of the 12th IEEE International Conference on Healthcare Informatics, 2024

Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage.

Justin Kim, Rahul Varki, Marco Oliva, Christina Boucher

Proceedings of the 32nd Annual European Symposium on Algorithms, 2024

Another virtue of wavelet forests.

Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh

Proceedings of the Data Compression Conference, 2024

Solving the Minimal Positional Substring Cover Problem in Sublinear Space.

Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola

Proceedings of the 35th Annual Symposium on Combinatorial Pattern Matching, 2024

2023

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni

Bioinform., September, 2023

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing.

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

Nucleic Acids Res., January, 2023

Special Issue: Algorithms in Bioinformatics.

Christina Boucher

Algorithms, January, 2023

Acceleration of FM-Index Queries Through Prefix-Free Parsing.

Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

Data Structures for SMEM-Finding in the PBWT.

Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi

Proceedings of the String Processing and Information Retrieval, 2023

Recursive Prefix-Free Parsing for Building Big BWTs.

Marco Oliva, Travis Gagie, Christina Boucher

Proceedings of the Data Compression Conference, 2023

LZ77 via Prefix-Free Parsing.

Aaron Hong, Massimiliano Rossi, Christina Boucher

Proceedings of the Symposium on Algorithm Engineering and Experiments, 2023

2022

Finding Overlapping Rmaps via Clustering.

Kingshuk Mukherjee, Daniel Dole-Muinos, Massimiliano Rossi, Ayomide Ajayi, Mattia Prosperi, Christina Boucher

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Computational graph pangenomics: a tutorial on data structures and their applications.

Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén

Nat. Comput., 2022

MONI: A Pangenomic Index for Finding Maximal Exact Matches.

Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher

J. Comput. Biol., 2022

Finding Maximal Exact Matches Using the r-Index.

Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher

J. Comput. Biol., 2022

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.

Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia Prosperi

CoRR, 2022

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing.

Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia Prosperi

Briefings Bioinform., 2022

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions.

Mattia Prosperi, Christina Boucher, Jiang Bian, Simone Marini

Artif. Intell. Medicine, 2022

Accessing the Suffix Array via φ ^-1-Forest.

Christina Boucher, Dominik Köppl, Herman Perera, Massimiliano Rossi

Proceedings of the String Processing and Information Retrieval, 2022

Building scalable indexes that can be efficiently queried.

Christina Boucher

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

CSTs for Terabyte-Sized Data.

Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher

Proceedings of the Data Compression Conference, 2022

2021

Succinct dynamic de Bruijn graphs.

Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher

Bioinform., August, 2021

Fast and exact quantification of motif occurrences in biological sequences.

Mattia Prosperi, Simone Marini, Christina Boucher

BMC Bioinform., 2021

Metagenome SNP calling via read-colored de Bruijn graphs.

Bahar Alipanahi, Martin D. Muggli, Musa Jundi, Noelle R. Noyes, Christina Boucher

Bioinform., 2021

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.

Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, Christina Boucher

Algorithms Mol. Biol., 2021

Computing the Original eBWT Faster, Simpler, and with Less Memory.

Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino

Proceedings of the String Processing and Information Retrieval, 2021

Efficiently Merging r-indexes.

Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher

Proceedings of the 31st Data Compression Conference, 2021

PHONI: Streamed Matching Statistics with Multi-Genome References.

Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi

Proceedings of the 31st Data Compression Conference, 2021

PFP Compressed Suffix Trees.

Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi

Proceedings of the Symposium on Algorithm Engineering and Experiments, 2021

2020

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data.

Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E. Belk, Noelle R. Noyes, Paul S. Morley

Nucleic Acids Res., 2020

Matching Reads to Many Genomes with the r-Index.

Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini

J. Comput. Biol., 2020

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.

Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini

J. Comput. Biol., 2020

PFP Data Structures.

Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi

CoRR, 2020

Fast and accurate correction of optical mapping data via spaced seeds.

Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Bioinform., 2020

Portable nanopore analytics: are we there yet?

Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol

Bioinform., 2020

2019

Aligning optical maps to de Bruijn graphs.

Kingshuk Mukherjee, Bahar Alipanahi, Tamer Kahveci, Leena Salmela, Christina Boucher

Bioinform., 2019

Building large updatable colored de Bruijn graphs via merging.

Martin D. Muggli, Bahar Alipanahi, Christina Boucher

Bioinform., 2019

Kohdista: an efficient method to index and query possible Rmap alignments.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Algorithms Mol. Biol., 2019

Prefix-free parsing for building big BWTs.

Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun

Algorithms Mol. Biol., 2019

Co-evolving Patterns in Temporal Networks of Varying Evolution.

Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Counting motifs in dynamic networks.

Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci

BMC Syst. Biol., 2018

Practical dynamic de Bruijn graphs.

Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie

Bioinform., 2018

A Succinct Solution to Rmap Alignment.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Prefix-Free Parsing for Building Big BWTs.

Christina Boucher, Travis Gagie, Alan Kuhnle, Giovanni Manzini

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Recoloring the Colored de Bruijn Graph.

Bahar Alipanahi, Alan Kuhnle, Christina Boucher

Proceedings of the String Processing and Information Retrieval, 2018

Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept.

Franco Milicchio, Marco Oliva, Christina Boucher, Mattia Prosperi

Proceedings of the 15th International Conference on Mobile Systems and Pervasive Computing (MobiSPC 2018) / The 13th International Conference on Future Networks and Communications (FNC-2018) / Affiliated Workshops, 2018

Identification of Co-evolving Temporal Networks.

Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

MEGARes: an antimicrobial resistance database for high throughput sequencing.

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

Nucleic Acids Res., 2017

Succinct colored de Bruijn graphs.

Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher

Bioinform., 2017

Disentangled Long-Read De Bruijn Graphs via Optical Maps.

Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016

Exploring Non-touchscreen Gestures for Smartwatches.

Shaikh Shawon Arefin Shimon, Courtney Lutton, Zichun Xu, Sarah Morrison-Smith, Christina Boucher, Jaime Ruiz

Proceedings of the 2016 CHI Conference on Human Factors in Computing Systems, 2016

2015

The Generating Function Approach for Peptide Identification in Spectral Networks.

Adrian Guthals, Christina Boucher, Nuno Bandeira

J. Comput. Biol., 2015

Misassembly detection using paired-end sequence reads and optical mapping data.

Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher

Bioinform., 2015

Relative Select.

Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2015

Consensus Patterns (Probably) Has no EPTAS.

Christina Boucher, Christine Lo, Daniel Lokshtanov

Proceedings of the Algorithms - ESA 2015, 2015

Variable-Order de Bruijn Graphs.

Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane

Proceedings of the 2015 Data Compression Conference, 2015

Elucidating the role and use of bioinformatics software in life science research.

Sarah Morrison-Smith, Christina Boucher, Andrea Bunt, Jaime Ruiz

Proceedings of the 2015 British HCI Conference, Lincoln, United Kingdom, July 13-17, 2015, 2015

Fast and efficient compression of high-throughput sequencing reads.

Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers.

Christine Lo, Boyko Kakaradov, Daniel Lokshtanov, Christina Boucher

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly.

Seyed Basir Shariat Razavi, Narjes Sadat Movahedi Tabrizi, Hamidreza Chitsaz, Christina Boucher

CoRR, 2014

Efficient Indexed Alignment of Contigs to Optical Maps.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013

On approximating string selection problems with outliers.

Christina Boucher, Gad M. Landau, Avivit Levy, David Pritchard, Oren Weimann

Theor. Comput. Sci., 2013

SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq.

Mark F. Rogers, Christina Boucher, Asa Ben-Hur

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

On the Hardness of Counting and Sampling Center Strings.

Christina Boucher, Mohamed Omar

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

SEQuel: improving the accuracy of genome assemblies.

Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner

Bioinform., 2012

2011

Outlier Detection for DNA Fragment Assembly

Christina Boucher, Christine Lo, Daniel Lokshtanov

CoRR, 2011

Closest string with outliers.

Christina Boucher, Bin Ma

BMC Bioinform., 2011

The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity.

Christina Boucher

Proceedings of the Mathematical Foundations of Computer Science 2011, 2011

2010

Combinatorial and Probabilistic Approaches to Motif Recognition.

Christina Anne Boucher

PhD thesis, 2010

Fast motif recognition via application of statistical thresholds.

Christina Boucher, James King

BMC Bioinform., 2010

Why Large Closest String Instances Are Easy to Solve in Practice.

Christina Boucher, Kathleen P. Wilkie

Proceedings of the String Processing and Information Retrieval, 2010

2009

Faster Algorithms for Sampling and Counting Biological Sequences.

Christina Boucher

Proceedings of the String Processing and Information Retrieval, 2009

Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding.

Christina Boucher, Daniel G. Brown

Proceedings of the Bioinformatics and Computational Biology, 2009

2008

On the Structure of Small Motif Recognition Instances.

Christina Boucher, Daniel G. Brown, Stephane Durocher

Proceedings of the String Processing and Information Retrieval, 2008

2007

A Graph Clustering Approach to Weak Motif Recognition.

Christina Boucher, Daniel G. Brown, Paul Church

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

An Ant Colony Optimization Heuristic for the Combinatorial Auction Problem.

Maja Omanovic, Christina Boucher

Proceedings of the 2007 International Conference on Artificial Intelligence, 2007

A Graphical Game Model of Drug Binding.

Christina Boucher, Maja Omanovic

Proceedings of the 2007 International Conference on Artificial Intelligence, 2007