A Graphical Game Model of Drug Binding. - Christina Boucher 001; Maja Omanovic (IC-AI, 2007)

An Ant Colony Optimization Heuristic for the Combinatorial Auction Problem. - Maja Omanovic; Christina Boucher 001 (IC-AI, 2007)

A Graph Clustering Approach to Weak Motif Recognition. - Christina Boucher 001; Daniel G. Brown 001; Paul Church (WABI, 2007)

On the Structure of Small Motif Recognition Instances. - Christina Boucher 001; Daniel G. Brown 001; Stephane Durocher (SPIRE, 2008)

Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding. - Christina Boucher 001; Daniel G. Brown 001 (BICoB, 2009)

Faster Algorithms for Sampling and Counting Biological Sequences. - Christina Boucher 001 (SPIRE, 2009)

Why Large Closest String Instances Are Easy to Solve in Practice. - Christina Boucher 001; Kathleen P. Wilkie (SPIRE, 2010)

Fast motif recognition via application of statistical thresholds. - Christina Boucher 001; James King 001 (BMC Bioinform., 2010)

Combinatorial and Probabilistic Approaches to Motif Recognition. - Christina Anne Boucher (2010)

The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity. - Christina Boucher 001 (MFCS, 2011)

Closest string with outliers. - Christina Boucher 001; Bin Ma 002 (BMC Bioinform., 2011)

Outlier Detection for DNA Fragment Assembly - Christina Boucher 001; Christine Lo; Daniel Lokshtanov (CoRR, 2011)

SEQuel: improving the accuracy of genome assemblies. - Roy Ronen; Christina Boucher 001; Hamidreza Chitsaz; Pavel A. Pevzner (Bioinform., 2012)

On the Hardness of Counting and Sampling Center Strings. - Christina Boucher 001; Mohamed Omar (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. - Mark F. Rogers; Christina Boucher 001; Asa Ben-Hur (BCB, 2013)

On approximating string selection problems with outliers. - Christina Boucher 001; Gad M. Landau; Avivit Levy; David Pritchard 001; Oren Weimann (Theor. Comput. Sci., 2013)

Efficient Indexed Alignment of Contigs to Optical Maps. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 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 001 (CoRR, 2014)

SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers. - Christine Lo; Boyko Kakaradov; Daniel Lokshtanov; Christina Boucher 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Fast and efficient compression of high-throughput sequencing reads. - Christopher Hoobin; Trey Kind; Christina Boucher 001; Simon J. Puglisi (BCB, 2015)

Elucidating the role and use of bioinformatics software in life science research. - Sarah Morrison-Smith; Christina Boucher 001; Andrea Bunt; Jaime Ruiz (BCS HCI, 2015)

Variable-Order de Bruijn Graphs. - Christina Boucher 001; Alexander Bowe; Travis Gagie; Simon J. Puglisi; Kunihiko Sadakane (DCC, 2015)

Consensus Patterns (Probably) Has no EPTAS. - Christina Boucher 001; Christine Lo; Daniel Lokshtanov (ESA, 2015)

Relative Select. - Christina Boucher 001; Alexander Bowe; Travis Gagie; Giovanni Manzini; Jouni Sirén (SPIRE, 2015)

Misassembly detection using paired-end sequence reads and optical mapping data. - Martin D. Muggli; Simon J. Puglisi; Roy Ronen; Christina Boucher 001 (Bioinform., 2015)

The Generating Function Approach for Peptide Identification in Spectral Networks. - Adrian Guthals; Christina Boucher 001; Nuno Bandeira (J. Comput. Biol., 2015)

Exploring Non-touchscreen Gestures for Smartwatches. - Shaikh Shawon Arefin Shimon; Courtney Lutton; Zichun Xu; Sarah Morrison-Smith; Christina Boucher 001; Jaime Ruiz (CHI, 2016)

Disentangled Long-Read De Bruijn Graphs via Optical Maps. - Bahar Alipanahi; Leena Salmela; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (WABI, 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 001 (Bioinform., 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; et al. (Nucleic Acids Res., 2017)

Identification of Co-evolving Temporal Networks. - Rasha Elhesha; Aisharjya Sarkar; Christina Boucher 001; Tamer Kahveci (BCB, 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 001; Mattia Prosperi (FNC/MobiSPC, 2018)

Recoloring the Colored de Bruijn Graph. - Bahar Alipanahi; Alan Kuhnle; Christina Boucher 001 (SPIRE, 2018)

Prefix-Free Parsing for Building Big BWTs. - Christina Boucher 001; Travis Gagie; Alan Kuhnle; Giovanni Manzini (WABI, 2018)

A Succinct Solution to Rmap Alignment. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 2018)

Practical dynamic de Bruijn graphs. - Victoria G. Crawford; Alan Kuhnle; Christina Boucher 001; Rayan Chikhi; Travis Gagie (Bioinform., 2018)

Counting motifs in dynamic networks. - Kingshuk Mukherjee; Md Mahmudul Hasan; Christina Boucher 001; Tamer Kahveci (BMC Syst. Biol., 2018)

Co-evolving Patterns in Temporal Networks of Varying Evolution. - Rasha Elhesha; Aisharjya Sarkar; Pietro Cinaglia; Christina Boucher 001; Tamer Kahveci (BCB, 2019)

Prefix-free parsing for building big BWTs. - Christina Boucher 001; Travis Gagie; Alan Kuhnle; Ben Langmead; Giovanni Manzini; Taher Mun (Algorithms Mol. Biol., 2019)

Kohdista: an efficient method to index and query possible Rmap alignments. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (Algorithms Mol. Biol., 2019)

Building large updatable colored de Bruijn graphs via merging. - Martin D. Muggli; Bahar Alipanahi; Christina Boucher 001 (Bioinform., 2019)

Aligning optical maps to de Bruijn graphs. - Kingshuk Mukherjee; Bahar Alipanahi; Tamer Kahveci; Leena Salmela; Christina Boucher 001 (Bioinform., 2019)

Portable nanopore analytics: are we there yet? - Marco Oliva; Franco Milicchio; Kaden King; Grace Benson; Christina Boucher 001; Mattia Prosperi; Inanç Birol (Bioinform., 2020)

Fast and accurate correction of optical mapping data via spaced seeds. - Leena Salmela; Kingshuk Mukherjee; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (Bioinform., 2020)

PFP Data Structures. - Christina Boucher 001; Ondrej Cvacho; Travis Gagie; Jan Holub 001; Giovanni Manzini; Gonzalo Navarro 001; Massimiliano Rossi 001 (CoRR, 2020)

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. - Alan Kuhnle; Taher Mun; Christina Boucher 001; Travis Gagie; Ben Langmead; Giovanni Manzini (J. Comput. Biol., 2020)

Matching Reads to Many Genomes with the r-Index. - Taher Mun; Alan Kuhnle; Christina Boucher 001; Travis Gagie; Ben Langmead; Giovanni Manzini (J. Comput. Biol., 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 001; Keith E. Belk; Noelle R. Noyes; Paul S. Morley (Nucleic Acids Res., 2020)

PFP Compressed Suffix Trees. - Christina Boucher 001; Ondrej Cvacho; Travis Gagie; Jan Holub 001; Giovanni Manzini; Gonzalo Navarro 001; Massimiliano Rossi 001 (ALENEX, 2021)

PHONI: Streamed Matching Statistics with Multi-Genome References. - Christina Boucher 001; Travis Gagie; Tomohiro I; Dominik Köppl; Ben Langmead; Giovanni Manzini; Gonzalo Navarro 001; Alejandro Pacheco; Massimiliano Rossi 001 (DCC, 2021)

Efficiently Merging r-indexes. - Marco Oliva; Massimiliano Rossi 001; Jouni Sirén; Giovanni Manzini; Tamer Kahveci; Travis Gagie; Christina Boucher 001 (DCC, 2021)

Computing the Original eBWT Faster, Simpler, and with Less Memory. - Christina Boucher 001; Davide Cenzato; Zsuzsanna Lipták; Massimiliano Rossi 001; Marinella Sciortino (SPIRE, 2021)

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. - Kingshuk Mukherjee; Massimiliano Rossi 001; Leena Salmela; Christina Boucher 001 (Algorithms Mol. Biol., 2021)

Metagenome SNP calling via read-colored de Bruijn graphs. - Bahar Alipanahi; Martin D. Muggli; Musa Jundi; Noelle R. Noyes; Christina Boucher 001 (Bioinform., 2021)

Fast and exact quantification of motif occurrences in biological sequences. - Mattia Prosperi; Simone Marini; Christina Boucher 001 (BMC Bioinform., 2021)

Succinct dynamic de Bruijn graphs. - Bahar Alipanahi; Alan Kuhnle; Simon J. Puglisi; Leena Salmela; Christina Boucher 001 (Bioinform., 2021)

CSTs for Terabyte-Sized Data. - Marco Oliva; Davide Cenzato; Massimiliano Rossi 001; Zsuzsanna Lipták; Travis Gagie; Christina Boucher 001 (DCC, 2022)

Building scalable indexes that can be efficiently queried. - Christina Boucher 001 (IPDPS Workshops, 2022)

Accessing the Suffix Array via φ -1-Forest. - Christina Boucher 001; Dominik Köppl; Herman Perera; Massimiliano Rossi 001 (SPIRE, 2022)

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. - Mattia Prosperi; Christina Boucher 001; Jiang Bian 001; Simone Marini (Artif. Intell. Medicine, 2022)

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. - Simone Marini; Rodrigo A. Mora; Christina Boucher 001; Noelle Robertson Noyes; Mattia Prosperi (Briefings Bioinform., 2022)

Syotti: scalable bait design for DNA enrichment. - Jarno N. Alanko; Ilya B. Slizovskiy; Daniel Lokshtanov; Travis Gagie; Noelle R. Noyes; Christina Boucher 001 (Bioinform., 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 001; J. Glenn Morris; Jiang Bian 001; Mattia Prosperi (CoRR, 2022)

Finding Maximal Exact Matches Using the r-Index. - Massimiliano Rossi 001; Marco Oliva; Paola Bonizzoni; Ben Langmead; Travis Gagie; Christina Boucher 001 (J. Comput. Biol., 2022)

MONI: A Pangenomic Index for Finding Maximal Exact Matches. - Massimiliano Rossi 001; Marco Oliva; Ben Langmead; Travis Gagie; Christina Boucher 001 (J. Comput. Biol., 2022)

Computational graph pangenomics: a tutorial on data structures and their applications. - Jasmijn A. Baaijens; Paola Bonizzoni; Christina Boucher 001; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Jouni Sirén (Nat. Comput., 2022)

Finding Overlapping Rmaps via Clustering. - Kingshuk Mukherjee; Daniel Dole-Muinos; Massimiliano Rossi 001; Ayomide Ajayi; Mattia Prosperi; Christina Boucher 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

LZ77 via Prefix-Free Parsing. - Aaron Hong; Massimiliano Rossi 001; Christina Boucher 001 (ALENEX, 2023)

Recursive Prefix-Free Parsing for Building Big BWTs. - Marco Oliva; Travis Gagie; Christina Boucher 001 (DCC, 2023)

Data Structures for SMEM-Finding in the PBWT. - Paola Bonizzoni; Christina Boucher 001; Davide Cozzi; Travis Gagie; Dominik Köppl; Massimiliano Rossi 001 (SPIRE, 2023)

Acceleration of FM-Index Queries Through Prefix-Free Parsing. - Aaron Hong; Marco Oliva; Dominik Köppl; Hideo Bannai; Christina Boucher 001; Travis Gagie (WABI, 2023)

Special Issue: Algorithms in Bioinformatics. - Christina Boucher 001 (Algorithms, 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 001 (Nucleic Acids Res., 2023)

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. - Davide Cozzi; Massimiliano Rossi 001; Simone Rubinacci; Travis Gagie; Dominik Köppl; Christina Boucher 001; Paola Bonizzoni (Bioinform., 2023)

Solving the Minimal Positional Substring Cover Problem in Sublinear Space. - Paola Bonizzoni; Christina Boucher 001; Davide Cozzi; Travis Gagie; Yuri Pirola (CPM, 2024)

Another virtue of wavelet forests. - Aaron Hong; Christina Boucher 001; Travis Gagie; Yansong Li; Norbert Zeh (DCC, 2024)

Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage. - Justin Kim; Rahul Varki; Marco Oliva; Christina Boucher 001 (ESA, 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 001 (ICHI, 2024)

Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. - Michael Aaron G. Sy; Mattia Prosperi; Mohammadali Serajian; Christina Boucher 001; Panayotis Takis Benos; Simone Marini (MIE, 2024)

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis. - Mohammadali Serajian; Simone Marini; Jarno N. Alanko; Noelle R. Noyes; Mattia Prosperi; Christina Boucher 001 (Bioinform., 2024)

The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices. - Carson Stillman; Jonathan E. Bravo; Christina Boucher 001; Sara Rampazzi (CoRR, 2024)

r-indexing the eBWT. - Christina Boucher 001; Davide Cenzato; Zsuzsanna Lipták; Massimiliano Rossi 001; Marinella Sciortino (Inf. Comput., 2024)

Pfp-fm: an accelerated FM-index. - Aaron Hong; Marco Oliva; Dominik Köppl; Hideo Bannai; Christina Boucher 001; Travis Gagie (Algorithms Mol. Biol., 2024)

Comparative Evaluation of Clinical Large Language Models and Machine Learning to Predict Antimicrobial Resistance in Hospital-Onset Sepsis. - Scott A. Cohen; Ziyi Chen; Jiang Bian 001; Christina Boucher 001; Yonghui Wu; Mattia Prosperi (AIME (1), 2025)

Phasing Data from Genotype Queries via the μ-PBWT. - Davide Cozzi; Paola Bonizzoni; Christina Boucher 001; Ben Langmead; Yuri Pirola (The Expanding World of Compressed Data, 2025)

Optimizing the Performance of the FM-Index for Large-Scale Data. - Eddie Ferro; Christina Boucher 001 (The Expanding World of Compressed Data, 2025)

Devider: Long-Read Reconstruction of Many Diverse Haplotypes. - Jim Shaw; Christina Boucher 001; Yun William Yu; Noelle R. Noyes; Heng Li (RECOMB, 2025)

Recursive Parsing and Grammar Compression in the Era of Pangenomics (Invited Talk). - Christina Boucher 001 (WABI, 2025)

Formal verification of bioinformatics software using model checking and theorem proving. - Hansika Weerasena; Aruna Jayasena; Christina Boucher 001; Prabhat Mishra 001 (Briefings Bioinform., 2025)

Enhancing Data Compression: Recent Innovations in LZ77 Algorithms. - Aaron Hong; Christina Boucher 001 (J. Comput. Biol., 2025)

SDSL-Mobile: Enabling space-efficient data structures for mobile applications. - Alexander Barquero; Anisha Wadhwani; Tyler Pencinger; Aaron Hong; Jaime Ruiz; Mattia Prosperi; Christina Boucher 001 (SoftwareX, 2025)