C. Boucher

发表

On the Structure of Small Motif Recognition Instances

Christina Boucher, Stephane Durocher, Daniel G. Brown, 2008, SPIRE.

Resistome SNP Calling via Read Colored de Bruijn Graphs

Martin D. Muggli, C. Boucher, N. Noyes, 2017, bioRxiv.

Expected Approximation Guarantees for the Demand Matching Problem

C. Boucher, D. Loker, 2006 .

aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events

Daniel B. Sloan, A. Ben-Hur, C. Boucher, 2016, PloS one.

Succinct Colored de Bruijn Graphs

Christina Boucher, Simon J. Puglisi, Travis Gagie, 2016 .

Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going?

Christina Boucher, Vikas Bansal, V. Bansal, 2019, iScience.

Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

Christina Boucher, Hua Yang, Dale R. Woerner, 2016, Applied and Environmental Microbiology.

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

Hua Yang, Kenneth L Jones, Kenneth L. Jones, 2016, Scientific Reports.

Resistome diversity in cattle and the environment decreases during beef production

Hua Yang, Shaun Cook, Kenneth L Jones, 2016, eLife.

On the Hardness of Counting and Sampling Center Strings

Christina Boucher, Mohamed Omar, C. Boucher, 2012, TCBB.

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period

Steven M. Lakin, C. Boucher, C. Dean, 2018, Front. Microbiol..

Identification of co-evolving temporal networks

Tamer Kahveci, C. Boucher, Rasha Elhesha, 2018, BMC Genomics.

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

C. Boucher, C. Dean, I. Slizovskiy, 2020, Frontiers in Microbiology.

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

B. Langmead, C. Boucher, G. Manzini, 2020, Journal of computational biology : a journal of computational molecular cell biology.

Error correcting optical mapping data Mukherjee , Kingshuk 2018-0525

Martin D. Muggli, C. Boucher, Leena Salmela, 2022 .

CSTs for Terabyte-Sized Data

C. Boucher, Z. Lipták, T. Gagie, 2022, 2022 Data Compression Conference (DCC).

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

Tamer Kahveci, C. Boucher, I. Slizovskiy, 2022, GigaScience.

Prefix-free parsing for building big BWTs

B. Langmead, C. Boucher, G. Manzini, 2019, Algorithms for molecular biology : AMB.

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

C. Boucher, J. Morris, S. Marini, 2022, ArXiv.

SPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests

B. Langmead, C. Boucher, T. Gagie, 2022, bioRxiv.

Development of a Prediction Model for Antibiotic-Resistant Urinary Tract Infections Using Integrated Electronic Health Records from Multiple Clinics in North-Central Florida

C. Boucher, J. Morris, K. Cherabuddi, 2022, Infectious Diseases and Therapy.

Compressed Data Structures for Population-Scale Positional Burrows–Wheeler Transforms

P. Bonizzoni, C. Boucher, T. Gagie, 2022, bioRxiv.

Genome Sequence of Xanthomonas arboricola pv. Corylina, Isolated from Turkish Filbert in Colorado

C. Boucher, Marcelo M. Zerillo, N. Tisserat, 2013, Genome Announcements.

Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences.

Martin D. Muggli, Steven M. Lakin, C. Boucher, 2019 .

Sequence analysis Portable nanopore analytics: are we there yet?

C. Boucher, M. Prosperi, F. Milicchio, 2020 .

Development of a Prediction Model for Antibiotic-Resistant Urinary Tract Infections Using Integrated Electronic Health Records from Multiple Clinics in North-Central Florida

C. Boucher, J. Morris, K. Cherabuddi, 2022, Infectious Diseases and Therapy.

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

C. Boucher, I. Slizovskiy, N. Noyes, 2022, Microbiome.

The K-mer antibiotic resistance gene variant analyzer (KARGVA)

C. Boucher, N. Noyes, M. Prosperi, 2022, bioRxiv.

ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks

J. Kaufman, C. Boucher, Ed Seabolt, 2022, Frontiers in Genetics.

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

P. Bonizzoni, C. Boucher, G. Della Vedova, 2022, Natural Computing.

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

C. Boucher, N. Noyes, E. Doster, 2022, Nucleic Acids Res..

Finding Overlapping Rmaps via Clustering

C. Boucher, M. Prosperi, Kingshuk Mukherjee, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Closest string with outliers

Bin Ma, Christina Boucher, B. Ma, 2011, BMC Bioinformatics.

Practical dynamic de Bruijn graphs

Christina Boucher, Travis Gagie, Rayan Chikhi, 2018, Bioinform..

Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains

C. Boucher, J. Morris, M. Prosperi, 2019, Applied and Environmental Microbiology.

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

Steven M. Lakin, Kenneth L. Jones, C. Boucher, 2017, Microbiome.

MEGARes: an antimicrobial resistance database for high throughput sequencing

Christina Boucher, Anne Spencer Ross, Jaime Ruiz, 2016, Nucleic Acids Res..

Succinct Colored de Bruijn Graphs

Christina Boucher, Simon J. Puglisi, Travis Gagie, 2016, bioRxiv.

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

Christina Boucher, Travis Gagie, Giovanni Manzini, 2018, bioRxiv.

Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

C. Boucher, N. Price, J. McKay, 2020, bioRxiv.

SEQuel: improving the accuracy of genome assemblies

Hamidreza Chitsaz, Christina Boucher, Pavel A. Pevzner, 2012, Bioinform..

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

Christina Boucher, Keith E. Belk, Christopher J. Dean, 2019, Nucleic Acids Res..

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Christina Boucher, Olivier Gascuel, Guy Baele, 2020, Proceedings of the National Academy of Sciences.

Data structures based on k-mers for querying large collections of sequencing data sets

Christina Boucher, Simon J. Puglisi, Paul Medvedev, 2019, bioRxiv.

Combinatorial and Probabilistic Approaches to Motif Recognition

Christina Anne Boucher, C. Boucher, 2010 .

Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems

Steven M. Lakin, C. Boucher, N. Noyes, 2019, Front. Microbiol..

Buffering updates enables efficient dynamic de Bruijn graphs

C. Boucher, T. Gagie, B. Alipanahi, 2021, bioRxiv.

Variable-Order de Bruijn Graphs

Christina Boucher, Kunihiko Sadakane, Simon J. Puglisi, 2014, 2015 Data Compression Conference.

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

Christina Boucher, Leena Salmela, Kingshuk Mukherjee, 2021, WABI.

Fast and accurate correction of optical mapping data via spaced seeds

Christina Boucher, Simon J Puglisi, Leena Salmela, 2019, Bioinformatics.

Aligning optical maps to de Bruijn graphs

Christina Boucher, Tamer Kahveci, Bahar Alipanahi, 2019, Bioinform..

Error correcting optical mapping data

Christina Boucher, Leena Salmela, Kingshuk Mukherjee, 2018, bioRxiv.

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

Christina Boucher, Simon J. Puglisi, Roy Ronen, 2014, Bioinform..

Efficient Indexed Alignment of Contigs to Optical Maps

Christina Boucher, Simon J. Puglisi, Martin D. Muggli, 2014, WABI.

Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

C. Boucher, M. Prosperi, Kingshuk Mukherjee, 2021, bioRxiv.

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

Christina Boucher, Simon J. Puglisi, Martin D. Muggli, 2019, Algorithms for Molecular Biology.

A Succinct Solution to Rmap Alignment

Christina Boucher, Simon J. Puglisi, Martin D. Muggli, 2018, WABI.

Disentangled Long-Read De Bruijn Graphs via Optical Maps

Christina Boucher, Simon J. Puglisi, Bahar Alipanahi, 2016, bioRxiv.

Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing

C. Boucher, T. Gagie, Marco Oliva, 2023, bioRxiv.

The SLOW GROWTH3 Pentatricopeptide Repeat Protein Is Required for the Splicing of Mitochondrial NADH Dehydrogenase Subunit7 Intron 2 in Arabidopsis1[OPEN]

C. Boucher, T. Harrison, M. Hsieh, 2015, Plant Physiology.

KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing

C. Boucher, M. Prosperi, Jaime Ruiz, 2022, Frontiers in Bioengineering and Biotechnology.

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

C. Boucher, N. Noyes, M. Prosperi, 2021, bioRxiv.

Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation

C. Boucher, M. Prosperi, I. Slizovskiy, 2021, Frontiers in Genetics.

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

P. Bonizzoni, G. D. Vedova, C. Boucher, 2022, Nat. Comput..

Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences

Martin D. Muggli, Steven M. Lakin, C. Boucher, 2019, Communications Biology.

μ-PBWT: Enabling the Storage and Use of UK Biobank Data on a Commodity Laptop

P. Bonizzoni, C. Boucher, D. Köppl, 2023, bioRxiv.

A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification

C. Boucher, N. Noyes, E. Doster, 2019, Front. Microbiol..

The Generating Function Approach for Peptide Identification in Spectral Networks

Christina Boucher, Nuno Bandeira, Adrian Guthals, 2014, RECOMB.

Co-evolving Patterns in Temporal Networks of Varying Evolution

Christina Boucher, Tamer Kahveci, Pietro Cinaglia, 2019, BCB.

Identification of co-evolving temporal networks

Tamer Kahveci, C. Boucher, Rasha Elhesha, 2018, bioRxiv.

Counting motifs in dynamic networks

Christina Boucher, Tamer Kahveci, Md Mahmudul Hasan, 2018, BMC Systems Biology.

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

C. Boucher, P. McDermott, Shaohua Zhao, 2022, bioRxiv.

Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina

C. Boucher, Marcelo M. Zerillo, N. Tisserat, 2014, Genome Announcements.

MONI: A Pangenomics Index for Finding MEMs

B. Langmead, C. Boucher, T. Gagie, 2021, bioRxiv.

Computing the original eBWT faster, simpler, and with less memory pdf

Christina Boucher, Marinella Sciortino, Massimiliano Rossi, 2021, SPIRE.

Efficiently Merging r-indexes

Christina Boucher, Tamer Kahveci, Travis Gagie, 2021, 2021 Data Compression Conference (DCC).

PFP Compressed Suffix Trees

Christina Boucher, Gonzalo Navarro, Jan Holub, 2021, ALENEX.

PFP Data Structures pdf

Christina Boucher, Gonzalo Navarro, Travis Gagie, 2020, ArXiv.

Building large updatable colored de Bruijn graphs via merging

Christina Boucher, Bahar Alipanahi, Martin D. Muggli, 2019, Bioinform..

Succinct De Bruijn Graph Construction for Massive Populations Through Space-Efficient Merging

Christina Boucher, Martin D. Muggli, C. Boucher, 2017, bioRxiv.

Challenges in large-scale bioinformatics projects

C. Boucher, Aleksandra Sarcevic, N. Noyes, 2022, Humanities and Social Sciences Communications.

Challenges in large-scale bioinformatics projects

C. Boucher, Aleksandra Sarcevic, N. Noyes, 2022, Humanities and Social Sciences Communications.

Pan-genomic matching statistics for targeted nanopore sequencing

M. Schatz, B. Langmead, C. Boucher, 2021, bioRxiv.

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

Andrea Bunt, Christina Boucher, Sarah Morrison-Smith, 2015, BCS HCI.

Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species

C. Boucher, M. Löchelt, S. Vandewoude, 2017, Journal of Clinical Microbiology.

MONI: A Pangenomic Index for Finding Maximal Exact Matches

B. Langmead, C. Boucher, T. Gagie, 2022, J. Comput. Biol..

PHONI: Streamed Matching Statistics with Multi-Genome References pdf

Christina Boucher, Gonzalo Navarro, Travis Gagie, 2020, 2021 Data Compression Conference (DCC).

Outlier Detection for DNA Fragment Assembly pdf

Christina Boucher, Daniel Lokshtanov, Christine Lo, 2011, ArXiv.

Propensity score synthetic augmentation matching using generative adversarial networks (PSSAM-GAN)

C. Boucher, J. Bian, Shantanu Ghosh, 2021, Computer methods and programs in biomedicine update.

SPUMONI 2: improved classification using a pangenome index of minimizer digests

B. Langmead, C. Boucher, T. Gagie, 2023, Genome Biology.

Exploring Non-touchscreen Gestures for Smartwatches

Christina Boucher, Sarah Morrison-Smith, Jaime Ruiz, 2016, CHI.

Fast and accurate correction of optical mapping data via spaced seeds

Martin D. Muggli, C. Boucher, S. Puglisi, 2020, Bioinform..

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

Martin D. Muggli, C. Boucher, S. Puglisi, 2019, Algorithms for Molecular Biology.

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, 2018, FNC/MobiSPC.

Prefix-free parsing for building big BWTs pdf

Travis Gagie, Giovanni Manzini, B. Langmead, 2018, Algorithms for Molecular Biology.

Metagenome SNP calling via read-colored de Bruijn graphs

Christina Boucher, Bahar Alipanahi, Martin D. Muggli, 2020, Bioinform..

Fast and exact quantification of motif occurrences in biological sequences

Christina Boucher, Simone Marini, Mattia C. F. Prosperi, 2021, BMC Bioinformatics.

Portable nanopore analytics: are we there yet?

Marco Oliva, Kaden King, Grace Benson, 2020, Bioinform..

Succinct Dynamic de Bruijn Graphs

Christina Boucher, Simon J. Puglisi, Bahar Alipanahi, 2020, bioRxiv.

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

Christina Boucher, Jiang Bian, Simone Marini, 2021, Artif. Intell. Medicine.

SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq

Christina Boucher, Asa Ben-Hur, Mark F. Rogers, 2013, BCB.

SeeSite: Efficiently Finding Co-occurring Splice Sites and Exon Splicing Enhancers

Christina Boucher, Daniel Lokshtanov, Christine Lo, 2012, 1206.5846.

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

Zaid Abdo, Keith E. Belk, Noelle R. Noyes, 2017, Microbiome.

Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences

Christina Boucher, Zaid Abdo, Bahar Alipanahi, 2019, Communications Biology.

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly

Hamidreza Chitsaz, Christina Boucher, Seyed Basir Shariat Razavi, 2014, BMC Genomics.

r-Indexing the eBWT

Christina Boucher, Marinella Sciortino, Zsuzsanna Lipták, 2021, SPIRE.

Consensus Patterns (Probably) Has no EPTAS

Christina Boucher, Daniel Lokshtanov, Christine Lo, 2015, ESA.