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2025
Estimating similarity and distance using FracMinHash
Algorithms for Molecular Biology
2025
K-mer-based Approaches to Bridging Pangenomics and Population Genetics
Molecular Biology and Evolution
2025
k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species
Evolution Letters
2025
The influence of depth on the global deep-sea plasmidome
Scientific Reports
2025
Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments
The ISME Journal
2025
Fermentation of native Brazilian fruits with kombucha: A novel opportunity for producing low-alcohol beverages
Food Bioscience
2025
Fractional hitting sets for efficient multiset sketching
Algorithms for Molecular Biology
2024
Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes
Scientific Reports
2024
Back to sequences: Find the origin of k-mers
Journal of Open Source Software
2024
2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA)
2024
Metagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments
Water Research
2024
MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data
Bioinformatics Advances
2023
Plankton biogeography in the 21st century and impacts of climate change: advances through genomics
Comptes Rendus. Biologies
2023
Comparison of k-mer-based de novo comparative metagenomic tools and approaches
Microbiome Research Reports
2023
Decoding the DNA and RNA viromes of a tropical urban lagoon
Environmental Microbiology
2023
A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures
PLOS Computational Biology
2023
Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments
ISME Communications
2022
Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms
Water Research
2022
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis
Bioinformatics
2022
From Sequences to Graphs
2022
kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections
Bioinformatics Advances
2022
Low-dose IL-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation
JCI Insight
2022
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
Functional & Integrative Genomics
2022
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
Nature
2022
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics
mSystems
2022
Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems
eLife
2022
Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment
Journal of Hazardous Materials
2022
Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
Frontiers in Microbiology
2022
Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
Genes
2021
2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS)
2021
Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history
BMC Genomics
2021
Comparison of microbiome samples: methods and computational challenges
Briefings in Bioinformatics
2021
Lecture Notes in Computer Science
2021
Metagenomic Geolocation Prediction Using an Adaptive Ensemble Classifier
Frontiers in Genetics
2021
A rapid and simple method for assessing and representing genome sequence relatedness
Peer Community Journal
2020
SimkaMin: fast and resource frugal de novo comparative metagenomics
Bioinformatics
2020
Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach
Scientific Reports
2020
A resource-frugal probabilistic dictionary and applications in bioinformatics
Discrete Applied Mathematics
2020
APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments
Systematic Biology
2020
ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies
International Journal of Environmental Research and Public Health
2020
Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes
mSystems
2020
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
Molecular Ecology
2020
Fast Approximation of Frequentk-Mers and Applications to Metagenomics
Journal of Computational Biology
2020
Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability
FEMS Microbiology Ecology
2020
Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system
Environment International
2020
Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
mSystems
2020
A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas
Frontiers in Microbiology
2019
Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity
PLOS Computational Biology
2019
Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
Microbiome
2019
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
PLOS Computational Biology
2019
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
BMC Bioinformatics
2019
Streaming histogram sketching for rapid microbiome analytics
Microbiome
2019
2019 15th International Conference on eScience (eScience)
2019
Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics
Frontiers in Microbiology
2019
Libra: scalable k-mer–based tool for massive all-vs-all metagenome comparisons
GigaScience
2019
Skmer: assembly-free and alignment-free sample identification using genome skims
Genome Biology
2019
Lecture Notes in Computer Science
2019
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
BMC Bioinformatics
2018
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
Bioinformatics
2018
A Data Adaptive Biological Sequence Representation for Supervised Learning
Journal of Healthcare Informatics Research
2018
Proceedings of the 9th Workshop on Scientific Cloud Computing
2018
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
Bioinformatics
2018
Alignment-Free Sequence Analysis and Applications
Annual Review of Biomedical Data Science
2018
Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome
Parasites & Vectors
2018
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2018
Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures
Frontiers in Microbiology
2018
Precise and Parallel Pairwise Metagenomic Comparisons
Journal of Computational Biology
2017
Lecture Notes in Computer Science
2017
Lecture Notes in Computer Science
2017
A submarine volcanic eruption leads to a novel microbial habitat
Nature Ecology & Evolution
2017
Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector
Science Advances
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