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2020
APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments
Systematic Biology
2020
Fast Approximation of Frequent k-Mers and Applications to Metagenomics
Journal of Computational Biology
2020
Comparison of microbiome samples: methods and computational challenges
Briefings in Bioinformatics
2020
A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas
Frontiers in Microbiology
2020
A resource-frugal probabilistic dictionary and applications in bioinformatics
Discrete Applied Mathematics
2020
Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system
Environment International
2020
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
Molecular Ecology
2020
Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach
Scientific Reports
2019
Libra: scalablek-mer–based tool for massive all-vs-all metagenome comparisons
GigaScience
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
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
BMC Bioinformatics
2019
Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
Microbiome
2019
SimkaMin: fast and resource frugal de novo comparative metagenomics
Bioinformatics
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
Lecture Notes in Computer Science
2019
2019 15th International Conference on eScience (eScience)
2019
Streaming histogram sketching for rapid microbiome analytics
Microbiome
2019
Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics
Frontiers in Microbiology
2019
Skmer: assembly-free and alignment-free sample identification using genome skims
Genome Biology
2018
Proceedings of the 9th Workshop on Scientific Cloud Computing - ScienceCloud'18
2018
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
Bioinformatics
2018
Precise and Parallel Pairwise Metagenomic Comparisons
Journal of Computational Biology
2018
Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome
Parasites & Vectors
2018
Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures
Frontiers in Microbiology
2018
Alignment-Free Sequence Analysis and Applications
Annual Review of Biomedical Data Science
2018
A Data Adaptive Biological Sequence Representation for Supervised Learning
Journal of Healthcare Informatics Research
2018
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
Bioinformatics
2017
Lecture Notes in Computer Science
2017
Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector
Science Advances
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