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Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections

mSystems, 2022-10, Vol.7 (5), p.e0047622-e0047622

2022

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A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

IEEE/ACM transactions on computational biology and bioinformatics, 2009-04, Vol.6 (2), p.180-189

2009

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IEEE_Xplore

Repetitive DNA and next-generation sequencing: computational challenges and solutions

Nature reviews. Genetics, 2012-01, Vol.13 (1), p.36

2012

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Deep sequencing of the oral microbiome reveals signatures of periodontal disease

PloS one, 2012-06, Vol.7 (6), p.e37919

2012

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Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

PLoS genetics, 2011-01, Vol.7 (1), p.e1001284

2011

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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

Genome Biology, 2018-10, Vol.19 (1), p.165-165, Article 165

2018

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Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome

Frontiers in immunology, 2018-11, Vol.9, p.2757-2757

2018

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Current progress and open challenges for applying deep learning across the biosciences

Nature communications, 2022-04, Vol.13 (1), p.1728-1728, Article 1728

2022

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Mash: fast genome and metagenome distance estimation using MinHash

Genome Biology, 2016-06, Vol.17 (1), p.132-132, Article 132

2016

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Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities

Bioinformatics (Oxford, England), 2023-06, Vol.39 (Supplement_1), p.i47-i56

2023

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Multiple genome alignment in the telomere-to-telomere assembly era

Genome Biology, 2022-08, Vol.23 (1), p.1-182, Article 182

2022

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Bambus 2: scaffolding metagenomes

Bioinformatics, 2011-11, Vol.27 (21), p.2964-2971

2011

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Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1140-1150

2019

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GAGE: A critical evaluation of genome assemblies and assembly algorithms

Genome research, 2012-03, Vol.22 (3), p.557

2012

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MethPhaser: methylation-based long-read haplotype phasing of human genomes

Nature communications, 2024-06, Vol.15 (1), p.5327-12, Article 5327

2024

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Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data

Nature communications, 2022-03, Vol.13 (1), p.1321-1321, Article 1321

2022

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Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation

Bioinformatics (Oxford, England), 2023-09, Vol.39 (9)

2023

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Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data

Nature methods, 2022-07, Vol.19 (7), p.845

2022

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To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics

Nucleic acids research, 2020-06, Vol.48 (10), p.5217

2020

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The long game of tenure

Nature biotechnology, 2023-10, Vol.41 (10), p.1373-1374

2023

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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Genome biology, 2013-01, Vol.14 (1), p.R2-R2

2013

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PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

Nature communications, 2021-02, Vol.12 (1), p.1167-1167, Article 1167

2021

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Fecal Microbiota Transplantation Derived from Alzheimer's Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls

International journal of molecular sciences, 2022-04, Vol.23 (9), p.4476

2022

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Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

Nature communications, 2023-05, Vol.14 (1), p.2834-2834, Article 2834

2023

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Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater

Nature communications, 2024-05, Vol.15 (1), p.4545-4545, Article 4545

2024

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Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

Repetitive DNA and next-generation sequencing: computational challenges and solutions

Deep sequencing of the oral microbiome reveals signatures of periodontal disease

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome

Current progress and open challenges for applying deep learning across the biosciences

Mash: fast genome and metagenome distance estimation using MinHash

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities

Multiple genome alignment in the telomere-to-telomere assembly era

Bambus 2: scaffolding metagenomes

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

GAGE: A critical evaluation of genome assemblies and assembly algorithms

MethPhaser: methylation-based long-read haplotype phasing of human genomes

Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation

Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data

To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics

The long game of tenure

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

Fecal Microbiota Transplantation Derived from Alzheimer's Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls

Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater

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