Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

Genome Evolution of Filamentous Cyanobacterium Nostoc Species: From Facultative Symbiosis to Free Living

(2021) Da Huo et al.   Microorganisms

Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

(2021) Yuu Hirose et al.   DNA RESEARCH

Deterministic Lateral Displacement: Challenges and Perspectives

(2020) Axel Hochstetter et al.   ACS Nano

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

(2020) Sidney P. Walker et al.   Scientific Reports

Limits of Life and the Habitability of Mars: The ESA Space Experiment BIOMEX on the ISS

(2019) Jean-Pierre de Vera et al.   ASTROBIOLOGY

Whole genome amplification of single epithelial cells dissociated from snap-frozen tissue samples in microfluidic platform

(2019) Yuguang Liu et al.   Biomicrofluidics

Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity

(2019) Yuguang Liu et al.   ANALYTICAL CHEMISTRY

ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data

(2019) Andrew J. Low et al.   PeerJ

Removing contaminants from databases of draft genomes

(2018) Jennifer Lu et al.   PLoS Computational Biology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms

(2018) Yuguang Liu et al.   Micromachines

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

(2017) Cedric C. Laczny et al.   NUCLEIC ACIDS RESEARCH

High-throughput automated microfluidic sample preparation for accurate microbial genomics

(2017) Soohong Kim et al.   Nature Communications

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics

(2017) Masahito Hosokawa et al.   Scientific Reports

Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

(2017) Nathan D. Olson et al.   PeerJ

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission

(2017) Kaisa Koskinen et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis

(2016) Maria Hammond et al.   Microbiome

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

(2014) Justin Chu et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents

(2014) S Motley et al.   BMC GENOMICS

Deterministic lateral displacement for particle separation: a review

(2014) J. McGrath et al.   LAB ON A CHIP

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

A review of the theory, methods and recent applications of high-throughput single-cell droplet microfluidics

(2013) Todd P Lagus et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Malassezia Fungi Are Specialized to Live on Skin and Associated with Dandruff, Eczema, and Other Skin Diseases

(2012) Charles W. Saunders et al.   PLoS Pathogens

Microfluidic Platforms for Single-Cell Analysis

(2010) Richard N. Zare et al.   Annual Review of Biomedical Engineering

Raman Spectroscopic Analysis of a Desert Cyanobacterium Nostoc sp. in Response to UVB Radiation

(2010) Gaohong Wang et al.   ASTROBIOLOGY

Bacillus oceanisediminis sp. nov., isolated from marine sediment

(2010) J. Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Digital MDA for enumeration of total nucleic acid contamination

(2010) P. C. Blainey et al.   NUCLEIC ACIDS RESEARCH

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal

Droplet microfluidics

(2008) Shia-Yen Teh et al.   LAB ON A CHIP