Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

(2019) Henrik Krehenwinkel et al.   GigaScience

NanoPipe—a web server for nanopore MinION sequencing data analysis

(2019) Victoria Shabardina et al.   GigaScience

Multiplex PCR targeting lineage specific SNP s ‐ A highly efficient and simple approach to block out predator sequences in molecular gut content analysis

(2019) Henrik Krehenwinkel et al.   Methods in Ecology and Evolution

High-Fidelity Nanopore Sequencing of Ultra-Short DNA Targets

(2019) Brandon D. Wilson et al.   ANALYTICAL CHEMISTRY

A 3D-printed hand-powered centrifuge for molecular biology

(2019) Gaurav Byagathvalli et al.   PLOS BIOLOGY

Playing a long game

(2019) Michael Eisenstein   NATURE METHODS

A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field

(2019) Maestri et al.   Genes

Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)

(2019) Deshpande et al.   Genes

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

(2019) Alexander M Piper et al.   GigaScience

Genomic biosurveillance of forest invasive alien enemies: A story written in code

(2019) Richard C. Hamelin et al.   Evolutionary Applications

Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

(2019) Ned Peel et al.   Methods in Ecology and Evolution

Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria

(2019) Harrison S. Edwards et al.   Scientific Reports

A Sequel to Sanger: amplicon sequencing that scales

(2018) Paul D. N. Hebert et al.   BMC GENOMICS

Phylogenetic scale in ecology and evolution

(2018) Catherine H. Graham et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing

(2018) Wendy Y. Wang et al.   Molecular Ecology Resources

A MinION™-based pipeline for fast and cost-effective DNA barcoding

(2018) Amrita Srivathsan et al.   Molecular Ecology Resources

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

(2018) Aaron Pomerantz et al.   GigaScience

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

(2018) Haotian Teng et al.   GigaScience

Rapid Detection and Monitoring of Flavobacterium psychrophilum in Water by Using a Handheld Field-Portable qPCR System

(2018) Phong L. Nguyen et al.   JOURNAL OF AQUATIC ANIMAL HEALTH

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

GenBank

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Climate-driven declines in arthropod abundance restructure a rainforest food web

(2018) Bradford C. Lister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

(2018) Ryan R. Wick et al.   PLoS Computational Biology

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

(2018) Szymon T Calus et al.   GigaScience

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

MinION as part of a biomedical rapidly deployable laboratory

(2017) Mathias C. Walter et al.   JOURNAL OF BIOTECHNOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

On site DNA barcoding by nanopore sequencing

(2017) Michele Menegon et al.   PLoS One

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

(2017) Peter R. Sternes et al.   GigaScience

Hand-powered ultralow-cost paper centrifuge

(2017) M. Saad Bhamla et al.   Nature Biomedical Engineering

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

More than 75 percent decline over 27 years in total flying insect biomass in protected areas

(2017) Caspar A. Hallmann et al.   PLoS One

Field-based species identification of closely-related plants using real-time nanopore sequencing

(2017) Joe Parker et al.   Scientific Reports

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Using mobile sequencers in an academic classroom

(2016) Sophie Zaaijer et al.   eLife

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

(2015) G.-J. Brandon-Mong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

‘Direct PCR’ optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

(2014) Wing Hing Wong et al.   Molecular Ecology Resources

Defaunation in the Anthropocene

(2014) R. Dirzo et al.   SCIENCE

Recent introduction of a chytrid fungus endangers Western Palearctic salamanders

(2014) A. Martel et al.   SCIENCE

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics and museum specimens

(2013) Michael W. Nachman   MOLECULAR ECOLOGY

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Approaching a state shift in Earth’s biosphere

(2012) Anthony D. Barnosky et al.   NATURE

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

(2011) KEVIN C. ROWE et al.   Molecular Ecology Resources

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

(2008) GARY M. BARKER   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY