List of works - Johan Bengtsson-Palme

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

scientific article published on 19 March 2015

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data

article published in 2018

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data.

scientific article

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

scientific article (publication date: 26 September 2016)

Antibiotic resistance genes in the environment: prioritizing risks.

scientific article published on 27 April 2015

Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?

scholarly article by Johan Bengtsson-Palme published April 2017 in Current opinion in food science

BacMet: antibacterial biocide and metal resistance genes database.

scientific article published on 03 December 2013

Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing?

article by Johan Bengtsson-Palme et al published January 2018 in Journal of Cleaner Production

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.

scientific article published on 17 November 2015

Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.

scientific article published on 16 November 2015

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

scientific article published on 7 May 2018

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

scientific article published in PLoS ONE

Does antifouling paint select for antibiotic resistance?

scientific article published on 08 March 2017

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

scientific article published on 16 August 2016

Environmental factors influencing the development and spread of antibiotic resistance

scientific article

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

scientific article

FARAO: the flexible all-round annotation organizer

scientific article published on 4 August 2016

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

scientific article

ITS1: a DNA barcode better than ITS2 in eukaryotes?

scientific article

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data.

scientific article published on 12 October 2017

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

article

Improving ITS sequence data for identification of plant pathogenic fungi

article

In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis

scientific article published on 10 July 2017

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities

scientific article published on 04 July 2019

Introducing ribosomal tandem repeat barcoding for fungi

METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.

scientific article published on 2 March 2015

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

scientific article published in Nature Communications

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

scientific article

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

scientific article published on 30 October 2015

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

scientific article

Metaxa, Overview

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

scholarly article by Johan Bengtsson-Palme published in June 2018

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

article

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

scientific article published on 15 June 2011

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.

scientific article

Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

scientific article published in 2019

Protection goals must guide risk assessment for antibiotics.

scientific article published on 31 October 2017

Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms

scientific article

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

scientific article

Strategies for Taxonomic and Functional Annotation of Metagenomes

Strategies to improve usability and preserve accuracy in biological sequence databases.

scientific article

Structure and function of the global topsoil microbiome

scientific article published in Nature

Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.

scientific article

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

scientific article

Taxonomic identification from metagenomic and metabarcoding data using any genetic marker

The European technical report on aquatic effect-based monitoring tools under the water framework directive

scientific article published in 2015

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents

scientific article published on 10 August 2015

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

scholarly article by Henrik Nilsson et al published 29 October 2018 in Nucleic Acids Research

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

The complete mitochondrial genome of the copepod Calanus glacialis

article by Marvin Choquet et al published 6 August 2017 in Mitochondrial DNA. Part B, Resources

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.

scientific article published on 7 July 2018

The relation between Blastocystis and the intestinal microbiota in Swedish travellers

scientific article published on 11 December 2017

The structure and diversity of human, animal and environmental resistomes

scientific article

Towards a unified paradigm for sequence-based identification of fungi

scientific article

Using metagenomics to investigate human and environmental resistomes

scientific article

List of works by Johan Bengtsson-Palme

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data.

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

Antibiotic resistance genes in the environment: prioritizing risks.

Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?

BacMet: antibacterial biocide and metal resistance genes database.

Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing?

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.

Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Does antifouling paint select for antibiotic resistance?

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Environmental factors influencing the development and spread of antibiotic resistance

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

FARAO: the flexible all-round annotation organizer

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

ITS1: a DNA barcode better than ITS2 in eukaryotes?

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data.

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Improving ITS sequence data for identification of plant pathogenic fungi

In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities

Introducing ribosomal tandem repeat barcoding for fungi

METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Metaxa, Overview

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.

Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

Protection goals must guide risk assessment for antibiotics.

Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

Strategies for Taxonomic and Functional Annotation of Metagenomes

Strategies to improve usability and preserve accuracy in biological sequence databases.

Structure and function of the global topsoil microbiome

Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

Taxonomic identification from metagenomic and metabarcoding data using any genetic marker

The European technical report on aquatic effect-based monitoring tools under the water framework directive

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

The complete mitochondrial genome of the copepod Calanus glacialis

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.

The relation between Blastocystis and the intestinal microbiota in Swedish travellers

The structure and diversity of human, animal and environmental resistomes

Towards a unified paradigm for sequence-based identification of fungi

Using metagenomics to investigate human and environmental resistomes