Johan Bengtsson-Palme

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DDLS Fellow: Cell and molecular biology

Primary: Shown in the list of current labels.

Year 2025

DOI Crossref
Strategies for taxonomic and functional annotation of metagenomes
Abramova A, Bengtsson-Palme J
- - (-) 57-81 [2025-00-00; online 2025-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2024

DOI Crossref
Fish are poor sentinels for surveillance of riverine AMR
Tskhay F, Köbsch C, Elena AX, ..., Berendonk TU, Klümper U
- - (-) - [2024-10-22; online 2024-10-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomic assemblies tend to break around antibiotic resistance genes.
Abramova A, Karkman A, Bengtsson-Palme J
BMC Genomics 25 (1) 959 [2024-10-14; online 2024-10-14]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Genetic Adaptation to Amoxicillin inEscherichia coli: The Limited Role ofdinBandkatE
Teichmann L, Wenne M, Luitwieler S, ..., Bengtsson-Palme J, Kuile Bt
- - (-) - [2024-10-06; online 2024-10-06]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
ISME Commun - (-) - [2024-09-24; online 2024-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.
Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ
FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Fluoroquinolone-Specific Resistance Trajectories inE. coliand their Dependence on the SOS-Response
Teichmann L, Luitwieler S, Bengtsson-Palme J, ter Kuile B
- - (-) - [2024-06-06; online 2024-06-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.
Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM
Sci Rep 14 (1) 7432 [2024-03-28; online 2024-03-28]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.
Jarquín-Díaz VH, Ferreira SCM, Balard A, ..., Forslund-Startceva SK, Heitlinger E
ISME Commun 4 (1) ycae053 [2024-01-00; online 2024-04-15]
DDLS Fellow Johan Bengtsson-Palme

Year 2023

PubMed DOI Crossref
Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
Bengtsson-Palme J, Abramova A, Berendonk TU, ..., Wester AL, Zahra R
Environ Int 178 (-) 108089 [2023-08-00; online 2023-07-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.
Abramova A, Berendonk TU, Bengtsson-Palme J
Environ Int 178 (-) 108084 [2023-08-00; online 2023-07-03]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.
Bargheet A, Klingenberg C, Esaiassen E, ..., Bengtsson-Palme J, Pettersen VK
EBioMedicine 92 (-) 104613 [2023-06-00; online 2023-05-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.
Inda-Díaz JS, Lund D, Parras-Moltó M, ..., Bengtsson-Palme J, Kristiansson E
Microbiome 11 (1) 44 [2023-03-08; online 2023-03-08]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants
Heß S, Bengtsson-Palme J
- - (-) - [2023-00-00; online 2023-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2022

DOI Crossref
The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers
Kampouris ID, Bengtsson-Palme J, Babin D, ..., Berendonk TU, Klümper U
- - (-) - [2022-11-15; online 2022-11-15]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.
Wikström T, Abrahamsson S, Bengtsson-Palme J, ..., Valentin L, Hagberg H
Clin Transl Med 12 (9) e1023 [2022-09-00; online 2022-09-15]
DDLS Fellow Johan Bengtsson-Palme

Year 2021

PubMed DOI Crossref
What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach.
Bengtsson-Palme J, Jonsson V, Heß S
Environ. Sci. Technol. 55 (23) 15734-15743 [2021-12-07; online 2021-11-18]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06861 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06860 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06859 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06858 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06856 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 4: β-Lactams: amoxicillin and penicillin V.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06855 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3: Amprolium.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06854 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Allende A, Koutsoumanis K, ..., Stella P, Peixe L
EFSA J 19 (10) e06853 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06852 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06865 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06864 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06863 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic acid.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06862 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Microbial retention and resistances in stormwater quality improvement devices treating road runoff
Liguori R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C
FEMS Microbes 2 (-) - [2021-08-03; online 2021-07-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Microbial Community Interactions Are Sensitive to Small Changes in Temperature.
Burman E, Bengtsson-Palme J
Front Microbiol 12 (-) 672910 [2021-05-21; online 2021-05-21]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
The Organelle in the Ointment: cryptic mitochondria account for many unknown sequences in cross-species microbiome comparisons
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
bioRxiv preprint - (-) - [2021-02-24; online 2021-02-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data.
Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J
Bioinformatics - (-) - [2021-01-04; online 2021-01-04]
DDLS Fellow Johan Bengtsson-Palme

Year 2020

PubMed DOI Crossref
Microbial model communities: To understand complexity, harness the power of simplicity.
Bengtsson-Palme J
Comput Struct Biotechnol J 18 (-) 3987-4001 [2020-12-02; online 2020-12-02]
DDLS Fellow Johan Bengtsson-Palme

Year 2019

PubMed DOI Crossref
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.
Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N
Water Res 162 (-) 437-445 [2019-10-01; online 2019-07-04]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Strategies to Reduce or Eliminate Resistant Pathogens in the Environment
Bengtsson‐Palme J, Heß S
Antibiotic Drug Resistance - (-) 637-673 [2019-09-09; online 2019-08-23]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data
Magesh S, Jonsson V, Bengtsson-Palme J
MBMG 3 (-) - [2019-09-04; online 2019-09-04]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia.
Guzman-Otazo J, Gonzales-Siles L, Poma V, ..., Iñiguez V, Sjöling Å
PLoS ONE 14 (1) e0210735 [2019-01-14; online 2019-01-14]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
Nilsson RH, Larsson KH, Taylor AFS, ..., Kõljalg U, Abarenkov K
Nucleic Acids Res. 47 (D1) D259-D264 [2019-01-08; online 2018-10-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Brown P, RELISH Consortium , Zhou Y
Database (Oxford) 2019 (-) - [2019-01-01; online 2019-01-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi.
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH
Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Assessment and Management of Risks Associated With Antibiotic Resistance in the Environment
Bengtsson-Palme J
Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment - (-) 243-263 [2019-00-00; online 2019-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2018

PubMed DOI Crossref
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.
Bengtsson-Palme J, Richardson RT, Meola M, ..., Hartmann M, Nilsson RH
Bioinformatics 34 (23) 4027-4033 [2018-12-01; online 2018-06-19]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Quantifying point-mutations in shotgun metagenomic data
Magesh S, Jonsson V, Bengtsson-Palme J
bioRxiv preprint - (-) - [2018-10-11; online 2018-10-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.
Pärnänen K, Karkman A, Hultman J, ..., Satokari R, Virta M
Nat Commun 9 (1) 3891 [2018-09-24; online 2018-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Structure and function of the global topsoil microbiome.
Bahram M, Hildebrand F, Forslund SK, ..., Tedersoo L, Bork P
Nature 560 (7717) 233-237 [2018-08-00; online 2018-08-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.
Larsson DGJ, Andremont A, Bengtsson-Palme J, ..., Wellington EM, Wernersson AS
Environ Int 117 (-) 132-138 [2018-08-00; online 2018-05-07]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.
Bengtsson-Palme J
Microbiome 6 (1) 125 [2018-07-07; online 2018-07-07]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms.
Kraupner N, Ebmeyer S, Bengtsson-Palme J, ..., Flach CF, Larsson DGJ
Environ Int 116 (-) 255-268 [2018-07-00; online 2018-04-25]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data
Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM
PeerJ 6 (-) e5126 [2018-06-26; online 2018-06-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.
Wahlgren WY, Dunevall E, North RA, ..., Ramaswamy S, Friemann R
Nat Commun 9 (1) 1753 [2018-05-01; online 2018-05-01]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Henrik Nilsson R
bioRxiv preprint - (-) - [2018-04-28; online 2018-04-28]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, ..., Venturi V, Van den Eede G
F1000Res 7 (-) 459 [2018-04-13; online 2018-04-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Protection goals must guide risk assessment for antibiotics.
Bengtsson-Palme J, Larsson DGJ
Environ Int 111 (-) 352-353 [2018-02-00; online 2017-10-31]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).
Nilsson RH, Taylor AFS, Adams RI, ..., Kõljalg U, Abarenkov K
MycoKeys - (28) 65-82 [2018-01-08; online 2018-01-08]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Environmental factors influencing the development and spread of antibiotic resistance.
Bengtsson-Palme J, Kristiansson E, Larsson DGJ
FEMS Microbiol Rev 42 (1) - [2018-01-01; online 2017-10-27]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing?
Bengtsson-Palme J, Gunnarsson L, Larsson DGJ
Journal of Cleaner Production 171 (-) 137-146 [2018-01-00; online 2018-01-00]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Strategies for Taxonomic and Functional Annotation of Metagenomes
Bengtsson-Palme J
Metagenomics: Perspectives, Methods, and Applications - (-) 55-79 [2018-00-00; online 2018-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2017

PubMed DOI Crossref
The relation between Blastocystis and the intestinal microbiota in Swedish travellers.
Forsell J, Bengtsson-Palme J, Angelin M, ..., Evengård B, Granlund M
BMC Microbiol. 17 (1) 231 [2017-12-11; online 2017-12-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data.
Berglund F, Marathe NP, Österlund T, ..., Larsson DGJ, Kristiansson E
Microbiome 5 (1) 134 [2017-10-12; online 2017-10-12]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Using metagenomics to investigate human and environmental resistomes.
Bengtsson-Palme J, Larsson DGJ, Kristiansson E
J Antimicrob Chemother 72 (10) 2690-2703 [2017-10-01; online 2017-07-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.
Thorell K, Bengtsson-Palme J, Liu OH, ..., Lundin SB, Sjöling Å
Infect. Immun. 85 (10) - [2017-10-00; online 2017-09-20]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.
Boulund F, Berglund F, Flach CF, ..., Larsson DGJ, Kristiansson E
BMC Genomics 18 (1) 682 [2017-09-02; online 2017-09-02]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The complete mitochondrial genome of the copepod Calanus glacialis.
Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G
Mitochondrial DNA B Resour 2 (2) 506-507 [2017-08-06; online 2017-08-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Does antifouling paint select for antibiotic resistance?
Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DGJ
Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data.
Richardson RT, Bengtsson-Palme J, Johnson RM
Mol Ecol Resour 17 (4) 760-769 [2017-07-00; online 2016-11-21]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?
Bengtsson-Palme J
Current Opinion in Food Science 14 (-) 66-71 [2017-04-00; online 2017-04-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2016

PubMed DOI Crossref
FARAO: the flexible all-round annotation organizer.
Hammarén R, Pal C, Bengtsson-Palme J
Bioinformatics 32 (23) 3664-3666 [2016-12-01; online 2016-08-04]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.
Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DGJ
Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-17]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The structure and diversity of human, animal and environmental resistomes.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
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)
Abarenkov K, Adams RI, Laszlo I, ..., Schriml L, Nilsson RH
MykoKeys 16 (-) 1-15 [2016-09-26; online 2016-09-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Strategies to improve usability and preserve accuracy in biological sequence databases.
Bengtsson-Palme J, Boulund F, Edström R, ..., Sanli K, Thorell K
Proteomics 16 (18) 2454-2460 [2016-09-00; online 2016-08-17]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.
Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DGJ
Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-22]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2
Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH
Ecological Informatics 33 (-) 45-50 [2016-05-00; online 2016-05-00]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.
Bengtsson-Palme J, Larsson DG
Environ Int 86 (-) 140-149 [2016-01-00; online 2015-11-17]
DDLS Fellow Johan Bengtsson-Palme

Year 2015

DOI Crossref
The European technical report on aquatic effect-based monitoring tools under the water framework directive
Wernersson AS, Carere M, Maggi C, ..., Kammann U, Kase R
Environ Sci Eur 27 (1) - [2015-12-00; online 2015-03-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
BMC Genomics 16 (-) 964 [2015-11-17; online 2015-11-17]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J, Hartmann M, Eriksson KM, ..., Larsson DG, Nilsson RH
Mol Ecol Resour 15 (6) 1403-1414 [2015-11-00; online 2015-03-23]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.
Sanli K, Bengtsson-Palme J, Nilsson RH, ..., Blanck H, Eriksson KM
Front Microbiol 6 (-) 1192 [2015-10-30; online 2015-10-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.
Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DG, Johansson A
Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-10]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Antibiotic resistance genes in the environment: prioritizing risks.
Bengtsson-Palme J, Larsson DG
Nat. Rev. Microbiol. 13 (6) 396 [2015-06-00; online 2015-04-27]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
ITS1: a DNA barcode better than ITS2 in eukaryotes?
Wang XC, Liu C, Huang L, ..., Cai D, Li JQ
Mol Ecol Resour 15 (3) 573-586 [2015-05-00; online 2014-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.
Nilsson RH, Tedersoo L, Ryberg M, ..., Edgar RC, Abarenkov K
Microbes Environ 30 (2) 145-150 [2015-03-19; online 2015-03-19]
DDLS Fellow Johan Bengtsson-Palme

Year 2014

PubMed DOI Crossref
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.
Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DG
Front Microbiol 5 (-) 648 [2014-12-02; online 2014-12-02]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.
Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A
BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Improving ITS sequence data for identification of plant pathogenic fungi
Nilsson RH, Hyde KD, Pawłowska J, ..., Kõljalg U, Abarenkov K
Fungal Diversity 67 (1) 11-19 [2014-07-00; online 2014-05-15]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
BacMet: antibacterial biocide and metal resistance genes database.
Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG
Nucleic Acids Res. 42 (Database issue) D737-D743 [2014-01-00; online 2013-12-03]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Metaxa, Overview
Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH
Encyclopedia of Metagenomics - (-) 1-5 [2014-00-00; online 2014-04-16]
DDLS Fellow Johan Bengtsson-Palme

Year 2013

PubMed DOI Crossref
Towards a unified paradigm for sequence-based identification of fungi.
Kõljalg U, Nilsson RH, Abarenkov K, ..., Weiss M, Larsson KH
Mol. Ecol. 22 (21) 5271-5277 [2013-11-00; online 2013-09-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
Bengtsson-Palme J, Ryberg M, Hartmann M, ..., Veldre V, Nilsson RH
Methods Ecol Evol - (-) n/a-n/a [2013-07-00; online 2013-07-19]
DDLS Fellow Johan Bengtsson-Palme

Year 2012

DOI Crossref
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
Nilsson RH, Tedersoo L, Abarenkov K, ..., Larsson E, Kõljalg U
MykoKeys 4 (-) 37-63 [2012-09-05; online 2012-09-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
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.
Bengtsson J, Hartmann M, Unterseher M, ..., Eriksson KM, Nilsson RH
Res. Microbiol. 163 (6-7) 407-412 [2012-07-00; online 2012-07-21]
DDLS Fellow Johan Bengtsson-Palme

Year 2011

PubMed DOI Crossref
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.
Bengtsson J, Eriksson KM, Hartmann M, ..., Rosenblad MA, Nilsson RH
Antonie Van Leeuwenhoek 100 (3) 471-475 [2011-10-00; online 2011-06-15]
DDLS Fellow Johan Bengtsson-Palme
SciLifeLab Data Centre
Publications 9.5.1