Peer-reviewed journal papers

  • Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E, Kõljalg U: Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys. Issue 4 (2012), 37–63. doi: 10.3897/mycokeys.4.3606 [Paper link]
  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH: 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. Research in Microbiology. Volume 163, Issues 6–7 (2012), 407–412, doi: 10.1016/j.resmic.2012.07.001. [Paper link]
  • Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: 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. Antonie van Leeuwenhoek. Volume 100, Number 3 (2011), 471-475, doi:10.1007/s10482-011-9598-6. [Paper link]

Peer-reviewed book chapters

  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: Metaxa, overview. In:Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg (2013). [Link]

Theses

  • Bengtsson J: Metagenomic Analysis of Marine Periphyton Communities: Taxonomic and Functional Perspectives on Natural Biofilm-forming Communities. Degree project for Master of Science in Systems Biology, Department of Cell and Molecular Biology, and Department of Plant and Environmental Sciences, University of Gothenburg, 2011.
  • Bengtsson J: Finding Genes Related to Detoxification in Metagenomic Data. Degree project for Bachelor of Science in Cell Biology, Department of Cell and Molecular Biology University of Gothenburg, 2009.

Posters

  • Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Using Large-Scale Sequencing Metagenomics to Assess the Antibiotic Resistome. 4th Next Generation Sequencing Congress, London, Great Britain, 2012.
  • Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: High-Throughput Diversity Analysis and Quality Control of Environmental Data Derived from Next-Generation Sequencing Studies. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Eriksson KM, Sanli K, Bengtsson-Palme J, Nilsson RH, Alm Rosenblad M, Blanck H: Starting to unravel the layer of life on surfaces in the sea: Metagenomics of complex marine biofilm communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Bengtsson J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012.
  • Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts. SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
  • Bengtsson J, Eriksson M, Alm Rosenblad M, Blanck H: Metagenomic Characterisation of Marine Periphyton Communitites. Deep Sequencing Techniques Workshop, Gothenburg, 2010.
  • Bengtsson J, Alm Rosenblad M, Forlin L, Celander M, Blanck H, Larsson DGJ, Molin M, Blomberg A: Distribution of Detoxification Genes in Marine Environments. Swedish Bioinformatics Workshop, Gothenburg, 2010.

Software packages

  • Bengtsson-Palme J, Veldre V, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, Bertrand Y, De Wit P, Sanchez M, Ebersberger I, Sanli K, de Souza F, Kristiansson E, Abarenkov K, Eriksson KM, Nilsson RH: ITSx – a software for improved detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
  • Bengtsson-Palme J: PETKit – a set of tools to ease the use of sequences from large-scale sequencing projects generating paired-end reads
  • Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa – a software package for automated identification and classification of small subunit (SSU) rRNA sequences from archaea, bacteria, eukaryotes, chloroplasts and mitochondria in metagenomic and environmental sequencing data sets
  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH: 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
  • Bengtsson J: Metaorf – a very simple gene finder adapted for the fragmentary nature of metagenomic data
  • Bengtsson-Palme J: Bloutminer – a script for mining data from BLAST reports