Peer-reviewed journal papers
° indicates equal contributions

    – 2017 –

  1. Forsell J, Bengtsson-Palme J, Angelin M, Johansson A, Evengård B, Granlund M: The relation between Blastocystis and the intestinal microbiota in Swedish travellers. BMC Microbiology, 17, 231 (2017). doi: 10.1186/s12866-017-1139-7 [Paper link]
  2. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, accepted manuscript (2017). doi: 10.1093/femsre/fux053 [Paper link]
  3. Berglund F, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach C-F, Larsson DGJ, Kristiansson E: Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome, 5, 134 (2017). doi: 10.1186/s40168-017-0353-8 [Paper link]
  4. Bengtsson-Palme J°, Gunnarsson L°, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? Journal of Cleaner Production, 171, 137–146 (2018). doi: 10.1016/j.jclepro.2017.09.247 [Paper link]
  5. Boulund F, Berglund F, Flach C-F, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E: Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics, 18, 682 (2017). doi: 10.1186/s12864-017-4064-0 [Paper link]
  6. Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G: The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2, 2, 506–507 (2017). doi: 10.1080/23802359.2017.1361357 [Paper link]
  7. Thorell K, Bengtsson-Palme J, Liu OH, Gonzales RVP, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å: In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis. Infection and Immunity, 85, 10, e00031-17 (2017). doi: 10.1128/IAI.00031-17 [Paper link]
  8. Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. Journal of Antimicrobial Chemotherapy, 72, 2690–2703 (2017). doi: 10.1093/jac/dkx199 [Paper link]
  9. Flach C-F, Pal C, Svensson CJ, Kristiansson E, Östman M, Bengtsson-Palme J, Tysklind M, Larsson DGJ: Does antifouling paint select for antibiotic resistance? Science of the Total Environment, 590–591, 461–468 (2017). doi: 10.1016/j.scitotenv.2017.01.213 [Paper link]
  10. – 2016 –

  11. Richardson RT, Bengtsson-Palme J, Johnson RM: Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Sequence Data. Molecular Ecology Resources, 17, 4, 760–769 (2017). doi: 10.1111/1755-0998.12628 [Paper link]
  12. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: The structure and diversity of human, animal and environmental resistomes. Microbiome, 4, 54 (2016). doi: 10.1186/s40168-016-0199-5 [Paper link]
  13. Abarenkov K, Adams RI, Laszlo I, Agan A, Ambrioso E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Untersehrer M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH: 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). MycoKeys, 16, 1–15 (2016). doi: 10.3897/mycokeys.16.10000 [Paper link]
  14. Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach C-F, Kristiansson E, Fick J, Tysklind M, Larsson DGJ: Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Science of the Total Environment, 572, 697–712 (2016). doi: 10.1016/j.scitotenv.2016.06.228 [Paper link]
  15. Hammarén R, Pal C, Bengtsson-Palme JFARAO: The Flexible All-Round Annotation Organizer. Bioinformatics, 32, 23, 3664-3666 (2016). doi: 10.1093/bioinformatics/btw499 [Paper link]
  16. Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH: Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2. Ecological Informatics, 33, 45–50 (2016). doi: 10.1016/j.ecoinf.2016.04.004 [Paper link]
  17. Lundström S, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Science of the Total Environment, 553, 587–595 (2016). doi: 10.1016/j.scitotenv.2016.02.103 [Paper link]
  18. – 2015 –

  19. Bengtsson-Palme J, Larsson DGJ: Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation. Environment International, 86, 140–149 (2016). doi: 10.1016/j.envint.2015.10.015 [Paper link]
  20. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics, 16, 964 (2015). doi: 10.1186/s12864-015-2153-5 [Paper link]
  21. Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM: Metagenomic sequencing of marine periphyton: Taxonomic and functional insights into biofilm communities. Frontiers in Microbiology, 6, 1192 (2015). doi: 10.3389/fmicb.2015.01192 [Paper link]
  22. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551–6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]
  23. Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker D, de Sousa F, Gamper HA, Larsson E, Larsson K-H, Kõljalg U, Edgar R, Abarenkov K: A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30, 2, 145–150 (2015). doi: 10.1264/jsme2.ME14121 [Paper link]
  24. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Dulio V, Broeg K, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, O’Toole S, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Hollert H, Di Paolo C, Brack W. Kammann U, Kase R: The European technical report on aquatic effect-based monitoring tools under the water framework directive. Environmental Sciences Europe, 27, 7 (2015). doi: 10.1186/s12302-015-0039-4 [Paper link]
  25. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]
  26. – 2014 –

  27. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648 [Paper link]
  28. Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q: ITS1: A DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources, 15, 3, 573–586 (2015). doi: 10.1111/1755-0998.12325 [Paper link]
  29. Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics, 15, 749 (2014). doi: 10.1186/1471-2164-15-749 [Paper link]
  30. Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F, Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson K-H, Kõljalg U, Abarenkov K: Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67, 1, 11–19 (2014). doi: 10.1007/s13225-014-0291-8 [Paper link]
  31. – 2013 –

  32. Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DGJ: BacMet: Antibacterial biocide and metal resistance genes database. Nucleic Acids Research, 42, D1, D737–D743 (2014). doi: 10.1093/nar/gkt1252 [Paper link]
  33. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M, Larsson KH: Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22, 21, 5271–5277 (2013). doi: 10.1111/mec.12481 [Paper link] (Cited more than 600 times)
  34. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Souza F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4, 10, 914–919 (2013). doi: 10.1111/2041-210X.12073 [Paper link] (Cited more than 150 times)
  35. – 2012 –

  36. 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, 4, 37–63 (2012). doi: 10.3897/mycokeys.4.3606 [Paper link]
  37. 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, 163, 6–7, 407–412 (2012). doi: 10.1016/j.resmic.2012.07.001. [Paper link]
  38. – 2011 –

  39. 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, 100, 3, 471–475 (2011). doi:10.1007/s10482-011-9598-6. [Paper link]

Opinion papers

  1. Bengtsson-Palme J, Larsson DGJ: Protection goals must guide risk assessment for antibiotics. Environment International, in press (2017). doi: 10.1016/j.envint.2017.10.019 [Paper link]
  2. Bengtsson-Palme J: Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Current Opinion in Food Science, 14, 66–71 (2017). doi: 10.1016/j.cofs.2017.01.010 [Paper link]
  3. Bengtsson-Palme J, Larsson DGJ: Why limit antibiotic pollution? The role of environmental selection in antibiotic resistance development. APUA Newsletter, 34, 2, 6-9 (2016). [Paper link].
  4. Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sánchez J, Sanli K, Thorell K: Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics, 16, 18, 2454–2460 (2016). doi: 10.1002/pmic.201600034 [Paper link]
  5. Bengtsson-Palme J, Larsson DGJ: Time to limit antibiotic pollution. The Medicine Maker, 0416, 302, 17–18 (2016). [Paper link]
  6. Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nature Reviews Microbiology, 13, 369 (2015). doi: 10.1038/nrmicro3399-c1 [Paper link]

Books, Book chapters and Theses

  1. Bengtsson-Palme J: Strategies for Taxonomic and Functional Annotation of Metagenomes. In: Nagarajan M (Ed.) Metagenomics: Perspectives, Methods, and Applications, 55–79. Academic Press, Elsevier, USA (2018). doi: 10.1016/B978-0-08-102268-9.00003-3 [Link]
  2. Bengtsson-Palme J: Antibiotic resistance in the environment: a contribution from metagenomic studies. Doctoral thesis (medicine), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 2016. [Link]
  3. 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). doi: 10.1007/978-1-4614-6418-1_239-6 [Link]
  4. 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.
  5. 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.

Contributions to official reports

  1. Joint Programming Initiative on Antimicrobial Resistance: JPIAMR Workshop on Environmental Dimensions of AMR: Summary and recommendations. JPIAMR (2017). [Link]
  2. Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099 [Link]
  3. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Broeg K, Kammann U, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kase R, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Dulio V, Hollert H, Di Paolo C, Brack W (2014). Technical Report on Aquatic Effect-Based Monitoring Tools. European Commission. Technical Report 2014-077, Office for Official Publications of European Communities, ISBN: 978-92-79-35787-9. doi:10.2779/7260 [Link]
  4. Länsstyrelsen i Västra Götalands län. (2012). Swedish monitoring of hazardous substances in the aquatic environment (No. 2012:23). In:Wernersson A-S (Ed.) Current vs required monitoring and potential developments. Länsstyrelsen i Västra Götalands län, vattenvårdsenheten. [Link]

Posters

  1. Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  2. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Using metagenomics to investigate human and environmental resistomes – Methodological considerations. 8th Next Generation Sequencing Congress, London, Great Britain, 2016.
  3. Bengtsson-Palme J, Lundström SV, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibiotics in complex microbial communities. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  4. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals on bacterial chromosomes and plasmids reveals novel insights into their co-selection potential. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  5. Flach C-F, Svensson C-J, Pal C, Bengtsson-Palme J, Östman M, Kristiansson E, Larsson DGJ: Antifouling paint co-selects for antibiotic resistant bacteria in the marine environment. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  6. Razavi M, Marathe NP, Bengtsson-Palme J, Flach C-F, Kristiansson E, Larsson DGJ: Identification of novel antibiotic resistance genes using amplicon sequencing of integrons from polluted environments in India. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  7. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals on bacterial chromosomes and plasmids reveals novel insights into their co-selection potential. ICETAR 2015: International Conference on the Evolution and Transfer of Antibiotic Resistance, Amsterdam, The Netherlands, 2015.
  8. Flach C-F, Svensson C-J, Pal C, Bengtsson-Palme J, Östman M, Kristiansson E, Larsson DGJ: Antifouling paint co-selects for antibiotic resistant bacteria in the marine environment. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  9. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  10. Hammarén R, Bengtsson-Palme J, Pal C, Flach C-F, Kristiansson E, Larsson DGJ: Elucidating co-selection of genes conferring resistance to biocides and metals with antibiotic resistance genes in Swedish wastewater treatment plants. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  11. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. ISME15 Conference, Seoul, South Korea, 2014.
  12. Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F, Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson K-H, Kõljalg U, Abarenkov K: Improving ITS sequence data for identification of plant pathogenic fungi. The 10th International Mycological Congress, Bangkok, Thailand, 2014.
  13. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Metagenomics Unravels the Antibiotic Resistome of Indian Soils. 2nd Thünen Symposium on Soil Metagenomics, Braunschweig, Germany, 2013.
  14. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Sequencing Depth is Central to Capture the Diversity of Antibiotic Resistance Genes in the Environment. 5th Next Generation Sequencing Congress, London, Great Britain, 2013.
  15. Sanli K, Eriksson KM, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H: Metagenomic Analysis of Periphyton: Taxonomic and Functional Insights into Marine Biofilm Communities. Swedish Bioinformatics Workshop, Skövde, Sweden, 2013.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. Bengtsson J, Eriksson M, Alm Rosenblad M, Blanck H: Metagenomic Characterisation of Marine Periphyton Communitites. Deep Sequencing Techniques Workshop, Gothenburg, 2010.
  23. 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.

Conference talks

Presenting author indicated by *

  1. Bengtsson-Palme J*, Gunnarsson L, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  2. Berglund F*, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Larsson DGJ, Kristiansson E: Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  3. Kraupner N*, Ebmeyer S, Bengtsson-Palme J, Fick J, Flach C-F, Larsson DGJ: Minimal selective concentration of ciprofloxacin for Escherichia coli grown in complex aquatic bacterial biofilms. 4th International symposium on the environmental dimension of antibiotic resistance (EDAR2017), Lansing, MI, USA, 2017.
  4. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Unravelling the structure and diversity of human, animal and environmental resistomes using metagenomics. NDPIA Network Meeting 2016, Gothenburg, Sweden, 2016.
  5. Bengtsson-Palme J*, Hammarén R, Pal C, Östman M, Björlenius B, Flach C-F, Kristiansson E, Fick J, Tysklind M, Larsson DGJ: Elucidating biocide and metal co-selection for antibiotic resistance in sewage treatment plants using metagenomics. The role of metals and biocides in the selection of antibiotic resistant bacteria, Stockholm, Sweden, 2016.
  6. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data. Swedish Bioinformatics Workshop, Stockholm, Sweden, 2015.
  7. Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 6th Congress of European Microbiologists (FEMS2015), Maastricht, The Netherlands, 2015.
  8. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into antibiotic resistance of bacterial communities using metagenomic data. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  9. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of antibacterial biocide, metal and antibiotic resistance genes in bacterial genomes and plasmids reveals novel insights in their co-selection potential. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  10. Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  11. Bengtsson-Palme J*, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: Metagenomics Reveals Changes in Antibiotic Resistance Gene Abundances in Gut Bacterial Communities Resulting from Long-range Traveling. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  12. Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Large-scale analysis of bacterial genomes and plasmids for antibiotic, biocide and metal resistance genes and their co-selection potential. Swedish Bioinformatics Workshop, Gothenburg, Sweden, 2014.
  13. Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Depth Matters: Sequencing depth is central to capture the diversity of antibiotic resistance genes in the environment. Swedish Bioinformatics Workshop 2013, Skövde, Sweden, 2013.
  14. 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.
  15. Bengtsson J*, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Analyzing antibiotic resistance using metagenomics. SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012
  16. 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.

Software packages

  1. Bengtsson-Palme J: COAT – Conservation-Oriented Alignment Tool (2017)
  2. Hammarén R, Pal C, Bengtsson-Palme J: FARAO – The Flexible All-Round Annotation Organizer (2015) [Paper link]
  3. Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH: Metaxa2 Diversity Tools (2015) (included with Metaxa2 2.1 and later) [Paper link]
  4. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2 – Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data (2014) [Paper link]
  5. Bengtsson-Palme J, Pal C: BacMet-Scan – A tool to scan sequence data against the BacMet database (2013) [Paper link]
  6. Bengtsson-Palme J: TriMetAss – Trinity-based Metagenomics Assembler (2013) [Paper link]
  7. Bengtsson-Palme J, Abarenkov K, Nilsson RH: Atosh – Assign to Species Hypothesis (2013) [This script underlies part of the UNITE database] [Paper link]
  8. 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 (2013) [Paper link]
  9. Bengtsson-Palme JPETKit – a set of tools to ease the use of sequences from large-scale sequencing projects generating paired-end reads (2012)
  10. 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 (2012) [Paper link]
  11. 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 (2011) [Paper link]
  12. Bengtsson J: Metaorf – a very simple gene finder adapted for the fragmentary nature of metagenomic data (2010)
  13. Bengtsson J: Bloutminer – a script for mining data from BLAST reports (2010)