2017

Bengtsson-Palme J, Kristiansson E, Larsson DGJ, Environmental factors influencing the development and spread of antibiotic resistance, FEMS Microbiology Reviews, 2017.

Berglund F, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach CF, Larsson DGJ, Kristiansson E, Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data, Microbiome 5(1) 2017.

Boulund F, Berglund F, Flach CF, 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(1) 2017.

Nilsson RH, Sánchez-García M, Ryberg MK, Abarenkov K, Wurzbacher C, Kristiansson E, Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory, MycoKeys 26(13) 2017.

Corcoll N, Österlund T, Sinclair L, Eiler A, Kristiansson E, Backhaus T, Eriksson KM, Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing, FEMS Microbiology Letters 364(14) 2017.

Marathe NP, Pal C, Gaikwad SS, Jonsson V, Kristiansson E, Larsson DGJ, Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics, Water research 124(388) 2017.

Flach CF, 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 Enviroment 590 2017.

Bengtsson-Palme J, Larsson DGJ, Kristiansson E, Using metagenomics to investigate human and environmental resistomes, Journal of Antimicrobial Chemotherapy 72(10) 2017.

Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, AL-Bayati O, Åhrén C, Moore ERB, Kristiansson E, TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry, Molecular & Cellular Proteomics 16(6) 2017.

Österlund T, Jonsson V, Kristiansson E, HirBin: High-resolution identification of differentially abundant functions in metagenomes, BMC Genomics 18(1) 2017.

Jakobsson HE, Salvà-Serra F, Thorell K, Karlsson R, Gonzales-Silès L, Boulund F, Engstrand L, Kristiansson E, Moore ERB, Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F, Genome announcements 5(14) 2017.

Jonsson V, Österlund T, Nerman O, Kristiansson E, Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes, Journal of Computational Biology 24(4) 2017.

Österlund T, Cvijovic M, Kristiansson E, Integrative analysis of omics data, book chapter in Systems biology, edited by Jens Nielsen and Stefan Hohmann, Wiley & Sons 2017.

Verbruggen B, Gunnarsson L, Kristiansson E, Österlund T, Owen SF, Snape JR, Tyler CR, ECOdrug: a database connecting drugs and conservation of their targets across species, Nucleic Acids Research, to appear, 2017.

Malmberg EBR, Ståhlman S, Rehammar A, Samuelsson T, Alm SJ, Kristiansson E, Abrahamsson J, Garelius H, Pettersson L, Ehinger M, Palmqvist L, Fogelstrand L, Patient‐tailored analysis of minimal residual disease in acute myeloid leukemia using next‐generation sequencing, European journal of haematology 98(1) 2017.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ, The structure and diversity of human, animal and environmental resistomes, Microbiome 4(1) 2016.

Johnning A, Jakobsson HE, Boulund F, Salvà-Serra F, Moore ERB, Åhrén C, Karami N, Kristiansson E, Draft genome sequence of extended-spectrum-β-lactamase-producing Escherichia coli strain CCUG 62462, isolated from a urine sample, Genome announcements 4(6) 2016.

Asker N, Albertsson E, Wijkmark E, Bergek S, Parkkonen J, Kammann U, Holmqvist I, Kristiansson E, Strand J, Gercken J, Förlin L, Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany, Marine environmental research 120 2016.

Abarenkov et al, 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 2016.

Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F, Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping, Scienfitic reports 6 2017.

Jonsson V, Österlund T, Nerman O, Kristiansson E, Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics, BMC Genomics, 17:78 2016.

Jakobsson HE, Salvà-Serra F, Thorell K, Gonzales-Siles L, Boulund F, Karlsson R, Sikora P, Engstrand L, Kristiansson E, Moore ERB, Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T, to appear in Genome Announcements 2016.

Salvà-Serra F, Jakobsson HE, Thorell K, Gonzales-Siles L, Hallbäck ET, Jaén-Luchoro D, Boulund F, Sikora P, Karlsson R, Svensson L, Bennasar A, Engstrand L, Kristiansson E, Moore ERB, Draft genome sequence of Streptococcus gordonii type strain CCUG 33482T, Genome Announcements 4(2) 2016.

Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach CF, Fick J, Kristiansson E, Tysklind M, Larsson DGJ, Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics, to appear in Science of the Total Environment, 2016.

Pereira MB, Kristiansson E, Axelsson-Fisk M, HattCI: fast and accurate attC site identification using hidden Markov models, to appear in Journal of Computational Biology, 2016.

Österlund T, Cvijovic M, Kristiansson E, Integrative analysis of omics data, book chapter, accepted to Biotechnology:Systems Biology, Editors Jens Nielsen and Stefan Hohmann, Wiley, 2016.

Malmberg E, Ståhlman S, Rehammar A, Samuelsson T, Alm SJ, Kristiansson E, Abrahamsson J, Garelius H, Palmqvist L, Fogelstrand L, Patient-tailored analysis of minimal residual disease in acute myeloid leukemia using next generation sequencing, accepted in European Journal of Haematology, 2016.

Nilsson RH, Wurzbacher C, Bahram M, Coimbra VRM, Larsson E, Tedersoo L, Eriksson J, Ritter CD, Svantesson S, Sánchez-García M, Ryberg M, Kristiansson E, Abarenkov K, Top 50 most wanted fungi, accepted for MycoKeys 2016.

Andersson E, Arvidsson Y, Swärd C, Hofving T, Wängberg B, Kristiansson E, Nilsson Ola, Profiling small intestine neuroendocrine tumors defines subgroups with clinical relevance, accepted for Modern Pathology 2016.

Karlsson R, Gonzales-Siles L, Boulund F, Lindgren Å, Svensson-Stadler L, Karlsson A, Kristiansson E, Moore ERB, Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms, to appear in “The Triumph of MALDI-TOF Mass Spectrometry and New Developments in Tandem Mass Spectrometry for Clinical Microbiology”, 2016.

Johnning A, Kristiansson E, Fick J, Weijdegård B, Larsson DGJ, Resistance mutations in gyrA and parC are common in bacterial communities of both pristine and fluoroquinolone-polluted environments, in press, Frontiers in Microbiology, 2015.

Wilzén A, Rehammar A, Muth A, Nilsson O, Tomić TT, Wängberg B, Kristiansson E, Abel F, Malignant pheochromocytomas/paragangliomas harbor mutations in transport and cell adhesion genes, Interational Journal of cancer, in press, 2015.

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(1) 2015.

Boulund F, Sjögren A, Kristiansson E, tentacle: a distributed framework for quantification of genes in metagenomes, GigaScience 4(40) 2015.

Karlsson R, Gonzales-Siles L, Boulund F, Svensson-Stadler L, Skovbjerg S, Karlsson A, Davidson M, Hulth S, Kristiansson E, Moore ERB, Proteotyping: Proteomic characterisation, classification and identification of microorganisms – a prospectus, Systematic and Applied Microbiology 38(4) 2015.

Nilsson HR, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K, A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts, Microbes and Environments 30(2) 2015.

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 doi: 10.1128/AAC.00933-15 2015.

Almroth, BC, Cuklev, F, Fick, J, Gunnarsson, L, Kristiansson, E, Förlin, L, Larsson, DGJ. Waterborne beclomethasone diproprionate affects fish while its metabolite beclomethasone is not taken up, Science of the Total Environment 511 2015.

Flach, CF, Johnning A, Nilsson I, Smalla K, Kristiansson E, Larsson DGJ, Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake, Journal of Antimicrobial Chemotherapy doi: 10.1093/jac/dkv167 2015.

Sanli K, Eriksson KM, Palme-Bengtsson J, Nilsson H, Kristiansson E, Alm-Rosenblad M, Blanck H, Metagenomic Sequencing of Periphyton: Taxonomic and Functional Insights into Marine Biofilm Communities, Frontiers in Microbiology 6 2015.

Johnning A, Kristiansson E, Angelin M, Marathe N, Shouche Y, Johansson A, Larsson DGJ, Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India, BMC Microbiology 15(1) 2015.

Asting AG, Lagerstedt KK, Kristiansson E, Lönnroth C, Andersson M, Rekabdar E, Hansson E, Nordgren S, Kressner U, Enlund F, Lundholm K, Genetic copy number variations in colon mucosa indicating risk for colorectal cancer, Journal of Cancer Therapy 5(14) 2014.

Palme-Bengtsson 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 2014.

Brown AR, Gunnarsson L, Kristiansson E, Tyler CR, Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology, Phil Trans R Soc B 2014 (DOI: 10.1098/rstb.2013.0576).

Rutgersson C, Fick J, Marathe N, Kristiansson E, Janzon A, Angelin M, Johansson A, Shouche Y, Flach CF, Larsson DGJ, Fluoroquinolones and qnr genes in sediment, water, soil and human fecal flora in an environment polluted by manufacturing discharges, Environment Science and Technology 48(14) 2014.

Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DGJ, BacMet: Antibacterial Biocides and Metal Resistance Genes Database, 2013, Nucleic Acids Research 42(D1) 2014.

Bergquist M, Nurkkala M, Rylander C, Kristiansson E, Hedenstierna G, Lindholm C, Expression of the glucocorticoid receptor is decreased in experimental Staphylococcus aureus sepsis, Journal of Infection 67(6) 2013.

Flach CF, Boulund F, Kristiansson E, Larsson DGJ, Functional Verification of Computationally Predicted qnr Genes, Annals of Clinical Microbiology and Antimicrobials 12(34) 2013

Johnning A, Moore ERB, Svensson-Stadler L, Shouche YS, Larsson DGJ, Kristiansson E. The acquired genetic mechanisms of a multi-resistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production, Applied Environmental Microbiology doi: 10.1128/AEM.02141-13

Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, Amend A, 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 analysis of environmental sequencing data, Methods in Ecology and Evolution 4(10) 2013.

Wilzén A, Krona C, Sveinbjörnsson B, Kristiansson E, Dalevi D, Øra I, De Preter K, Stallings R L, Maris J, Versteeg R, Nilsson S, Kogner P, Abel F, ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours, Molecular Cancer 12(70) 2013.

Rutgersson C, Gunnarsson L, Kristiansson E, Larsson DGJ. Oral exposure to industrial effluent with exceptionally high levels of drugs does not indicate acute toxic effects in rats, Environmental Science and Chemistry 32(2) 2013.

Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M, Kauserud H, Ryberg M, Kristiansson E, Nilsson RH, Incorporating molecular data in fungal systematics: a guide for aspiring researchers. 2013. To appear in Current Research in Environmental & Applied Mycology.

Asker N, Kristiansson E, Albertsson E, Larsson DGJ, Förlin L, Hepatic transcriptome profiling indicates differential mRNA expression of apoptosis and immune related genes in eelpout (Zoarces viviparus) caught at Göteborg harbor, Sweden, Aquatic Toxicology 130-131 2013.

Kristiansson, E, Österlund, T, Gunnarsson, L, Arne, G, Larsson, DGJ, Nerman O. A novel method for cross-species gene expression analysis. BMC Bioinformatics, 14:70, 2013.

Boulund F, Johnning A, Pereira M, Larsson DGJ, Kristiansson, E. A method for identification of quinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequence data, BMC Genomics, 13:694, 2012.

Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Nylander J, Bergsten J, Porter T, Jumpponen A, Vaishampayan P, Hallenberg N, Bengtsson J, Eriksson M, Larsson K-H, Larsson E, Kõljalg U, Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences, MycoKeys 4 2012.

Cuklev F, Fick J, Cvijovic M, Kristiansson E, Förlin L, Larsson DGJ. Does ketoprofen or diclofenac pose the lowest risk to fish?, Journal of Hazardous Materials 229-230: 100-106 2012.

Gjertsson I, Lagerquist MK, Kristiansson E, Carlsten H, Lindholm C. Estrogen ameliorates arthritis and protects against systemic bone loss in Staphylococcus aureus infection in mice. Arthritis Research & Therapy, 14:R76 2012.

Cuklev F, Cvijovic M, Kristiansson E, Gunnarsson L, Rutgersson C, Björlenius B, Larsson DGJ. Global hepatic gene expression in rainbow trout exposed to sewage effluents: A comparison of different sewage treatment technologies. 427-428:106-14 2012.

Arne G, Nilsson B, Dahlmo J, Forssell-Aronsson, E, Kristiansson E, Ahlman H, Nilsson O. Gastrointestinal stromal tumors (GISTs) express somatostatin receptors and bind radiolabeled somatostatin analogs. Acta Oncologica 52(4):783-92.

2011

Cuklev F, Kristiansson E, Fick J, Asker N, Förlin L, Larsson DGJ. Diclofenac in fish –blood plasma levels similar to human therapeutic levels affect global hepatic gene expression. Environmental Toxicology and Chemistry 30(9) 2011.

Janzon A, Kristiansson E, Larsson DGJ. Environmental microbial communities living under very high antibiotic selection pressure. Book Chapter. 2011.

Lennquist A, Asker N, Kristiansson E, Brenthel A, Thrandur Björnsson B, Kling P, Hultman M, Larsson DJG, Förlin L. Physiology and mRNA expression in rainbow trout (Oncorhynchus mykiss) after long-term exposure to the new antifoulant medetomidine. Comparative Biochemistry and Physiology 154(3) 2011.

Kristiansson E, Fick J, Janzon A, Gabric R, Rutgersson C, Weidegård B, Söderström H, Larsson DGJ. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements PLoS ONE 6(2) 2011.

Gunnarsson L, Kristiansson E, Larsson DGJ. Environmental Comparative Pharmacology: Theory and Application. Human Pharmaceuticals in the Environment: Current and Future Perspectives. Eds: B Brooks, D Huggett Springer Verlag 2011.

Arne G, Kristiansson E, Nerman O, Kindblom LG, Ahlman H, Nilsson B and Nilsson O. Expression profiling of GIST demonstrates CD133 in tumors associated with poor survival. International Journal of Cancer 129(5) 2011.

2010
Lennquist A, Mårtensson LGE, Hedberg D, Kristiansson E, Förlin L. Colour and melanophore function in rainbow trout after long term exposure to the new antifoulant medetomidine. Chemosphere 80(9) 2010.

Nilsson HR, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson,E, Ryberg M, Jumpponen A, Abarenkov K. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecology 3(4) 2010.

Lagerstedt KK, Kristiansson E, Lönnroth C, Andersson M, Gustafsson A, Hansson E, Kressner U, Nordgren S, Lundholm K. Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients. Cancer Informatics 9 2010.

Nilsson HR, Abarenkov K, Veldre V, Nylinder S, De Wit P, Brosché S, Alfredsson JF,
Ryberg M, Kristiansson E. An open source chimera checker for the fungal ITS region. Molecular Ecology Resources 10(6) 2010.

Arvidsson Y, Bergström A, Arvidsson L, Kristiansson E, Ahlman H, Nilsson O. Hypoxia
stimulates CXCR4 signalling in ileal carcinoids. Endocrine-related cancer 17(2) 2010.

Selpi S, Bryant CH, Kemp GJ, Sarv J, Kristiansson E, Sunnerhagen P. Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC Bioinformatics 40(451) 2010.

2009
Kristiansson E, Hugenholtz P, Dalevi D. ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes, Bioinformatics 25(20) 2009.

Kristiansson E, Asker N, Förlin L, Larsson DGJ. Charaterization of the Zoarces viviparus liver transcriptome using massivly parallel pyrosequencing, BMC Genomics 10(345) 2009.

Gunnarsson L, Kristiansson E, Rutgersson C, Larsson DGJ (2009). Pharmaceutical industry effluent diluted 1:500 affect global gene expression, CYP1A activity and plasma phosphate in fish. Environmental Toxicology and Chemistry, 28(12) 2009.

Thorsen M, Perrone G, Kristiansson E, Traini M, Sohrman M, Dawes IW, Peter M, Nerman O, Tamás M. Genetic basis of arsenite and cadmium tolerance in yeast. BMC Genomics 10(105) 2009.

Kristiansson E, Thorsen M, Tamas M, Nerman O. Evolutonary forces act on promoter length: identification of enriched of cis-regulatory elements. Molecular Biology and Evolution 26(6) 2009.

Nilsson HR, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Letters in Ecology 296(1) 2009.

Nilsson HR, Bok G, Ryberg M, Kristiansson E, Hallenberg N. A software pipeline for processing and identification of fungal ITS sequences. Source Code for Biology and Medicine 4(1) 2009.

Ryberg M, Kristiansson E, Sjökvist E, Nilsson HR. An outlook on the fungal ITS sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytologist 181(2) 2009.

2008
Gunnarsson L, Jauhiainen A, Kristiansson E, Nerman, O, Larsson, DGJ. Evolutionary Conservation of Human Drug Targets in Organisms used for Environmental Risk Assessments. Environmental Science and Technology 42(15) 2008.

Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH. Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and its Implications for Molecular Species Identification. Evolutionary Bioinformatics 4 2008.

Ryberg M, Nilsson HR, Kristiansson E, Töpel M, Jacobsson S, Larsson E. Mining metadata from unidentified ITS sequences in GenBank: a case study of Inocybe (Basidiomycota). BMC Evolutionary Biology 8(50) 2008.

2007
Sjögren A, Kristiansson E, Rudemo, M, Nerman, O. Weighted Analysis of General Microarray Experiments. BMC Bioinformatics 8(387) 2007.

Thorsen M, Lagniel G, Kristiansson E, Junot C, Nerman O, Labarre J, Tamas M. Quantitative transcriptome, proteome and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological Genomics 30(1) 2007.

Gunnarsson L, Kristiansson E, Förlin L, Nerman O, Larsson DGJ. Sensitive and robust gene expression changes in fish exposed to estrogen - a microarray approach. BMC Genomics 8(132) 2007.

2006
Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K, Kõljalg U. Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective. PLoS ONE 1(1) 2006.

Kristiansson E, Sjögren A, Rudemo M, Nerman O. Quality Optimised Analysis of General Paired Microarray Experiments. Statistical Applications in Genetics and Molecular Biology 5(1) 2006.

2005
Kristiansson E, Sjögren A, Rudemo M, Nerman O. Weighted Analysis of Paired Microarray Experiments. Statistical Applications in Genetics and Molecular Biology 4(1) 2005.

Nilsson RH, Kristiansson E, Ryberg M, Larsson KH. Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi. BMC Bioinformatics 6(88) 2005.

Nelander S, Larsson E, Kristiansson E, Månsson R, Nerman O, Sigvardsson M, Mostad P, Lindahl, P. Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. BMC Genomics 6(68) 2005.