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Items: 1 to 50 of 98

1.

Pharmacology beyond the patient - The environmental risks of human drugs.

Gunnarsson L, Snape JR, Verbruggen B, Owen SF, Kristiansson E, Margiotta-Casaluci L, Österlund T, Hutchinson K, Leverett D, Marks B, Tyler CR.

Environ Int. 2019 Aug;129:320-332. doi: 10.1016/j.envint.2019.04.075. Epub 2019 May 28.

2.

Identification and reconstruction of novel antibiotic resistance genes from metagenomes.

Berglund F, Österlund T, Boulund F, Marathe NP, Larsson DGJ, Kristiansson E.

Microbiome. 2019 Apr 1;7(1):52. doi: 10.1186/s40168-019-0670-1.

3.

CMY-1/MOX-family AmpC β-lactamases MOX-1, MOX-2 and MOX-9 were mobilized independently from three Aeromonas species.

Ebmeyer S, Kristiansson E, Larsson DGJ.

J Antimicrob Chemother. 2019 Feb 7. doi: 10.1093/jac/dkz025. [Epub ahead of print]

4.

177Lu-octreotate therapy for neuroendocrine tumours is enhanced by Hsp90 inhibition.

Hofving T, Sandblom V, Arvidsson Y, Shubbar E, Altiparmak G, Swanpalmer J, Almobarak B, Elf AK, Johanson V, Elias E, Kristiansson E, Forssell-Aronsson E, Nilsson O.

Endocr Relat Cancer. 2019 Feb 1. pii: ERC-18-0509.R1. doi: 10.1530/ERC-18-0509. [Epub ahead of print]

5.

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics.

Karlsson R, Gonzales-Siles L, Gomila M, Busquets A, Salvà-Serra F, Jaén-Luchoro D, Jakobsson HE, Karlsson A, Boulund F, Kristiansson E, Moore ERB.

PLoS One. 2018 Dec 10;13(12):e0208804. doi: 10.1371/journal.pone.0208804. eCollection 2018.

6.

Modelling of zero-inflation improves inference of metagenomic gene count data.

Jonsson V, Österlund T, Nerman O, Kristiansson E.

Stat Methods Med Res. 2018 Nov 25:962280218811354. doi: 10.1177/0962280218811354. [Epub ahead of print]

PMID:
30474490
7.

The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis.

Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000233. Epub 2018 Nov 21.

8.

PER extended-spectrum β-lactamases originate from Pararheinheimera spp.

Ebmeyer S, Kristiansson E, Larsson DGJ.

Int J Antimicrob Agents. 2019 Feb;53(2):158-164. doi: 10.1016/j.ijantimicag.2018.10.019. Epub 2018 Nov 2.

PMID:
30395985
9.

Accurate and Sensitive Analysis of Minimal Residual Disease in Acute Myeloid Leukemia Using Deep Sequencing of Single Nucleotide Variations.

Delsing Malmberg E, Rehammar A, Pereira MB, Abrahamsson J, Samuelsson T, Ståhlman S, Asp J, Tierens A, Palmqvist L, Kristiansson E, Fogelstrand L.

J Mol Diagn. 2019 Jan;21(1):149-162. doi: 10.1016/j.jmoldx.2018.08.004. Epub 2018 Sep 29.

PMID:
30273780
10.

Introducing ribosomal tandem repeat barcoding for fungi.

Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH.

Mol Ecol Resour. 2019 Jan;19(1):118-127. doi: 10.1111/1755-0998.12944. Epub 2018 Oct 24.

PMID:
30240145
11.

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

Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach CF, Larsson DGJ.

Environ Int. 2018 Jul;116:255-268. doi: 10.1016/j.envint.2018.04.029. Epub 2018 Apr 25.

PMID:
29704804
12.

Comparison of normalization methods for the analysis of metagenomic gene abundance data.

Pereira MB, Wallroth M, Jonsson V, Kristiansson E.

BMC Genomics. 2018 Apr 20;19(1):274. doi: 10.1186/s12864-018-4637-6.

13.

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines.

Hofving T, Arvidsson Y, Almobarak B, Inge L, Pfragner R, Persson M, Stenman G, Kristiansson E, Johanson V, Nilsson O.

Endocr Relat Cancer. 2018 Apr;25(4):X1-X2. doi: 10.1530/ERC-17-0445e. No abstract available.

PMID:
29540494
14.

Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.

Dvirnas A, Pichler C, Stewart CL, Quaderi S, Nyberg LK, Müller V, Kumar Bikkarolla S, Kristiansson E, Sandegren L, Westerlund F, Ambjörnsson T.

PLoS One. 2018 Mar 9;13(3):e0193900. doi: 10.1371/journal.pone.0193900. eCollection 2018.

15.

miRNA profiling of small intestinal neuroendocrine tumors defines novel molecular subtypes and identifies miR-375 as a biomarker of patient survival.

Arvidsson Y, Rehammar A, Bergström A, Andersson E, Altiparmak G, Swärd C, Wängberg B, Kristiansson E, Nilsson O.

Mod Pathol. 2018 Aug;31(8):1302-1317. doi: 10.1038/s41379-018-0010-1. Epub 2018 Feb 27.

PMID:
29487354
16.

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines.

Hofving T, Arvidsson Y, Almobarak B, Inge L, Pfragner R, Persson M, Stenman G, Kristiansson E, Johanson V, Nilsson O.

Endocr Relat Cancer. 2018 Mar;25(3):367-380. doi: 10.1530/ERC-17-0445. Erratum in: Endocr Relat Cancer. 2018 Apr;25(4):X1-X2.

17.

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste.

Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ.

Environ Int. 2018 Mar;112:279-286. doi: 10.1016/j.envint.2017.12.036. Epub 2018 Jan 6.

PMID:
29316517
18.

Corrigendum: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.

Nyberg LK, Quaderi S, Emilsson G, Karami N, Lagerstedt E, Müller V, Noble C, Hammarberg S, Nilsson AN, Sjöberg F, Fritzsche J, Kristiansson E, Sandegren L, Ambjörnsson T, Westerlund F.

Sci Rep. 2017 Dec 22;7:46911. doi: 10.1038/srep46911.

19.

Discovery of the fourth mobile sulfonamide resistance gene.

Razavi M, Marathe NP, Gillings MR, Flach CF, Kristiansson E, Joakim Larsson DG.

Microbiome. 2017 Dec 15;5(1):160. doi: 10.1186/s40168-017-0379-y.

20.

ECOdrug: a database connecting drugs and conservation of their targets across species.

Verbruggen B, Gunnarsson L, Kristiansson E, Österlund T, Owen SF, Snape JR, Tyler CR.

Nucleic Acids Res. 2018 Jan 4;46(D1):D930-D936. doi: 10.1093/nar/gkx1024.

21.

Environmental factors influencing the development and spread of antibiotic resistance.

Bengtsson-Palme J, Kristiansson E, Larsson DGJ.

FEMS Microbiol Rev. 2018 Jan 1;42(1). doi: 10.1093/femsre/fux053. Review.

22.

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

Berglund F, Marathe NP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach CF, Larsson DGJ, Kristiansson E.

Microbiome. 2017 Oct 12;5(1):134. doi: 10.1186/s40168-017-0353-8.

23.

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.

Boulund F, Berglund F, Flach CF, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E.

BMC Genomics. 2017 Sep 2;18(1):682. doi: 10.1186/s12864-017-4064-0.

24.

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.

Marathe NP, Pal C, Gaikwad SS, Jonsson V, Kristiansson E, Larsson DGJ.

Water Res. 2017 Nov 1;124:388-397. doi: 10.1016/j.watres.2017.07.060. Epub 2017 Jul 25.

PMID:
28780361
25.

Using metagenomics to investigate human and environmental resistomes.

Bengtsson-Palme J, Larsson DGJ, Kristiansson E.

J Antimicrob Chemother. 2017 Oct 1;72(10):2690-2703. doi: 10.1093/jac/dkx199. Review.

PMID:
28673041
26.

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing.

Corcoll N, Österlund T, Sinclair L, Eiler A, Kristiansson E, Backhaus T, Eriksson KM.

FEMS Microbiol Lett. 2017 Aug 1;364(14). doi: 10.1093/femsle/fnx139.

PMID:
28673033
27.

HirBin: high-resolution identification of differentially abundant functions in metagenomes.

Österlund T, Jonsson V, Kristiansson E.

BMC Genomics. 2017 Apr 21;18(1):316. doi: 10.1186/s12864-017-3686-6.

28.

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics.

Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, Al-Bayati O, Åhrén C, Moore ERB, Kristiansson E.

Mol Cell Proteomics. 2017 Jun;16(6):1052-1063. doi: 10.1074/mcp.M116.061721. Epub 2017 Apr 18.

29.

Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.

Jakobsson HE, Salvà-Serra F, Thorell K, Karlsson R, Gonzales-Silès L, Boulund F, Engstrand L, Kristiansson E, Moore ER.

Genome Announc. 2017 Apr 6;5(14). pii: e00125-17. doi: 10.1128/genomeA.00125-17.

30.

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, Kristiansson E, Östman M, Bengtsson-Palme J, Tysklind M, Larsson DGJ.

Sci Total Environ. 2017 Jul 15;590-591:461-468. doi: 10.1016/j.scitotenv.2017.01.213. Epub 2017 Mar 8.

PMID:
28284638
31.

Draft Genome Sequence of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample.

Johnning A, Jakobsson HE, Boulund F, Salvà-Serra F, Moore ER, Åhrén C, Karami N, Kristiansson E.

Genome Announc. 2016 Dec 15;4(6). pii: e01382-16. doi: 10.1128/genomeA.01382-16.

32.

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.

Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F.

Sci Rep. 2016 Dec 1;6:37938. doi: 10.1038/srep37938.

33.

Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes.

Jonsson V, Österlund T, Nerman O, Kristiansson E.

J Comput Biol. 2017 Apr;24(4):311-326. doi: 10.1089/cmb.2016.0180. Epub 2016 Nov 28.

PMID:
27892712
34.

The structure and diversity of human, animal and environmental resistomes.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG.

Microbiome. 2016 Oct 7;4(1):54.

35.

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

Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach CF, Fick J, Kristiansson E, Tysklind M, Larsson DGJ.

Sci Total Environ. 2016 Dec 1;572:697-712. doi: 10.1016/j.scitotenv.2016.06.228. Epub 2016 Aug 17.

PMID:
27542633
36.

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.

Nyberg LK, Quaderi S, Emilsson G, Karami N, Lagerstedt E, Müller V, Noble C, Hammarberg S, Nilsson AN, Sjöberg F, Fritzsche J, Kristiansson E, Sandegren L, Ambjörnsson T, Westerlund F.

Sci Rep. 2016 Jul 27;6:30410. doi: 10.1038/srep30410. Erratum in: Sci Rep. 2017 Dec 22;7:46911.

37.

HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models.

Pereira MB, Wallroth M, Kristiansson E, Axelson-Fisk M.

J Comput Biol. 2016 Nov;23(11):891-902. Epub 2016 Jul 18.

PMID:
27428829
38.

Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany.

Asker N, Albertsson E, Wijkmark E, Bergek S, Parkkonen J, Kammann U, Holmqvist I, Kristiansson E, Strand J, Gercken J, Förlin L.

Mar Environ Res. 2016 Sep;120:32-43. doi: 10.1016/j.marenvres.2016.07.002. Epub 2016 Jul 7.

PMID:
27423807
39.

Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.

Jakobsson HE, Salvà-Serra F, Thorell K, Gonzales-Siles L, Boulund F, Karlsson R, Sikora P, Engstrand L, Kristiansson E, Moore ER.

Genome Announc. 2016 Jun 16;4(3). pii: e00552-16. doi: 10.1128/genomeA.00552-16.

40.

Patient-tailored analysis of minimal residual disease in acute myeloid leukemia using next-generation sequencing.

Malmberg EB, Ståhlman S, Rehammar A, Samuelsson T, Alm SJ, Kristiansson E, Abrahamsson J, Garelius H, Pettersson L, Ehinger M, Palmqvist L, Fogelstrand L.

Eur J Haematol. 2017 Jan;98(1):26-37. doi: 10.1111/ejh.12780. Epub 2016 Jun 8.

PMID:
27197529
41.

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

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 ER.

Genome Announc. 2016 Mar 24;4(2). pii: e00175-16. doi: 10.1128/genomeA.00175-16.

42.

Expression profiling of small intestinal neuroendocrine tumors identifies subgroups with clinical relevance, prognostic markers and therapeutic targets.

Andersson E, Arvidsson Y, Swärd C, Hofving T, Wängberg B, Kristiansson E, Nilsson O.

Mod Pathol. 2016 Jun;29(6):616-29. doi: 10.1038/modpathol.2016.48. Epub 2016 Mar 11.

43.

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics.

Jonsson V, Österlund T, Nerman O, Kristiansson E.

BMC Genomics. 2016 Jan 25;17:78. doi: 10.1186/s12864-016-2386-y.

44.

Resistance Mutations in gyrA and parC are Common in Escherichia Communities of both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments.

Johnning A, Kristiansson E, Fick J, Weijdegård B, Larsson DG.

Front Microbiol. 2015 Dec 9;6:1355. doi: 10.3389/fmicb.2015.01355. eCollection 2015.

45.

Malignant pheochromocytomas/paragangliomas harbor mutations in transport and cell adhesion genes.

Wilzén A, Rehammar A, Muth A, Nilsson O, Tešan Tomić T, Wängberg B, Kristiansson E, Abel F.

Int J Cancer. 2016 May 1;138(9):2201-11. doi: 10.1002/ijc.29957. Epub 2015 Dec 30.

46.

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

Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM.

Front Microbiol. 2015 Oct 30;6:1192. doi: 10.3389/fmicb.2015.01192. eCollection 2015.

47.

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. 2015 Nov 17;16:964. doi: 10.1186/s12864-015-2153-5.

48.

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.

Johnning A, Kristiansson E, Angelin M, Marathe N, Shouche YS, Johansson A, Larsson DG.

BMC Microbiol. 2015 Oct 24;15:235. doi: 10.1186/s12866-015-0574-6.

49.

Tentacle: distributed quantification of genes in metagenomes.

Boulund F, Sjögren A, Kristiansson E.

Gigascience. 2015 Sep 7;4:40. doi: 10.1186/s13742-015-0078-1. eCollection 2015.

50.

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

Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DG, Johansson A.

Antimicrob Agents Chemother. 2015 Oct;59(10):6551-60. doi: 10.1128/AAC.00933-15. Epub 2015 Aug 10.

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