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Items: 1 to 50 of 61

1.

Predicting the origin of stains from whole miRNome massively parallel sequencing data.

Dørum G, Ingold S, Hanson E, Ballantyne J, Russo G, Aluri S, Snipen L, Haas C.

Forensic Sci Int Genet. 2019 May;40:131-139. doi: 10.1016/j.fsigen.2019.02.015. Epub 2019 Feb 15.

PMID:
30818157
2.

Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell.

Liu B, Zhang X, Bakken LR, Snipen L, Frostegård Å.

Front Microbiol. 2019 Jan 8;9:3208. doi: 10.3389/fmicb.2018.03208. eCollection 2018.

3.

Optimizing body fluid recognition from microbial taxonomic profiles.

Hanssen EN, Liland KH, Gill P, Snipen L.

Forensic Sci Int Genet. 2018 Nov;37:13-20. doi: 10.1016/j.fsigen.2018.07.012. Epub 2018 Jul 30.

PMID:
30071492
4.

Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota.

Ravi A, Avershina E, Angell IL, Ludvigsen J, Manohar P, Padmanaban S, Nachimuthu R, Snipen L, Rudi K.

J Microbiol Methods. 2018 Jun;149:44-52. doi: 10.1016/j.mimet.2018.02.016. Epub 2018 Mar 1.

PMID:
29501688
5.

Predicting the origin of stains from next generation sequencing mRNA data.

Dørum G, Ingold S, Hanson E, Ballantyne J, Snipen L, Haas C.

Forensic Sci Int Genet. 2018 May;34:37-48. doi: 10.1016/j.fsigen.2018.01.001. Epub 2018 Jan 6.

PMID:
29413634
6.

Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon.

Rudi K, Angell IL, Pope PB, Vik JO, Sandve SR, Snipen LG.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01974-17. doi: 10.1128/AEM.01974-17. Print 2018 Jan 15.

7.

Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome.

McLeod A, Mosleth EF, Rud I, Branco Dos Santos F, Snipen L, Liland KH, Axelsson L.

PLoS One. 2017 Nov 3;12(11):e0187542. doi: 10.1371/journal.pone.0187542. eCollection 2017.

8.

Cecal microbiota association with tumor load in a colorectal cancer mouse model.

Bråten LS, Sødring M, Paulsen JE, Snipen LG, Rudi K.

Microb Ecol Health Dis. 2017 Jan 1;28(1):1352433. doi: 10.1080/16512235.2017.1352433. eCollection 2017.

9.

Body fluid prediction from microbial patterns for forensic application.

Hanssen EN, Avershina E, Rudi K, Gill P, Snipen L.

Forensic Sci Int Genet. 2017 Sep;30:10-17. doi: 10.1016/j.fsigen.2017.05.009. Epub 2017 Jun 1.

PMID:
28605650
10.

microclass: an R-package for 16S taxonomy classification.

Liland KH, Vinje H, Snipen L.

BMC Bioinformatics. 2017 Mar 16;18(1):172. doi: 10.1186/s12859-017-1583-2.

11.

The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.

Bohlin J, Eldholm V, Pettersson JH, Brynildsrud O, Snipen L.

BMC Genomics. 2017 Feb 10;18(1):151. doi: 10.1186/s12864-017-3543-7.

12.

Evolution of the immune system influences speciation rates in teleost fishes.

Malmstrøm M, Matschiner M, Tørresen OK, Star B, Snipen LG, Hansen TF, Baalsrud HT, Nederbragt AJ, Hanel R, Salzburger W, Stenseth NC, Jakobsen KS, Jentoft S.

Nat Genet. 2016 Oct;48(10):1204-10. doi: 10.1038/ng.3645. Epub 2016 Aug 22.

PMID:
27548311
13.

A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

Mehmood T, Bohlin J, Snipen L.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):560-7. doi: 10.1109/TCBB.2014.2366146.

PMID:
26357267
14.

Comparing K-mer based methods for improved classification of 16S sequences.

Vinje H, Liland KH, Almøy T, Snipen L.

BMC Bioinformatics. 2015 Jul 1;16:205. doi: 10.1186/s12859-015-0647-4.

15.

micropan: an R-package for microbial pan-genomics.

Snipen L, Liland KH.

BMC Bioinformatics. 2015 Mar 12;16:79. doi: 10.1186/s12859-015-0517-0.

16.

A genomic virulence reference map of Enterococcus faecalis reveals an important contribution of phage03-like elements in nosocomial genetic lineages to pathogenicity in a Caenorhabditis elegans infection model.

La Rosa SL, Snipen LG, Murray BE, Willems RJ, Gilmore MS, Diep DB, Nes IF, Brede DA.

Infect Immun. 2015 May;83(5):2156-67. doi: 10.1128/IAI.02801-14. Epub 2015 Mar 16.

17.

CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data.

Brynildsrud O, Snipen LG, Bohlin J.

Bioinformatics. 2015 Jun 1;31(11):1708-15. doi: 10.1093/bioinformatics/btv070. Epub 2015 Feb 1.

PMID:
25644268
18.

An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.

Bohlin J, Brynildsrud OB, Sekse C, Snipen L.

BMC Genomics. 2014 Oct 9;15:882. doi: 10.1186/1471-2164-15-882.

19.

Rotation gene set testing for longitudinal expression data.

Dørum G, Snipen L, Solheim M, Saebø S.

Biom J. 2014 Nov;56(6):1055-75. doi: 10.1002/bimj.201100178. Epub 2014 Sep 22.

PMID:
25243581
20.

Transcriptomic and functional analysis of NaCl-induced stress in Enterococcus faecalis.

Solheim M, La Rosa SL, Mathisen T, Snipen LG, Nes IF, Brede DA.

PLoS One. 2014 Apr 22;9(4):e94571. doi: 10.1371/journal.pone.0094571. eCollection 2014.

21.

Exact computation of the distribution of likelihood ratios with forensic applications.

Dørum G, Bleka Ø, Gill P, Haned H, Snipen L, Sæbø S, Egeland T.

Forensic Sci Int Genet. 2014 Mar;9:93-101. doi: 10.1016/j.fsigen.2013.11.008. Epub 2013 Dec 9.

PMID:
24528587
22.

A systematic search for discriminating sites in the 16S ribosomal RNA gene.

Vinje H, Almøy T, Liland KH, Snipen L.

Microb Inform Exp. 2014 Jan 27;4(1):2. doi: 10.1186/2042-5783-4-2.

23.

Staphylococcus aureus nasal isolates from healthy individuals cause highly variable host cell responses in vitro: the Tromsø Staph and Skin Study.

Askarian F, Sangvik M, Hanssen AM, Snipen L, Sollid JU, Johannessen M.

Pathog Dis. 2014 Mar;70(2):158-66. doi: 10.1111/2049-632X.12099. Epub 2013 Oct 11.

PMID:
24115641
24.

Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression.

Mehmood T, Warringer J, Snipen L, Sæbø S.

BMC Bioinformatics. 2012 Dec 8;13:327. doi: 10.1186/1471-2105-13-327.

25.

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli.

Snipen L, Wassenaar TM, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knøchel S, Ussery DW, Meinersmann RJ.

Microb Inform Exp. 2012 Aug 28;2(1):8. doi: 10.1186/2042-5783-2-8.

26.

Microarray-based transcriptome of Listeria monocytogenes adapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid.

Tessema GT, Møretrø T, Snipen L, Heir E, Holck A, Naterstad K, Axelsson L.

Can J Microbiol. 2012 Sep;58(9):1112-23. doi: 10.1139/w2012-091. Epub 2012 Aug 22.

PMID:
22913877
27.

Exploration of multivariate analysis in microbial coding sequence modeling.

Mehmood T, Bohlin J, Kristoffersen AB, Sæbø S, Warringer J, Snipen L.

BMC Bioinformatics. 2012 May 14;13:97. doi: 10.1186/1471-2105-13-97.

28.

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands.

Bohlin J, van Passel MW, Snipen L, Kristoffersen AB, Ussery D, Hardy SP.

BMC Genomics. 2012 Feb 10;13:66. doi: 10.1186/1471-2164-13-66.

29.

A domain sequence approach to pangenomics: applications to Escherichia coli.

Snipen LG, Ussery DW.

Version 2. F1000Res. 2012 Oct 1 [revised 2013 Jan 1];1:19. doi: 10.12688/f1000research.1-19.v2. eCollection 2012.

30.

A Partial Least Squares based algorithm for parsimonious variable selection.

Mehmood T, Martens H, Sæbø S, Warringer J, Snipen L.

Algorithms Mol Biol. 2011 Dec 5;6(1):27. doi: 10.1186/1748-7188-6-27.

31.

Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase.

Mehmeti I, Faergestad EM, Bekker M, Snipen L, Nes IF, Holo H.

Appl Environ Microbiol. 2012 Jan;78(1):170-6. doi: 10.1128/AEM.06604-11. Epub 2011 Oct 28.

32.

Target recognition, resistance, immunity and genome mining of class II bacteriocins from Gram-positive bacteria.

Kjos M, Borrero J, Opsata M, Birri DJ, Holo H, Cintas LM, Snipen L, Hernández PE, Nes IF, Diep DB.

Microbiology. 2011 Dec;157(Pt 12):3256-67. doi: 10.1099/mic.0.052571-0. Epub 2011 Oct 6. Review.

PMID:
21980118
33.

Mining for genotype-phenotype relations in Saccharomyces using partial least squares.

Mehmood T, Martens H, Saebø S, Warringer J, Snipen L.

BMC Bioinformatics. 2011 Aug 3;12:318. doi: 10.1186/1471-2105-12-318.

34.

Global transcriptome response in Lactobacillus sakei during growth on ribose.

McLeod A, Snipen L, Naterstad K, Axelsson L.

BMC Microbiol. 2011 Jun 24;11:145. doi: 10.1186/1471-2180-11-145.

35.

Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant.

Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF.

J Bacteriol. 2011 May;193(9):2377-8. doi: 10.1128/JB.00183-11. Epub 2011 Mar 11.

36.

Comparative genomics of Lactobacillus sakei with emphasis on strains from meat.

Nyquist OL, McLeod A, Brede DA, Snipen L, Aakra Å, Nes IF.

Mol Genet Genomics. 2011 Apr;285(4):297-311. doi: 10.1007/s00438-011-0608-1. Epub 2011 Mar 3.

PMID:
21369871
37.

Standard operating procedure for computing pangenome trees.

Snipen L, Ussery DW.

Stand Genomic Sci. 2010 Jan 28;2(1):135-41. doi: 10.4056/sigs.38923.

38.

Global transcriptional analysis of spontaneous sakacin P-resistant mutant strains of Listeria monocytogenes during growth on different sugars.

Tessema GT, Møretrø T, Snipen L, Axelsson L, Naterstad K.

PLoS One. 2011 Jan 6;6(1):e16192. doi: 10.1371/journal.pone.0016192.

39.
40.

Smoothing gene expression data with network information improves consistency of regulated genes.

Dørum G, Snipen L, Solheim M, Saebo S.

Stat Appl Genet Mol Biol. 2011 Aug 9;10(1). pii: /j/sagmb.2011.10.issue-1/sagmb.2011.10.1.1618/sagmb.2011.10.1.1618.xml. doi: 10.2202/1544-6115.1618.

PMID:
23089828
41.

Genomic characterization of Campylobacter jejuni strain M1.

Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW.

PLoS One. 2010 Aug 26;5(8):e12253. doi: 10.1371/journal.pone.0012253.

42.

Comparative genomic analysis of pathogenic and probiotic Enterococcus faecalis isolates, and their transcriptional responses to growth in human urine.

Vebø HC, Solheim M, Snipen L, Nes IF, Brede DA.

PLoS One. 2010 Aug 31;5(8):e12489. doi: 10.1371/journal.pone.0012489.

43.

Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods.

Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J.

BMC Evol Biol. 2010 Aug 13;10:249. doi: 10.1186/1471-2148-10-249.

44.

Analysis of intra-genomic GC content homogeneity within prokaryotes.

Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Dønsvik T, Skjerve E, Ussery DW.

BMC Genomics. 2010 Aug 6;11:464. doi: 10.1186/1471-2164-11-464.

45.

The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment.

Aakra A, Vebø H, Indahl U, Snipen L, Gjerstad O, Lunde M, Nes IF.

Int J Microbiol. 2010;2010:483048. doi: 10.1155/2010/483048. Epub 2010 Jun 15.

46.

The abi proteins and their involvement in bacteriocin self-immunity.

Kjos M, Snipen L, Salehian Z, Nes IF, Diep DB.

J Bacteriol. 2010 Apr;192(8):2068-76. doi: 10.1128/JB.01553-09. Epub 2010 Feb 12.

47.

The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood.

Vebø HC, Snipen L, Nes IF, Brede DA.

PLoS One. 2009 Nov 4;4(11):e7660. doi: 10.1371/journal.pone.0007660.

48.

On the origins of a Vibrio species.

Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW.

Microb Ecol. 2010 Jan;59(1):1-13. doi: 10.1007/s00248-009-9596-7.

49.

Microbial comparative pan-genomics using binomial mixture models.

Snipen L, Almøy T, Ussery DW.

BMC Genomics. 2009 Aug 19;10:385. doi: 10.1186/1471-2164-10-385.

50.

Rotation testing in gene set enrichment analysis for small direct comparison experiments.

Dørum G, Snipen L, Solheim M, Saebø S.

Stat Appl Genet Mol Biol. 2009;8:Article34. doi: 10.2202/1544-6115.1418. Epub 2009 Jul 27.

PMID:
19645689

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