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Cluster analysis on high dimensional RNA-seq data with applications to cancer research - An evaluation study.

Vidman L, Källberg D, Rydén P.

PLoS One. 2019 Dec 5;14(12):e0219102. doi: 10.1371/journal.pone.0219102. eCollection 2019.


Gene expression profiles define molecular subtypes of prostate cancer bone metastases with different outcomes and morphology traceable back to the primary tumor.

Thysell E, Vidman L, Ylitalo EB, Jernberg E, Crnalic S, Iglesias-Gato D, Flores-Morales A, Stattin P, Egevad L, Widmark A, Rydén P, Bergh A, Wikström P.

Mol Oncol. 2019 Aug;13(8):1763-1777. doi: 10.1002/1878-0261.12526. Epub 2019 Jun 27.


A panel of correlates predicts vaccine-induced protection of rats against respiratory challenge with virulent Francisella tularensis.

De Pascalis R, Hahn A, Brook HM, Ryden P, Donart N, Mittereder L, Frey B, Wu TH, Elkins KL.

PLoS One. 2018 May 25;13(5):e0198140. doi: 10.1371/journal.pone.0198140. eCollection 2018.


Temporal and long-term gut microbiota variation in allergic disease: A prospective study from infancy to school age.

Simonyté Sjödin K, Hammarström ML, Rydén P, Sjödin A, Hernell O, Engstrand L, West CE.

Allergy. 2019 Jan;74(1):176-185. doi: 10.1111/all.13485. Epub 2018 Oct 18.


Vaccine-Mediated Mechanisms Controlling Replication of Francisella tularensis in Human Peripheral Blood Mononuclear Cells Using a Co-culture System.

Eneslätt K, Golovliov I, Rydén P, Sjöstedt A.

Front Cell Infect Microbiol. 2018 Feb 7;8:27. doi: 10.3389/fcimb.2018.00027. eCollection 2018.


Bioethanol production from spent mushroom compost derived from chaff of millet and sorghum.

Ryden P, Efthymiou MN, Tindyebwa TAM, Elliston A, Wilson DR, Waldron KW, Malakar PK.

Biotechnol Biofuels. 2017 Aug 4;10:195. doi: 10.1186/s13068-017-0880-3. eCollection 2017.


Erratum to: A new concept and a comprehensive evaluation of SYSMEX UF-1000i flow cytometer to identify culture-negative urine specimens in patients with UTI.

Monsen T, Ryden P.

Eur J Clin Microbiol Infect Dis. 2017 Sep;36(9):1705. doi: 10.1007/s10096-017-3059-8. No abstract available.


SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.

Stattin EL, Henning P, Klar J, McDermott E, Stecksen-Blicks C, Sandström PE, Kellgren TG, Rydén P, Hallmans G, Lönnerholm T, Ameur A, Helfrich MH, Coxon FP, Dahl N, Wikström J, Lerner UH.

Sci Rep. 2017 Jun 7;7(1):3012. doi: 10.1038/s41598-017-02533-2.


A statistically compiled test battery for feasible evaluation of knee function after rupture of the Anterior Cruciate Ligament - derived from long-term follow-up data.

Schelin L, Tengman E, Ryden P, Häger C.

PLoS One. 2017 May 1;12(5):e0176247. doi: 10.1371/journal.pone.0176247. eCollection 2017.


A new concept and a comprehensive evaluation of SYSMEX UF-1000i  flow cytometer to identify culture-negative urine specimens in patients with UTI.

Monsen T, Ryden P.

Eur J Clin Microbiol Infect Dis. 2017 Sep;36(9):1691-1703. doi: 10.1007/s10096-017-2964-1. Epub 2017 Apr 6. Erratum in: Eur J Clin Microbiol Infect Dis. 2017 Jul 15;:.


High-risk regions and outbreak modelling of tularemia in humans.

Desvars-Larrive A, Liu X, Hjertqvist M, Sjöstedt A, Johansson A, Rydén P.

Epidemiol Infect. 2017 Feb;145(3):482-490. doi: 10.1017/S0950268816002478. Epub 2016 Nov 3.


Durum wheat particle size affects starch and protein digestion in vitro.

Mandalari G, Merali Z, Ryden P, Chessa S, Bisignano C, Barreca D, Bellocco E, Laganà G, Faulks RM, Waldron KW.

Eur J Nutr. 2018 Feb;57(1):319-325. doi: 10.1007/s00394-016-1321-y. Epub 2016 Oct 26.


Results of application of the ISPD guidelines to the management of peritoneal dialysis in a single center in Sudan.

Kheir SM, Kafi SK, Ryden P, Elbir H, Soliman MA, Ali S, Abulikailik R, Ahamed K, Abu-Aisha H.

J Infect Public Health. 2017 May - Jun;10(3):348-352. doi: 10.1016/j.jiph.2016.08.008. Epub 2016 Oct 5.


Comparison of saccharification and fermentation of steam exploded rice straw and rice husk.

Wood IP, Cao HG, Tran L, Cook N, Ryden P, Wilson DR, Moates GK, Collins SR, Elliston A, Waldron KW.

Biotechnol Biofuels. 2016 Sep 5;9(1):193. doi: 10.1186/s13068-016-0599-6. eCollection 2016.


Emerging evidence of the role of gut microbiota in the development of allergic diseases.

Simonyte Sjödin K, Vidman L, Rydén P, West CE.

Curr Opin Allergy Clin Immunol. 2016 Aug;16(4):390-5. doi: 10.1097/ACI.0000000000000277. Review.


Ethanol from a biorefinery waste stream: Saccharification of amylase, protease and xylanase treated wheat bran.

Wood IP, Cook NM, Wilson DR, Ryden P, Robertson JA, Waldron KW.

Food Chem. 2016 May 1;198:125-31. doi: 10.1016/j.foodchem.2015.09.108. Epub 2015 Oct 23.


Gut microbiome and innate immune response patterns in IgE-associated eczema.

West CE, Rydén P, Lundin D, Engstrand L, Tulic MK, Prescott SL.

Clin Exp Allergy. 2015 Sep;45(9):1419-29. doi: 10.1111/cea.12566.


Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates.

Field SJ, Ryden P, Wilson D, James SA, Roberts IN, Richardson DJ, Waldron KW, Clarke TA.

Biotechnol Biofuels. 2015 Feb 26;8:33. doi: 10.1186/s13068-015-0217-z. eCollection 2015.


Mutations in collagen, type XVII, alpha 1 (COL17A1) cause epithelial recurrent erosion dystrophy (ERED).

Jonsson F, Byström B, Davidson AE, Backman LJ, Kellgren TG, Tuft SJ, Koskela T, Rydén P, Sandgren O, Danielson P, Hardcastle AJ, Golovleva I.

Hum Mutat. 2015 Apr;36(4):463-73. doi: 10.1002/humu.22764.


Epidemiology and ecology of tularemia in Sweden, 1984-2012.

Desvars A, Furberg M, Hjertqvist M, Vidman L, Sjöstedt A, Rydén P, Johansson A.

Emerg Infect Dis. 2015 Jan;21(1):32-9. doi: 10.3201/eid2101.140916.


Within-population distribution of trimethoprim resistance in Escherichia coli before and after a community-wide intervention on trimethoprim use.

Sundqvist M, Granholm S, Naseer U, Rydén P, Brolund A, Sundsfjord A, Kahlmeter G, Johansson A.

Antimicrob Agents Chemother. 2014 Dec;58(12):7492-500. doi: 10.1128/AAC.03228-14. Epub 2014 Oct 6.


What happens to food choices when a gluten-free diet is required? A prospective longitudinal population-based study among Swedish adolescent with coeliac disease and their peers.

Kautto E, Rydén PJ, Ivarsson A, Olsson C, Norström F, Högberg L, Carlsson A, Hagfors L, Hörnell A.

J Nutr Sci. 2014 Feb 13;3:e2. doi: 10.1017/jns.2013.24. eCollection 2014.


Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias.

Degerman S, Landfors M, Siwicki JK, Revie J, Borssén M, Evelönn E, Forestier E, Chrzanowska KH, Rydén P, Keith WN, Roos G.

Neoplasia. 2014 Jul;16(7):606-15. doi: 10.1016/j.neo.2014.07.001. Epub 2014 Jul 22.


Models derived from in vitro analyses of spleen, liver, and lung leukocyte functions predict vaccine efficacy against the Francisella tularensis Live Vaccine Strain (LVS).

De Pascalis R, Chou AY, Ryden P, Kennett NJ, Sjöstedt A, Elkins KL.

mBio. 2014 Apr 8;5(2):e00936. doi: 10.1128/mBio.00936-13.


OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants.

Srivastava V, Obudulu O, Bygdell J, Löfstedt T, Rydén P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnström J, Karlsson J, Melzer M, Moritz T, Trygg J, Hvidsten TR, Wingsle G.

BMC Genomics. 2013 Dec 17;14:893. doi: 10.1186/1471-2164-14-893.


Functional studies of the yeast med5, med15 and med16 mediator tail subunits.

Larsson M, Uvell H, Sandström J, Rydén P, Selth LA, Björklund S.

PLoS One. 2013 Aug 22;8(8):e73137. doi: 10.1371/journal.pone.0073137. eCollection 2013.


The shared genome is a pervasive constraint on the evolution of sex-biased gene expression.

Griffin RM, Dean R, Grace JL, Rydén P, Friberg U.

Mol Biol Evol. 2013 Sep;30(9):2168-76. doi: 10.1093/molbev/mst121. Epub 2013 Jun 29.


Cycles of light and dark co-ordinate reversible colony differentiation in Listeria monocytogenes.

Tiensuu T, Andersson C, Rydén P, Johansson J.

Mol Microbiol. 2013 Feb;87(4):909-24. doi: 10.1111/mmi.12140. Epub 2013 Jan 21.


EGFR gene variants are associated with specific somatic aberrations in glioma.

Wibom C, Ghasimi S, Van Loo P, Brännström T, Trygg J, Lau C, Henriksson R, Bergenheim T, Andersson U, Rydén P, Melin B.

PLoS One. 2012;7(12):e47929. doi: 10.1371/journal.pone.0047929. Epub 2012 Dec 7.


Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable -10 element.

Del Peso-Santos T, Landfors M, Skärfstad E, Ryden P, Shingler V.

Nucleic Acids Res. 2012 Dec;40(22):11308-20. doi: 10.1093/nar/gks934. Epub 2012 Oct 11.


Impact of steam explosion on biogas production from rape straw in relation to changes in chemical composition.

Vivekanand V, Ryden P, Horn SJ, Tapp HS, Wellner N, Eijsink VG, Waldron KW.

Bioresour Technol. 2012 Nov;123:608-15. doi: 10.1016/j.biortech.2012.06.088. Epub 2012 Jul 4.


Normalization of high dimensional genomics data where the distribution of the altered variables is skewed.

Landfors M, Philip P, Rydén P, Stenberg P.

PLoS One. 2011;6(11):e27942. doi: 10.1371/journal.pone.0027942. Epub 2011 Nov 22.


Outbreaks of tularemia in a boreal forest region depends on mosquito prevalence.

Rydén P, Björk R, Schäfer ML, Lundström JO, Petersén B, Lindblom A, Forsman M, Sjöstedt A, Johansson A.

J Infect Dis. 2012 Jan 15;205(2):297-304. doi: 10.1093/infdis/jir732. Epub 2011 Nov 28.


DNA-repair gene variants are associated with glioblastoma survival.

Wibom C, Sjöström S, Henriksson R, Brännström T, Broholm H, Rydén P, Johansen C, Collatz-Laier H, Hepworth S, McKinney PA, Bethke L, Houlston RS, Andersson U, Melin BS.

Acta Oncol. 2012 Mar;51(3):325-32. doi: 10.3109/0284186X.2011.616284. Epub 2011 Oct 21.


Classification of microarrays; synergistic effects between normalization, gene selection and machine learning.

Önskog J, Freyhult E, Landfors M, Rydén P, Hvidsten TR.

BMC Bioinformatics. 2011 Oct 7;12:390. doi: 10.1186/1471-2105-12-390.


Elongator complex influences telomeric gene silencing and DNA damage response by its role in wobble uridine tRNA modification.

Chen C, Huang B, Eliasson M, Rydén P, Byström AS.

PLoS Genet. 2011 Sep;7(9):e1002258. doi: 10.1371/journal.pgen.1002258. Epub 2011 Sep 1.


Persistence of cell-mediated immunity three decades after vaccination with the live vaccine strain of Francisella tularensis.

Eneslätt K, Rietz C, Rydén P, Stöven S, House RV, Wolfraim LA, Tärnvik A, Sjöstedt A.

Eur J Immunol. 2011 Apr;41(4):974-80. doi: 10.1002/eji.201040923. Epub 2011 Feb 21.


Diet cost, diet quality and socio-economic position: how are they related and what contributes to differences in diet costs?

Rydén PJ, Hagfors L.

Public Health Nutr. 2011 Sep;14(9):1680-92. doi: 10.1017/S1368980010003642. Epub 2011 Jan 24.


Implementing and sustaining dietary change in the context of social relationships.

Rydén PJ, Sydner YM.

Scand J Caring Sci. 2011 Sep;25(3):583-90. doi: 10.1111/j.1471-6712.2010.00867.x. Epub 2011 Jan 19.


Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.

Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RHY, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JDG, McDowell JM, Beynon J, Tyler BM.

Science. 2010 Dec 10;330(6010):1549-1551. doi: 10.1126/science.1195203.


miRNA analysis of formalin-fixed squamous cell carcinomas of the tongue is affected by age of the samples.

Rentoft M, Fahlén J, Coates PJ, Laurell G, Sjöström B, Rydén P, Nylander K.

Int J Oncol. 2011 Jan;38(1):61-9.


Molecular immune responses to aerosol challenge with Francisella tularensis in mice inoculated with live vaccine candidates of varying efficacy.

Shen H, Harris G, Chen W, Sjostedt A, Ryden P, Conlan W.

PLoS One. 2010 Oct 12;5(10):e13349. doi: 10.1371/journal.pone.0013349.


Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering.

Freyhult E, Landfors M, Önskog J, Hvidsten TR, Rydén P.

BMC Bioinformatics. 2010 Oct 11;11:503. doi: 10.1186/1471-2105-11-503.


Directed screen of Francisella novicida virulence determinants using Drosophila melanogaster.

Ahlund MK, Rydén P, Sjöstedt A, Stöven S.

Infect Immun. 2010 Jul;78(7):3118-28. doi: 10.1128/IAI.00146-10. Epub 2010 May 17.


Effects of climate change on tularaemia disease activity in Sweden.

Rydén P, Sjöstedt A, Johansson A.

Glob Health Action. 2009 Nov 11;2. doi: 10.3402/gha.v2i0.2063.


MC-normalization: a novel method for dye-normalization of two-channel microarray data.

Landfors M, Fahlén J, Rydén P.

Stat Appl Genet Mol Biol. 2009;8:Article 42. doi: 10.2202/1544-6115.1459. Epub 2009 Oct 1.


Buffering of segmental and chromosomal aneuploidies in Drosophila melanogaster.

Stenberg P, Lundberg LE, Johansson AM, Rydén P, Svensson MJ, Larsson J.

PLoS Genet. 2009 May;5(5):e1000465. doi: 10.1371/journal.pgen.1000465. Epub 2009 May 1.

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