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Aspirin Use and Respiratory Morbidity in COPD: A Propensity Score-Matched Analysis in Subpopulations and Intermediate Outcome Measures in COPD Study.

Fawzy A, Putcha N, Aaron CP, Bowler RP, Comellas AP, Cooper CB, Dransfield MT, Han MK, Hoffman EA, Kanner RE, Krishnan JA, Labaki WW, Paine R 3rd, Paulin LM, Peters SP, Wise R, Barr RG, Hansel NN; SPIROMICS Investigators.

Chest. 2018 Dec 26. pii: S0012-3692(18)32887-3. doi: 10.1016/j.chest.2018.11.028. [Epub ahead of print]


Benzodiazepines Safe in Chronic Obstructive Pulmonary Disease? Don't Hold Your Breath.

Koch AL, Paulin LM.

Ann Am Thorac Soc. 2019 Jan;16(1):53-55. doi: 10.1513/AnnalsATS.201809-618ED. No abstract available.


Reply to: Socioeconomic Disparities and Health Outcomes.

Raju S, Keet CA, Paulin LM, Matsui EC, Peng RD, Hansel NN, McCormack MC.

Am J Respir Crit Care Med. 2018 Dec 22. doi: 10.1164/rccm.201811-2185LE. [Epub ahead of print] No abstract available.


Bracketing phenogenotypic limits of mammalian hybridization.

Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J.

R Soc Open Sci. 2018 Nov 28;5(11):180903. doi: 10.1098/rsos.180903. eCollection 2018 Nov.


Rural Residence and Poverty are Independent Risk Factors for COPD in the United States.

Raju S, Keet CA, Paulin LM, Matsui EC, Peng RD, Hansel NN, McCormack MC.

Am J Respir Crit Care Med. 2018 Nov 2. doi: 10.1164/rccm.201807-1374OC. [Epub ahead of print]


The Receptor-like Pseudokinase GHR1 Is Required for Stomatal Closure.

Sierla M, Hõrak H, Overmyer K, Waszczak C, Yarmolinsky D, Maierhofer T, Vainonen JP, Salojärvi J, Denessiouk K, Laanemets K, Tõldsepp K, Vahisalu T, Gauthier A, Puukko T, Paulin L, Auvinen P, Geiger D, Hedrich R, Kollist H, Kangasjärvi J.

Plant Cell. 2018 Nov;30(11):2813-2837. doi: 10.1105/tpc.18.00441. Epub 2018 Oct 25.


Occupational Exposures and Computed Tomographic Imaging Characteristics in the SPIROMICS Cohort.

Paulin LM, Smith BM, Koch A, Han M, Hoffman EA, Martinez C, Ejike C, Blanc PD, Rous J, Barr RG, Peters SP, Paine R 3rd, Pirozzi C, Cooper CB, Dransfield MT, Comellas AP, Kanner RE, Drummond MB, Putcha N, Hansel NN.

Ann Am Thorac Soc. 2018 Dec;15(12):1411-1419. doi: 10.1513/AnnalsATS.201802-150OC.


Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family.

Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T.

Nat Commun. 2018 Oct 3;9(1):3735. doi: 10.1038/s41467-018-06138-9.


Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent.

Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H.

Int J Syst Evol Microbiol. 2018 Nov;68(11):3479-3486. doi: 10.1099/ijsem.0.003012. Epub 2018 Sep 18.


Acidipropionibacterium virtanenii sp. nov., isolated from malted barley.

Deptula P, Smolander OP, Laine P, Roberts RJ, Edelmann M, Peltola P, Piironen V, Paulin L, Storgårds E, Savijoki K, Laitila A, Auvinen P, Varmanen P.

Int J Syst Evol Microbiol. 2018 Oct;68(10):3175-3183. doi: 10.1099/ijsem.0.002965. Epub 2018 Aug 29.


Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress.

Laine MA, Trontti K, Misiewicz Z, Sokolowska E, Kulesskaya N, Heikkinen A, Saarnio S, Balcells I, Ameslon P, Greco D, Mattila P, Ellonen P, Paulin L, Auvinen P, Jokitalo E, Hovatta I.

eNeuro. 2018 Jul 11;5(4). pii: ENEURO.0166-18.2018. doi: 10.1523/ENEURO.0166-18.2018. eCollection 2018 Jul-Aug.


BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.

Somervuo P, Koskinen P, Mei P, Holm L, Auvinen P, Paulin L.

BMC Bioinformatics. 2018 Jul 5;19(1):257. doi: 10.1186/s12859-018-2262-7.


Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening.

Duru IC, Laine P, Andreevskaya M, Paulin L, Kananen S, Tynkkynen S, Auvinen P, Smolander OP.

Int J Food Microbiol. 2018 May 19;281:10-22. doi: 10.1016/j.ijfoodmicro.2018.05.017. [Epub ahead of print]


Dietary supplementation with yeast hydrolysate in pregnancy influences colostrum yield and gut microbiota of sows and piglets after birth.

Hasan S, Junnikkala S, Peltoniemi O, Paulin L, Lyyski A, Vuorenmaa J, Oliviero C.

PLoS One. 2018 May 24;13(5):e0197586. doi: 10.1371/journal.pone.0197586. eCollection 2018.


Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition.

Andreevskaya M, Jääskeläinen E, Johansson P, Ylinen A, Paulin L, Björkroth J, Auvinen P.

Appl Environ Microbiol. 2018 Jun 18;84(13). pii: e00554-18. doi: 10.1128/AEM.00554-18. Print 2018 Jul 1.


Lower serum IgA is associated with COPD exacerbation risk in SPIROMICS.

Putcha N, Paul GG, Azar A, Wise RA, O'Neal WK, Dransfield MT, Woodruff PG, Curtis JL, Comellas AP, Drummond MB, Lambert AA, Paulin LM, Fawzy A, Kanner RE, Paine R 3rd, Han MK, Martinez FJ, Bowler RP, Barr RG, Hansel NN; SPIROMICS investigators.

PLoS One. 2018 Apr 12;13(4):e0194924. doi: 10.1371/journal.pone.0194924. eCollection 2018.


Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes.

Åvall-Jääskeläinen S, Taponen S, Kant R, Paulin L, Blom J, Palva A, Koort J.

PeerJ. 2018 Mar 30;6:e4560. doi: 10.7717/peerj.4560. eCollection 2018.


The complexity of titin splicing pattern in human adult skeletal muscles.

Savarese M, Jonson PH, Huovinen S, Paulin L, Auvinen P, Udd B, Hackman P.

Skelet Muscle. 2018 Mar 29;8(1):11. doi: 10.1186/s13395-018-0156-z.


Rural Residence and COPD Exacerbations: Analysis of the SPIROMICS Cohort.

Burkes RM, Gassett AJ, Ceppe AS, Anderson W, O'Neal WK, Woodruff PG, Krishnan JA, Barr RG, Han MK, Martinez FJ, Comellas AP, Lambert AA, Kaufman JD, Dransfield MT, Wells JM, Kanner RE, Paine R 3rd, Bleecker ER, Paulin LM, Hansel NN, Drummond MB; SPIROMICS Investigators.

Ann Am Thorac Soc. 2018 Mar 27. doi: 10.1513/AnnalsATS.201710-837OC. [Epub ahead of print]


BK polyomavirus microRNA expression and sequence variation in polyomavirus-associated nephropathy.

Virtanen E, Seppälä H, Helanterä I, Laine P, Lautenschlager I, Paulin L, Mannonen L, Auvinen P, Auvinen E.

J Clin Virol. 2018 May;102:70-76. doi: 10.1016/j.jcv.2018.02.007. Epub 2018 Feb 12.


Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells.

Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT.

Nucleic Acids Res. 2018 Jun 1;46(10):5209-5226. doi: 10.1093/nar/gky159.


Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains.

Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K.

Microb Biotechnol. 2018 May;11(3):510-526. doi: 10.1111/1751-7915.13254. Epub 2018 Feb 28.


Association of thrombocytosis with COPD morbidity: the SPIROMICS and COPDGene cohorts.

Fawzy A, Putcha N, Paulin LM, Aaron CP, Labaki WW, Han MK, Wise RA, Kanner RE, Bowler RP, Barr RG, Hansel NN; SPIROMICS and COPDGene Investigators.

Respir Res. 2018 Jan 26;19(1):20. doi: 10.1186/s12931-018-0717-z.


Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering.

Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H.

Nucleic Acids Res. 2018 May 18;46(9):4649-4661. doi: 10.1093/nar/gkx1281.


Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1.

Niemi O, Laine P, Koskinen P, Pasanen M, Pennanen V, Harjunpää H, Nykyri J, Holm L, Paulin L, Auvinen P, Palva ET, Pirhonen M.

Stand Genomic Sci. 2017 Dec 20;12:87. doi: 10.1186/s40793-017-0301-z. eCollection 2017.


Breakpoint mapping and haplotype analysis of translocation t(1;12)(q43;q21.1) in two apparently independent families with vascular phenotypes.

Luukkonen TM, Mehrjouy MM, Pöyhönen M, Anttonen AK, Lahermo P, Ellonen P, Paulin L, Tommerup N, Palotie A, Varilo T.

Mol Genet Genomic Med. 2018 Jan;6(1):56-68. doi: 10.1002/mgg3.346. Epub 2017 Nov 23.


Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum.

Hasan S, Aho V, Pereira P, Paulin L, Koivusalo SB, Auvinen P, Eriksson JG.

Acta Obstet Gynecol Scand. 2018 Jan;97(1):38-46. doi: 10.1111/aogs.13252.


Complete Genome Sequence of Eubacterium hallii Strain L2-7.

Shetty SA, Ritari J, Paulin L, Smidt H, De Vos WM.

Genome Announc. 2017 Oct 26;5(43). pii: e01167-17. doi: 10.1128/genomeA.01167-17.


De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii.

Deptula P, Laine PK, Roberts RJ, Smolander OP, Vihinen H, Piironen V, Paulin L, Jokitalo E, Savijoki K, Auvinen P, Varmanen P.

BMC Genomics. 2017 Oct 16;18(1):790. doi: 10.1186/s12864-017-4165-9.


Archetype JC Polyomavirus (JCPyV) Prevails in a Rare Case of JCPyV Nephropathy and in Stable Renal Transplant Recipients With JCPyV Viruria.

Seppälä HM, Helanterä IT, Laine PKS, Lautenschlager IT, Paulín LG, Jahnukainen TJ, Auvinen POV, Auvinen E.

J Infect Dis. 2017 Nov 15;216(8):981-989. doi: 10.1093/infdis/jix435.


Design of the Subpopulations and Intermediate Outcome Measures in COPD (SPIROMICS) AIR Study.

Hansel NN, Paulin LM, Gassett AJ, Peng RD, Alexis N, Fan VS, Bleecker E, Bowler R, Comellas AP, Dransfield M, Han MK, Kim V, Krishnan JA, Pirozzi C, Cooper CB, Martinez F, Woodruff PG, Breysse PJ, Barr RG, Kaufman JD.

BMJ Open Respir Res. 2017 May 18;4(1):e000186. doi: 10.1136/bmjresp-2017-000186. eCollection 2017.


Impact of Physical Activity on Reporting of Childhood Asthma Symptoms.

Nnodum BN, McCormack MC, Putcha N, Hwang S, Paulin LM, Brigham EP, Fawzy A, Romero K, Diette GB, Hansel NN.

Lung. 2017 Dec;195(6):693-698. doi: 10.1007/s00408-017-0049-7. Epub 2017 Sep 15.


More than constipation - bowel symptoms in Parkinson's disease and their connection to gut microbiota.

Mertsalmi TH, Aho VTE, Pereira PAB, Paulin L, Pekkonen E, Auvinen P, Scheperjans F.

Eur J Neurol. 2017 Nov;24(11):1375-1383. doi: 10.1111/ene.13398. Epub 2017 Sep 11.


24-h Nitrogen dioxide concentration is associated with cooking behaviors and an increase in rescue medication use in children with asthma.

Paulin LM, Williams D'L, Peng R, Diette GB, McCormack MC, Breysse P, Hansel NN.

Environ Res. 2017 Nov;159:118-123. doi: 10.1016/j.envres.2017.07.052. Epub 2017 Aug 7.


Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia.

Pereira P, Aho V, Arola J, Boyd S, Jokelainen K, Paulin L, Auvinen P, Färkkilä M.

PLoS One. 2017 Aug 10;12(8):e0182924. doi: 10.1371/journal.pone.0182924. eCollection 2017.


Clonal Analysis of Regulatory T Cell Defect in Patients with Autoimmune Polyendocrine Syndrome Type 1 Suggests Intrathymic Impairment.

Koivula TT, Laakso SM, Niemi HJ, Kekäläinen E, Laine P, Paulin L, Auvinen P, Arstila TP.

Scand J Immunol. 2017 Oct;86(4):221-228. doi: 10.1111/sji.12586.


Correction: Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system.

Nissilä E, Douillard FP, Ritari J, Paulin L, Järvinen HM, Rasinkangas P, Haapasalo K, Meri S, Jarva H, de Vos WM.

PLoS One. 2017 Jul 10;12(7):e0181292. doi: 10.1371/journal.pone.0181292. eCollection 2017.


Performance of microbiological, serological, molecular, and modified seminal plasma methods in the diagnosis of Brucella abortus in semen and serum of bovine bulls.

Nardi Júnior G, Megid J, Mathias LA, Paulin L, Vicente AF, Cortez A, Listoni FJP, Lara GHB, Motta RG, Chacur MGM, Monteiro FM, Ribeiro MG.

Biologicals. 2017 Jul;48:6-9. doi: 10.1016/j.biologicals.2017.06.005. Epub 2017 Jun 27.


Colder temperature is associated with increased COPD morbidity.

McCormack MC, Paulin LM, Gummerson CE, Peng RD, Diette GB, Hansel NN.

Eur Respir J. 2017 Jun 29;49(6). pii: 1601501. doi: 10.1183/13993003.01501-2016. Print 2017 Jun. No abstract available.


Isotretinoin and lymecycline treatments modify the skin microbiota in acne.

Kelhälä HL, Aho VTE, Fyhrquist N, Pereira PAB, Kubin ME, Paulin L, Palatsi R, Auvinen P, Tasanen K, Lauerma A.

Exp Dermatol. 2018 Jan;27(1):30-36. doi: 10.1111/exd.13397. Epub 2017 Sep 14.


Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system.

Nissilä E, Douillard FP, Ritari J, Paulin L, Järvinen HM, Rasinkangas P, Haapasalo K, Meri S, Jarva H, de Vos WM.

PLoS One. 2017 May 11;12(5):e0176739. doi: 10.1371/journal.pone.0176739. eCollection 2017. Erratum in: PLoS One. 2017 Jul 10;12 (7):e0181292.


Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J.

Nat Genet. 2017 Jun;49(6):904-912. doi: 10.1038/ng.3862. Epub 2017 May 8.


Single-Molecule Sequencing Revealing the Presence of Distinct JC Polyomavirus Populations in Patients With Progressive Multifocal Leukoencephalopathy.

Seppälä H, Virtanen E, Saarela M, Laine P, Paulín L, Mannonen L, Auvinen P, Auvinen E.

J Infect Dis. 2017 Mar 15;215(6):889-895. doi: 10.1093/infdis/jiw399.


Oral and nasal microbiota in Parkinson's disease.

Pereira PAB, Aho VTE, Paulin L, Pekkonen E, Auvinen P, Scheperjans F.

Parkinsonism Relat Disord. 2017 May;38:61-67. doi: 10.1016/j.parkreldis.2017.02.026. Epub 2017 Feb 22.


Skin Microbiome in Small- and Large-plaque Parapsoriasis.

Salava A, Pereira P, Aho V, Väkevä L, Paulin L, Auvinen P, Ranki A, Lauerma A.

Acta Derm Venereol. 2017 Jun 9;97(6):685-691. doi: 10.2340/00015555-2631.


Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia.

Ruokolainen L, Paalanen L, Karkman A, Laatikainen T, von Hertzen L, Vlasoff T, Markelova O, Masyuk V, Auvinen P, Paulin L, Alenius H, Fyhrquist N, Hanski I, Mäkelä MJ, Zilber E, Jousilahti P, Vartiainen E, Haahtela T.

Clin Exp Allergy. 2017 May;47(5):665-674. doi: 10.1111/cea.12895. Epub 2017 Mar 6.


Loss of cutaneous microbial diversity during first 3 weeks of life in very low birthweight infants.

Salava A, Aho V, Lybeck E, Pereira P, Paulin L, Nupponen I, Ranki A, Auvinen P, Andersson S, Lauerma A.

Exp Dermatol. 2017 Oct;26(10):861-867. doi: 10.1111/exd.13312. Epub 2017 May 3.


Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.

Ouwerkerk JP, Koehorst JJ, Schaap PJ, Ritari J, Paulin L, Belzer C, de Vos WM.

Genome Announc. 2017 Jan 5;5(1). pii: e01098-16. doi: 10.1128/genomeA.01098-16.


An Inducible Operon Is Involved in Inulin Utilization in Lactobacillus plantarum Strains, as Revealed by Comparative Proteogenomics and Metabolic Profiling.

Buntin N, Hongpattarakere T, Ritari J, Douillard FP, Paulin L, Boeren S, Shetty SA, de Vos WM.

Appl Environ Microbiol. 2016 Dec 30;83(2). pii: e02402-16. doi: 10.1128/AEM.02402-16. Print 2017 Jan 15.


Comparative genomics and physiology of the butyrate-producing bacterium Intestinimonas butyriciproducens.

Bui TP, Shetty SA, Lagkouvardos I, Ritari J, Chamlagain B, Douillard FP, Paulin L, Piironen V, Clavel T, Plugge CM, de Vos WM.

Environ Microbiol Rep. 2016 Dec;8(6):1024-1037. doi: 10.1111/1758-2229.12483. Epub 2016 Nov 9.


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