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Items: 26

1.

Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster.

Deptula P, Loivamaa I, Smolander OP, Laine P, Roberts RJ, Piironen V, Paulin L, Savijoki K, Auvinen P, Varmanen P.

Microorganisms. 2019 Oct 30;7(11). pii: E512. doi: 10.3390/microorganisms7110512.

2.

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output.

Kammonen JI, Smolander OP, Paulin L, Pereira PAB, Laine P, Koskinen P, Jernvall J, Auvinen P.

PLoS One. 2019 Sep 9;14(9):e0216885. doi: 10.1371/journal.pone.0216885. eCollection 2019.

3.

Notum produced by Paneth cells attenuates regeneration of aged intestinal epithelium.

Pentinmikko N, Iqbal S, Mana M, Andersson S, Cognetta AB 3rd, Suciu RM, Roper J, Luopajärvi K, Markelin E, Gopalakrishnan S, Smolander OP, Naranjo S, Saarinen T, Juuti A, Pietiläinen K, Auvinen P, Ristimäki A, Gupta N, Tammela T, Jacks T, Sabatini DM, Cravatt BF, Yilmaz ÖH, Katajisto P.

Nature. 2019 Jul;571(7765):398-402. doi: 10.1038/s41586-019-1383-0. Epub 2019 Jul 10.

PMID:
31292548
4.

Author Correction: 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. 2019 Jul;51(7):1187-1189. doi: 10.1038/s41588-019-0442-7. No abstract available.

PMID:
31197270
5.

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi.

Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T.

BMC Genomics. 2019 May 28;20(1):430. doi: 10.1186/s12864-019-5817-8.

6.

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.

7.

Alternative oxidase-mediated respiration prevents lethal mitochondrial cardiomyopathy.

Rajendran J, Purhonen J, Tegelberg S, Smolander OP, Mörgelin M, Rozman J, Gailus-Durner V, Fuchs H, Hrabe de Angelis M, Auvinen P, Mervaala E, Jacobs HT, Szibor M, Fellman V, Kallijärvi J.

EMBO Mol Med. 2019 Jan;11(1). pii: e9456. doi: 10.15252/emmm.201809456.

8.

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.

PMID:
30156530
9.

Poststroke delivery of MANF promotes functional recovery in rats.

Mätlik K, Anttila JE, Kuan-Yin T, Smolander OP, Pakarinen E, Lehtonen L, Abo-Ramadan U, Lindholm P, Zheng C, Harvey B, Arumäe U, Lindahl M, Airavaara M.

Sci Adv. 2018 May 23;4(5):eaap8957. doi: 10.1126/sciadv.aap8957. eCollection 2018 May.

10.

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 Sep 20;281:10-22. doi: 10.1016/j.ijfoodmicro.2018.05.017. Epub 2018 May 19.

11.

NAD+ repletion produces no therapeutic effect in mice with respiratory chain complex III deficiency and chronic energy deprivation.

Purhonen J, Rajendran J, Tegelberg S, Smolander OP, Pirinen E, Kallijärvi J, Fellman V.

FASEB J. 2018 May 21:fj201800090R. doi: 10.1096/fj.201800090R. [Epub ahead of print]

PMID:
29782205
12.

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.

13.

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. Erratum in: Nat Genet. 2019 Jul;51(7):1187-1189.

PMID:
28481341
14.

NOGO-A/RTN4A and NOGO-B/RTN4B are simultaneously expressed in epithelial, fibroblast and neuronal cells and maintain ER morphology.

Rämö O, Kumar D, Gucciardo E, Joensuu M, Saarekas M, Vihinen H, Belevich I, Smolander OP, Qian K, Auvinen P, Jokitalo E.

Sci Rep. 2016 Oct 27;6:35969. doi: 10.1038/srep35969.

15.

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose.

Kuuskeri J, Häkkinen M, Laine P, Smolander OP, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T.

Biotechnol Biofuels. 2016 Sep 5;9(1):192. doi: 10.1186/s13068-016-0608-9. eCollection 2016.

16.

Cytokinin and Auxin Display Distinct but Interconnected Distribution and Signaling Profiles to Stimulate Cambial Activity.

Immanen J, Nieminen K, Smolander OP, Kojima M, Alonso Serra J, Koskinen P, Zhang J, Elo A, Mähönen AP, Street N, Bhalerao RP, Paulin L, Auvinen P, Sakakibara H, Helariutta Y.

Curr Biol. 2016 Aug 8;26(15):1990-1997. doi: 10.1016/j.cub.2016.05.053. Epub 2016 Jul 14.

17.

Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T).

Koskinen P, Deptula P, Smolander OP, Tamene F, Kammonen J, Savijoki K, Paulin L, Piironen V, Auvinen P, Varmanen P.

Stand Genomic Sci. 2015 Oct 24;10:83. doi: 10.1186/s40793-015-0082-1. eCollection 2015.

18.

Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47.

Andreevskaya M, Johansson P, Laine P, Smolander OP, Sonck M, Rahkila R, Jääskeläinen E, Paulin L, Auvinen P, Björkroth J.

Appl Environ Microbiol. 2015 Jun;81(11):3800-11. doi: 10.1128/AEM.00320-15. Epub 2015 Mar 27.

19.

Increased transcriptome sequencing efficiency with modified Mint-2 digestion-ligation protocol.

Kammonen JI, Smolander OP, Sipilä T, Overmyer K, Auvinen P, Paulin L.

Anal Biochem. 2015 May 15;477:38-40. doi: 10.1016/j.ab.2014.12.001. Epub 2014 Dec 13.

PMID:
25513723
20.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I.

Nat Commun. 2014 Sep 5;5:4737. doi: 10.1038/ncomms5737.

21.

Transcriptome dynamics-based operon prediction in prokaryotes.

Fortino V, Smolander OP, Auvinen P, Tagliaferri R, Greco D.

BMC Bioinformatics. 2014 May 16;15:145. doi: 10.1186/1471-2105-15-145.

22.

Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter.

Smolander OP, Kandhavelu M, Mannerström H, Lihavainen E, Kalaichelvan S, Healy S, Yli-Harja O, Karp M, Ribeiro AS.

BMC Mol Biol. 2011 May 14;12:21. doi: 10.1186/1471-2199-12-21.

23.

Information propagation within the Genetic Network of Saccharomyces cerevisiae.

Chowdhury S, Lloyd-Price J, Smolander OP, Baici WC, Hughes TR, Yli-Harja O, Chua G, Ribeiro AS.

BMC Syst Biol. 2010 Oct 26;4:143. doi: 10.1186/1752-0509-4-143.

24.

Delayed stochastic model of transcription at the single nucleotide level.

Ribeiro AS, Smolander OP, Rajala T, Häkkinen A, Yli-Harja O.

J Comput Biol. 2009 Apr;16(4):539-53. doi: 10.1089/cmb.2008.0153.

PMID:
19361326
25.

RMBNToolbox: random models for biochemical networks.

Aho T, Smolander OP, Niemi J, Yli-Harja O.

BMC Syst Biol. 2007 May 24;1:22.

26.

Simulation tools for biochemical networks: evaluation of performance and usability.

Pettinen A, Aho T, Smolander OP, Manninen T, Saarinen A, Taattola KL, Yli-Harja O, Linne ML.

Bioinformatics. 2005 Feb 1;21(3):357-63. Epub 2004 Sep 9.

PMID:
15358616

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