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Year Number of Results
2010 2
2011 1
2012 4
2013 1
2014 3
2015 4
2016 2
2017 2
2018 1
2019 2
2024 0

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21 results

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Page 1
Genome sequence of Lactobacillus crispatus ST1.
Ojala T, Kuparinen V, Koskinen JP, Alatalo E, Holm L, Auvinen P, Edelman S, Westerlund-Wikström B, Korhonen TK, Paulin L, Kankainen M. Ojala T, et al. Among authors: koskinen jp. J Bacteriol. 2010 Jul;192(13):3547-8. doi: 10.1128/JB.00399-10. Epub 2010 Apr 30. J Bacteriol. 2010. PMID: 20435723 Free PMC article.
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. Koskinen P, et al. Stand Genomic Sci. 2015 Oct 24;10:83. doi: 10.1186/s40793-015-0082-1. eCollection 2015. Stand Genomic Sci. 2015. PMID: 26500719 Free PMC article.
A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. Radivojac P, et al. Among authors: koskinen p. Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27. Nat Methods. 2013. PMID: 23353650 Free PMC article.
Transcriptome analysis reveals signature of adaptation to landscape fragmentation.
Somervuo P, Kvist J, Ikonen S, Auvinen P, Paulin L, Koskinen P, Holm L, Taipale M, Duplouy A, Ruokolainen A, Saarnio S, Sirén J, Kohonen J, Corander J, Frilander MJ, Ahola V, Hanski I. Somervuo P, et al. Among authors: koskinen p. PLoS One. 2014 Jul 2;9(7):e101467. doi: 10.1371/journal.pone.0101467. eCollection 2014. PLoS One. 2014. PMID: 24988207 Free PMC article.
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. Niemi O, et al. Among authors: koskinen p. Stand Genomic Sci. 2017 Dec 20;12:87. doi: 10.1186/s40793-017-0301-z. eCollection 2017. Stand Genomic Sci. 2017. PMID: 29276572 Free PMC article.
Genome sequence of Pectobacterium sp. strain SCC3193.
Koskinen JP, Laine P, Niemi O, Nykyri J, Harjunpää H, Auvinen P, Paulin L, Pirhonen M, Palva T, Holm L. Koskinen JP, et al. J Bacteriol. 2012 Nov;194(21):6004. doi: 10.1128/JB.00681-12. J Bacteriol. 2012. PMID: 23045508 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: koskinen p. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
21 results