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Items: 47

1.

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.

Lin YC, Wang J, Delhomme N, Schiffthaler B, Sundström G, Zuccolo A, Nystedt B, Hvidsten TR, de la Torre A, Cossu RM, Hoeppner MP, Lantz H, Scofield DG, Zamani N, Johansson A, Mannapperuma C, Robinson KM, Mähler N, Leitch IJ, Pellicer J, Park EJ, Van Montagu M, Van de Peer Y, Grabherr M, Jansson S, Ingvarsson PK, Street NR.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10970-E10978. doi: 10.1073/pnas.1801437115. Epub 2018 Oct 29.

2.

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.

Kunath BJ, Delogu F, Naas AE, Arntzen MØ, Eijsink VGH, Henrissat B, Hvidsten TR, Pope PB.

ISME J. 2018 Oct 12. doi: 10.1038/s41396-018-0290-y. [Epub ahead of print]

PMID:
30315317
3.

The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.

Varadharajan S, Sandve SR, Gillard GB, Tørresen OK, Mulugeta TD, Hvidsten TR, Lien S, Asbjørn Vøllestad L, Jentoft S, Nederbragt AJ, Jakobsen KS.

Genome Biol Evol. 2018 Oct 1;10(10):2785-2800. doi: 10.1093/gbe/evy201.

4.

Subfunctionalization versus neofunctionalization after whole-genome duplication.

Sandve SR, Rohlfs RV, Hvidsten TR.

Nat Genet. 2018 Jul;50(7):908-909. doi: 10.1038/s41588-018-0162-4. No abstract available.

PMID:
29955176
5.

Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.

Felten J, Vahala J, Love J, Gorzsás A, Rüggeberg M, Delhomme N, Leśniewska J, Kangasjärvi J, Hvidsten TR, Mellerowicz EJ, Sundberg B.

New Phytol. 2018 May;218(3):999-1014. doi: 10.1111/nph.15078. Epub 2018 Mar 12.

PMID:
29528503
6.

Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication.

Tylewicz S, Petterle A, Marttila S, Miskolczi P, Azeez A, Singh RK, Immanen J, Mähler N, Hvidsten TR, Eklund DM, Bowman JL, Helariutta Y, Bhalerao RP.

Science. 2018 Apr 13;360(6385):212-215. doi: 10.1126/science.aan8576. Epub 2018 Mar 8.

PMID:
29519919
7.

Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon.

Gillard G, Harvey TN, Gjuvsland A, Jin Y, Thomassen M, Lien S, Leaver M, Torgersen JS, Hvidsten TR, Vik JO, Sandve SR.

Mol Ecol. 2018 Mar;27(5):1200-1213. doi: 10.1111/mec.14533. Epub 2018 Mar 12.

PMID:
29431879
8.

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees.

Obudulu O, Mähler N, Skotare T, Bygdell J, Abreu IN, Ahnlund M, Latha Gandla M, Petterle A, Moritz T, Hvidsten TR, Jönsson LJ, Wingsle G, Trygg J, Tuominen H.

BMC Genomics. 2018 Jan 3;19(1):11. doi: 10.1186/s12864-017-4411-1.

9.

AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula.

Sundell D, Street NR, Kumar M, Mellerowicz EJ, Kucukoglu M, Johnsson C, Kumar V, Mannapperuma C, Delhomme N, Nilsson O, Tuominen H, Pesquet E, Fischer U, Niittylä T, Sundberg B, Hvidsten TR.

Plant Cell. 2017 Jul;29(7):1585-1604. doi: 10.1105/tpc.17.00153. Epub 2017 Jun 27.

10.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification.

Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ.

Genome Biol. 2017 Jun 14;18(1):111. doi: 10.1186/s13059-017-1241-z.

11.

Gene co-expression network connectivity is an important determinant of selective constraint.

Mähler N, Wang J, Terebieniec BK, Ingvarsson PK, Street NR, Hvidsten TR.

PLoS Genet. 2017 Apr 13;13(4):e1006402. doi: 10.1371/journal.pgen.1006402. eCollection 2017 Apr.

12.

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

Jokipii-Lukkari S, Sundell D, Nilsson O, Hvidsten TR, Street NR, Tuominen H.

New Phytol. 2017 Oct;216(2):482-494. doi: 10.1111/nph.14458. Epub 2017 Feb 10.

13.

Towards integration of population and comparative genomics in forest trees.

Ingvarsson PK, Hvidsten TR, Street NR.

New Phytol. 2016 Oct;212(2):338-44. doi: 10.1111/nph.14153. Epub 2016 Aug 30. Review.

14.

Extracting functional trends from whole genome duplication events using comparative genomics.

Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA.

Biol Proced Online. 2016 May 10;18:11. doi: 10.1186/s12575-016-0041-2. eCollection 2016. Review.

15.

The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.

PMID:
27088604
16.

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

Obudulu O, Bygdell J, Sundberg B, Moritz T, Hvidsten TR, Trygg J, Wingsle G.

BMC Genomics. 2016 Feb 18;17:119. doi: 10.1186/s12864-016-2458-z.

17.

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR.

PLoS One. 2015 Sep 28;10(9):e0139080. doi: 10.1371/journal.pone.0139080. eCollection 2015.

18.

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin YC, Sjödin A, Van de Peer Y, Jansson S, Hvidsten TR, Street NR.

New Phytol. 2015 Dec;208(4):1149-56. doi: 10.1111/nph.13557. Epub 2015 Jul 20.

19.

Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803.

Mähler N, Cheregi O, Funk C, Netotea S, Hvidsten TR.

PLoS One. 2014 Nov 24;9(11):e113496. doi: 10.1371/journal.pone.0113496. eCollection 2014.

20.

Populus tremula (European aspen) shows no evidence of sexual dimorphism.

Robinson KM, Delhomme N, Mähler N, Schiffthaler B, Onskog J, Albrectsen BR, Ingvarsson PK, Hvidsten TR, Jansson S, Street NR.

BMC Plant Biol. 2014 Oct 16;14:276. doi: 10.1186/s12870-014-0276-5.

21.

Genome interplay in the grain transcriptome of hexaploid bread wheat.

Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR; International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA.

Science. 2014 Jul 18;345(6194):1250091. doi: 10.1126/science.1250091.

22.

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa.

Netotea S, Sundell D, Street NR, Hvidsten TR.

BMC Genomics. 2014 Feb 6;15:106. doi: 10.1186/1471-2164-15-106.

23.

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.

24.

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica.

Immanen J, Nieminen K, Duchens Silva H, Rodríguez Rojas F, Meisel LA, Silva H, Albert VA, Hvidsten TR, Helariutta Y.

BMC Genomics. 2013 Dec 16;14:885. doi: 10.1186/1471-2164-14-885.

25.

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.

PMID:
23698360
26.

Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress.

Miranda H, Cheregi O, Netotea S, Hvidsten TR, Moritz T, Funk C.

J Proteomics. 2013 Jan 14;78:294-311. doi: 10.1016/j.jprot.2012.09.036. Epub 2012 Oct 9.

PMID:
23063787
27.

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.

28.

Activity-dormancy transition in the cambial meristem involves stage-specific modulation of auxin response in hybrid aspen.

Baba K, Karlberg A, Schmidt J, Schrader J, Hvidsten TR, Bako L, Bhalerao RP.

Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3418-23. doi: 10.1073/pnas.1011506108. Epub 2011 Feb 2.

29.

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.

Street NR, Jansson S, Hvidsten TR.

BMC Plant Biol. 2011 Jan 13;11:13. doi: 10.1186/1471-2229-11-13.

30.

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.

31.

A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity.

Hvidsten TR, Laegreid A, Kryshtafovych A, Andersson G, Fidelis K, Komorowski J.

PLoS One. 2009 Jul 15;4(7):e6266. doi: 10.1371/journal.pone.0006266.

32.

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.

Björkholm P, Daniluk P, Kryshtafovych A, Fidelis K, Andersson R, Hvidsten TR.

Bioinformatics. 2009 May 15;25(10):1264-70. doi: 10.1093/bioinformatics/btp149. Epub 2009 Mar 16.

33.

Gene expression trends and protein features effectively complement each other in gene function prediction.

Wabnik K, Hvidsten TR, Kedzierska A, Van Leene J, De Jaeger G, Beemster GT, Komorowski J, Kuiper MT.

Bioinformatics. 2009 Feb 1;25(3):322-30. doi: 10.1093/bioinformatics/btn625. Epub 2008 Dec 2.

PMID:
19050035
34.
35.

Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space.

Strömbergsson H, Daniluk P, Kryshtafovych A, Fidelis K, Wikberg JE, Kleywegt GJ, Hvidsten TR.

J Chem Inf Model. 2008 Nov;48(11):2278-88. doi: 10.1021/ci800200e.

PMID:
18937438
36.

A segmental maximum a posteriori approach to genome-wide copy number profiling.

Andersson R, Bruder CE, Piotrowski A, Menzel U, Nord H, Sandgren J, Hvidsten TR, Diaz de Ståhl T, Dumanski JP, Komorowski J.

Bioinformatics. 2008 Mar 15;24(6):751-8. doi: 10.1093/bioinformatics/btn003. Epub 2008 Jan 19.

PMID:
18204059
37.

Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors.

Andersson CR, Hvidsten TR, Isaksson A, Gustafsson MG, Komorowski J.

BMC Syst Biol. 2007 Oct 16;1:45.

38.

Differential gene expression in the olfactory bulb following exposure to the olfactory toxicant 2,6-dichlorophenyl methylsulphone and its 2,5-dichlorinated isomer in mice.

Bergström U, Olsson JA, Hvidsten TR, Komorowski J, Brandt I.

Neurotoxicology. 2007 Nov;28(6):1120-8. Epub 2007 Jun 2.

PMID:
17655932
39.

Using local gene expression similarities to discover regulatory binding site modules.

Wilczyński B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

BMC Bioinformatics. 2006 Nov 17;7:505.

40.

Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures.

Strömbergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JE, Komorowski J, Hvidsten TR.

Proteins. 2006 Nov 15;65(3):568-79.

PMID:
16948162
41.

Discovering regulatory binding-site modules using rule-based learning.

Hvidsten TR, Wilczyński B, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

Genome Res. 2005 Jun;15(6):856-66.

42.

Markers of adenocarcinoma characteristic of the site of origin: development of a diagnostic algorithm.

Dennis JL, Hvidsten TR, Wit EC, Komorowski J, Bell AK, Downie I, Mooney J, Verbeke C, Bellamy C, Keith WN, Oien KA.

Clin Cancer Res. 2005 May 15;11(10):3766-72.

43.

A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins.

Hvidsten TR, Kryshtafovych A, Komorowski J, Fidelis K.

Bioinformatics. 2003 Oct;19 Suppl 2:ii81-91.

PMID:
14534176
44.

Learning rule-based models of biological process from gene expression time profiles using gene ontology.

Hvidsten TR, Laegreid A, Komorowski J.

Bioinformatics. 2003 Jun 12;19(9):1116-23.

PMID:
12801872
45.

Predicting gene ontology biological process from temporal gene expression patterns.

Lagreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK.

Genome Res. 2003 May;13(5):965-79. Epub 2003 Apr 14.

46.

[New knowledge derived from measurement of gene expression with the DNA microarray method].

Komorowski J, Hvidsten TR, Jenssen TK, Tjeldvoll D, Hovig E, Laegreid A, Sandvik AK.

Tidsskr Nor Laegeforen. 2001 Apr 20;121(10):1229-32. Norwegian.

47.

Predicting gene function from gene expressions and ontologies.

Hvidsten TR, Komorowski J, Sandvik AK, Laegreid A.

Pac Symp Biocomput. 2001:299-310.

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