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Items: 25

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 Oct 29. pii: 201801437. doi: 10.1073/pnas.1801437115. [Epub ahead of print]

2.

The gut microbiome participates in transgenerational inheritance of low temperature responses in Drosophila melanogaster.

Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P.

FEBS Lett. 2018 Oct 29. doi: 10.1002/1873-3468.13278. [Epub ahead of print]

PMID:
30372516
3.

A genetic network mediating the control of bud break in hybrid aspen.

Singh RK, Maurya JP, Azeez A, Miskolczi P, Tylewicz S, Stojkovič K, Delhomme N, Busov V, Bhalerao RP.

Nat Commun. 2018 Oct 9;9(1):4173. doi: 10.1038/s41467-018-06696-y.

4.

PORCUPINE regulates development in response to temperature through alternative splicing.

Capovilla G, Delhomme N, Collani S, Shutava I, Bezrukov I, Symeonidi E, de Francisco Amorim M, Laubinger S, Schmid M.

Nat Plants. 2018 Aug;4(8):534-539. doi: 10.1038/s41477-018-0176-z. Epub 2018 Jul 9.

PMID:
29988152
5.

Ethylene-Related Gene Expression Networks in Wood Formation.

Seyfferth C, Wessels B, Jokipii-Lukkari S, Sundberg B, Delhomme N, Felten J, Tuominen H.

Front Plant Sci. 2018 Mar 14;9:272. doi: 10.3389/fpls.2018.00272. eCollection 2018.

6.

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
7.

Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival.

Law SR, Chrobok D, Juvany M, Delhomme N, Lindén P, Brouwer B, Ahad A, Moritz T, Jansson S, Gardeström P, Keech O.

Plant Physiol. 2018 May;177(1):132-150. doi: 10.1104/pp.18.00062. Epub 2018 Mar 9.

8.

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, Ramachandran P, Dalman K, Nilsson O, Minina EA, Bozhkov PV.

PLoS One. 2018 Mar 2;13(3):e0192945. doi: 10.1371/journal.pone.0192945. eCollection 2018.

9.

Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.

Jokipii-Lukkari S, Delhomme N, Schiffthaler B, Mannapperuma C, Prestele J, Nilsson O, Street NR, Tuominen H.

Plant Physiol. 2018 Apr;176(4):2851-2870. doi: 10.1104/pp.17.01590. Epub 2018 Feb 27.

PMID:
29487121
10.

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.

11.

A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism.

Laitinen T, Morreel K, Delhomme N, Gauthier A, Schiffthaler B, Nickolov K, Brader G, Lim KJ, Teeri TH, Street NR, Boerjan W, Kärkönen A.

Plant Physiol. 2017 Jul;174(3):1449-1475. doi: 10.1104/pp.17.00085. Epub 2017 May 18.

12.

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.

Schiffthaler B, Kostadima M; NGS Trainer Consortium, Delhomme N, Rustici G.

PLoS Comput Biol. 2016 Jun 16;12(6):e1004937. doi: 10.1371/journal.pcbi.1004937. eCollection 2016 Jun.

13.

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.

14.

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.

15.

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.

16.

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
17.

The genomic and transcriptomic landscape of a HeLa cell line.

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM.

G3 (Bethesda). 2013 Aug 7;3(8):1213-24. doi: 10.1534/g3.113.005777.

18.

easyRNASeq: a bioconductor package for processing RNA-Seq data.

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM.

Bioinformatics. 2012 Oct 1;28(19):2532-3. Epub 2012 Jul 30.

19.

Nos2 inactivation promotes the development of medulloblastoma in Ptch1(+/-) mice by deregulation of Gap43-dependent granule cell precursor migration.

Haag D, Zipper P, Westrich V, Karra D, Pfleger K, Toedt G, Blond F, Delhomme N, Hahn M, Reifenberger J, Reifenberger G, Lichter P.

PLoS Genet. 2012;8(3):e1002572. doi: 10.1371/journal.pgen.1002572. Epub 2012 Mar 15.

20.

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE.

Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064.

PMID:
22231485
21.

Seamless gene tagging by endonuclease-driven homologous recombination.

Khmelinskii A, Meurer M, Duishoev N, Delhomme N, Knop M.

PLoS One. 2011;6(8):e23794. doi: 10.1371/journal.pone.0023794. Epub 2011 Aug 22.

22.

Differential retinoic acid signaling in tumors of long- and short-term glioblastoma survivors.

Barbus S, Tews B, Karra D, Hahn M, Radlwimmer B, Delhomme N, Hartmann C, Felsberg J, Krex D, Schackert G, Martinez R, Reifenberger G, Lichter P.

J Natl Cancer Inst. 2011 Apr 6;103(7):598-606. doi: 10.1093/jnci/djr036. Epub 2011 Feb 23.

PMID:
21346226
23.

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.

Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E.

PLoS Genet. 2010 Sep 9;6(9):e1001109. doi: 10.1371/journal.pgen.1001109.

24.

Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain.

Stange DE, Engel F, Longerich T, Koo BK, Koch M, Delhomme N, Aigner M, Toedt G, Schirmacher P, Lichter P, Weitz J, Radlwimmer B.

Gut. 2010 Sep;59(9):1236-44. doi: 10.1136/gut.2009.195701. Epub 2010 May 17.

PMID:
20479215
25.

FACT--a framework for the functional interpretation of high-throughput experiments.

Kokocinski F, Delhomme N, Wrobel G, Hummerich L, Toedt G, Lichter P.

BMC Bioinformatics. 2005 Jun 28;6:161.

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