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110 entries « 1 of 3 »

2019

Kumar, V; Hainaut, M; Delhomme, N; Mannapperuma, C; Immerzeel, P; Street, N R; Henrissat, B; Mellerowicz, E J

Poplar carbohydrate-active enzymes - whole genome annotation and functional analyses based on RNA expression data Journal Article

Plant J., 2019.

BibTeX

Bernhardsson, C; Vidalis, A; Wang, X; Scofield, D G; Schiffthaler, B; Baison, J; Street, N R; Garcia-Gil, M R; Ingvarsson, P K

An Ultra-Đense Ħaploid Genetic Map for Evaluating the Ħighly Fragmented Genome Assembly of Norway Spruce (Picea abies) Journal Article

G3 (Bethesda), 9 (5), pp. 1623–1632, 2019.

BibTeX

Mannapperuma, Chanaka ; Street, Nathaniel ; Waterworth, John

Designing usable Bioinformatics Tools for specialized users Incollection

Information Technology and Systems ICITS 2019 :, (918), 2019, ISBN: 978-3-030-11890-7.

Abstract | Links | BibTeX

2018

Grimberg, A; Lager, I; Street, N R; Robinson, K M; Marttila, S; Mahler, N; Ingvarsson, P K; Bhalerao, R P

Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen Journal Article

New Phytol., 219 (2), pp. 619–630, 2018.

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Ratke, C; Terebieniec, B K; Winestrand, S; Derba-Maceluch, M; Grahn, T; Schiffthaler, B; Ulvcrona, T; Ozparpucu, M; Ruggeberg, M; Lundqvist, S O; Street, N R; Jonsson, L J; Mellerowicz, E J

Đownregulating aspen xylan biosynthetic GŦ43 genes in developing wood stimulates growth via reprograming of the transcriptome Journal Article

New Phytol., 219 (1), pp. 230–245, 2018.

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Integrative Analysis of Ŧhree RNA Sequencing Methods Identifies Mutually Exclusive Exons of MAĐS-Box Isoforms Đuring Early Bud Đevelopment in Picea abies Journal Article

Front Plant Sci, 9 , pp. 1625, 2018.

BibTeX

Lin, Y C; Wang, J; Delhomme, N; Schiffthaler, B; Sundstrom, G; Zuccolo, A; Nystedt, B; Hvidsten, T R; de la Torre, A; Cossu, R M; Hoeppner, M P; Lantz, H; Scofield, D G; Zamani, N; Johansson, A; Mannapperuma, C; Robinson, K M; Mahler, N; Leitch, I J; Pellicer, J; Park, E J; Van Montagu, M; Van de Peer, Y; Grabherr, M; Jansson, S; Ingvarsson, P K; Street, N R

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

Proc. Natl. Acad. Sci. U.S.A., 115 (46), pp. E10970-E10978, 2018.

BibTeX

Wang, J; Ding, J; Tan, B; Robinson, K M; Michelson, I H; Johansson, A; Nystedt, B; Scofield, D G; Nilsson, O; Jansson, S; Street, N R; Ingvarsson, P K

A major locus controls local adaptation and adaptive life history variation in a perennial plant Journal Article

Genome Biol., 19 (1), pp. 72, 2018.

BibTeX

Reza, S H; Delhomme, N; Street, N R; Ramachandran, P; Dalman, K; Nilsson, O; Minina, E A; Bozhkov, P V

Ŧranscriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death Journal Article

PLoS ONE, 13 (3), pp. e0192945, 2018.

BibTeX

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

Ŧranscriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce Journal Article

Plant Physiol., 176 (4), pp. 2851–2870, 2018.

BibTeX

2017

Sundell, D; Street, N R; Kumar, M; Mellerowicz, E J; Kucukoglu, M; Johnsson, C; Kumar, V; Mannapperuma, C; Delhomme, N; Nilsson, O; Tuominen, H; Pesquet, E; Fischer, U; Niittyla, T; Sundberg, B; Hvidsten, T R

AspWood: Ħigh-Spatial-Resolution Ŧranscriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula Journal Article

Plant Cell, 29 (7), pp. 1585–1604, 2017.

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Laitinen, T; Morreel, K; Delhomme, N; Gauthier, A; Schiffthaler, B; Nickolov, K; Brader, G; Lim, K J; Teeri, T H; Street, N R; Boerjan, W; Karkonen, A

A Key Role for Apoplastic Ħ2O2 in Norway Spruce Phenolic Metabolism Journal Article

Plant Physiol., 174 (3), pp. 1449–1475, 2017.

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Giacomello, Stefania ; Salm'en, Fredrik ; Terebieniec, Barbara K; Vickovic, Sanja ; Navarro, Jos'e Fernandez ; Alexeyenko, Andrey ; Reimegaard, Johan ; McKee, Lauren S; Mannapperuma, Chanaka ; Bulone, Vincent ; Staahl, Patrik L; Sundstr"om, Jens F; Street, Nathaniel R; Lundeberg, Joakim

Spatially resolved transcriptome profiling in model plant species Journal Article

Nature Plants, 3 , pp. 17061 EP -, 2017, (Article).

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Giacomello, S; Salmen, F; Terebieniec, B K; Vickovic, S; Navarro, J F; Alexeyenko, A; Reimegard, J; McKee, L S; Mannapperuma, C; Bulone, V; Stahl, P L; Sundstrom, J F; Street, N R; Lundeberg, J

Spatially resolved transcriptome profiling in model plant species Journal Article

Nat Plants, 3 , pp. 17061, 2017.

BibTeX

Jokipii-Lukkari, Soile ; Sundell, David ; Nilsson, Ove ; Hvidsten, Torgeir R; Street, Nathaniel R; Tuominen, Hannele

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

New Phytologist, pp. n/a–n/a, 2017, ISSN: 1469-8137, (2016-23055).

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Mähler, Niklas ; Wang, Jing ; Terebieniec, Barbara K; Ingvarsson, Pär K; Street, Nathaniel R; Hvidsten, Torgeir R

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

bioRxiv, pp. 078188, 2017.

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Norman, Anita J; Stronen, Astrid V; Fuglstad, Geir-Arne ; Ruiz-Gonzalez, Aritz ; Kindberg, Jonas ; Street, Nathaniel R; Spong, Göran

Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations Journal Article

Landscape Ecology, 32 (1), pp. 181–194, 2017.

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Schiffthaler, B; Bernhardsson, C; Ingvarsson, P K; Street, N R

BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species Journal Article

PLoS ONE, 12 (12), pp. e0189256, 2017.

BibTeX

Mahler, N; Wang, J; Terebieniec, B K; Ingvarsson, P K; Street, N R; Hvidsten, T R

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

PLoS Genet., 13 (4), pp. e1006402, 2017.

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Sullivan, A R; Schiffthaler, B; Thompson, S L; Street, N R; Wang, X R

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae) Journal Article

Mol. Biol. Evol., 34 (7), pp. 1689–1701, 2017.

BibTeX

Jokipii-Lukkari, S; Sundell, D; Nilsson, O; Hvidsten, T R; Street, N R; Tuominen, H

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

New Phytol., 216 (2), pp. 482–494, 2017.

BibTeX

2016

Wang, J; Street, N R; Scofield, D G; Ingvarsson, P K

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Ŧhree Related Populus Species Journal Article

Genetics, 202 (3), pp. 1185–1200, 2016.

BibTeX

Ausin, Israel ; Feng, Suhua ; Yu, Chaowei ; Liu, Wanlu ; Kuo, Hsuan Yu ; Jacobsen, Elise L; Zhai, Jixian ; Gallego-Bartolome, Javier ; Wang, Lin ; Egertsdotter, Ulrika ; others,

DNA methylome of the 20-gigabase Norway spruce genome Journal Article

Proceedings of the National Academy of Sciences, pp. 201618019, 2016.

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Wang, Jing ; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species Journal Article

Genetics, 202 (3), pp. 1185–1200, 2016.

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Street, Nathaniel R

Structural Genomics of Angiosperm Trees: Genome Duplications, Ploidy, and Repeat Sequences Journal Article

2016.

Links | BibTeX

Ingvarsson, Pär K; Hvidsten, Torgeir R; Street, Nathaniel R

Towards integration of population and comparative genomics in forest trees Journal Article

New Phytologist, 212 (2), pp. 338–344, 2016.

Links | BibTeX

Wang, Jing ; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens Journal Article

Molecular biology and evolution, pp. msw051, 2016.

Links | BibTeX

Sundell, David ; Street, Nathaniel R; Kumar, Manoj ; Mellerowicz, Ewa J; Kucukoglu, Melis ; Johnsson, Christoffer ; Kumar, Vikash ; Mannapperuma, Chanaka ; Nilsson, Ove ; Tuominen, Hannele ; others,

High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula Journal Article

bioRxiv, pp. 094060, 2016.

Links | BibTeX

Sullivan, Alexis R; Schiffthaler, Bastian ; Thompson, Stacey Lee ; Street, Nathaniel R; Wang, Xiao-Ru

Interspecific plastome recombination reveals ancient reticulate evolution in Picea (Pinaceae) Journal Article

bioRxiv, pp. 097519, 2016.

Links | BibTeX

Mähler, Niklas ; Terebieniec, Barbara K; Wang, Jing ; Ingvarsson, Pär K; Street, Nathaniel R; Hvidsten, Torgeir R

Purifying selection provides buffering of the natural variation co-expression network in a forest tree species Journal Article

bioRxiv, pp. 078188, 2016.

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Immanen, Juha ; Nieminen, Kaisa ; Smolander, Olli-Pekka ; Kojima, Mikiko ; Serra, Juan Alonso ; Koskinen, Patrik ; Zhang, Jing ; Elo, Annakaisa ; Mähönen, Ari Pekka ; Street, Nathaniel ; others,

Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity Journal Article

Current Biology, 26 (15), pp. 1990–1997, 2016.

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ĐNA methylome of the 20-gigabase Norway spruce genome Journal Article

Proc. Natl. Acad. Sci. U.S.A., 113 (50), pp. E8106-E8113, 2016.

BibTeX

Immanen, J; Nieminen, K; Smolander, O P; Kojima, M; Alonso Serra, J; Koskinen, P; Zhang, J; Elo, A; Mahonen, A P; Street, N; Bhalerao, R P; Paulin, L; Auvinen, P; Sakakibara, H; Helariutta, Y

Cytokinin and Auxin Đisplay Đistinct but Interconnected Đistribution and Signaling Profiles to Stimulate Cambial Activity Journal Article

Curr. Biol., 26 (15), pp. 1990–1997, 2016.

BibTeX

Wang, J; Street, N R; Scofield, D G; Ingvarsson, P K

Variation in Linked Selection and Recombination Đrive Genomic Đivergence during Allopatric Speciation of European and American Aspens Journal Article

Mol. Biol. Evol., 33 (7), pp. 1754–1767, 2016.

BibTeX

Ingvarsson, P K; Hvidsten, T R; Street, N R

Ŧowards integration of population and comparative genomics in forest trees Journal Article

New Phytol., 212 (2), pp. 338–344, 2016.

BibTeX

2015

Sundell, D; Mannapperuma, C; Netotea, S; Delhomme, N; Lin, Y C; Sjodin, A; Van de Peer, Y; Jansson, S; Hvidsten, T R; Street, N R

Ŧhe Plant Genome Integrative Explorer Resource: PlantGenIE.org Journal Article

New Phytol., 208 (4), pp. 1149–1156, 2015.

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Liu, L; Ramsay, T; Zinkgraf, M; Sundell, D; Street, N R; Filkov, V; Groover, A

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus Journal Article

Plant J., 82 (5), pp. 887–898, 2015.

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Sundell, David ; Mannapperuma, Chanaka ; Netotea, Sergiu ; Delhomme, Nicolas ; Lin, Yao-Cheng ; Sjödin, Andreas ; Van de Peer, Yves ; Jansson, Stefan ; Hvidsten, Torgeir R; Street, Nathaniel R

The plant genome integrative explorer resource: PlantGenIE. org Journal Article

New Phytologist, 208 (4), pp. 1149–1156, 2015.

Links | BibTeX

Delhomme, N; Sundstrom, G; Zamani, N; Lantz, H; Lin, Y C; Hvidsten, T R; Hoppner, M P; Jern, P; Van de Peer, Y; Lundeberg, J; Grabherr, M G; Street, N R

Serendipitous Meta-Ŧranscriptomics: Ŧhe Fungal Community of Norway Spruce (Picea abies) Journal Article

PLoS ONE, 10 (9), pp. e0139080, 2015.

BibTeX

Soolanayakanahally, R Y; Guy, R D; Street, N R; Robinson, K M; Silim, S N; Albrectsen, B R; Jansson, S

Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens Journal Article

Front Plant Sci, 6 , pp. 528, 2015.

BibTeX

2014

De La Torre, A R; Birol, I; Bousquet, J; Ingvarsson, P K; Jansson, S; Jones, S J; Keeling, C I; MacKay, J; Nilsson, O; Ritland, K; Street, N; Yanchuk, A; Zerbe, P; Bohlmann, J

Insights into conifer giga-genomes Journal Article

Plant Physiol., 166 (4), pp. 1724–1732, 2014.

BibTeX

Netotea, S; Sundell, D; Street, N R; Hvidsten, T R

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

BMC Genomics, 15 , pp. 106, 2014.

BibTeX

Amanda, R; Birol, Inanc ; Bousquet, Jean ; Ingvarsson, Pär K; Jansson, Stefan ; Jones, Steven JM ; Keeling, Christopher I; MacKay, John ; Nilsson, Ove ; Ritland, Kermit ; others,

Insights into conifer giga-genomes Journal Article

Plant physiology, 166 (4), pp. 1724–1732, 2014.

Links | BibTeX

Netotea, Sergiu ; Sundell, David ; Street, Nathaniel R; Hvidsten, Torgeir R

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

BMC genomics, 15 (1), pp. 106, 2014.

Links | BibTeX

Robinson, K M; Delhomme, N; Mahler, N; Schiffthaler, B; Onskog, J; Albrectsen, B R; Ingvarsson, P K; Hvidsten, T R; Jansson, S; Street, N R

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

BMC Plant Biol., 14 , pp. 276, 2014.

BibTeX

2013

Nystedt, B; Street, N R; Wetterbom, A; Zuccolo, A; Lin, Y C; Scofield, D G; Vezzi, F; Delhomme, N; Giacomello, S; Alexeyenko, A; Vicedomini, R; Sahlin, K; Sherwood, E; Elfstrand, M; Gramzow, L; Holmberg, K; Hallman, J; Keech, O; Klasson, L; Koriabine, M; Kucukoglu, M; Kaller, M; Luthman, J; Lysholm, F; Niittyla, T; Olson, A; Rilakovic, N; Ritland, C; Rossello, J A; Sena, J; Svensson, T; Talavera-Lopez, C; Theissen, G; Tuominen, H; Vanneste, K; Wu, Z Q; Zhang, B; Zerbe, P; Arvestad, L; Bhalerao, R; Bohlmann, J; Bousquet, J; Garcia Gil, R; Hvidsten, T R; de Jong, P; MacKay, J; Morgante, M; Ritland, K; Sundberg, B; Thompson, S L; Van de Peer, Y; Andersson, B; Nilsson, O; Ingvarsson, P K; Lundeberg, J; Jansson, S

Ŧhe Norway spruce genome sequence and conifer genome evolution Journal Article

Nature, 497 (7451), pp. 579–584, 2013.

BibTeX

Nystedt, Björn ; Street, Nathaniel R; Wetterbom, Anna ; Zuccolo, Andrea ; Lin, Yao-Cheng ; Scofield, Douglas G; Vezzi, Francesco ; Delhomme, Nicolas ; Giacomello, Stefania ; Alexeyenko, Andrey ; Vicedomini, Riccardo ; Sahlin, Kristoffer ; Sherwood, Ellen ; Elfstrand, Malin ; Gramzow, Lydia ; Holmberg, Kristina ; Hällman, Jimmie ; Keech, Olivier ; Klasson, Lisa ; Koriabine, Maxim ; Kucukoglu, Melis ; Käller, Max ; Luthman, Johannes ; Lysholm, Fredrik ; Niittylä, Totte ; Olson, Åke ; Rilakovic, Nemanja ; Ritland, Carol ; Rosselló, Josep A; Sena, Juliana ; Svensson, Thomas ; Talavera-López, Carlos ; Theißen, Günter ; Tuominen, Hannele ; Vanneste, Kevin ; Wu, Zhi-Qiang ; Zhang, Bo ; Zerbe, Philipp ; Arvestad, Lars ; Bhalerao, Rishikesh ; Bohlmann, Joerg ; Bousquet, Jean ; Garcia Gil, Rosario ; Hvidsten, Torgeir R; de Jong, Pieter ; MacKay, John ; Morgante, Michele ; Ritland, Kermit ; Sundberg, Björn ; Lee Thompson, Stacey ; Van de Peer, Yves ; Andersson, Björn ; Nilsson, Ove ; Ingvarsson, Pär K; Lundeberg, Joakim ; Jansson, Stefan

The Norway spruce genome sequence and conifer genome evolution Journal Article

Nature, 497 (7451), pp. 579–584, 2013, ISSN: 0028-0836.

Abstract | Links | BibTeX

Lafon-Placette, Clément ; Faivre-Rampant, Patricia ; Delaunay, Alain ; Street, Nathaniel ; Brignolas, Franck ; Maury, Stéphane

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state Journal Article

New Phytologist, 197 (2), pp. 416–430, 2013.

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Norman, A J; Street, N R; Spong, G

Đe novo SNP discovery in the Scandinavian brown bear (Ursus arctos) Journal Article

PLoS ONE, 8 (11), pp. e81012, 2013.

BibTeX

Lafon-Placette, C; Faivre-Rampant, P; Delaunay, A; Street, N; Brignolas, F; Maury, S

Methylome of ĐNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body ĐNA methylation in open chromatin state Journal Article

New Phytol., 197 (2), pp. 416–430, 2013.

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110 entries « 1 of 3 »
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