2012 Publications

Molecular insights into how a deficiency of amylose affects carbon allocation - carbohydrate and oil analyses and gene expression profiling in the seeds of a rice waxy mutant (2012) Zhang MZ, Fang JH, Yan X, Liu J, Bao JS, Fransson G, Andersson R, Jansson C, Åman P, Sun C
BMC Plant Biology 12: 230

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms (2012) Chen J, Uebbing S, Gyllenstrand N, Lagercrantz U, Lascoux, M, Kallman T
BMC Genomics 13: 589

Sesquiterpenes from the conifer root rot pathogen Heterobasidion occidentale (2012) Hansson D, Menkis A, Himmelstrand K,Thelander M, Olson A, Stenlid J, Karlsson M, Broberg A
Phytochemistry 82: 158-165

Spatial and temporal determinants of genetic structure in Gentianella bohemica (2012) Koniger J, Rebernig, CA, Brabec J, Kiehl K, Greimler J
Ecology and Evolution 2: 636-648

The potato mop-top virus TGB2 protein and viral RNA associate with chloroplasts and viral infection induces inclusions in the plastids (2012) Cowan GH, Roberts AG, Chapman SN, Ziegler A, Savenkov EI, Torrance L
Frontiers in Plant Science 3:290 

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry (2012) de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE
PLoS Genetics Nov;8(11):e1003088 

Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans (2012) Vetukuri RR, Åsman AKM, Tellgren-Roth C, Jahan SN, Reimegård J, Fogelqvist J, Savenkov E, Söderbom F, Avrova AO, Whisson, SC, Dixelius C
PLoS ONE 7: e51399

Distinct modes of DNA accessibility in plant chromatin (2012) Shu H, Wildhaber T, Siretskiy A, Gruissem W, Hennig L
Nature Communications 11, 3:1281

Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks (2012) Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I
Plant Cell 24: 3859-3875

Integration of stress-related and ROS-mediated signals by Topoisomerase VI in Arabidopsis thaliana (2012) Šimková K, Moreau F, Pawlak P, Vriet C, Baruah A, Alexandre CM, Hennig L, Apel K, Laloi C
Proceedings of the National Academy of Sciences USA 109: 16360-16365

The polyamines and their catabolic products are significant players in the turnover of nitrogenous molecules in plants (2012) Moschou PN, Wu J, Cona A, Tavladoraki P, Angelini R, Roubelakis-Angelakis KA
Journal of Experimental Botany 63: 5003-5015

Evolution, function, and regulation of genomic imprinting in plant seed development (2012) Jiang H, Köhler C
Journal of Experimental Botany 63: 4713-4722

Tearing down barriers: understanding the molecular mechanisms of interploidy hybridizations (2012) Schatlowski N, Köhler C
Journal of Experimental Botany 63: 6059-6067 

Patterning during somatic embryogenesis in Scots pine in relation to polar auxin transport and programmed cell death (2012) Abrahamsson M, Valladares S, Larsson E, Clapham D, von Arnold S
Plant Cell Tissue Organ Cult 109, 391–400 

Varied response of Spodoptera littoralis against Arabidopsis thaliana with metabolically engineered glucosinolate profiles (2012) Bejai S, Fridborg I, and Ekbom B
Plant Physiol Biochem 50, 72–78

Interactions among Glomus irregulare, arbuscular mycorrhizal spore-associated bacteria, and plant pathogens under in vitro conditions (2012) Bharadwaj DP, Alstrom S, and Lundquist P-O Mycorrhiza 22, 437–447

Two loci in sorghum with NB-LRR encoding genes confer resistance to Colletotrichum sublineolum  (2012) Biruma M, Martin T, Fridborg I, Okori P, Dixelius C 
Theor Appl Genet 124, 1005–1015

Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies) (2012) Chen J, Kallman T, Ma X, Gyllenstrand N, Zaina G, Morgante M, Bousquet J, Eckert A, Wegrzyn J, Neale D, et al 
Genetics 191, 865–U377

Gene silencing mechanisms in Phytophthora infestans (2012) Vetukuri, Ramesh Raju
Dissertation Acta Universitatis agriculturae Sueciae 1652-6880; 2012:26

European agricultural policy goes down the tubers (2012) Dixelius C, Fagerstrom T, Sundstrom JF
Nat Biotechnol 30, 492–493

A fruitful chromatin harvest: meeting summary of the Second European Workshop on Plant Chromatin 2011 in Versailles, France (2012) Houba-Hérin N, Hennig L, Köhler C, Gaudin V
Epigenetics 7:307

Ageratum conyzoides: a host to a unique begomovirus disease complex in Cameroon (2012) Leke WN, Brown JK, Ligthart ME, Sattar N, Njualem D, Kvarnheden A
Virus Research 163:229-237

Sesquiterpenes from the conifer root rot pathogen Heterobasidion occidentale (2012) Hansson D, Menkis A, Himmelstrand K, Thelander M, Olson Å, Stenlid J, Karlsson M, Broberg A 
Phytochemistry 82, 158–165

Ageratum conyzoides: a host to a unique begomovirus disease complex in Cameroon (2012) Leke WN, Brown JK, Ligthart ME, Sattar N, Njualem D, Kvarnheden A
Virus Research 163:229-237

Stop worrying; start growing. Risk research on GM crops is a dead parrot: it is time to start reaping the benefits of GM (2012) Fagerström T, Dixelius C, Magnusson U, Sundström JF
Embo Reports 

Endosperm cellularization defines an important developmental transition for embryo development (2012) Hehenberger E, Kradolfer D, Köhler C
Development 139, 2031-2039

The Arabidopsis thaliana transcriptional activator STYLISH1 regulates genes affecting stamen development, cell expansion and timing of flowering (2012) Ståldal V, Cierlik I, Chen S, Landberg K, Baylis T, Myrenås M, Sundström JF, Eklund DM, Ljung K, Sundberg E
Plant Mol Biol DOI 10.1007/s11103-012-9888-z

Endosperm cellularization defines an important developmental transition for embryo development (2012) Hehenberger, E, Kradolfer, D, Kohler, C
Development 139, 2031-2039

A rare major plant QTL determines non-responsiveness to a gall-forming insect in willow (2012) Hoglund S, Ronnberg-Wastljung AC, Lagercrantz U, Larsson S
Tree Genet Genomes 8, 1051–1060

Stop worrying; start growing. Risk research on GM crops is a dead parrot: it is time to start reaping the benefits of GM (2012) Fagerström T, Dixelius C, Magnusson U, Sundström JF
Embo Reports

Evolution, function, and regulation of genomic imprinting in plant seed development (2012) Jiang H, Kohler C
J Exp Bot 63, 4713–4722

Epigenetic Mechanisms Underlying Genomic Imprinting in Plants (2012) Kohler C, Wolff P, Spillane C
Annual Review of Plant Biology 63, 331–352

Differential regulation of Knotted1-like genes during establishment of the shoot apical meristem in Norway spruce (Picea abies) (2012) Larsson E, Sitbon F, von Arnold S
Plant Cell Reports 31, 1053–1060

W chromosome expression responds to female-specific selection (2012) Moghadam HK, Pointer MA, Wright AE, Berlin S, Mank JE
Proc Natl Acad Sci U S A 109, 8207–8211

Separases: biochemistry and function (2012) Moschou PN, Bozhkov PV
Physiol Plant 145, 67–76

Evaluation of alternative RNA labeling protocols for transcript  profiling with Arabidopsis AGRONOMICS1 tiling arrays (2012) Mueller M, Patrignani A, Rehrauer H, Gruissem W, Hennig L
Plant Methods 13:18

Development of an efficient Tissue Culture after Crossing (TCC) system for transgenic improvement of barley as a bioenergy crop (2012) Nalawade S, Nalawade S, Liu C, Jansson C, Sun C
Appl Energy 91, 405–411

The Arabidopsis thaliana transcriptional activator STYLISH1 regulates genes affecting stamen development, cell expansion and timing of  flowering (2012) Staldal V, Cierlik I, Chen S, Landberg K, Baylis T, Myrenas M, Sundstrom JF, Eklund DM, Ljung K, Sundberg E
Plant Mol Biol 78, 545–559

Arabidopsis thaliana TERMINAL FLOWER2 is involved in light-controlled signalling during seedling photomorphogenesis (2012) Valdes AE, Rizzardi K, Johannesson H, Para A, Sundås-Larsson A, Landberg K
Plant Cell Environ 35, 1013–1025

Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells (2012) Westholm JO, Tronnersjo S, Nordberg N, Olsson I, Komorowski J, Ronne H
PLoS One 7, article e31577

Meristem culture of selected sweet potato (Ipomoea batatas L Lam) cultivars to produce virus-free planting material (2012) Wondimu T, Feyissa T, Bedada G
J Horticult Sci Biotechnol 87, 255–260

Guidelines for the use and interpretation of assays for monitoring autophagy (2012) Klionsky DJ et al (incl Bozhkov P)
Autophagy 8: 445-544 

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit (2012) Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W
Molecular Systems Biology 8, 606

Causal Stability Ranking (2012) Stekhoven DJ, Izabel Moraes I, Sveinbjörnsson G, Hennig L, Maathuis MH, Bühlmann P
Bioinformatics Epub ahead of print

Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans? (2012) Whisson SC, Vetukuri RR, Avrova AO, Dixelius C
Mobile Genetic Elements 2: 110-114
 

Expression of genes of cellulose and lignin synthesis in Eucalyptus urophylla and its relation to some economic traits (2012) Quang T, Hallingbäck H, Gyllenstrand N, von Arnold S, Clapham D
Trees – Strucure and Function  3: 893-901

Expression of PaNAC01, a Picea abies CUP-SHAPED COTYLEDON orthologue, is regulated by polar auxin transport and associated with differentiation of the shoot apical meristem and formation of separated cotyledons (2012) Larsson E, Sundström J, Sitbon F, von Arnold S
Annals of Botany 110: 923-934

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