Rohde A, Bhalerao RP: Plant dormancy in the perennial context. Trends Plant Sci. 2007, 12: 217-223. 10.1016/j.tplants.2007.03.012.
Article
CAS
PubMed
Google Scholar
Faust M, Erez A, Rowland LJ, Wang SY, Norman HA: Bud dormancy in perennial fruit trees: physiological basis for dormancy induction, maintenance, and release. HortSci. 1997, 32: 623-629.
Google Scholar
Lang GA, Early JD, Martin GC, Darnell RL: Endo-, Para-, and Ecodormancy: physiological terminology and classification for dormancy research. HortSci. 1987, 22: 371-377.
Google Scholar
Naor A, Flaishman M, Stern R, Moshe A, Erez A: Temperature effects on dormancy completion of vegetative buds in apple. J Amer Soc Hort Sci. 2003, 128: 636-641.
Google Scholar
Guerriero R, Monteleone P, Viti R: Evaluation of end of dormancy in several apricot cultivars according to different methodological approaches. Acta Hort. 2006, 701: 99-103.
Article
Google Scholar
Horvath DP, Anderson JV, Chao WS, Foley ME: Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci. 2003, 8: 534-540. 10.1016/j.tplants.2003.09.013.
Article
CAS
PubMed
Google Scholar
Chuine , Cour P: Climatic determinants of budburst seasonality in four temperate-zone tree species. New Phytol. 1999, 143: 339-349. 10.1046/j.1469-8137.1999.00445.x.
Article
Google Scholar
Kalcsits L, Silim S, Tanino K: Warm temperature accelerates short photoperiod-induced growth cessation and dormancy induction in hybrid poplar (Populus × spp.). Trees - Structure and Function. 2009, 23: 971-979. 10.1007/s00468-009-0339-7.
Article
Google Scholar
Chmielewski FM, Muller A, Bruns E: Climate change and trends in phenology of fruit trees and field crops in germany, 1961–2000. Agric For Meteorol. 2004, 121: 69-78. 10.1016/S0168-1923(03)00161-8.
Article
Google Scholar
Menzel A, Fabian P: Growing season extended in Europe. Nature. 1999, 397: 659-10.1038/17709.
Article
CAS
Google Scholar
Ducousso A, Guyon JP, Kremer A: Latitudinal and altitudinal variation of bud burst in western populations of sessile oak (Quercus petraea (Matt) Liebl). Annales Des Sciences Forestieres. 1996, 53: 775-782. 10.1051/forest:19960253.
Article
Google Scholar
Tsarouhas V, Gullberg U, Lagercrantz U: Mapping of quantitative trait loci controlling timing of bud flush in Salix. Hereditas. 2003, 138: 172-178. 10.1034/j.1601-5223.2003.01695.x.
Article
PubMed
Google Scholar
Bradshaw HD, Stettler RF: Molecular genetics of growth and development in populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics. 1995, 139: 963-973.
CAS
PubMed
Google Scholar
Saintagne C, Bodenes C, Barreneche T, Pot D, Plomion C, Kremer A: Distribution of genomic regions differentiating oak species assessed by QTL detection. Heredity. 2004, 92: 20-30. 10.1038/sj.hdy.6800358.
Article
CAS
PubMed
Google Scholar
Derory J, Scotti-Saintagne C, Bertocchi E, Le Dantec L, Graignic N, Jauffres A, Casasoli M, Chancerel E, Bodenes C, Alberto F, Kremer A: Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks. Heredity. 2010, 104: 438-448. 10.1038/hdy.2009.134.
Article
CAS
PubMed
Google Scholar
Ibanez C, Kozarewa I, Johansson M, Ogren E, Rohde A, Eriksson M: Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees. Plant Physiol. 2010, 153: 1823-1833. 10.1104/pp.110.158220.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rohde A, Ruttink T, Hostyn V, Sterck L, Van Driessche K, Boerjan W: Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar. J Exp Bot. 2007, 58: 4047-4060. 10.1093/jxb/erm261.
Article
CAS
PubMed
Google Scholar
Allona I, Ramos A, Ibanez C, Contreras A, Casado R, Aragoncillo C: Molecular control of winter dormancy establishment in trees. Span J Agric Res. 2008, 6: 201-210.
Article
Google Scholar
Bohlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O: CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science. 2006, 312: 1040-1043. 10.1126/science.1126038.
Article
PubMed
Google Scholar
Walton E, Wu R, Schaffer R, Thodey K, Janssen B, Richardson A, Hellens R, Rae G, Wood M: Genetic regulation of budbreak in kiwi. Acta Hort. 2007, 753: 561-566.
Article
CAS
Google Scholar
Mathiason K, He D, Grimplet J, Venkateswari J, Galbraith DW, Or E, Fennell A: Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. Funct Integr Genomics. 2009, 9: 81-96. 10.1007/s10142-008-0090-y.
Article
CAS
PubMed
Google Scholar
Campbell M, Segear E, Beers L, Knauber D, Suttle J: Dormancy in potato tuber meristems: chemically induced cessation in dormancy matches the natural process based on transcript profiles. Funct Integr Genomics. 2008, 8: 317-328. 10.1007/s10142-008-0079-6.
Article
CAS
PubMed
Google Scholar
Mazzitelli L, Hancock RD, Haupt S, Walker PG, Pont SD, McNicol J, Cardle L, Morris J, Viola R, Brennan R: Co-ordinated gene expression during phases of dormancy release in raspberry (Rubus idaeus L.) buds. J Exp Bot. 2007, 58: 1035-1045. 10.1093/jxb/erl266.
Article
CAS
PubMed
Google Scholar
Horvath DP, Sung S, Kim D, Chao W, Anderson J: Characterization, expression and function of DORMANCY ASSOCIATED MADS-BOX genes from leafy spurge. Plant Mol Biol. 2010, 73: 169-179. 10.1007/s11103-009-9596-5.
Article
CAS
PubMed
Google Scholar
Derory J, Leger P, Garcia V, Schaeffer J, Hauser MT, Salin F, Luschnig C, Plomion C, Glossl J, Kremer A: Transcriptome analysis of bud burst in sessile oak (Quercus petraea). New Phytol. 2006, 170: 723-738. 10.1111/j.1469-8137.2006.01721.x.
Article
CAS
PubMed
Google Scholar
Ruttink T, Arend M, Morreel K, Storme V, Rombauts S, Fromm J, Bhalerao RP, Boerjan W, Rohde A: A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell. 2007, 19: 2370-2390. 10.1105/tpc.107.052811.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jimenez S, Li Z, Reighard G, Bielenberg D: Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant. BMC Plant Biol. 2010, 10: 25-10.1186/1471-2229-10-25.
Article
PubMed Central
PubMed
Google Scholar
Ueno S, Le Provost G, Leger V, Klopp C, Noirot C, Frigerio JM, Salin F, Salse J, Abrouk M, Murat F: Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics. 2010, 11: 650-10.1186/1471-2164-11-650.
Article
PubMed Central
PubMed
Google Scholar
Stekel DJ, Git Y, Falciani F: The comparison of gene expression from multiple cDNA libraries. Genome Res. 2000, 10: 2055-2061. 10.1101/gr.GR-1325RR.
Article
PubMed Central
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009, 26: 139-140.
Article
PubMed Central
PubMed
Google Scholar
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11: R106-10.1186/gb-2010-11-10-r106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pacey-Miller T, Scott K, Ablett E, Tingey S, Ching A, Henry R: Genes associated with the end of dormancy in grapes. Funct Integr Genomics. 2003, 3: 144-152. 10.1007/s10142-003-0094-6.
Article
CAS
PubMed
Google Scholar
Casey R: Distribution and some properties of seed globulins. Seed proteins. Edited by: Shewry P, Casey R. 1999, Dordrecht: Kluwer Academic Publishers, 159-169.
Chapter
Google Scholar
Shewry PR, Halford NG: Cereal seed storage proteins: structures, properties and role in grain utilization. J Exp Bot. 2002, 53: 947-958. 10.1093/jexbot/53.370.947.
Article
CAS
PubMed
Google Scholar
Rivin CJ, Grudt T: Abscisic Acid and the developmental regulation of embryo storage proteins in maize. Plant Physiol. 1991, 95: 358-365. 10.1104/pp.95.2.358.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shutov AD, Vaintraub IA: Degradation of storage proteins in germinating seeds. Phytochemistry. 1987, 26: 1557-1566. 10.1016/S0031-9422(00)82245-1.
Article
CAS
Google Scholar
Anderson JV, Gesch RW, Jia Y, Chao WS, Horvath DP: Seasonal shifts in dormancy status, carbohydrate metabolism, and related gene expression in crown buds of leafy spurge. Plant Cell Environ. 2005, 28: 1567-1578. 10.1111/j.1365-3040.2005.01393.x.
Article
CAS
Google Scholar
Yokoyama R, Nishitani K: A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant Cell Physiol. 2001, 42: 1025-1033. 10.1093/pcp/pce154.
Article
CAS
PubMed
Google Scholar
Catala C, Rose JK, York WS, Albersheim P, Darvill AG, Bennett AB: Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls. Plant Physiol. 2001, 127: 1180-1192. 10.1104/pp.010481.
Article
PubMed Central
CAS
PubMed
Google Scholar
Purugganan MM, Braam J, Fry SC: The Arabidopsis TCH4 xyloglucan endotransglycosylase. Substrate specificity, pH optimum, and cold tolerance. Plant Physiol. 1997, 115: 181-190. 10.1104/pp.115.1.181.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J, Nilsson P, Bhalerao RP: Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J. 2004, 40: 173-187. 10.1111/j.1365-313X.2004.02199.x.
Article
CAS
PubMed
Google Scholar
Leida C, Terol J, Marti G, Agusti M, Llacer G, Badenes ML, Rios G: Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. Tree Physiol. 2010, 30: 655-666. 10.1093/treephys/tpq008.
Article
CAS
PubMed
Google Scholar
Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I: Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics. 2010, 11: 630-10.1186/1471-2164-11-630.
Article
PubMed Central
PubMed
Google Scholar
Hortensteiner S: Chlorophyll degradation during senescence. Annu Rev Plant Biol. 2006, 57: 55-77. 10.1146/annurev.arplant.57.032905.105212.
Article
CAS
PubMed
Google Scholar
Nomura K, Takahashi N, Hirose M, Nakamura S, Yagi F: Overall carbohydrate-binding properties of Castanea crenata agglutinin (CCA). Carbohydr Res. 2005, 340: 2004-2009. 10.1016/j.carres.2005.05.020.
Article
CAS
PubMed
Google Scholar
Horvath D: Bud Dormancy and Growth. Plant Developmental Biology - Biotechnological Perspectives. Edited by: Pua EC, Davey MR. 2010, Berlin Heidelberg: Springer, 53-70.
Chapter
Google Scholar
Anderson J, Doğramacı M, Horvath D, Foley M, Chao W, Suttle J, Thimmapuram J, Hernandez A, Ali S, Mikel M: Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense). Funct Integr Genomics. 2012, 12: 515-531. 10.1007/s10142-012-0280-5.
Article
CAS
PubMed
Google Scholar
Meyer G, Kloppstech K: A rapidly light-induced chloroplast protein with a high turnover coded for by pea nuclear DNA. Eur J Biochem. 1984, 138: 201-207. 10.1111/j.1432-1033.1984.tb07900.x.
Article
CAS
PubMed
Google Scholar
Montane MH, Kloppstech K: The family of light-harvesting-related proteins (LHCs, ELIPs, HLIPs): was the harvesting of light their primary function?. Gene. 2000, 258: 1-8. 10.1016/S0378-1119(00)00413-3.
Article
CAS
PubMed
Google Scholar
Montané M-H, Dreyer S, Triantaphylides C, Kloppstech K: Early light-inducible proteins during long-term acclimation of barley to photooxidative stress caused by light and cold: high level of accumulation by posttranscriptional regulation. Planta. 1997, 202: 293-302. 10.1007/s004250050131.
Article
Google Scholar
Savenstrand H, Olofsson M, Samuelsson M, Strid A: Induction of early light-inducible protein gene expression in Pisum sativum after exposure to low levels of UV-B irradiation and other environmental stresses. Plant Cell Rep. 2004, 22: 532-536. 10.1007/s00299-003-0743-1.
Article
CAS
PubMed
Google Scholar
Dhanaraj AL, Slovin JP, Rowland LJ: Analysis of gene expression associated with cold acclimation in blueberry floral buds using expressed sequence tags. Plant Sci. 2004, 166: 863-872. 10.1016/j.plantsci.2003.11.013.
Article
CAS
Google Scholar
Chung S, Parish RW: Combinatorial interactions of multiple cis-elements regulating the induction of the Arabidopsis XERO2 dehydrin gene by abscisic acid and cold. Plant J. 2008, 54: 15-29.
Article
CAS
PubMed
Google Scholar
Jung SH, Lee JY, Lee DH: Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol Biol. 2003, 52: 553-567. 10.1023/A:1024866716987.
Article
CAS
PubMed
Google Scholar
Close TJ: Dehydrins: Emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant. 1996, 97: 795-803. 10.1111/j.1399-3054.1996.tb00546.x.
Article
CAS
Google Scholar
Yakovlev I, Asante D, Fossdal C, Partanen J, Junttila O, Johnsen Ø: Dehydrins expression related to timing of bud burst in Norway spruce. Planta. 2008, 228: 459-472. 10.1007/s00425-008-0750-0.
Article
CAS
PubMed
Google Scholar
Yang L, Zheng B, Mao C, Yi K, Liu F, Wu Y, Tao Q, Wu P: cDNA-AFLP analysis of inducible gene expression in rice seminal root tips under a water deficit. Gene. 2003, 314: 141-148.
Article
CAS
PubMed
Google Scholar
Kovtun Y, Chiu WL, Tena G, Sheen J: Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants. Proc Natl Acad Sci USA. 2000, 97: 2940-2945. 10.1073/pnas.97.6.2940.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dure L, Greenway SC, Galau GA: Developmental biochemistry of cottonseed embryogenesis and germination: changing messenger ribonucleic acid populations as shown by in vitro and in vivo protein synthesis. Biochemistry. 1981, 20: 4162-4168. 10.1021/bi00517a033.
Article
CAS
PubMed
Google Scholar
Galau GA, Hughes DW, Dure L: Abscisic acid induction of cloned cotton late embryogenesis-abundant (Lea) mRNAs. Plant Mol Biol. 1986, 7: 155-170. 10.1007/BF00021327.
Article
CAS
PubMed
Google Scholar
Horvath DP, Chao WS, Suttle JC, Thimmapuram J, Anderson JV: Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.). BMC Genomics. 2008, 9: 536-10.1186/1471-2164-9-536.
Article
PubMed Central
PubMed
Google Scholar
Hundertmark M, Hincha DK: LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics. 2008, 9: 118-10.1186/1471-2164-9-118.
Article
PubMed Central
PubMed
Google Scholar
Sakai A, Larcher W: Frost survival of plants: responses and adaptation to freezing stress. 1987, Berlin: Springer-Verlag
Book
Google Scholar
Medina J, Catala R, Salinas J: Developmental and stress regulation of RCI2A and RCI2B, two cold-inducible genes of arabidopsis encoding highly conserved hydrophobic proteins. Plant Physiol. 2001, 125: 1655-1666. 10.1104/pp.125.4.1655.
Article
PubMed Central
CAS
PubMed
Google Scholar
Davik J, Koehler G, From B, Torp T, Rohloff J, Eidem P, Wilson RC, Sonsteby A, Randall SK, Alsheikh M: Dehydrin, alcohol dehydrogenase, and central metabolite levels are associated with cold tolerance in diploid strawberry (Fragaria spp.). Planta. 2013, 237: 265-277. 10.1007/s00425-012-1771-2.
Article
CAS
PubMed
Google Scholar
Doğramacı M, Horvath D, Christoffers M, Anderson J: Dehydration and vernalization treatments identify overlapping molecular networks impacting endodormancy maintenance in leafy spurge crown buds. Funct Integr Genomics. 2011, 11: 611-626. 10.1007/s10142-011-0239-y.
Article
PubMed
Google Scholar
Cong L, Zheng H-C, Zhang Y-X, Chai T-Y: Arabidopsis DREB1A confers high salinity tolerance and regulates the expression of GA dioxygenases in Tobacco. Plant Sci. 2008, 174: 156-164. 10.1016/j.plantsci.2007.11.002.
Article
CAS
Google Scholar
Doğramacı M, Horvath DP, Chao WS, Foley ME, Christoffers MJ, Anderson JV: Low temperatures impact dormancy status, flowering competence, and transcript profiles in crown buds of leafy spurge. Plant Mol Biol. 2010, 73: 207-226. 10.1007/s11103-010-9621-8.
Article
PubMed
Google Scholar
Herzog M, Dorne AM, Grellet F: GASA, a gibberellin-regulated gene family from Arabidopsis thaliana related to the tomato GAST1 gene. Plant Mol Biol. 1995, 27: 743-752. 10.1007/BF00020227.
Article
CAS
PubMed
Google Scholar
Shi L, Gast RT, Gopalraj M, Olszewski NE: Characterization of a shoot-specific, GA3- and ABA-regulated gene from tomato. Plant J. 1992, 2: 153-159.
CAS
PubMed
Google Scholar
Aubert D, Chevillard M, Dorne AM, Arlaud G, Herzog M: Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Mol Biol. 1998, 36: 871-883. 10.1023/A:1005938624418.
Article
CAS
PubMed
Google Scholar
Roxrud I, Lid SE, Fletcher JC, Schmidt ED, Opsahl-Sorteberg HG: GASA4, one of the 14-member Arabidopsis GASA family of small polypeptides, regulates flowering and seed development. Plant Cell Physiol. 2007, 48: 471-483. 10.1093/pcp/pcm016.
Article
CAS
PubMed
Google Scholar
Suttle JC: Involvement of endogenous gibberellins in potato tuber dormancy and early sprout growth: a critical assessment. J Plant Physiol. 2004, 161: 157-164. 10.1078/0176-1617-01222.
Article
CAS
PubMed
Google Scholar
Garcia-Martinez JL, Gil J: Light regulation of gibberellin biosynthesis and mode of action. J Plant Growth Regul. 2001, 20: 354-368. 10.1007/s003440010033.
Article
CAS
PubMed
Google Scholar
Ueguchi-Tanaka M, Nakajima M, Motoyuki A, Matsuoka M: Gibberellin receptor and its role in gibberellin signaling in plants. Annu Rev Plant Biol. 2007, 58: 183-198. 10.1146/annurev.arplant.58.032806.103830.
Article
CAS
PubMed
Google Scholar
Rinne PL, Welling A, Vahala J, Ripel L, Ruonala R, Kangasjarvi J, van der Schoot C: Chilling of dormant buds hyperinduces FLOWERING LOCUS T and recruits GA-inducible 1,3-beta-glucanases to reopen signal conduits and release dormancy in Populus. Plant Cell. 2011, 23: 130-146. 10.1105/tpc.110.081307.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dixon DP, Lapthorn A, Edwards R: Plant glutathione transferases. Genome Biol. 2002, 3: REVIEWS 3004.1-3004.10.
Google Scholar
Halaly T, Pang X, Batikoff T, Crane O, Keren A, Venkateswari J, Ogrodovitch A, Sadka A, Lavee S, Or E: Similar mechanisms might be triggered by alternative external stimuli that induce dormancy release in grape buds. Planta. 2008, 228: 79-88. 10.1007/s00425-008-0720-6.
Article
CAS
PubMed
Google Scholar
Hedley PE, Russell JR, Jorgensen L, Gordon S, Morris JA, Hackett CA, Cardle L, Brennan R: Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.). BMC Plant Biol. 2010, 10: 202-10.1186/1471-2229-10-202.
Article
PubMed Central
PubMed
Google Scholar
Prasad T: Mechanisms of chilling-induced oxidative stress injury and tolerance in developing maize seedlings: changes in antioxidant system, oxidation of proteins and lipids, and protease activities. Plant J. 1996, 10: 1017-1026. 10.1046/j.1365-313X.1996.10061017.x.
Article
CAS
Google Scholar
Stafstrom JP, Ripley BD, Devitt ML, Drake B: Dormancy-associated gene expression in pea axillary buds. Cloning and expression of PsDRM1 and PsDRM2. Planta. 1998, 205: 547-552. 10.1007/s004250050354.
Article
CAS
PubMed
Google Scholar
Naik D, Dhanaraj AL, Arora R, Rowland LJ: Identification of genes associated with cold acclimation in blueberry (Vaccinium corymbosum L.) using a subtractive hybridization approach. Plant Sci. 2007, 173: 213-222. 10.1016/j.plantsci.2007.05.003.
Article
CAS
Google Scholar
Koike M, Takezawa D, Arakawa K, Yoshida S: Accumulation of 19-kDa plasma membrane polypeptide during induction of freezing tolerance in wheat suspension-cultured cells by abscisic acid. Plant Cell Physiol. 1997, 38: 707-716. 10.1093/oxfordjournals.pcp.a029224.
Article
CAS
PubMed
Google Scholar
Guy C: Molecular responses of plants to cold shock and cold acclimation. J Mol Microbiol Biotechnol. 1999, 1: 231-242.
CAS
PubMed
Google Scholar
Le Provost G, Herrera R, Paiva J, Chaumeil P, Salin F, Plomion C: A micromethod for high throughput RNA extraction in forest trees. Biol Res. 2007, 40: 291-297.
Article
CAS
PubMed
Google Scholar
Documentation for phrap and cross_match. http://bozeman.mbt.washington.edu/phrap.docs/phrap.html,
SeqClean. http://sourceforge.net/projects/seqclean/,
Jerome M, Noirot C, Klopp C: Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC research notes. 2011, 4: 149-10.1186/1756-0500-4-149.
Article
PubMed Central
PubMed
Google Scholar
Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000, 7: 203-214. 10.1089/10665270050081478.
Article
CAS
PubMed
Google Scholar
Wilhelm BT, Landry JR: RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods. 2009, 48: 249-257. 10.1016/j.ymeth.2009.03.016.
Article
CAS
PubMed
Google Scholar
R Development Core Team: A Language and Environment for Statistical Computing. 2010, Vienna, Austria: R Foundation for Statistical Computing
Google Scholar
Young MD, Wakefield MJ, Smyth GK, Oshlack A: Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010, 11: R14-10.1186/gb-2010-11-2-r14.
Article
PubMed Central
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
CAS
PubMed
Google Scholar
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, Phan I: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003, 31: 365-370. 10.1093/nar/gkg095.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.
Article
CAS
PubMed
Google Scholar
Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E: PGC-1[alpha]-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003, 34: 267-273. 10.1038/ng1180.
Article
CAS
PubMed
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005, 102: 15545-15550. 10.1073/pnas.0506580102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Paiva JA, Garces M, Alves A, Garnier-Gere P, Rodrigues JC, Lalanne C, Porcon S, Le Provost G, Perez Dda S, Brach J: Molecular and phenotypic profiling from the base to the crown in maritime pine wood-forming tissue. New Phytol. 2008, 178: 283-301. 10.1111/j.1469-8137.2008.02379.x.
Article
CAS
PubMed
Google Scholar
Rozen S, Skaletsky HJ: Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Edited by: Krawetz SA, Misener S. 2000, Totowa/NJ: Humana Press, 365-386.
Google Scholar
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3: RESEARCH0034
Google Scholar