Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome
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[1] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[2] S. Kelly,et al. TransRate: reference-free quality assessment of de novo transcriptome assemblies , 2015, bioRxiv.
[3] Rafael A. Cañas,et al. De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. , 2014, Plant biotechnology journal.
[4] Hans A. Vasquez-Gross,et al. Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation , 2014, Genetics.
[5] S. Salzberg,et al. Sequencing and Assembly of the 22-Gb Loblolly Pine Genome , 2014, Genetics.
[6] Matthew Fraser,et al. InterProScan 5: genome-scale protein function classification , 2014, Bioinform..
[7] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[8] R. Sturrock,et al. Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola , 2013, BMC Genomics.
[9] J. Harrow,et al. Assessment of transcript reconstruction methods for RNA-seq , 2013, Nature Methods.
[10] Kazunori Okada,et al. WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance , 2013, Journal of experimental botany.
[11] Colin N. Dewey,et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.
[12] Michael Ott,et al. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity , 2013 .
[13] Douglas G. Scofield,et al. The Norway spruce genome sequence and conifer genome evolution , 2013, Nature.
[14] Steven J. M. Jones,et al. Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana) , 2013, BMC Plant Biology.
[15] Ning Leng,et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments , 2013, Bioinform..
[16] Nagarjun Vijay,et al. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA‐seq experiments , 2013, Molecular ecology.
[17] R. Marsh,et al. Comparative analysis of de novo transcriptome assembly , 2013, Science China Life Sciences.
[18] Stephen A. Smith,et al. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics , 2013, BMC Genomics.
[19] T. Itoh,et al. Characterisation of the wheat (triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat , 2013, BMC Genomics.
[20] Shilin Chen,et al. FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads , 2012, PloS one.
[21] Jun Liu,et al. Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses , 2012, PloS one.
[22] Philippe Rigault,et al. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers , 2012, BMC Biology.
[23] Jialei Duan,et al. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data , 2012, BMC Genomics.
[24] D. Neale,et al. Uniform standards for genome databases in forest and fruit trees , 2012, Tree Genetics & Genomes.
[25] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[26] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[27] Stijn van Dongen,et al. Using MCL to extract clusters from networks. , 2012, Methods in molecular biology.
[28] P. Lockhart,et al. Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants , 2012, BMC Genomics.
[29] Y. van de Peer,et al. Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W] , 2011, Plant Physiology.
[30] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[31] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[32] Darío Guerrero-Fernández,et al. EuroPineDB: a high-coverage web database for maritime pine transcriptome , 2011, BMC Genomics.
[33] P. Rigault,et al. A White Spruce Gene Catalog for Conifer Genome Analyses1[W][OA] , 2011, Plant Physiology.
[34] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[35] N. Friedman,et al. Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .
[36] Gang Wu,et al. Inference of gene networks - application to Bifidobacterium , 2011, Bioinform..
[37] M. Wingfield,et al. Pitch canker caused by Fusarium circinatum — a growing threat to pine plantations and forests worldwide , 2008, Australasian Plant Pathology.
[38] Janos Kriston-Vizi,et al. Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3D segmentation algorithms , 2011, BMC Bioinformatics.
[39] G. Sherlock,et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads , 2010, BMC Genomics.
[40] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[41] Patrick J. Biggs,et al. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data , 2010, BMC Bioinformatics.
[42] A. Kononowicz,et al. R proteins as fundamentals of plant innate immunity , 2010, Cellular & Molecular Biology Letters.
[43] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[44] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[45] Jill L. Wegrzyn,et al. TreeGenes: A Forest Tree Genome Database , 2008, International journal of plant genomics.
[46] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[47] R. Sederoff,et al. Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion. , 2007, Tree physiology.
[48] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[49] R. Croteau,et al. Simple isolation of functional RNA from woody stems of gymnosperms , 1994, Plant Molecular Biology Reporter.
[50] K. Shokat,et al. Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4. , 2006, The Plant journal : for cell and molecular biology.
[51] B. Hall,et al. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. , 2006, Molecular phylogenetics and evolution.
[52] Steven Salzberg,et al. Beware of mis-assembled genomes , 2005, Bioinform..
[53] Juan Miguel García-Gómez,et al. BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .
[54] Thomas D. Wu,et al. GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..
[55] W. Dvorak,et al. Differential responses of Central American and Mexican pine species and Pinus radiata to infection by the pitch canker fungus , 2000, New Forests.
[56] M. Wingfield,et al. The future of exotic plantation forestry in the tropics and southern Hemisphere: Lessons from pitch canker , 2002 .
[57] Anton J. Enright,et al. An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.
[58] W. Dvorak,et al. Flow Cytometric Analysis of DNA Content for Tropical and Temperate New World Pines , 2000 .
[59] W. B. Critchfield,et al. Geographic distribution of the pines of the world , 1966 .