Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

[1]  Florian P Breitwieser,et al.  Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification , 2019, Bioinform..

[2]  R. Varshney,et al.  Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement , 2019, Trends in plant science.

[3]  Manja Marz,et al.  De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers , 2019, GigaScience.

[4]  Elena Bushmanova,et al.  rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data , 2018, bioRxiv.

[5]  D. Gilbert Genes of the pig, Sus scrofa, reconstructed with EvidentialGene , 2018, bioRxiv.

[6]  Alejandro A. Schäffer,et al.  VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening , 2018, Bioinform..

[7]  Kazutaka Katoh,et al.  Parallelization of MAFFT for large-scale multiple sequence alignments , 2018, Bioinform..

[8]  Xuehui Huang,et al.  Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice , 2018, Nature Genetics.

[9]  Qun Xu,et al.  Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice , 2018, Nature Genetics.

[10]  Fabian Sievers,et al.  Clustal Omega for making accurate alignments of many protein sequences , 2018, Protein science : a publication of the Protein Society.

[11]  E. M. Farré,et al.  Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato , 2017, Proceedings of the National Academy of Sciences.

[12]  Robert M. Waterhouse,et al.  BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.

[13]  C. K. Chan,et al.  The pangenome of hexaploid bread wheat , 2017, The Plant journal : for cell and molecular biology.

[14]  Bernd Rinn,et al.  FAIRDOMHub: a repository and collaboration environment for sharing systems biology research , 2016, Nucleic Acids Res..

[15]  S. Sauer,et al.  Efficient Application of De Novo RNA Assemblers for Proteomics Informed by Transcriptomics. , 2016, Journal of proteome research.

[16]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[17]  Cheng He,et al.  Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation , 2015, Scientific Reports.

[18]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[19]  Daniel Standage,et al.  The khmer software package: enabling efficient nucleotide sequence analysis , 2015, F1000Research.

[20]  S. Kelly,et al.  TransRate: reference-free quality assessment of de novo transcriptome assemblies , 2015, bioRxiv.

[21]  A. Allan,et al.  Comparative Transcriptome Analysis of White and Purple Potato to Identify Genes Involved in Anthocyanin Biosynthesis , 2015, PloS one.

[22]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[23]  Yi-Zheng Zhang,et al.  Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms , 2015, BMC Genomics.

[24]  Ruiqiang Li,et al.  De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits , 2014, Nature Biotechnology.

[25]  S. Kelly,et al.  Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis , 2014, PLoS genetics.

[26]  C. Buell,et al.  Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding , 2014 .

[27]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[28]  M. A. Pedraza,et al.  Insights into the Maize Pan-Genome and Pan-Transcriptome[W][OPEN] , 2014, Plant Cell.

[29]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[30]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[31]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[32]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[33]  Martin Vingron,et al.  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..

[34]  Vipin T. Sreedharan,et al.  Multiple reference genomes and transcriptomes for Arabidopsis thaliana , 2011, Nature.

[35]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[36]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[37]  Vladimir Batagelj,et al.  Exploratory social network analysis with Pajek. - 2nd ed. , 2011 .

[38]  Daniel R Zerbino,et al.  Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies , 2010, Current protocols in bioinformatics.

[39]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[40]  Chris Sander,et al.  MView: a web-compatible database search or multiple alignment viewer , 1998, Bioinform..