Review and Important Papers:


1.    Jiao, Y., Li, J., Tang, H. & Paterson, A. H. Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots. The Plant cell 26, 2792 (2014).

2.   Project, A. G. et al. [Research Article] The Amborella Genome and the Evolution of Flowering Plants.  (2013).

3.    Ming, R. et al. The pineapple genome and the evolution of CAM photosynthesis. Nature genetics 47, 1435 (2015).

4.   Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644 (2011).

5.   Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9, R7 (2008).

6.   I, K. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004).

7.   A, L., V, T., YO, C. & M, B. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic acids research 33, 6494-6506 (2005).

8.   Stanke, M., Schöffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).

9.   Consortium, T. G. O. Gene Ontology Consortium: going forward. Nucleic Acids Research 43, D1049 (2015).

10.   Finn, R. D. et al. InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Research 45, D190 (2017).

11.   Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240 (2014).

12.   Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 27, 29-34 (2000).

13.   C, X. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic acids research 39, W316 (2011).

14.   Rozen, S. & Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132, 365 (2000).

15.   Schuler, G. D. Sequence mapping by electronic PCR. Genome Research 7, 541 (1997).

16.   Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform.  (Oxford University Press, 2009).

17.   Li, H., Handsaker, B., Wysoker, A., Fennell, T. & Ruan, J. The Sequence Alignment-Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).

18.   Mckenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 1297-1303 (2010).

19.   Lee, T. H., Guo, H., Wang, X., Kim, C. & Paterson, A. H. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC genomics 15, 162 (2014).

20.   Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (Oxford, England) 30, 2114 (2014).

21.   Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature protocols 11, 1650 (2016).

22.   Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 562 (2012).

23.   Ma, C. & Wang, X. Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis. Chinese Nursing Management 160, 192 (2008).

24.   H, T. et al. Synteny and collinearity in plant genomes. Science 320, 486-488 (2008).

25.   Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J. & Holmes, I. H. JBrowse: a next-generation genome browser. Genome Research 19, 1630 (2009).

26.   SF, A., W, G., W, M., EW, M. & DJ, L. Basic local alignment search tool. Journal of Molecular Biology 215, 403-410 (1990).

27.   Deng, W., Nickle, D. C., Learn, G. H., Maust, B. & Mullins, J. I. ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 23, 2334-2336 (2007).

28.   Bindler, G. et al. A high density genetic map of tobacco ( Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theoretical & Applied Genetics 123, 219 (2011).

29.   D'Hont, A. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488, 213-217 (2012).



30.   Moyle, R. L., Crowe, M. L., Ripi-Koia, J., Fairbairn, D. J. & Botella, J. R. PineappleDB: An online pineapple bioinformatics resource. BMC plant biology 5, 21 (2005).