TY - JOUR AU - Andrews, S. J. AU - Rothnagel, J. A. PY - 2014 DA - 2014// TI - Emerging evidence for functional peptides encoded by short open reading frames JO - Nat Rev Genet VL - 15 UR - https://doi.org/10.1038/nrg3520 DO - 10.1038/nrg3520 ID - Andrews2014 ER - TY - JOUR AU - Aalen, R. B. PY - 2013 DA - 2013// TI - Maturing peptides open for communication JO - J Exp Bot VL - 64 UR - https://doi.org/10.1093/jxb/ert378 DO - 10.1093/jxb/ert378 ID - Aalen2013 ER - TY - JOUR AU - Tavormina, P. AU - Coninck, B. AU - Nikonorova, N. AU - Smet, I. AU - Cammue, B. P. A. PY - 2015 DA - 2015// TI - The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions JO - Plant Cell VL - 27 UR - https://doi.org/10.1105/tpc.15.00440 DO - 10.1105/tpc.15.00440 ID - Tavormina2015 ER - TY - JOUR AU - Ghorbani, S. AU - Lin, Y. C. AU - Parizot, B. AU - Fernandez, A. AU - Njo, M. F. AU - Peer, Y. PY - 2015 DA - 2015// TI - Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays JO - J Exp Bot VL - 66 UR - https://doi.org/10.1093/jxb/erv346 DO - 10.1093/jxb/erv346 ID - Ghorbani2015 ER - TY - JOUR AU - Krishnakumar, V. AU - Hanlon, M. R. AU - Contrino, S. AU - Ferlanti, E. S. AU - Karamycheva, S. AU - Kim, M. PY - 2015 DA - 2015// TI - Araport: The Arabidopsis Information Portal JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1200 DO - 10.1093/nar/gku1200 ID - Krishnakumar2015 ER - TY - JOUR AU - Lease, K. A. AU - Walker, J. C. PY - 2006 DA - 2006// TI - The Arabidopsis unannotated secreted peptide database, a resource for plant peptidomics JO - Plant Physiol VL - 142 UR - https://doi.org/10.1104/pp.106.086041 DO - 10.1104/pp.106.086041 ID - Lease2006 ER - TY - STD TI - Hanada K, Zhang X, Borevitz JO, Li W, Shiu S. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res. 2007;17:632–40. ID - ref7 ER - TY - JOUR AU - Hanada, K. AU - Higuchi-Takeuchi, M. AU - Okamoto, M. AU - Yoshizumi, T. AU - Shimizu, M. AU - Nakaminami, K. PY - 2013 DA - 2013// TI - Small open reading frames associated with morphogenesis are hidden in plant genomes JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1213958110 DO - 10.1073/pnas.1213958110 ID - Hanada2013 ER - TY - STD TI - CIPHER by c-guzman [Internet]. Available from: https://c-guzman.github.io/cipher-website/. cited 16 Dec 2016. UR - https://c-guzman.github.io/cipher-website/ ID - ref9 ER - TY - JOUR AU - Tang, S. AU - Lomsadze, A. AU - Borodovsky, M. PY - 2015 DA - 2015// TI - Identification of protein coding regions in RNA transcripts JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv024 DO - 10.1093/nar/gkv024 ID - Tang2015 ER - TY - STD TI - TransDecoder (Find Coding Regions Within Transcripts) [Internet]. Available from: https://transdecoder.github.io/. cited 16 Dec 2016. UR - https://transdecoder.github.io/ ID - ref11 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. AU - Adiconis, X. AU - Fan, L. AU - Raychowdhury, R. AU - Zeng, Q. AU - Chen, Z. AU - Mauceli, E. AU - Hacohen, N. AU - Gnirke, A. AU - Rhind, N. AU - Palma, F. AU - Friedman, B. W. N. AU - Regev, A. PY - 2013 DA - 2013// TI - Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2013 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat : discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - BOOK AU - Skinner, M. E. AU - Uzilov, A. V. AU - Stein, L. D. AU - Mungall, C. J. AU - Holmes, I. H. PY - 2009 DA - 2009// TI - JBrowse : A next-generation genome browser ID - Skinner2009 ER - TY - JOUR AU - Barrett, T. AU - Wilhite, S. E. AU - Ledoux, P. AU - Evangelista, C. AU - Kim, I. F. AU - Tomashevsky, M. PY - 2013 DA - 2013// TI - NCBI GEO: Archive for functional genomics data sets–Update JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1193 DO - 10.1093/nar/gks1193 ID - Barrett2013 ER - TY - JOUR AU - Coninck, B. AU - Carron, D. AU - Tavormina, P. AU - Willem, L. AU - Craik, D. J. AU - Vos, C. PY - 2013 DA - 2013// TI - Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance JO - J Exp Bot VL - 64 UR - https://doi.org/10.1093/jxb/ert295 DO - 10.1093/jxb/ert295 ID - Coninck2013 ER - TY - JOUR AU - Lamesch, P. AU - Berardini, T. Z. AU - Li, D. AU - Swarbreck, D. AU - Wilks, C. AU - Sasidharan, R. PY - 2012 DA - 2012// TI - The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1090 DO - 10.1093/nar/gkr1090 ID - Lamesch2012 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. PY - 2009 DA - 2009// TI - 2C-Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: Phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Suyama, M. AU - Torrents, D. AU - Bork, P. PY - 2006 DA - 2006// TI - PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl315 DO - 10.1093/nar/gkl315 ID - Suyama2006 ER - TY - JOUR AU - Jin, J. AU - Liu, J. AU - Wang, H. AU - Wong, L. AU - Chua, N. H. PY - 2013 DA - 2013// TI - PLncDB: Plant long non-coding RNA database JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt107 DO - 10.1093/bioinformatics/btt107 ID - Jin2013 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: A flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - JOUR AU - Silverstein, K. A. T. AU - Moskal, W. A. AU - Wu, H. C. AU - Underwood, B. A. AU - Graham, M. A. AU - Town, C. D. PY - 2007 DA - 2007// TI - Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants JO - Plant J VL - 51 UR - https://doi.org/10.1111/j.1365-313X.2007.03136.x DO - 10.1111/j.1365-313X.2007.03136.x ID - Silverstein2007 ER - TY - JOUR AU - Silverstein, K. A. T. AU - Graham, M. A. AU - Paape, T. D. AU - VandenBosch, K. A. PY - 2005 DA - 2005// TI - Genome organization of more than 300 defensin-like genes in Arabidopsis JO - Plant Physiol VL - 138 UR - https://doi.org/10.1104/pp.105.060079 DO - 10.1104/pp.105.060079 ID - Silverstein2005 ER - TY - JOUR AU - Giacomelli, L. AU - Nanni, V. AU - Lenzi, L. AU - Zhuang, J. AU - Serra, M. D. AU - Banfield, M. J. PY - 2012 DA - 2012// TI - Identification and Characterization of the Defensin-Like Gene Family of Grapevine JO - Mol Plant-Microbe Interact VL - 25 UR - https://doi.org/10.1094/MPMI-12-11-0323 DO - 10.1094/MPMI-12-11-0323 ID - Giacomelli2012 ER - TY - JOUR AU - Zhou, P. AU - Silverstein, K. A. AU - Gao, L. AU - Walton, J. D. AU - Nallu, S. AU - Guhlin, J. PY - 2013 DA - 2013// TI - Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application) JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-335 DO - 10.1186/1471-2105-14-335 ID - Zhou2013 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2014 DA - 2014// TI - Pfam: The protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 ER - TY - JOUR AU - Eddy, S. R. PY - 2011 DA - 2011// TI - Accelerated profile HMM searches JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002195 DO - 10.1371/journal.pcbi.1002195 ID - Eddy2011 ER - TY - JOUR AU - Petersen, T. N. AU - Brunak, S. AU - Heijne, G. AU - Nielsen, H. PY - 2011 DA - 2011// TI - SignalP 4.0: discriminating signal peptides from transmembrane regions JO - Nat Methods VL - 8 UR - https://doi.org/10.1038/nmeth.1701 DO - 10.1038/nmeth.1701 ID - Petersen2011 ER - TY - JOUR AU - Krogh, A. AU - Larsson, B. AU - Heijne, G. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes JO - J Mol Biol VL - 305 UR - https://doi.org/10.1006/jmbi.2000.4315 DO - 10.1006/jmbi.2000.4315 ID - Krogh2001 ER - TY - JOUR AU - Castro, E. AU - Sigrist, C. J. A. AU - Gattiker, A. AU - Bulliard, V. AU - Langendijk-Genevaux, P. S. AU - Gasteiger, E. PY - 2006 DA - 2006// TI - ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl124 DO - 10.1093/nar/gkl124 ID - Castro2006 ER - TY - JOUR AU - Dinkel, H. AU - Michael, S. AU - Weatheritt, R. J. AU - Davey, N. E. AU - Roey, K. AU - Altenberg, B. PY - 2012 DA - 2012// TI - ELM–The database of eukaryotic linear motifs JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1064 DO - 10.1093/nar/gkr1064 ID - Dinkel2012 ER - TY - STD TI - van Dongen S. Graph clustering. Graph Stimul. by flow Clust. PhD thesis. Utrecht: University of Utrecht; 2000. ID - ref36 ER - TY - JOUR AU - Masselot, A. PY - 2014 DA - 2014// TI - Visualization of protein sequence features using JavaScript and SVG with pViz.js JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu567 DO - 10.1093/bioinformatics/btu567 ID - Masselot2014 ER - TY - JOUR AU - Martin, A. C. R. PY - 2014 DA - 2014// TI - Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV) JO - F1000Res VL - 3 ID - Martin2014 ER - TY - JOUR AU - Castellana, N. E. AU - Payne, S. H. AU - Shen, Z. AU - Stanke, M. AU - Bafna, V. AU - Briggs, S. P. PY - 2008 DA - 2008// TI - Discovery and revision of Arabidopsis genes by proteogenomics JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0811066106 DO - 10.1073/pnas.0811066106 ID - Castellana2008 ER -