Acta Biológica Colombiana

Adams MJ. DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Res. 2006;34(90001):D382-D385. Doi: http://dx.doi.org/10.1093/nar/gkj023

Adams I, Fox A. Diagnosis of Plant Viruses Using Next-Generation Sequencing and Metagenomic Analysis. In: Wang A, Zhou X, editors. Current Research Topics in Plant Virology. Cham: Springer International Publishing, 2016. p. 323-335.

Adams IP, Braidwood LA, Stomeo F, Phiri N, Uwumukiza B, Feyissa B, et al. Characterising maize viruses associated with maize lethal necrosis symptoms in sub Saharan Africa. bioRxiv. 2017:161489. Doi: http://dx.doi.org/10.1101/161489

Alexander MM, Cilia M. A molecular tug-of-war: Global plant proteome changes during viral infection. Curr. Plant Biol. 2016;5:13-24. Doi: http://dx.doi.org/10.1016/j.cpb.2015.10.003

Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci. Rep. 2017;7(1). Doi: http://dx.doi.org/10.1038/s41598-017-09617-z

Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. Doi: http://dx.doi.org/10.1186/gb-2010-11-10-r106

Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31(2):166-169. Doi: http://dx.doi.org/10.1093/bioinformatics/btu638

Anjanappa RB, Mehta D, Okoniewski MJ, Szabelska-Berȩsewicz A, Gruissem W, Vanderschuren H. Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response. Mol. Plant Pathol. 2018;19(2):476-489. Doi: http://dx.doi.org/10.1111/mpp.12565

Barba M, Czosnek H, Hadidi A. Historical Perspective, Development and Applications of Next-Generation Sequencing in Plant Virology. Viruses. 2014;6(1):106-136. Doi: http://dx.doi.org/10.3390/v6010106

Bengyella L, Waikhom SD, Allie F, Rey C. Virus tolerance and recovery from viral induced-symptoms in plants are associated with transcriptome reprograming. Plant Mol. Biol. 2015;89(3):243-252. Doi: http://dx.doi.org/10.1007/s11103-015-0362-6

Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung K-H, Miller PL, et al. X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers. ‎J. Proteome Res. 2008;7(1):293-299. Doi: http://dx.doi.org/10.1021/pr0701198

Blawid R, Silva JMF, Nagata T. Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline. Ann. Appl. Biol. 2017;170(3):301-314. Doi: http://dx.doi.org/10.1111/aab.12345

Blazquez MA, Zheng W, Ma L, Zhao J, Li Z, Sun F, et al. Comparative Transcriptome Analysis of Two Rice Varieties in Response to Rice Stripe Virus and Small Brown Planthoppers during Early Interaction. PLoS One. 2013;8(12):e82126. Doi: http://dx.doi.org/10.1371/journal.pone.0082126

Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 2016;34(5):525-527. Doi: http://dx.doi.org/10.1038/nbt.3519

Bronzato Badial A, Sherman D, Stone A, Gopakumar A, Wilson V, Schneider W, et al. Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues. Plant Dis. 2018;102(8):1648-1652. Doi: http://dx.doi.org/10.1094/pdis-04-17-0488-re

Carvajal-Yepes M, Olaya C, Lozano I, Cuervo M, Castaño M, Cuellar WJ. Unraveling complex viral infections in cassava (Manihot esculenta Crantz) from Colombia. Virus Res. 2014;186:76-86. Doi: http://dx.doi.org/10.1016/j.virusres.2013.12.011

Chakrabarty D, Ghorbani A, Izadpanah K, Dietzgen RG. Changes in maize transcriptome in response to maize Iranian mosaic virus infection. PLoS One. 2018;13(4):e0194592. Doi: http://dx.doi.org/10.1371/journal.pone.0194592

Chandrasekhar K, Dileep A, Lebonah DE, Kumari JP. A Short Review on Proteomics and its Applications. Int. Lett. Nat. Sci. 2014;17:77-84. Doi: http://dx.doi.org/10.18052/www.scipress.com/ILNS.17.77

Choi H, Fermin D, Nesvizhskii AI. Significance Analysis of Spectral

Count Data in Label-free Shotgun Proteomics. Mol. Cell. Proteom. 2008;7(12):2373-2385. Doi: http://dx.doi.org/10.1074/mcp.M800203-MCP200

De La Fuente Van Bentem S, Roitinger E, Anrather D, Csaszar E, Hirt H. Phosphoproteomics as a tool to unravel plant regulatory mechanisms. Physiol. Plant. 2006;126(1):110-119. Doi: http://dx.doi.org/10.1111/j.1399-3054.2006.00615.x

Di Carli M, Villani ME, Bianco L, Lombardi R, Perrotta G, Benvenuto E, et al. Proteomic Analysis of the Plant−Virus Interaction in Cucumber Mosaic Virus (CMV) Resistant Transgenic Tomato. ‎J. Proteome Res. 2010;9(11):5684-5697. Doi: http://dx.doi.org/10.1021/pr100487x

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. Doi: http://dx.doi.org/10.1093/bioinformatics/bts635

Dong Q. PlantGDB, plant genome database and analysis tools. Nucleic Acids Res. 2004;32(90001):354D-359. Doi: http://dx.doi.org/10.1093/nar/gkh046

Dória MS, Pirovani CP. Proteomic Response of Host Plants to Citrus tristeza virus. 2019;2015:209-218. Doi: http://dx.doi.org/10.1007/978-1-4939-9558-5_15

Fang DD, Maruthi MN, Bouvaine S, Tufan HA, Mohammed IU, Hillocks RJ. Transcriptional Response of Virus-Infected Cassava and Identification of Putative Sources of Resistance for Cassava Brown Streak Disease. PLoS One. 2014;9(5):e96642. Doi: http://dx.doi.org/10.1371/journal.pone.0096642

Fellers J, Webb C, Fellers M, Shoup Rupp J, De Wolf E. Wheat virus identification within infected tissue using nanopore sequencing technology. Plant Dis. 2019. Doi: http://dx.doi.org/10.1094/pdis-09-18-1700-re

Filloux D, Fernandez E, Loire E, Claude L, Galzi S, Candresse T, et al. Nanopore-based detection and characterization of yam viruses. Sci. Rep. 2018;8(1). Doi: http://dx.doi.org/10.1038/s41598-018-36042-7

Gallo Y, Toro LF, Jaramillo H, Gutiérrez PA, Marín M. Identificación y caracterización molecular del genoma completo de tres virus en cultivos de lulo (Solanum quitoense) de Antioquia (Colombia). rev.colomb.cienc.hortic. 2018;12(2):281-292. Doi: http://dx.doi.org/10.17584/rcch.2018v12i2.7692

Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, et al. Open Mass Spectrometry Search Algorithm. ‎J. Proteome Res. 2004;3(5):958-964. Doi: http://dx.doi.org/10.1021/pr0499491

Glaus P, Honkela A, Rattray M. Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics. 2012;28(13):1721-1728. Doi: http://dx.doi.org/10.1093/bioinformatics/bts260

Goecks J, Nekrutenko A, Taylor J, Galaxy Team T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86. Doi: http://dx.doi.org/10.1186/gb-2010-11-8-r86

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178-D1186. Doi: http://dx.doi.org/10.1093/nar/gkr944

Goodwin S, Mcpherson JD, Mccombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 2016;17(6):333-351. Doi: http://dx.doi.org/10.1038/nrg.2016.49

Goyer A, Hamlin L, Crosslin JM, Buchanan A, Chang JH. RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection. BMC genomics. 2015;16(1). Doi: http://dx.doi.org/10.1186/s12864-015-1666-2

Gutiérrez-Sánchez P, Alzate-Restrepo J, Marín-Montoya M. Caracterización del viroma de ARN en tejido radical de Solanum phureja mediante pirosecuenciación 454 GS-FLX. Bioagro. 2014;26(2):89-98.

Gutiérrez P, Mesa HJ, Marín Montoya M. Genome sequence of a divergent Colombian isolate of potato virus V (PVV) infecting Solanum phureja. ActaVirol. 2016;60(01):49-54. Doi: http://dx.doi.org/10.4149/av_2016_01_49

Gutiérrez PA, Alzate JF, Marín Montoya M. Genome sequence of a virus isolate from tamarillo (Solanum betaceum) in Colombia: evidence for a new potyvirus. Arch. Virol. 2014;160(2):557-560. Doi: http://dx.doi.org/10.1007/s00705-014-2296-8

Gutiérrez PA, Alzate JF, Montoya MM. Complete genome sequence of an isolate of Potato virus X (PVX) infecting Cape gooseberry (Physalis peruviana) in Colombia. Virus Genes. 2015;50(3):518-522. Doi: http://dx.doi.org/10.1007/s11262-015-1181-1

Gutiérrez PA, Marín-Montoya M, Muñoz-Baena L. Genome sequencing of two Bell pepper endornavirus (BPEV) variants infecting Capsicum annuum in Colombia. Agron. Colomb. 2017;35(1):44. Doi: http://dx.doi.org/10.15446/agron.colomb.v35n1.60626

Gutiérrez Sánchez PA, Jaramillo Mesa H, Marin Montoya M. Next generation sequence analysis of the forage peanut (Arachis pintoi) virome. Rev Fac Nac Agron. 2016;69(2):7881. Doi: http://dx.doi.org/10.15446/rfna.v69n2.59133

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 2013;8(8):1494-1512. Doi: http://dx.doi.org/10.1038/nprot.2013.084

Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol. 2016;7. Doi: http://dx.doi.org/10.3389/fmicb.2016.01325

Hanley-Bowdoin L, Settlage SB, Robertson D. Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication. Mol. Plant Pathol. 2004;5(2):149-156. Doi: http://dx.doi.org/10.1111/j.1364-3703.2004.00214.x

Hardcastle TJ, Kelly KA. baySeq: Empirical Bayesian methods for

identifying differential expression in sequence count data. BMC Bioinform. 2010;11(1):422. Doi: http://dx.doi.org/10.1186/1471-2105-11-422

Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016;107(1):1-8. Doi: http://dx.doi.org/10.1016/j.ygeno.2015.11.003

Hernandez R. Sequencing Within Reach. Genet Eng Biotechn N. 2018;38(4):1,22,25. Doi: http://dx.doi.org/10.1089/gen.38.04.01

Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF. The transcriptomics of an experimentally evolved plant-virus interaction. Sci. Rep. 2016;6(1). Doi: http://dx.doi.org/10.1038/srep24901

Howe EA, Sinha R, Schlauch D, Quackenbush J. RNA-Seq analysis in MeV. Bioinformatics. 2011;27(22):3209-3210. Doi: http://dx.doi.org/10.1093/bioinformatics/btr490

Hull R. Plant Virus Viromics. In: Plant Virology. Ciudad: Academic Press, 2014. p. 929-971.

Hull R. Plant Viruses and Their Classification. In: Hull R, editor. Plant Virology. Ciudad: Academic Press, 2014. p. 15-68.

Hulo C, De Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, et al. ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res. 2011;39(suppl_1):D576-D582. Doi: http://dx.doi.org/10.1093/nar/gkq901

International Human Genome Sequencing C. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931-45. Doi: http://dx.doi.org/10.1038/nature03001

Jaramillo Mesa H, Marín Montoya M, Gutiérrez PA. Molecular characterization of Soybean mosaic virus (SMV) infecting Purple passion fruit (Passiflora edulis f. edulis) in Antioquia, Colombia. Arch Phytopathology Plant Protect. 2018;51(11-12):617-636. Doi: http://dx.doi.org/10.1080/03235408.2018.1505411

Jaramillo Mesa H, Marín Montoya MA, Gutiérrez Sánchez P. Complete genome sequence of a Passion fruit yellow mosaic virus (PFYMV) isolate infecting purple passionfruit (Passiflora edulis f. edulis). Rev Fac Nac Agron Medellin. 2019;72(1):8643-8654. Doi: http://dx.doi.org/10.15446/rfnam.v72n1.69438

Jayaraman D, Forshey KL, Grimsrud PA, Ané J-M. Leveraging Proteomics to Understand Plant–Microbe Interactions. Front. Plant Sci. 2012;3. Doi: http://dx.doi.org/10.3389/fpls.2012.00044

Jeske H. Barcoding of Plant Viruses with Circular Single-Stranded DNA Based on Rolling Circle Amplification. Viruses. 2018;10(9):469. Doi: http://dx.doi.org/10.3390/v10090469

Jimenez J, Carvajal-Yepes M, Leiva AM, Cruz M, Romero LE, Bolaños CA, et al. Complete Genome Sequence of Rice hoja blanca tenuivirus Isolated from a Susceptible Rice Cultivar in Colombia. Genome Announc. 2018;6(7):e01490-17. Doi: http://dx.doi.org/10.1128/genomeA.01490-17

Kanehisa M, Goto S. KEGG: kyoto encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27-30. Doi: http://dx.doi.org/10.1093/nar/28.1.27

Kchouk M, Gibrat JF, Elloumi M. Generations of Sequencing Technologies: From First to Next Generation. Biol. Med. 2017;09(03). Doi: http://dx.doi.org/10.4172/0974-8369.1000395

Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods. 2015;12(4):357-360. Doi: http://dx.doi.org/10.1038/nmeth.3317

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. Doi: http://dx.doi.org/10.1186/gb-2013-14-4-r36

Kulski JK. Next-generation sequencing—an overview of the history, tools, and “Omic” applications. In: Next Generation Sequencing-Advances, Applications and Challenges. IntechOpen, 2016.

Kundu S, Chakraborty D, Kundu A, Pal A. Proteomics approach combined with biochemical attributes to elucidate compatible and incompatible plant-virus interactions between Vigna mungo and Mungbean Yellow Mosaic India Virus. Proteome Sci. 2013;11(1):15. Doi: http://dx.doi.org/10.1186/1477-5956-11-15

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011;12(1):323. Doi: http://dx.doi.org/10.1186/1471-2105-12-323

Li Z, Adams RM, Chourey K, Hurst GB, Hettich RL, Pan C. Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos. ‎J. Proteome Res. 2012;11(3):1582-1590. Doi: http://dx.doi.org/10.1021/pr200748h

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013;30(7):923-930. Doi: http://dx.doi.org/10.1093/bioinformatics/btt656

Lin P-C, Hu W-C, Lee S-C, Chen Y-L, Lee C-Y, Chen Y-R, et al. Application of an Integrated Omics Approach for Identifying Host Proteins That Interact WithOdontoglossum ringspot virusCapsid Protein. Mol Plant Microbe In. 2015;28(6):711-726. Doi: http://dx.doi.org/10.1094/mpmi-08-14-0246-r

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012;40(W1):W622-W627. Doi: http://dx.doi.org/10.1093/nar/gks540

Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics. 2014;30(23):3399-3401. Doi: http://dx.doi.org/10.1093/bioinformatics/btu555

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12). Doi: http://dx.doi.org/10.1186/s13059-014-0550-8

Madroñero J, Rodrigues SP, Antunes TFS, Abreu PMV, Ventura JA, Fernandes AaR, et al. Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya. Plant cell reports. 2018;37(7):967-980. Doi: http://dx.doi.org/10.1007/s00299-018-2281-x

Megias E, Do Carmo LST, Nicolini C, Silva LP, Blawid R, Nagata T, et al. Chloroplast proteome of nicotiana benthamiana infected by Tomato Blistering mosaic virus. Protein J. 2018;37(3):290-299. Doi: http://dx.doi.org/10.1007/s10930-018-9775-9

Mehta D, Hirsch-Hoffmann M, Were M, Patrignani A, Zaidi SS-E-A, Were H, et al. A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic Acids Res. 2019;47(2):e9-e9. Doi: http://dx.doi.org/10.1093/nar/gky914

Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, et al. Linking Virus Genomes with Host Taxonomy. Viruses. 2016;8(3):66. Doi: http://dx.doi.org/10.3390/v8030066

Mochida K, Shinozaki K. Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions. Plant Cell Physiol. 2011;52(12):2017-2038. Doi: http://dx.doi.org/10.1093/pcp/pcr153

Mosa KA, Ismail A, Helmy M. Omics and System Biology Approaches in Plant Stress Research. In: Plant Stress Tolerance. SpringerBriefs in Systems Biology. Ciudad: Springer, Cham, 2017. p. 21-34.

Muñoz Baena L, Gutiérrez Sánchez PA, Marín Montoya M. Secuenciación del genoma completo del Potato yellow vein virus (PYVV) en tomate (Solanum lycopersicum) en Colombia. Acta biol. colomb. 2017;22(1):5-17. Doi: http://dx.doi.org/10.15446/abc.v22n1.59211

Muñoz E, Gutiérrez S, Marín M. Detection and genome characterization of Potato virus Y isolates infecting potato (Solanum tuberosum L.) in La Union (Antioquia, Colombia). Agron. Colomb. 2016;34(3):317-328. Doi: http://dx.doi.org/http://dx.doi.org/10.15446/agron.colomb.v34n3.59973

Naito FYB, Melo FL, Fonseca MEN, Santos CaF, Chanes CR, Ribeiro BM, et al. Nanopore sequencing of a novel bipartite New World begomovirus infecting cowpea. Arch. Virol. 2019;164(7):1907-1910. Doi: http://dx.doi.org/10.1007/s00705-019-04254-5

Nicaise VR. Crop immunity against viruses: outcomes and future challenges. Front. Plant Sci. 2014;5. Doi: http://dx.doi.org/10.3389/fpls.2014.00660

NIH. The Cost of Sequencing a Human Genome [cited 2019 24/04/2019]. Available from: https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost.

O'leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, Mcveigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733-D745. Doi: http://dx.doi.org/10.1093/nar/gkv1189

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 2017;14(4):417-419. Doi: http://dx.doi.org/10.1038/nmeth.4197

Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat. Biotechnol. 2014;32(5):462-464. Doi: http://dx.doi.org/10.1038/nbt.2862

Pavan Kumar BK, Kanakala S, Malathi VG, Gopal P, Usha R. Transcriptomic and proteomic analysis of yellow mosaic diseased soybean. J Plant Biochem Biot. 2016;26(2):224-234. Doi: http://dx.doi.org/10.1007/s13562-016-0385-3

Peck SC. Proteomics: Setting the Stage for Systems Biology. 2018;35:243-257. Doi: http://dx.doi.org/10.1002/9781119312994.apr0379

Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N, et al. Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches. Front Microbiol. 2017;8. Doi: http://dx.doi.org/10.3389/fmicb.2017.01998

Peng Y, Leung HCM, Yiu S-M, Lv M-J, Zhu X-G, Chin FYL. IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. Bioinformatics. 2013;29(13):i326-i334. Doi: http://dx.doi.org/10.1093/bioinformatics/btt219

Proost S, Van bel M, Vaneechoutte D, Van de peer Y, Inzé D, Mueller-Roeber B, et al. PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res. 2015;43(D1):D974-D981. Doi: http://dx.doi.org/10.1093/nar/gku986

Rang FJ, Kloosterman WP, De Ridder J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 2018;19(1):90. Doi: http://dx.doi.org/10.1186/s13059-018-1462-9

Rhoads A, Au KF. PacBio Sequencing and Its Applications. Genom Proteom Bioinf. 2015;13(5):278-289. Doi: http://dx.doi.org/10.1016/j.gpb.2015.08.002

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, et al. De novo assembly and analysis of RNA-seq data. Nat. Methods. 2010;7(11):909-912. Doi: http://dx.doi.org/10.1038/nmeth.1517

Robinson MD, Mccarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26(1):139-140. Doi: http://dx.doi.org/10.1093/bioinformatics/btp616

Rodríguez MH, Niño NE, Cutler J, Langer J, Casierra-Posada F, Miranda D, et al. Certificación de material vegetal sano en Colombia: Un análisis crítico de oportunidades y retos para controlar enfermedades ocasionadas por virus. rev.colomb.cienc.hortic. 2016;10(1):164-175. Doi: http://dx.doi.org/10.17584/rcch.2016v10i1.4921

Roossinck MJ, Martin DP, Roumagnac P. Plant Virus Metagenomics: Advances in Virus Discovery. Phytopathology. 2015;105(6):716-727. Doi: http://dx.doi.org/10.1094/phyto-12-14-0356-rvw

Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, et al. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2012;41(D1):D475-D482. Doi: http://dx.doi.org/10.1093/nar/gks1200

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat. Methods. 2016;13(9):741-748. Doi: http://dx.doi.org/10.1038/nmeth.3959

Roy A, Zhang Y. Protein Structure Prediction. 2012. Doi: http://dx.doi.org/10.1002/9780470015902.a0003031.pub2

Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28(8):1086-1092. Doi: http://dx.doi.org/10.1093/bioinformatics/bts094

Shannon P. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-2504. Doi: http://dx.doi.org/10.1101/gr.1239303

Soares EDA, Werth EG, Madroñero LJ, Ventura JA, Rodrigues SP, Hicks LM, et al. Label-free quantitative proteomic analysis of pre-flowering PMeV-infected Carica papaya L. J. Proteom. 2017;151:275-283. Doi: http://dx.doi.org/10.1016/j.jprot.2016.06.025

Souza PFN, Garcia-Ruiz H, Carvalho FEL. What proteomics can reveal about plant–virus interactions? Photosynthesis-related proteins on the spotlight. Theor Exp Plant Phys. 2019;31(1):227-248. Doi: http://dx.doi.org/10.1007/s40626-019-00142-0

Srivastava A, Sarkar H, Gupta N, Patro R. RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. Bioinformatics. 2016;32(12):i192-i200. Doi: http://dx.doi.org/10.1093/bioinformatics/btw277

Stagljar I. The power of OMICs. Biochemical and biophysical research communications. 2016;479(4):607-609. Doi: http://dx.doi.org/10.1016/j.bbrc.2016.09.095

Stano M, Beke G, Klucar L. viruSITE—integrated database for viral genomics. Database. 2016;2016:baw162. Doi: http://dx.doi.org/10.1093/database/baw162

Stare T, Stare K, Weckwerth W, Wienkoop S, Gruden K. Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection. Proteomes. 2017;5(4):14. Doi: http://dx.doi.org/10.3390/proteomes5030014

Sun F, Fang P, Li J, Du L, Lan Y, Zhou T, et al. RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis. Virol. J. 2016;13(1):202. Doi: http://dx.doi.org/10.1186/s12985-016-0663-7

Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, et al. Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004;37(6):914-939. Doi: http://dx.doi.org/10.1111/j.1365-313X.2004.02016.x

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature biotechnology. 2013;31:46-53. Doi: http://dx.doi.org/10.1038/nbt.2450

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012;7:562-578. Doi: http://dx.doi.org/10.1038/nprot.2012.016

Tyanova S, Cox J. Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research. 2018;1711:133-148. Doi: http://dx.doi.org/10.1007/978-1-4939-7493-1_7

Tyanova S, Temu T, Carlson A, Sinitcyn P, Mann M, Cox J. Visualization of LC-MS/MS proteomics data in MaxQuant. Proteomics. 2015;15(8):1453-1456. Doi: http://dx.doi.org/10.1002/pmic.201400449

Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods. 2016;13(9):731-740. Doi: http://dx.doi.org/10.1038/nmeth.3901

Vallejo C D, Gutiérrez S PA, Marín M M. Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk. Agron. Colomb. 2016;34(1):51-60. Doi: http://dx.doi.org/10.15446/agron.colomb.v34n1.53161

Varela ALN, Komatsu S, Wang X, Silva RGG, Souza PFN, Lobo AKM, et al. Gel-free/label-free proteomic, photosynthetic, and biochemical analysis of cowpea (Vigna unguiculata [L.] Walp.) resistance against Cowpea severe mosaic virus (CPSMV). J. Proteom. 2017;163:76-91. Doi: http://dx.doi.org/10.1016/j.jprot.2017.05.003

Villamil-Garzón A, Cuellar WJ, Guzmán-Barney M. Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia. Agron. Colomb. 2014;32(2):213-223. Doi: http://dx.doi.org/10.15446/agron.colomb.v32n2.43968

Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. Phytopathology. 2019;109(5):716-725. Doi: http://dx.doi.org/10.1094/phyto-07-18-0257-rvw

Vowinckel J, Capuano F, Campbell K, Deery MJ, Lilley KS, Ralser M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. F1000. 2014;2:272. Doi: http://dx.doi.org/10.12688/f1000research.2-272.v2

Wan Y, Renner DW, Albert I, Szpara ML. VirAmp: a galaxy-based viral genome assembly pipeline. GigaScience. 2015;4(1). Doi: http://dx.doi.org/10.1186/s13742-015-0060-y

Wilkins MR, Sanchez J-C, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, et al. Progress with Proteome Projects: Why all Proteins Expressed by a Genome Should be Identified and How To Do It. Biotechnol Genet Eng. 1996;13(1):19-50. Doi: http://dx.doi.org/10.1080/02648725.1996.10647923

Wong S-M, Cho WK, Lian S, Kim S-M, Seo BY, Jung JK, et al. Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection. PLoS One. 2015;10(8):e0136736. Doi: http://dx.doi.org/10.1371/journal.pone.0136736

Wu C, Li X, Guo S, Wong S-M. Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana. Sci. Rep. 2016;6(1). Doi: http://dx.doi.org/10.1038/srep36007

Wu L, Han Z, Wang S, Wang X, Sun A, Zu X, et al. Comparative proteomic analysis of the plant–virus interaction in resistant and susceptible ecotypes of maize infected with sugarcane mosaic virus. J. Proteom. 2013;89:124-140. Doi: http://dx.doi.org/10.1016/j.jprot.2013.06.005

Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30(12):1660-1666. Doi: http://dx.doi.org/10.1093/bioinformatics/btu077

Xu K, D. Nagy P. Dissecting Virus-Plant Interactions Through Proteomics Approaches. Curr Proteomics. 2010;7(4):316-327. Doi: http://dx.doi.org/10.2174/157016410793611792

Yamashita A, Sekizuka T, Kuroda M. VirusTAP: Viral Genome-Targeted Assembly Pipeline. Front Microbiol. 2016;7. Doi: http://dx.doi.org/10.3389/fmicb.2016.00032

Zanardo LG, De Souza GB, Alves MS. Transcriptomics of plant–virus interactions: a review. Theor Exp Plant Phys. 2019;31(1):103-125. Doi: http://dx.doi.org/10.1007/s40626-019-00143-z

Zaynab M, Fatima M, Abbas S, Sharif Y, Jamil K, Ashraf A, et al. Proteomics Approach Reveals Importance of Herbal Plants in Curing Diseases. Mol. Microbiol. 2018;1(1):23-28.