Zpracování dat z vysokokapacitního DNA sekvenování pro studium variability genomu a transkriptomu.

• Název práce v češtině: Zpracování dat z vysokokapacitního DNA sekvenování pro studium variability genomu a transkriptomu.
• Název v anglickém jazyce: Study of genome and transcriptome variability employing data processing from massive parallel DNA sequencing.
• Klíčová slova: masivní paralelní sekvenování, Diamond-Blackfanova anémie, RPS7, anotace DNA variant, RNA sekvenování, stres suchem u rostlin
• Klíčová slova anglicky: massive parallel sequencing, Diamond-Blackfan anaemia, RPS7, DNA variant annotation, RNA sequencing, effect drought stress on plants
• Akademický rok vypsání: 2009/2010
• Typ práce: disertační práce
• Jazyk práce: čeština
• Ústav: Mimofakultní pracoviště (13-999)
• Vedoucí / školitel: doc. MUDr. Marián Hajdúch, Ph.D.
• Řešitel: skrytý - zadáno a potvrzeno stud. odd.
• Datum přihlášení: 03.09.2014
• Datum zadání: 03.09.2014
• Datum potvrzení stud. oddělením: 03.09.2014
• Datum a čas obhajoby: 12.09.2018 12:30
• Datum odevzdání elektronické podoby: 25.06.2018
• Datum odevzdání tištěné podoby: 25.06.2018
• Datum proběhlé obhajoby: 12.09.2018
• Oponenti: Mgr. Eva Budinská, Ph.D.
• Konzultanti: prof. MUDr. Milan Macek, DrSc.

Seznam odborné literatury

[1] Adessi C. (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Research 28, 87e–87.
[2] Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., et al. (2010) A method and server for predicting damaging missense mutations. Nature Methods 7, 248–249.
[3] Afgan E., Baker D., van den Beek M., Blankenberg D., Bouvier D., Čech M., et al. (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic acids research 44, W3–W10.
[4] Alonso-Ramirez A., Rodriguez D., Reyes D., Jimenez J.A., Nicolas G., Lopez-Climent M., et al. (2009) Evidence for a Role of Gibberellins in Salicylic Acid-Modulated Early Plant Responses to Abiotic Stress in Arabidopsis Seeds. PLANT PHYSIOLOGY 150, 1335–1344.
[5] Altschul S.F., Gish W., Miller W., Myers E.W. & Lipman D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.
[6] Anders S., Pyl P.T. & Huber W. (2015) HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169.
[7] Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. (2000) Gene ontology: Tool for the unification of biology. Nature Genetics 25, 25–29.
[8] Audo I., Bujakowska K.M., Léveillard T., Mohand-Sad S., Lancelot M.E., Germain A., et al. (2012) Development and application of a next-generation-sequencing (NGS) approach to detect known and novel gene defects underlying retinal diseases. Orphanet Journal of Rare Diseases 7, 8.
[9] Aziz R.K., Bartels D., Best A., DeJongh M., Disz T., Edwards R.A., et al. (2008) The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9, 75.
[10] Azuma M., Toyama R., Laver E. & Dawid I.B. (2006) Perturbation of rRNA synthesis in the bap28 mutation leads to apoptosis mediated by p53 in the zebrafish central nervous system. Journal of Biological Chemistry 281, 13309–13316.
[11] Badhai J., Fröjmark A.S., J. Davey E., Schuster J. & Dahl N. (2009) Ribosomal protein S19 and S24 insufficiency cause distinct cell cycle defects in Diamond-Blackfan anemia. Biochimica et Biophysica Acta - Molecular Basis of Disease 1792, 1036–1042.
[12] Baldwin I.T., Schmelz E.A. & Ohnmeiss T.E. (1994) Wound-induced changes in root and shoot jasmonic acid pools correlate with induced nicotine synthesis in Nicotiana sylvestris spegazzini and comes. Journal of Chemical Ecology 20, 2139–2157.
[13] Ball S. (2011) Diamond Blackfan anemia. Hematology Am Soc Hematol Educ Program 2011, 487–491.
[14] Barbazuk W.B., Emrich S.J., Chen H.D., Li L. & Schnable P.S. (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal 51, 910–918.
[15] Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59.
[16] Bergmann C. (2018) Genetics of Autosomal Recessive Polycystic Kidney Disease and Its Differential Diagnoses. Frontiers in Pediatrics 5, 221.
[17] Blume K.G., Kaplan J.C., Löhr G.W., Ramot B. & Valentine W.N. (1977) International Committee for Standardization in Haematology: Recommended Methods for Red‐Cell Enzyme Analysis. British Journal of Haematology 35, 331–340.
[18] Bolger A.M., Lohse M. & Usadel B. (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
[19] Bortolomeazzi M., Gaffo E. & Bortoluzzi S. (2017) A survey of software tools for microRNA discovery and characterization using RNA-seq. Briefings in Bioinformatics.
[20] Branton D., Deamer D.W., Marziali A., Bayley H., Benner S.A., Butler T., et al. (2008) The potential and challenges of nanopore sequencing. Nature Biotechnology 26, 1146–1153.
[21] Brown T.L. & Meloche T.M. (2016) Exome sequencing a review of new strategies for rare genomic disease research. Genomics 108, 109–114.
[22] Busby M.A., Stewart C., Miller C.A., Grzeda K.R. & Marth G.T. (2013) Scotty: A web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics 29, 656–657.
[23] Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., et al. (2009) BLAST+: Architecture and applications. BMC Bioinformatics 10, 421.
[24] Cantarel B.L., Korf I., Robb S.M.C., Parra G., Ross E., Moore B., et al. (2008) MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18, 188–196.
[25] Capriotti E., Fariselli P. & Casadio R. (2005) I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research 33, W306-10.
[26] Carapito R., Radosavljevic M. & Bahram S. (2016) Next-Generation Sequencing of the HLA locus: Methods and impacts on HLA typing, population genetics and disease association studies. Human Immunology 77, 1016–1023.
[27] Carbon S., Dietze H., Lewis S.E., Mungall C.J., Munoz-Torres M.C., Basu S., et al. (2017) Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium. Nucleic Acids Research 45, D331–D338.
[28] Cariaso M. & Lennon G. (2012) SNPedia: A wiki supporting personal genome annotation, interpretationand analysis. Nucleic Acids Research 40, D1308-12.
[29] Cario H., Bode H., Gustavsson P., Dahl N. & Kohne E. (1999) A microdeletion syndrome due to a 3-Mb deletion on 19q13.2--Diamond-Blackfan anemia associated with macrocephaly, hypotonia, and psychomotor retardation. Clinical genetics 55, 487–92.
[30] Cass C.L., Peraldi A., Dowd P.F., Mottiar Y., Santoro N., Karlen S.D., et al. (2015) Effects of PHENYLALANINE AMMONIA LYASE (PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses in Brachypodium. Journal of Experimental Botany 66, 4317–4335.
[31] Chakraborty A., Uechi T., Nakajima Y., Gazda H.T., O„Donohue M.F., Gleizes P.E., et al. (2017) Cross talk between TP53 and c-Myc in the pathophysiology of Diamond-Blackfan anemia: Evidence from RPL11-deficient in vivo and in vitro models. Biochemical and Biophysical Research Communications 495, 1839–1845.
[32] Cheng J., Randall A. & Baldi P. (2005) Prediction of protein stability changes for single-site mutations using support vector machines. Proteins: Structure, Function, and Bioinformatics 62, 1125–1132.
[33] Chhangawala S., Rudy G., Mason C.E. & Rosenfeld J.A. (2015) The impact of read length on quantification of differentially expressed genes and splice junction detection. Genome Biology 16, 131.
[34] Chiabrando D., Marro S., Mercurio S., Giorgi C., Petrillo S., Vinchi F., et al. (2012) The mitochondrial heme exporter FLVCR1b mediates erythroid differentiation. Journal of Clinical Investigation 122, 4569–4579.
[35] Chyra Kufova Z., Sevcikova T., Januska J., Vojta P., Boday A., Vanickova P., et al. (2018) Newly designed 11-gene panel reveals first case of hereditary amyloidosis captured by massive parallel sequencing. Journal of Clinical Pathology, jclinpath-2017-204978.
[36] Cingolani P., Platts A., Wang L.L., Coon M., Nguyen T., Wang L., et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92.
[37] Cmejlova J., Dolezalova L., Pospisilova D., Petrtylova K., Petrak J. & Cmejla R. (2006) Translational efficiency in patients with Diamond-Blackfan anemia. Haematologica 91, 1456–1464.
[38] Collart M.A., Baeuerle P. & Vassalli P. (1990) Regulation of tumor necrosis factor alpha transcription in macrophages: involvement of four kappa B-like motifs and of constitutive and inducible forms of NF-kappa B. Molecular and cellular biology 10, 1498–506.
[39] Conesa A., Götz S., García-Gómez J.M., Terol J., Talón M. & Robles M. (2005) Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676.
[40] Danecek P., Auton A., Abecasis G., Albers C.A., Banks E., DePristo M.A., et al. (2011) The variant call format and VCFtools. Bioinformatics 27, 2156–2158.
[41] Danilova N., Sakamoto K.M. & Lin S. (2008) Ribosomal protein S19 deficiency in zebrafish leads to developmental abnormalities and defective erythropoiesis through activation of p53 protein family. Blood 112, 5228–5237.
[42] Danilova N., Wilkes M., Bibikova E., Youn M.Y., Sakamoto K.M. & Lin S. (2018) Innate immune system activation in zebrafish and cellular models of Diamond Blackfan Anemia. Scientific Reports 8, 5165.
[43] Deisenroth C. & Zhang Y. (2010) Ribosome biogenesis surveillance: Probing the ribosomal protein-Mdm2-p53 pathway. Oncogene 29, 4253–4260.
[44] DePristo M.A., Banks E., Poplin R., Garimella K. V, Maguire J.R., Hartl C., et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics 43, 491–8.
[45] Diao Y., Yang C., Yan M., Zheng X., Jin S., Wang Y., et al. (2014) De novo transcriptome and small RNA analyses of two Amorphophallus species. PLoS ONE 9, e95428.
[46] Van Dijk E.L., Jaszczyszyn Y. & Thermes C. (2014) Library preparation methods for next-generation sequencing: Tone down the bias. Experimental Cell Research 322, 12–20.
[47] DiNardo C.D., Routbort M.J., Bannon S.A., Benton C.B., Takahashi K., Kornblau S.M., et al. (2018) Improving the detection of patients with inherited predispositions to hematologic malignancies using next-generation sequencing-based leukemia prognostication panels. Cancer.
[48] Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., et al. (2013) STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21.
[49] Donati G., Montanaro L. & Derenzini M. (2012) Ribosome biogenesis and control of cell proliferation: p53 is not alone. Cancer Research 72, 1602–1607.
[50] Dressman D., Yan H., Traverso G., Kinzler K.W. & Vogelstein B. (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proceedings of the National Academy of Sciences 100, 8817–8822.
[51] Dunn P., Albury C.L., Maksemous N., Benton M.C., Sutherland H.G., Smith R.A., et al. (2018) Next generation sequencing methods for diagnosis of epilepsy syndromes. Frontiers in Genetics 9, 20.
[52] Ebbert M.T.W., Wadsworth M.E., Staley L.A., Hoyt K.L., Pickett B., Miller J., et al. (2016) Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. BMC Bioinformatics 17, 239.
[53] Eden E., Navon R., Steinfeld I., Lipson D. & Yakhini Z. (2009) GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48.
[54] Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138.
[55] Errichiello E., Vetro A., Mina T., Wischmeijer A., Berrino E., Carella M., et al. (2017) Whole exome sequencing in the differential diagnosis of Diamond-Blackfan anemia: Clinical and molecular study of three patients with novel RPL5 and mosaic RPS19 mutations. Blood Cells, Molecules, and Diseases 64, 38–44.
[56] Fabregat A., Jupe S., Matthews L., Sidiropoulos K., Gillespie M., Garapati P., et al. (2018) The Reactome Pathway Knowledgebase. Nucleic Acids Research 46, D649–D655.
[57] Farrar J.E. & Dahl N. (2011) Untangling the phenotypic heterogeneity of diamond Blackfan anemia. Seminars in Hematology 48, 124–135.
[58] Feussner I. & Wasternack C. (2002) THE LIPOXYGENASE PATHWAY. Annual Review of Plant Biology 53, 275–297.
[59] Finn R.D., Clements J. & Eddy S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic acids research 39, W29-37.
[60] Finn R.D., Coggill P., Eberhardt R.Y., Eddy S.R., Mistry J., Mitchell A.L., et al. (2016) The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Research 44, D279–D285.
[61] Fokkema I.F.A.C., Taschner P.E.M., Schaafsma G.C.P., Celli J., Laros J.F.J. & den Dunnen J.T. (2011) LOVD v.2.0: The next generation in gene variant databases. Human Mutation 32, 557–563.
[62] Galichet A., Hoyerova K., Kaminek M. & Gruissem W. (2008) Farnesylation Directs AtIPT3 Subcellular Localization and Modulates Cytokinin Biosynthesis in Arabidopsis. PLANT PHYSIOLOGY 146, 1155–1164.
[63] Gan S. & Amasino R.M. (1995) Inhibition of Leaf Senescence by Autoregulated Production of Cytokinin. Science 270, 1986–1988.
[64] Garrison E. & Marth G. (2012) Haplotype-based variant detection from short-read sequencing. arxiv:1207.3907.
[65] Gazda H.T., Sheen M.R., Vlachos A., Choesmel V., O„Donohue M.F., Schneider H., et al. (2008) Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients. American Journal of Human Genetics 83, 769–780.
[66] Gerrard G., Valgañón M., Foong H.E., Kasperaviciute D., Iskander D., Game L., et al. (2013) Target enrichment and high-throughput sequencing of 80 ribosomal protein genes to identify mutations associated with Diamond-Blackfan anaemia. British Journal of Haematology 162, 530–536.
[67] Ghanem M.E., Albacete A., Smigocki A.C., Frébort I., Pospíilová H., Martínez-Andújar C., et al. (2011) Root-synthesized cytokinins improve shoot growth and fruit yield in salinized tomato (Solanum lycopersicum L.) plants. Journal of Experimental Botany 62, 125–140.
[68] Giardine B., Riemer C., Hardison R.C., Burhans R., Elnitski L., Shah P., et al. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Research 15, 1451–1455.
[69] Gibbs R.A., Boerwinkle E., Doddapaneni H., Han Y., Korchina V., Kovar C., et al. (2015) A global reference for human genetic variation. Nature 526, 68–74.
[70] Ginsberg D. (2002) E2F1 pathways to apoptosis. FEBS Letters 529, 122–125.
[71] Goldstein S. & Samuni A. (2005) Intra- and intermolecular oxidation of oxymyoglobin and oxyhemoglobin induced by hydroxyl and carbonate radicals. Free Radical Biology and Medicine 39, 511–519.
[72] Goudarzi K.M. & Lindström M.S. (2016) Role of ribosomal protein mutations in tumor development (Review). International Journal of Oncology 48, 1313–1324.
[73] Griffiths J.A., Scialdone A. & Marioni J.C. (2018) Using single‐cell genomics to understand developmental processes and cell fate decisions. Molecular Systems Biology 14, e8046.
[74] Gripp K.W., Curry C., Olney A.H., Sandoval C., Fisher J., Chong J.X.L., et al. (2014) Diamond-Blackfan anemia with mandibulofacial dystostosis is heterogeneous, including the novel DBA genes TSR2 and RPS28. American Journal of Medical Genetics, Part A 164, 2240–2249.
[75] Gustavsson P., Willig T.N., Haeringen A. V., Tchernia G., Dianzani I., Donner M., et al. (1997) Diamond-blackfan anaemia: Genetic homogeneity for a gene on chromosome 19q13 restricted to 1.8 Mb. Nature Genetics 16, 368–371.
[76] Ha S., Vankova R., Yamaguchi-Shinozaki K., Shinozaki K. & Tran L.S.P. (2012) Cytokinins: Metabolism and function in plant adaptation to environmental stresses. Trends in Plant Science 17, 172–179.
[77] Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8, 1494–1512.
[78] Hasan M.S. habbi., Wu X. & Zhang L. (2015) Performance evaluation of indel calling tools using real short-read data. Human genomics 9, 20.
[79] Havlova M., Dobrev P.I., Motyka V., Storchova H., Libus J., Dobr?? J., et al. (2008) The role of cytokinins in responses to water deficit in tobacco plants over-expressing trans-zeatin O-glucosyltransferase gene under 35S or SAG12 promoters. Plant, Cell and Environment 31, 341–353.
[80] Heijnen H.F., van Wijk R., Pereboom T.C., Goos Y.J., Seinen C.W., van Oirschot B.A., et al. (2014) Ribosomal Protein Mutations Induce Autophagy through S6 Kinase Inhibition of the Insulin Pathway. PLoS Genetics 10, e1004371.
[81] Huang D.W., Sherman B.T. & Lempicki R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57.
[82] Huber W., Carey V.J., Gentleman R., Anders S., Carlson M., Carvalho B.S., et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12, 115–121.
[83] Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. (2009) InterPro: The integrative protein signature database. Nucleic Acids Research 37, D211-5.
[84] Ichimura T., Yoshida K., Okuno Y., Yujiri T., Nagai K., Nishi M., et al. (2017) Diagnostic challenge of Diamond-Blackfan anemia in mothers and children by whole-exome sequencing. International journal of hematology 105, 515–520.
[85] Idury R.M. & Waterman M.S. (1995) A New Algorithm for DNA Sequence Assembly. Journal of Computational Biology 2, 291–306.
[86] Ikeda F., Yoshida K., Toki T., Uechi T., Ishida S., Nakajima Y., et al. (2016) Exome sequencing identified RPS15A as a novel causative gene for Diamond-Blackfan anemia. Haematologica 102, e93–e96.
[87] Itan Y., Shang L., Boisson B., Patin E., Bolze A., Moncada-Vélez M., et al. (2015) The human gene damage index as a gene-level approach to prioritizing exome variants. Proceedings of the National Academy of Sciences 112, 13615–13620.
[88] Jelin A.C. & Vora N. (2018) Whole Exome Sequencing: Applications in Prenatal Genetics. Obstetrics and Gynecology Clinics of North America 45, 69–81.
[89] Jennings L.J., Arcila M.E., Corless C., Kamel-Reid S., Lubin I.M., Pfeifer J., et al. (2017) Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. Journal of Molecular Diagnostics 19, 341–365.
[90] Jia Q., Zhang Q., Zhang Z., Wang Y., Zhang W., Zhou Y., et al. (2013) Transcriptome analysis of the zebrafish model of Diamond-Blackfan anemia from RPS19 deficiency via p53-dependent and -independent pathways. PloS one 8, e71782.
[91] Joslin J.M., Fernald A.A., Tennant T.R., Davis E.M., Kogan S.C., Anastasi J., et al. (2007) Haploinsufficiency of EGR1, a candidate gene in the del(5q), leads to the development of myeloid disorders. Blood 110, 719–726.
[92] Keeton A.B., Bortoff K.D., Bennett W.L., Franklin J.L., Venable D.Y. & Messina J.L. (2003) Insulin-Regulated Expression of Egr-1 and Krox20: Dependence on ERK1/2 and Interaction with p38 and PI3-Kinase Pathways. Endocrinology 144, 5402–5410.
[93] Kim D., Langmead B. & Salzberg S.L. (2015) HISAT: A fast spliced aligner with low memory requirements. Nature Methods 12, 357–360.
[94] Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R. & Salzberg S.L. (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14, R36.
[95] Kinde I., Wu J., Papadopoulos N., Kinzler K.W. & Vogelstein B. (2011) Detection and quantification of rare mutations with massively parallel sequencing. Proceedings of the National Academy of Sciences 108, 9530–9535.
[96] Kinsella R.J., Kähäri A., Haider S., Zamora J., Proctor G., Spudich G., et al. (2011) Ensembl BioMarts: A hub for data retrieval across taxonomic space. Database 2011, bar030-bar030.
[97] Koboldt D.C., Zhang Q., Larson D.E., Shen D., McLellan M.D., Lin L., et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research 22, 568–576.
[98] Kohany O., Gentles A.J., Hankus L. & Jurka J. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7, 474.
[99] Köhler S., Vasilevsky N.A., Engelstad M., Foster E., McMurry J., Aymé S., et al. (2017) The human phenotype ontology in 2017. Nucleic Acids Research 45, D865–D876.
[100] Kokas F., Vojta P. & Galuszka P. (2016) Dataset for transcriptional response of barley (Hordeum vulgare) exposed to drought and subsequent re-watering. Data in Brief 8, 334–341.
[101] Krumm N., Sudmant P.H., Ko A., O„Roak B.J., Malig M., Coe B.P., et al. (2012) Copy number variation detection and genotyping from exome sequence data. Genome Research 22, 1525–1532.
[102] Kufova Z., Sevcikova T., Growkova K., Vojta P., Filipova J., Adam Z., et al. (2017) Biomarkers in immunoglobulin light chain amyloidosis. Klinicka Onkologie 30.
[103] Kuppu S., Mishra N., Hu R., Sun L., Zhu X., Shen G., et al. (2013) Water-Deficit Inducible Expression of a Cytokinin Biosynthetic Gene IPT Improves Drought Tolerance in Cotton. PLoS ONE 8, e64190.
[104] Lai Z., Markovets A., Ahdesmaki M., Chapman B., Hofmann O., Mcewen R., et al. (2016) VarDict: A novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Research 44.
[105] Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., et al. (2014) ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research 42, D980-5.
[106] Langmead B., Trapnell C., Pop M. & Salzberg S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10, R25.
[107] Lapin V., Mighion L.C., da Silva C.P., Cuperus Y., Bean L.J.H. & Hegde M.R. (2016) Regulating whole exome sequencing as a diagnostic test. Human Genetics 135, 655–673.
[108] Leek J.T., Johnson W.E., Parker H.S., Jaffe A.E. & Storey J.D. (2012) The SVA package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882–883.
[109] Lek M., Karczewski K.J., Minikel E. V., Samocha K.E., Banks E., Fennell T., et al. (2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291.
[110] Li H. & Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760.
[111] Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079.
[112] Li Y.H., Yu C.Y., Li X.X., Zhang P., Tang J., Yang Q., et al. (2018) Therapeutic target database update 2018: Enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Research 46, D1121–D1127.
[113] Liao Y., Smyth G.K. & Shi W. (2014) FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930.
[114] Lin Y., Golovnina K., Chen Z.-X., Lee H.N., Negron Y.L.S., Sultana H., et al. (2016) Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster. BMC Genomics 17, 28.
[115] Liu L., Li Y., Li S., Hu N., He Y., Pong R., et al. (2012) Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology 2012, 1–11.
[116] Liu X., Wu C., Li C. & Boerwinkle E. (2016) dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. Human Mutation 37, 235–241.
[117] Love M.I., Huber W. & Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550.
[118] Majeska-Cudejkova M., Vojta P., Valarik J. & Galuszka P. (2016) Quantitative and qualitative transcriptome analysis of four industrial strains of Claviceps purpurea with respect to ergot alkaloid production. New Biotechnology 33, 743–754.
[119] Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.
[120] Matthijs G., Souche E., Alders M., Corveleyn A., Eck S., Feenstra I., et al. (2016) Guidelines for diagnostic next-generation sequencing. European Journal of Human Genetics 24, 2–5.
[121] McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., et al. (2010) The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 1297–1303.
[122] McLaren W., Gil L., Hunt S.E., Riat H.S., Ritchie G.R.S., Thormann A., et al. (2016) The Ensembl Variant Effect Predictor. Genome Biology 17.
[123] Medina I., Carbonell J., Pulido L., Madeira S.C., Goetz S., Conesa A., et al. (2010) Babelomics: An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research 38, W210–W213.
[124] Merewitz E.B., Gianfagna T. & Huang B. (2011) Photosynthesis, water use, and root viability under water stress as affected by expression of SAG12-ipt controlling cytokinin synthesis in Agrostis stolonifera. Journal of Experimental Botany 62, 383–395.
[125] Metzker M.L. (2010) Sequencing technologies the next generation. Nature Reviews Genetics 11, 31–46.
[126] Moon J., Parry G. & Estelle M. (2004) The ubiquitin-proteasome pathway and plant development. The Plant cell 16, 3181–3195.
[127] Moortgat S., Lederer D., Deprez M., Buzatu M., Clapuyt P., Boulanger S., et al. (2018) Expanding the phenotypic spectrum associated with OPHN1 mutations: Report of 17 individuals with intellectual disability but no cerebellar hypoplasia. European Journal of Medical Genetics.
[128] Mortazavi A., Williams B.A., McCue K., Schaeffer L. & Wold B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628.
[129] Narasimhan V., Danecek P., Scally A., Xue Y., Tyler-Smith C. & Durbin R. (2016) BCFtools/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32, 1749–1751.
[130] Nishi H., Inagi R., Kato H., Tanemoto M., Kojima I., Son D., et al. (2008) Hemoglobin Is Expressed by Mesangial Cells and Reduces Oxidant Stress. Journal of the American Society of Nephrology 19, 1500–1508.
[131] Nishiyama R., Watanabe Y., Fujita Y., Le D.T., Kojima M., Werner T., et al. (2011) Analysis of Cytokinin Mutants and Regulation of Cytokinin Metabolic Genes Reveals Important Regulatory Roles of Cytokinins in Drought, Salt and Abscisic Acid Responses, and Abscisic Acid Biosynthesis. The Plant Cell 23, 2169–2183.
[132] Nishiyama R., Watanabe Y., Leyva-Gonzalez M.A., Van Ha C., Fujita Y., Tanaka M., et al. (2013) Arabidopsis AHP2, AHP3, and AHP5 histidine phosphotransfer proteins function as redundant negative regulators of drought stress response. Proceedings of the National Academy of Sciences 110, 4840–4845.
[133] O’Brien J.A. & Benková E. (2013) Cytokinin cross-talking during biotic and abiotic stress responses. Frontiers in Plant Science 4, 451.
[134] O’Brien K.A., Seidel N.E., Farrar J., Vlachos A., Anderson S.M., An X., et al. (2013) Autosomal recessive diamond-blackfan anemia: Identification of mutations in MCM2 and FLNB. In: Blood. .
[135] Ogata H., Goto S., Sato K., Fujibuchi W., Bono H. & Kanehisa M. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 27, 29–34.
[136] Okonechnikov K., Golosova O. & Fursov M. (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28, 1166–1167.
[137] Oono Y., Kobayashi F., Kawahara Y., Yazawa T., Handa H., Itoh T., et al. (2013) 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. BMC Genomics 14, 77.
[138] Peleg Z. & Blumwald E. (2011) Hormone balance and abiotic stress tolerance in crop plants. Current Opinion in Plant Biology 14, 290–295.
[139] Peleg Z., Reguera M., Tumimbang E., Walia H. & Blumwald E. (2011) Cytokinin-mediated source/sink modifications improve drought tolerance and increase grain yield in rice under water-stress. Plant Biotechnology Journal 9, 747–758.
[140] Pertea M., Kim D., Pertea G.M., Leek J.T. & Salzberg S.L. (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature protocols 11, 1650–1667.
[141] Pertea M., Pertea G.M., Antonescu C.M., Chang T.C., Mendell J.T. & Salzberg S.L. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33, 290–295.
[142] Petrovski S., Wang Q., Heinzen E.L., Allen A.S. & Goldstein D.B. (2013) Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes. PLoS Genetics 9, e1003709.
[143] Pevzner P.A., Tang H. & Waterman M.S. (2001) An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences 98, 9748–9753.
[144] Plagnol V., Curtis J., Epstein M., Mok K.Y., Stebbings E., Grigoriadou S., et al. (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 28, 2747–2754.
[145] Plutino M., Chaussenot A., Rouzier C., Ait-El-Mkadem S., Fragaki K., Paquis-Flucklinger V., et al. (2018) Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases. BMC Medical Genetics 19, 57.
[146] Pospisilova D., Cmejlova J., Ludikova B., Stary J., Cerna Z., Hak J., et al. (2012) The Czech National Diamond-Blackfan Anemia Registry: Clinical data and ribosomal protein mutations update. Blood Cells, Molecules, and Diseases 48, 209–218.
[147] Pospíšilová H., Jiskrová E., Vojta P., Mrízová K., Kokáš F., Čudejková M.M., et al. (2016) Transgenic barley overexpressing a cytokinin dehydrogenase gene shows greater tolerance to drought stress. New Biotechnology 33, 692–705.
[148] Quinlan A.R. & Hall I.M. (2010) BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.
[149] Reguera M., Peleg Z., Abdel-Tawab Y.M., Tumimbang E.B., Delatorre C.A. & Blumwald E. (2013) Stress-Induced Cytokinin Synthesis Increases Drought Tolerance through the Coordinated Regulation of Carbon and Nitrogen Assimilation in Rice. PLANT PHYSIOLOGY 163, 1609–1622.
[150] Rehrauer H., Opitz L., Tan G., Sieverling L. & Schlapbach R. (2013) Blind spots of quantitative RNA-seq: The limits for assessing abundance, differential expression, and isoform switching. BMC Bioinformatics 14, 370.
[151] Richards S., Aziz N., Bale S., Bick D., Das S., Gastier-Foster J., et al. (2015) Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine 17, 405–424.
[152] Van Riggelen J. & Felsher D.W. (2010) Myc and a Cdk2 senescence switch. Nature Cell Biology 12, 7–9.
[153] Riley M.F. & Lozano G. (2012) The Many Faces of MDM2 Binding Partners. Genes and Cancer 3, 226–239.
[154] Rimmer A., Phan H., Mathieson I., Iqbal Z., Twigg S.R.F., Wilkie A.O.M., et al. (2014) Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics 46, 912–918.
[155] Rippert P. & Matringe M. (2002) Molecular and biochemical characterization of an Arabidopsis thaliana arogenate dehydrogenase with two. Plant molecular biology 48, 361–368.
[156] Risso D., Ngai J., Speed T.P. & Dudoit S. (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology 32, 896–902.
[157] Rivero R.M., Gimeno J., Van Deynze A., Walia H. & Blumwald E. (2010) Enhanced cytokinin synthesis in tobacco plants expressing PSARK::IPT Prevents the degradation of photosynthetic protein complexes during drought. Plant and Cell Physiology 51, 1929–1941.
[158] Rivero R.M., Kojima M., Gepstein A., Sakakibara H., Mittler R., Gepstein S., et al. (2007) Delayed leaf senescence induces extreme drought tolerance in a flowering plant. Proceedings of the National Academy of Sciences 104, 19631–19636.
[159] Robinson M.D., McCarthy D.J. & Smyth G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England) 26, 139–40.
[160] Roggero S., Quarello P., Vinciguerra T., Longo F., Piga A. & Ramenghi U. (2009) Severe iron overload in Blackfan-Diamond anemia: A case-control study. American Journal of Hematology 84, 729–732.
[161] Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348–352.
[162] Russell J.L., Powers J.T., Rounbehler R.J., Rogers P.M., Conti C.J. & Johnson D.G. (2002) ARF differentially modulates apoptosis induced by E2F1 and Myc. Molecular and cellular biology 22, 1360–1368.
[163] Ruzicka K., Ljung K., Vanneste S., Podhorska R., Beeckman T., Friml J., et al. (2007) Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport-Dependent Auxin Distribution. THE PLANT CELL ONLINE 19, 2197–2212.
[164] Sandmann S., De Graaf A.O., Karimi M., Van Der Reijden B.A., Hellström-Lindberg E., Jansen J.H., et al. (2017) Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data. Scientific Reports 7, 43169.
[165] Sankaran V.G., Ghazvinian R., Do R., Thiru P., Vergilio J.A., Beggs A.H., et al. (2012) Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. Journal of Clinical Investigation 122, 2439–2443.
[166] Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., et al. (2005) Molecular biology: Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732.
[167] Sherry S.T. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 29, 308–311.
[168] Smetanina N.S., Mersiyanova I. V., Kurnikova M.A., Ovsyannikova G.S., Hachatryan L.A., Bobrynina V.O., et al. (2015) Clinical and genomic heterogeneity of Diamond Blackfan anemia in the Russian Federation. Pediatric Blood and Cancer 62, 1597–1600.
[169] Song B., Zhang Q., Zhang Z., Wan Y., Jia Q., Wang X., et al. (2014) Systematic transcriptome analysis of the zebrafish model of diamond-blackfan anemia induced by RPS24 deficiency. BMC Genomics 15, 759.
[170] Stanke M., Keller O., Gunduz I., Hayes A., Waack S. & Morgenstern B. (2006) AUGUSTUS: A b initio prediction of alternative transcripts. Nucleic Acids Research 34, W435-9.
[171] Sun L., Zhang Q., Wu J., Zhang L., Jiao X., Zhang S., et al. (2014) Two Rice Authentic Histidine Phosphotransfer Proteins, OsAHP1 and OsAHP2, Mediate Cytokinin Signaling and Stress Responses in Rice. PLANT PHYSIOLOGY 165, 335–345.
[172] Sýkorová B., Kurešová G., Daskalova S., Trčková M., Hoyerová K., Raimanová I., et al. (2008) Senescence-induced ectopic expression of the A. tumefaciens ipt gene in wheat delays leaf senescence, increases cytokinin content, nitrate influx, and nitrate reductase activity, but does not affect grain yield. Journal of Experimental Botany 59, 377–387.
[173] Teixeira M.R. (2006) Recurrent fusion oncogenes in carcinomas. Critical reviews in oncogenesis 12, 257–271.
[174] Thorvaldsdóttir H., Robinson J.T. & Mesirov J.P. (2013) Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Briefings in Bioinformatics 14, 178–192.
[175] Tian D., Tooker J., Peiffer M., Chung S.H. & Felton G.W. (2012) Role of trichomes in defense against herbivores: Comparison of herbivore response to woolly and hairless trichome mutants in tomato (Solanum lycopersicum). Planta 236, 1053–1066.
[176] Tian S., Yan H., Kalmbach M. & Slager S.L. (2016) Impact of post-alignment processing in variant discovery from whole exome data. BMC Bioinformatics 17, 403.
[177] Tran L.-S.P., Urao T., Qin F., Maruyama K., Kakimoto T., Shinozaki K., et al. (2007) Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proceedings of the National Academy of Sciences 104, 20623–20628.
[178] Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7, 562–578.
[179] Travers K.J., Chin C.S., Rank D.R., Eid J.S. & Turner S.W. (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Research 38, e159–e159.
[180] Tsuchisaka A. & Theologis A. (2004) Unique and Overlapping Expression Patterns among the Arabidopsis 1-Amino-Cyclopropane-1-Carboxylate Synthase Gene Family Members. Plant Physiology 136, 2982–3000.
[181] Tulpová Z., Luo M.C., Toegelová H., Visendi P., Hayashi S., Vojta P., et al. (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology.
[182] Ueda J. & Kato J. (1982) Identification of jasmonic acid and abscisic acid as senescence-promoting substances from cleyera ochnacea dc. Agricultural and Biological Chemistry 46, 1975–1976.
[183] Utsugisawa T., Uchiyama T., Toki T., Ogura H., Aoki T., Hamaguchi I., et al. (2016) Erythrocyte glutathione is a novel biomarker of Diamond-Blackfan anemia. Blood Cells, Molecules, and Diseases 59, 31–36.
[184] Virolle T., Adamson E.D., Baron V., Birle D., Mercola D., Mustelin T., et al. (2001) The Egr-1 transcription factor directly activates PTEN during irradiation-induced signalling. Nature Cell Biology 3, 1124–1128.
[185] Vlachos A., Ball S., Dahl N., Alter B.P., Sheth S., Ramenghi U., et al. (2008) Diagnosing and treating Diamond Blackfan anaemia: Results of an international clinical consensus conference. British Journal of Haematology 142, 859–876.
[186] Vlamis J. & Williams D.E. (1962) Ion Competition in Manganese Uptake by Barley Plants. PLANT PHYSIOLOGY 37, 650–655.
[187] Voelkerding K. V., Dames S. & Durtschi J.D. (2010) Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: A Paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology. Journal of Molecular Diagnostics 12, 539–551.
[188] Vojta P., Kokáš F., Husičková A., Grúz J., Bergougnoux V., Marchetti C.F., et al. (2016) Whole transcriptome analysis of transgenic barley with altered cytokinin homeostasis and increased tolerance to drought stress. New Biotechnology 33, 676–691.
[189] Volejnikova J., Zapletalova J., Jarosova M., Urbankova H., Vojta P., Klaskova E., et al. (2018) Acute lymphoblastic leukemia in a child with leri-weill syndrome and complete shox gene deletion: A case report. Biomedical Papers 162, 65–70.
[190] Vyroubalova S., Vaclavikova K., Tureckova V., Novak O., Smehilova M., Hluska T., et al. (2009) Characterization of New Maize Genes Putatively Involved in Cytokinin Metabolism and Their Expression during Osmotic Stress in Relation to Cytokinin Levels. PLANT PHYSIOLOGY 151, 433–447.
[191] Wagner G.P., Kin K. & Lynch V.J. (2012) Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences 131, 281–285.
[192] Wan Y., Zhang Q., Zhang Z., Song B., Wang X., Zhang Y., et al. (2016) Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia. BMC Medical Genomics 9, 13.
[193] Wang C., Yang A., Yin H. & Zhang J. (2008) Influence of water stress on endogenous hormone contents and cell damage of maize seedlings. Journal of Integrative Plant Biology 50, 427–434.
[194] Wang K., Li M. & Hakonarson H. (2010) ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38.
[195] Wang L., Wang Z., Xu Y., Joo S.H., Kim S.K., Xue Z., et al. (2009) OsGSR1 is involved in crosstalk between gibberellins and brassinosteroids in rice. Plant Journal 57, 498–510.
[196] Warden C.D., Adamson A.W., Neuhausen S.L. & Wu X. (2014) Detailed comparison of two popular variant calling packages for exome and targeted exon studies. PeerJ 2, e600.
[197] Wasternack C. (2014) Action of jasmonates in plant stress responses and development - Applied aspects. Biotechnology Advances 32, 31–39.
[198] Watkins-Chow D.E., Cooke J., Pidsley R., Edwards A., Slotkin R., Leeds K.E., et al. (2013) Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes. PLoS Genetics 9, e1003094.
[199] Wei W., Alexandersson E., Golldack D., Miller A.J., Kjellbom P.O. & Fricke W. (2007) HvPIP1;6, a barley (Hordeum vulgare L.) plasma membrane water channel particularly expressed in growing compared with non-growing leaf tissues. Plant and Cell Physiology 48, 1132–1147.
[200] Weiss M.M., Van der Zwaag B., Jongbloed J.D.H., Vogel M.J., Brüggenwirth H.T., Lekanne Deprez R.H., et al. (2013) Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: A national collaborative study of dutch genome diagnostic laboratories. Human Mutation 34, 1313–1321.
[201] Willig T.N., Draptchinskaia N., Dianzani I., Ball S., Niemeyer C., Ramenghi U., et al. (1999) Mutations in ribosomal protein S19 gene and diamond blackfan anemia: wide variations in phenotypic expression. Blood 94, 4294–4306.
[202] Xuan J., Yu Y., Qing T., Guo L. & Shi L. (2013) Next-generation sequencing in the clinic: Promises and challenges. Cancer Letters 340, 284–295.
[203] Ye C., Hill C.M., Wu S., Ruan J. & Ma Z. (2016) DBG2OLC: Efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Scientific Reports 6, 31900.
[204] Zalabák D., Pospíšilová H., Šmehilová M., Mrízová K., Frébort I. & Galuszka P. (2013) Genetic engineering of cytokinin metabolism: Prospective way to improve agricultural traits of crop plants. Biotechnology Advances 31, 97–117.
[205] Zatopkova M., Filipova J., Jelinek T., Vojta P., Sevcikova T., Simicek M., et al. (2017) Whole exome sequencing of aberrant plasma cells in a patient with multiple myeloma minimal residual disease. Klinicka Onkologie 30.
[206] Zerbino D.R., Achuthan P., Akanni W., Amode M.R., Barrell D., Bhai J., et al. (2018) Ensembl 2018. Nucleic Acids Research 46, D754–D761.
[207] Zerbino D.R. & Birney E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18, 821–829.
[208] Zhang S.-W., Li C.-H., Cao J., Zhang Y.-C., Zhang S.-Q., Xia Y.-F., et al. (2009) Altered Architecture and Enhanced Drought Tolerance in Rice via the Down-Regulation of Indole-3-Acetic Acid by TLD1/OsGH3.13 Activation. PLANT PHYSIOLOGY 151, 1889–1901.
[209] Zhang Z., Jia H., Zhang Q., Wan Y., Zhou Y., Jia Q., et al. (2013) Assessment of hematopoietic failure due to Rpl11 deficiency in a zebrafish model of Diamond-Blackfan anemia by deep sequencing. BMC Genomics 14, 896.
[210] Zhang Z., Theurkauf W.E., Weng Z. & Zamore P.D. (2012) Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.
[211] Zook J.M., Chapman B., Wang J., Mittelman D., Hofmann O., Hide W., et al. (2014) Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nature Biotechnology 32, 246–251.
[212] Zubo Y.O., Yamburenko M. V., Selivankina S.Y., Shakirova F.M., Avalbaev A.M., Kudryakova N. V., et al. (2008) Cytokinin Stimulates Chloroplast Transcription in Detached Barley Leaves. PLANT PHYSIOLOGY 148, 1082–1093.