Biyoinformatiğe Giriş
Özet
Biyoinformatik, biyolojik verileri anlamak ve yorumlamak için kullanılan yöntemlerin ve teknolojilerin bir kümesidir. Biyoinformatik, genetik verileri, protein yapılarını, metabolik verileri veya güncel biyolojik verileri analiz etmek için kullanılırken biyoinfomatik veri tabanları bu verileri saklamak ve erişmek için kullanılır. Bu veritabanları, verileri kullanarak ilaç veya tedavi seçenekleri gibi uygulamaların geliştirilmesi için imkanlar sağlar. Biyoinformatik ile genomik, transkriptomik, proteomik ve metabolomik gibi omik teknolojiler aracılığıyla elde edilen verilerin analizi yapılır. Genetik yapı ve özellikleri iyileştirmek için veri madenciliği yöntemleri kullanılabilir, hastalıkların patogenezini ve tedavisini araştırmak için veri analizleri gerçekleştirilebilir. Biyoinformatik, dizi hizalama ve filogenetik analiz gibi konularda önemli rol oynayan bir bilim dalıdır. Dizi hizalama, biyolojik diziler arasındaki benzerlikleri belirlemek için kullanılırken filogenetik analiz ise, canlıların evrimsel kökenlerini ve ilişkilerini belirlemek için kullanılmaktadır. Biyoinformatik ayrıca, farmakogenomik, nöroinformatik, onkoloji gibi çeşitli alanlarda da önemli roller oynayan bir bilimdir. Bu veritabanları, bu verileri kullanarak ilaç veya tedavi seçenekleri gibi uygulamaların geliştirilmesi için imkanlar sağlar. Biyoinformatik, biyolojik verilerin anlaşılması ve yorumlanması için önemli bir araçtır ve sağlık, tarım, çevre ve enerji gibi çeşitli alanlarda önemli bir rol oynayan bir bilim dalıdır.
Referanslar
Franco ML, Cediel JF, Payan, C. Breve historia de la bioinformática. Colombia Médica. 2008; 39(1): 117-120.
Zhang X, Zhou X, Wang X. Chapter1: Basics for Bioinformatics. Jiang R, Zhang X, Zhang MQ (ed.) Basics of Bioinformatics: Lecture Notes of the Graduate Summer School on Bioin- formatics of China içinde. Tsinghua University Press, Beijing and Springer-Verlag Berlin Heidelberg; 2013. p. 1-25.
Mirsaydaliyevich YI. History of Bioinformatics. Journal of Social Sciences &Interdiscipli- nary Research. 2022; 11(7): 72-76.
Sharma MK, Dhar MK, Kaul S. Bioinformatics: An introduction and Overview. Internatio- nal Journal of Engineering Research and Development. 2012; 3(8): 88-99.
Fenstermacher D. Introduction to Bioinformatics. Journal of the Amerıcan Society for Infor- mation Science and Technology. 2005; 56(5): 440-446.
Atalay RÇ. Neden Biyoinformatik? Avrasya Dosyası. 2022; 8(3): 127-139.
Ünel NM, Önal İK, Çetin F, et al. Biyoinformatiğe Giriş. Baloğlu MC (ed.) Biyoinformatik Temelleri ve Uygulamaları içinde. Pegem Akademi; 2020: p. 2-16.
Keklik G, Özcan BD. An Overview of Bioinformatics as a Multidisciplinary Science. OKU Journal of The Institute of Science and Technology. 2022; 5(2): 1082-1091.
Fu J, Zhang Y, Liu J, et al. Pharmacometabonomics: data processing and statistical analysis.
Briefings in Bioinformatics. 2021; 22(5): 1-25.
Chen YPP. Introduction to Bioinformatics. Chen YPP. (ed.) Bioinformatics Technologies. Springer-Verlag Berlin Heidelberg: 2005: p. 1-13.
O’Donoghue SI. Grand Challenges in Bioinformatics Data Visualization. Frontiers in Bio- informatics. 2021; 1: 669186. doi: 10.3389/fbinf.2021.669186
Çelik Altunoğlu Y, Ceylan KB, Ceylan Y, et al. Biyolojik Veri Tabanları. Baloğlu MC (ed.) Biyoinformatik Temelleri ve Uygulamaları içinde. Pegem Akademi; 2020: p. 19-44.
Kamble A, Khairkar R. Basics of Bioinformatics in Biological Research. International Journal of Applied Sciences and Bİotechnology. 2016; 4(4): 425-429. doi:10.3126/ijasbt. v4i4.16252
Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Research. 2001; 11(5): 863-874. doi:10.1101/GR.176601
Gollery M. Bioinformatics: Sequence and Genome Analysis. 2nd ed. Clinical Chemistry. 2005; 51(11): 2219-2220.
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. Journal of Molecular Biology. 1990; 215(3): 403–410. doi: S0022-2836(05)80360-2
Elias I. Settling the intractability of multiple alignment. Journal of Computational Bio- logy: A Journal of Computational Molecular Cell Biology. 2006; 13(7): 1323-1339. doi: CMB.2006.13.1323
Wang L, Jiang T. On the complexity of multiple sequence alignment. Journal of Computati- onal Biology : A Journal of Computational Molecular Cell Biology. 1994; 1(4): 337-348. doi: CMB.1994.1.337
Thompson JD, Higgins DG, Gibson, TJ. CLUSTAL W: improving the sensitivity of prog- ressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994; 22(22): 4673-4680. doi: 10.1093/NAR/22.22.4673
Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology. 2000; 302(1): 205-217. doi: 10.1006/JMBI.2000.4042
Ortet P, Bastien O. Where Does the Alignment Score Distribution Shape Come from? Evo- lutionary Bioinformatics Online. 2010; 6(6): 159. doi: 10.4137/EBO.S5875
Dayhoff MO, Eck RV. Atlas of protein sequence and structure. Silver Spring, Md.: National Biomedical Research Foundation; 1972.
Pevsner J. Bioinformatics and functional genomics. (3. Baskı). West Sussex, UK: John Wiley & Sons; 2015.
Dai X, Shen L. Advances and Trends in Omics Technology Development. Frontiers in Me- dicine. 2022; 9: 1546. doi: 10.3389/FMED.2022.911861/BIBTEX
Orgogozo V, Peluffo AE, Morizot B. The “Mendelian Gene” and the “Molecular Gene”: Two Relevant Concepts of Genetic Units. Current Topics in Developmental Biology, 2016; 119: 1-26. doi: 10.1016/BS.CTDB.2016.03.002
Debnath M, Prasad GB, Bisen PS. Introduction to Molecular Diagnostic. Mousumi Deb- nath, Godavarthi B.K.S. Prasad, Prakash S. Bisen (Eds.), Molecular Diagnostics: Promises and Possibilities içinde. Netherlands: Springer, Dordrecht; 2010. p. 1-10.
Davies H. A role for “omics” technologies in food safety assessment. Food Control. 2010; 21(12): 1601-1610. doi: 10.1016/J.FOODCONT.2009.03.002
Budak ŞÖ, Dönmez S. Gıda Biliminde Yeni Omik Teknolojileri. Gıda. 2012; 37(3): 173-179.
Bilello J. The agony and ecstasy of “OMIC” technologies in drug development. Current Molecular Medicine, 2005; 5(1): 39-52. doi: 10.2174/1566524053152898
Alabert C, Groth A. Chromatin replication and epigenome maintenance. Nature reviews Molecular Cell Biology, 2012; 13(3): 153-167.
Horton P, Park KJ, Obayashi T, et al. WoLF PSORT: protein localization predictor. Nucleic acids research. 2007; 35(suppl_2): W585-W587.
Fischer HP. Towards quantitative biology: integration of biological information to eluci- date disease pathways and to guide drug discovery. Biotechnology Annual Review. 2005; 11(SUPPL.): 1-68. doi:10.1016/S1387-2656(05)11001-1
Huang S, Chaudhary K, Garmire LX. More Is Better: Recent Progress in Multi-Omics Data Integration Methods. Frontiers in Genetics. 2017; 8(JUN): 84. doi: 10.3389/FGE- NE.2017.00084
Kim M, Tagkopoulos I. Data integration and predictive modeling methods for multi-omics datasets. Molecular Omics. 2018; 14(1): 8-25. doi: 10.1039/C7MO00051K
Lin E, Lane HY. Machine learning and systems genomics approaches for multi-omics data.
Biomarker Research. 2017; 5(1): 1-6. doi: 10.1186/S40364-017-0082-Y/FIGURES/3
Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome biology. 2017; 18(1): 83. doi: 10.1186/s13059-017-1215-1
Aborode AT, Awuah WA, Mikhailova T, et al. OMICs Technologies for Natural Compoun- ds-based Drug Development. Current Topics in Medicinal Chemistry. 2022; 22(21): 1751- 1765. doi: 10.2174/1568026622666220726092034
Zhao K, Rhee SY. Omics-guided metabolic pathway discovery in plants: Resources, ap- proaches, and opportunities. Current Opinion in Plant Biology. 2022; 67: 102222. doi: 10.1016/J.PBI.2022.102222
Tyers M, Mann M. From genomics to proteomics. Nature. 2003; 422(6928): 193-197.
Debnath M, Prasad GB, Bisen PS. Omics technology. Mousumi Debnath, Godavarthi
B.K.S. Prasad, Prakash S. Bisen (Eds.), Molecular Diagnostics: Promises and Possibilities
içinde. Netherlands: Springer, Dordrecht; 2010. p. 11-31.
Russell C, Rahman A, Mohammed, AR. Application of genomics, proteomics and meta- bolomics in drug discovery, development and clinic. Therapeutic Delivery. 2013; 4(3): 395- 413.
Martin DB, Nelson PS. From genomics to proteomics: techniques and applications in can- cer research. Trends Cell Biol. 2001; 11: 60-65.
Unamba CI, Nag A, Sharma RK. Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Frontiers in Plant Science. 2015; 6: 1074.
Horgan RP, Kenny LC. ‘Omic’technologies: genomics, transcriptomics, proteomics and metabolomics. The Obstetrician & Gynaecologist. 2011; 13(3): 189-195.
Bal SH, Budak F. Genomik, proteomik kavramlarına genel bakış ve uygulama alanları. Ulu- dağ Üniversitesi Tıp Fakültesi Dergisi. 2013; 39(1): 65-69.
Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, et al. Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar). Fron- tiers in Genetics, 2020; 10: 1406.
Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: new develop- ments in KEGG. Nucleic Acids Research. 2006; 34: D354–D357.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics. 2009; 10(1): 57. doi: 10.1038/NRG2484
Jiménez-Chillarón JC, Díaz R, Ramón-Krauel M. Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications. Comprehensive Analytical Chemistry. 2014; 63: 81-110. doi: 10.1016/B978-0-444-62651-6.00004-0
Kodama Y, Shumway M, Leinonen R, et al. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Research. 2012; 40(Database issue): D54–D56. doi: 10.1093/nar/gkr854
Dunn MJ. Proteomics comes of age. Proteomics. 2014; 14(1): 1-2.
Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, et al. Platelet genomics and proteomics in human health and disease. The Journal of Clinical Investigation. 2005; 115(12): 3370- 3377.
Kenyon GL, DeMarini DM, Fuchs E, et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Molecular & Cellular Proteomics. 2002; 1(10): 763- 780.
Pierce JD, Fakhari M, Works KV, et al. Understanding proteomics. Nursing & Health Scien- ces. 2007; 9(1): 54-60.
Horgan RP, Kenny LC. ‘Omic’technologies: genomics, transcriptomics, proteomics and metabolomics. The Obstetrician & Gynaecologist. 2001; 13(3): 189-195.
Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nature Biotechnology. 2010; 28(7): 695-709.
O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. Journal of Bio- logical Chemistry. 1975; 250(10): 4007-4021.
Cho A, Normile D. Nobel Prize in chemistry. Mastering macromolecules. Science. 2002; 298: 527–528.
Blueggel M, Chamrad D, Meyer HE. Bioinformatics in proteomics. Current Pharmaceutical Biotechnology. 2004; 5(1): 79-88.
Ludvigsen M, Honoré B. Transcriptomics and proteomics: integration? eLS, 2018; 1-7.
Wen B, Zeng WF, Liao Y, Shi Z, et al. Deep learning in proteomics. Proteomics. 2020; 20(21- 22): 1900335.
Oliver SG, Winson MK, Kell DB, Systematic functional analysis of the yeast genome. Tren- ds in Biotechnology. 1998; 16(9): 373-378.
Wishart DS, Tzur D, Knox C, et al. HMDB: the human metabolome database. Nucleic Acids Research. 2007; 35(suppl_1): D521-D526.
Ramautar R, Demirci A, de Jong GJ. Capillary electrophoresis in metabolomics. TrAC Trends in Analytical Chemistry. 2006; 25(5): 455-466.
Monton MRN, Soga T. Metabolome analysis by capillary electrophoresis–mass spectro- metry. Journal of Chromatography A. 2007; 1168(1-2): 237-246.
Cevallos‐Cevallos JM, Rouseff R, Reyes‐De‐Corcuera JI. Untargeted metabolite analysis of healthy and Huanglongbing‐infected orange leaves by CE‐DAD. Electrophoresis. 2009; 30(7): 1240-1247.
Cevallos-Cevallos JM, Reyes-De-Corcuera JI, Etxeberria E, et al. Metabolomic analysis in food science: a review. Trends in Food Science & Technology. 2009; 20(11-12): 557-566.
Vautz W, Zimmermann D, Hartmann M, et al. Ion mobility spectrometry for food quality and safety. Food Additives and Contaminants. 2006; 23(11): 1064-1073.
Cho IH, Kim YS, Choi HK. Metabolomic discrimination of different grades of pine-mush- room (Tricholoma matsutake Sing.) using 1H NMR spectrometry and multivariate data analysis. Journal of Pharmaceutical and Biomedical Analysis. 2007; 43(3): 900-904.
Beckmann M, Enot DP, Overy DP, et al. Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars. Journal of Agricultural and Food Chemistry. 2007; 55(9): 3444-3451.
van der Greef J, Davidov E, Verheij E, et al. The Role of Metabolomics in Systems Biology. Harrigan GG, Royston Goodacre (Eds), Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis içinde. New York: Springer New York; 2003. p. 171-198.
Kaddurah-Daouk R, Krishnan K. Metabolomics: a global biochemical approach to the study of central nervous system diseases. Neuropsychopharmacology. 2009; 34(1): 173-186.
German JB, Hammock BD, Watkins SM. Metabolomics: building on a century of bioche- mistry to guide human health. Metabolomics. 2005; 1(1): 3-9.
Li S, Tian Y, Jiang P, et al. Recent advances in the application of metabolomics for food safety control and food quality analyses. Critical Reviews in Food Science and Nutrition. 2021; 61(9): 1448-1469.
Cowan MM. Plant products as antimicrobial agents. Clinical Microbiology Reviews. 1999; 12(4): 564-582.
Patwardhan B, Warude D, Pushpangadan P, et al. Ayurveda and traditional Chinese me- dicine: a comparative overview. Evidence-based Complementary and Alternative Medicine. 2005; 2(4): 465-473.
Saito K, Matsuda F. Metabolomics for functional genomics, systems biology, and biotech- nology. Annual Review of Plant Biology. 2010; 61: 463-489.
Rocca-Serra P, Brazma A, Parkinson H, et al. ArrayExpress: a public database of gene exp- ression data at EBI. Comptes Rendus Biologies. 2003; 326(10-11): 1075-1078.
Barrett T, Edgar R. Gene Expression Omnibus: microarray data storage, submission, retrie- val, and analysis. Methods in Enzymology. 2006; 411: 352-369.
Wise RP, Caldo RA, Hong L, et al. Barleybase/plexdb. In Plant bioinformatics. Humana Press; 2007. pp. 347-363.
Leinonen R, Sugawara H, Shumway M, et al. The sequence read archive. Nucleic Acids Re- search, 2010; 39(suppl_1): D19-D21.
Harishchander A. A review on application of bioinformatics in medicinal plant research.
Bioinformatics & Proteomics Open Access Journal. 2017; 1(1): 000104.
Kanehisa M. Representation and analysis of molecular networks involving diseases and drugs. Genome Informatics 2009: Genome Informatics Series. 2009; 23: 212-213.
Kaul S, Koo HL, Jenkins J, et al. Analysis of the genome sequence of the flowering plant
Arabidopsis thaliana. Nature. 2000; 408(6814): 796-815.
Matsumoto T, Wu JZ, Kanamori H, et al. The map-based sequence of the rice genome.
Nature. 2005; 436(7052): 793–800.
Skuse GR, Du C. Bioinformatics tools for plant genomics. International Journal of Plant Genomics, 2008; 2008: 910474.
Batley J, Edwards D. The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current Opinion in Plant Biology. 2016; 30: 78-81.
Shafi A. Haq E. Fazili K.M. et al. Impact of Bioinformatics on Plant Science Research and Crop Improvement. Hakeem KR, Shaik NA, Banaganapalli B, et al. (Eds.), Essentials of Bio- informatics, Volume III içinde. Cham: Springer; 2019. p. 29-46.
Henry RJ. Genomics Strategies for Germplasm Characterization and the Development of Climate Resilient Crops. Santosh Kumar (Ed.) Crop breeding: bioinformatics and prepa- ring for climate change içinde. New York: Apple Academic Press; 2016. p. 3-12.
Takeda S, Matsuoka M. Genetic approaches to crop improvement: responding to environ- mental and population changes. Nature Reviews Genetics. 2008; 9(6): 444-457.
Ahmad P, Ashraf, M, Younis M, et al. Role of transgenic plants in agriculture and biophar- ming. Biotechnology advances, 2012; 30(3): 524-540.
Tester M, Langridge P. Breeding technologies to increase crop production in a changing world. Science. 2010; 327(5967): 818-822.
Cogburn LA, Porter TE, Duclos MJ, et al. Functional genomics of the chicken-a model organism. Poultry Science, 2007; 86(10): 2059-2094.
AH. Genomics of Sorghum. International Journal of Plant Genomics. 2008; 2008: 362451.
Malav AK, Chandrawat I, Chandrawat KS. Gene pyramiding: an overview. International Journal of Current Research inBiosciences and Plant Biology. 2016; 3(7): 22-28.
Feltus FA, Wan J, Schulze SR, et al. An SNP resource for rice genetics and breeding ba- sed on subspecies indica and japonica genome alignments. Genome Research. 2004; 14(9): 1812-1819.
Varshney RK, Graner A, Sorrells ME. Genomics-assisted breeding for crop improvement.
Trends in Plant Science. 2005; 10(12): 621-630.
Pandey SP, Somssich IE. The role of WRKY transcription factors in plant immunity. Plant Physiology. 2009; 150(4): 1648-1655.
Schenk PM, Carvalhais LC, Kazan K. Unraveling plant–microbe interactions: can mul- ti-species transcriptomics help? Trends in Biotechnology, 2012; 30(3): 177-184.
Hu H, Scheben A, Edwards D. Advances in integrating genomics and bioinformatics in the plant breeding pipeline. Agriculture. 2008; 8(6): 75.
Jorgensen WL. The many roles of computation in drug discovery. Science. 2004; 303(5665): 1813-1818.
Kavitha K, Venkataraman G, Parida A. An oxidative and salinity stress induced peroxiso- mal ascorbate peroxidase from Avicennia marina: molecular and functional characteriza- tion. Plant Physiology and Biochemistry. 2008; 46(8-9): 794-804.
Cabral A, Stassen JH, Seidl MF, et al. Identification of Hyaloperonospora arabidopsidis transcript sequences expressed during infection reveals isolate-specific effectors. PLoS One, 2011; 6(5): e19328.
Yuan D, Tu L, Zhang X. Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One. 2011; 6(7): e22758.
Referanslar
Franco ML, Cediel JF, Payan, C. Breve historia de la bioinformática. Colombia Médica. 2008; 39(1): 117-120.
Zhang X, Zhou X, Wang X. Chapter1: Basics for Bioinformatics. Jiang R, Zhang X, Zhang MQ (ed.) Basics of Bioinformatics: Lecture Notes of the Graduate Summer School on Bioin- formatics of China içinde. Tsinghua University Press, Beijing and Springer-Verlag Berlin Heidelberg; 2013. p. 1-25.
Mirsaydaliyevich YI. History of Bioinformatics. Journal of Social Sciences &Interdiscipli- nary Research. 2022; 11(7): 72-76.
Sharma MK, Dhar MK, Kaul S. Bioinformatics: An introduction and Overview. Internatio- nal Journal of Engineering Research and Development. 2012; 3(8): 88-99.
Fenstermacher D. Introduction to Bioinformatics. Journal of the Amerıcan Society for Infor- mation Science and Technology. 2005; 56(5): 440-446.
Atalay RÇ. Neden Biyoinformatik? Avrasya Dosyası. 2022; 8(3): 127-139.
Ünel NM, Önal İK, Çetin F, et al. Biyoinformatiğe Giriş. Baloğlu MC (ed.) Biyoinformatik Temelleri ve Uygulamaları içinde. Pegem Akademi; 2020: p. 2-16.
Keklik G, Özcan BD. An Overview of Bioinformatics as a Multidisciplinary Science. OKU Journal of The Institute of Science and Technology. 2022; 5(2): 1082-1091.
Fu J, Zhang Y, Liu J, et al. Pharmacometabonomics: data processing and statistical analysis.
Briefings in Bioinformatics. 2021; 22(5): 1-25.
Chen YPP. Introduction to Bioinformatics. Chen YPP. (ed.) Bioinformatics Technologies. Springer-Verlag Berlin Heidelberg: 2005: p. 1-13.
O’Donoghue SI. Grand Challenges in Bioinformatics Data Visualization. Frontiers in Bio- informatics. 2021; 1: 669186. doi: 10.3389/fbinf.2021.669186
Çelik Altunoğlu Y, Ceylan KB, Ceylan Y, et al. Biyolojik Veri Tabanları. Baloğlu MC (ed.) Biyoinformatik Temelleri ve Uygulamaları içinde. Pegem Akademi; 2020: p. 19-44.
Kamble A, Khairkar R. Basics of Bioinformatics in Biological Research. International Journal of Applied Sciences and Bİotechnology. 2016; 4(4): 425-429. doi:10.3126/ijasbt. v4i4.16252
Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Research. 2001; 11(5): 863-874. doi:10.1101/GR.176601
Gollery M. Bioinformatics: Sequence and Genome Analysis. 2nd ed. Clinical Chemistry. 2005; 51(11): 2219-2220.
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. Journal of Molecular Biology. 1990; 215(3): 403–410. doi: S0022-2836(05)80360-2
Elias I. Settling the intractability of multiple alignment. Journal of Computational Bio- logy: A Journal of Computational Molecular Cell Biology. 2006; 13(7): 1323-1339. doi: CMB.2006.13.1323
Wang L, Jiang T. On the complexity of multiple sequence alignment. Journal of Computati- onal Biology : A Journal of Computational Molecular Cell Biology. 1994; 1(4): 337-348. doi: CMB.1994.1.337
Thompson JD, Higgins DG, Gibson, TJ. CLUSTAL W: improving the sensitivity of prog- ressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994; 22(22): 4673-4680. doi: 10.1093/NAR/22.22.4673
Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology. 2000; 302(1): 205-217. doi: 10.1006/JMBI.2000.4042
Ortet P, Bastien O. Where Does the Alignment Score Distribution Shape Come from? Evo- lutionary Bioinformatics Online. 2010; 6(6): 159. doi: 10.4137/EBO.S5875
Dayhoff MO, Eck RV. Atlas of protein sequence and structure. Silver Spring, Md.: National Biomedical Research Foundation; 1972.
Pevsner J. Bioinformatics and functional genomics. (3. Baskı). West Sussex, UK: John Wiley & Sons; 2015.
Dai X, Shen L. Advances and Trends in Omics Technology Development. Frontiers in Me- dicine. 2022; 9: 1546. doi: 10.3389/FMED.2022.911861/BIBTEX
Orgogozo V, Peluffo AE, Morizot B. The “Mendelian Gene” and the “Molecular Gene”: Two Relevant Concepts of Genetic Units. Current Topics in Developmental Biology, 2016; 119: 1-26. doi: 10.1016/BS.CTDB.2016.03.002
Debnath M, Prasad GB, Bisen PS. Introduction to Molecular Diagnostic. Mousumi Deb- nath, Godavarthi B.K.S. Prasad, Prakash S. Bisen (Eds.), Molecular Diagnostics: Promises and Possibilities içinde. Netherlands: Springer, Dordrecht; 2010. p. 1-10.
Davies H. A role for “omics” technologies in food safety assessment. Food Control. 2010; 21(12): 1601-1610. doi: 10.1016/J.FOODCONT.2009.03.002
Budak ŞÖ, Dönmez S. Gıda Biliminde Yeni Omik Teknolojileri. Gıda. 2012; 37(3): 173-179.
Bilello J. The agony and ecstasy of “OMIC” technologies in drug development. Current Molecular Medicine, 2005; 5(1): 39-52. doi: 10.2174/1566524053152898
Alabert C, Groth A. Chromatin replication and epigenome maintenance. Nature reviews Molecular Cell Biology, 2012; 13(3): 153-167.
Horton P, Park KJ, Obayashi T, et al. WoLF PSORT: protein localization predictor. Nucleic acids research. 2007; 35(suppl_2): W585-W587.
Fischer HP. Towards quantitative biology: integration of biological information to eluci- date disease pathways and to guide drug discovery. Biotechnology Annual Review. 2005; 11(SUPPL.): 1-68. doi:10.1016/S1387-2656(05)11001-1
Huang S, Chaudhary K, Garmire LX. More Is Better: Recent Progress in Multi-Omics Data Integration Methods. Frontiers in Genetics. 2017; 8(JUN): 84. doi: 10.3389/FGE- NE.2017.00084
Kim M, Tagkopoulos I. Data integration and predictive modeling methods for multi-omics datasets. Molecular Omics. 2018; 14(1): 8-25. doi: 10.1039/C7MO00051K
Lin E, Lane HY. Machine learning and systems genomics approaches for multi-omics data.
Biomarker Research. 2017; 5(1): 1-6. doi: 10.1186/S40364-017-0082-Y/FIGURES/3
Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome biology. 2017; 18(1): 83. doi: 10.1186/s13059-017-1215-1
Aborode AT, Awuah WA, Mikhailova T, et al. OMICs Technologies for Natural Compoun- ds-based Drug Development. Current Topics in Medicinal Chemistry. 2022; 22(21): 1751- 1765. doi: 10.2174/1568026622666220726092034
Zhao K, Rhee SY. Omics-guided metabolic pathway discovery in plants: Resources, ap- proaches, and opportunities. Current Opinion in Plant Biology. 2022; 67: 102222. doi: 10.1016/J.PBI.2022.102222
Tyers M, Mann M. From genomics to proteomics. Nature. 2003; 422(6928): 193-197.
Debnath M, Prasad GB, Bisen PS. Omics technology. Mousumi Debnath, Godavarthi
B.K.S. Prasad, Prakash S. Bisen (Eds.), Molecular Diagnostics: Promises and Possibilities
içinde. Netherlands: Springer, Dordrecht; 2010. p. 11-31.
Russell C, Rahman A, Mohammed, AR. Application of genomics, proteomics and meta- bolomics in drug discovery, development and clinic. Therapeutic Delivery. 2013; 4(3): 395- 413.
Martin DB, Nelson PS. From genomics to proteomics: techniques and applications in can- cer research. Trends Cell Biol. 2001; 11: 60-65.
Unamba CI, Nag A, Sharma RK. Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Frontiers in Plant Science. 2015; 6: 1074.
Horgan RP, Kenny LC. ‘Omic’technologies: genomics, transcriptomics, proteomics and metabolomics. The Obstetrician & Gynaecologist. 2011; 13(3): 189-195.
Bal SH, Budak F. Genomik, proteomik kavramlarına genel bakış ve uygulama alanları. Ulu- dağ Üniversitesi Tıp Fakültesi Dergisi. 2013; 39(1): 65-69.
Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, et al. Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar). Fron- tiers in Genetics, 2020; 10: 1406.
Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: new develop- ments in KEGG. Nucleic Acids Research. 2006; 34: D354–D357.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics. 2009; 10(1): 57. doi: 10.1038/NRG2484
Jiménez-Chillarón JC, Díaz R, Ramón-Krauel M. Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications. Comprehensive Analytical Chemistry. 2014; 63: 81-110. doi: 10.1016/B978-0-444-62651-6.00004-0
Kodama Y, Shumway M, Leinonen R, et al. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Research. 2012; 40(Database issue): D54–D56. doi: 10.1093/nar/gkr854
Dunn MJ. Proteomics comes of age. Proteomics. 2014; 14(1): 1-2.
Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, et al. Platelet genomics and proteomics in human health and disease. The Journal of Clinical Investigation. 2005; 115(12): 3370- 3377.
Kenyon GL, DeMarini DM, Fuchs E, et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Molecular & Cellular Proteomics. 2002; 1(10): 763- 780.
Pierce JD, Fakhari M, Works KV, et al. Understanding proteomics. Nursing & Health Scien- ces. 2007; 9(1): 54-60.
Horgan RP, Kenny LC. ‘Omic’technologies: genomics, transcriptomics, proteomics and metabolomics. The Obstetrician & Gynaecologist. 2001; 13(3): 189-195.
Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nature Biotechnology. 2010; 28(7): 695-709.
O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. Journal of Bio- logical Chemistry. 1975; 250(10): 4007-4021.
Cho A, Normile D. Nobel Prize in chemistry. Mastering macromolecules. Science. 2002; 298: 527–528.
Blueggel M, Chamrad D, Meyer HE. Bioinformatics in proteomics. Current Pharmaceutical Biotechnology. 2004; 5(1): 79-88.
Ludvigsen M, Honoré B. Transcriptomics and proteomics: integration? eLS, 2018; 1-7.
Wen B, Zeng WF, Liao Y, Shi Z, et al. Deep learning in proteomics. Proteomics. 2020; 20(21- 22): 1900335.
Oliver SG, Winson MK, Kell DB, Systematic functional analysis of the yeast genome. Tren- ds in Biotechnology. 1998; 16(9): 373-378.
Wishart DS, Tzur D, Knox C, et al. HMDB: the human metabolome database. Nucleic Acids Research. 2007; 35(suppl_1): D521-D526.
Ramautar R, Demirci A, de Jong GJ. Capillary electrophoresis in metabolomics. TrAC Trends in Analytical Chemistry. 2006; 25(5): 455-466.
Monton MRN, Soga T. Metabolome analysis by capillary electrophoresis–mass spectro- metry. Journal of Chromatography A. 2007; 1168(1-2): 237-246.
Cevallos‐Cevallos JM, Rouseff R, Reyes‐De‐Corcuera JI. Untargeted metabolite analysis of healthy and Huanglongbing‐infected orange leaves by CE‐DAD. Electrophoresis. 2009; 30(7): 1240-1247.
Cevallos-Cevallos JM, Reyes-De-Corcuera JI, Etxeberria E, et al. Metabolomic analysis in food science: a review. Trends in Food Science & Technology. 2009; 20(11-12): 557-566.
Vautz W, Zimmermann D, Hartmann M, et al. Ion mobility spectrometry for food quality and safety. Food Additives and Contaminants. 2006; 23(11): 1064-1073.
Cho IH, Kim YS, Choi HK. Metabolomic discrimination of different grades of pine-mush- room (Tricholoma matsutake Sing.) using 1H NMR spectrometry and multivariate data analysis. Journal of Pharmaceutical and Biomedical Analysis. 2007; 43(3): 900-904.
Beckmann M, Enot DP, Overy DP, et al. Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars. Journal of Agricultural and Food Chemistry. 2007; 55(9): 3444-3451.
van der Greef J, Davidov E, Verheij E, et al. The Role of Metabolomics in Systems Biology. Harrigan GG, Royston Goodacre (Eds), Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis içinde. New York: Springer New York; 2003. p. 171-198.
Kaddurah-Daouk R, Krishnan K. Metabolomics: a global biochemical approach to the study of central nervous system diseases. Neuropsychopharmacology. 2009; 34(1): 173-186.
German JB, Hammock BD, Watkins SM. Metabolomics: building on a century of bioche- mistry to guide human health. Metabolomics. 2005; 1(1): 3-9.
Li S, Tian Y, Jiang P, et al. Recent advances in the application of metabolomics for food safety control and food quality analyses. Critical Reviews in Food Science and Nutrition. 2021; 61(9): 1448-1469.
Cowan MM. Plant products as antimicrobial agents. Clinical Microbiology Reviews. 1999; 12(4): 564-582.
Patwardhan B, Warude D, Pushpangadan P, et al. Ayurveda and traditional Chinese me- dicine: a comparative overview. Evidence-based Complementary and Alternative Medicine. 2005; 2(4): 465-473.
Saito K, Matsuda F. Metabolomics for functional genomics, systems biology, and biotech- nology. Annual Review of Plant Biology. 2010; 61: 463-489.
Rocca-Serra P, Brazma A, Parkinson H, et al. ArrayExpress: a public database of gene exp- ression data at EBI. Comptes Rendus Biologies. 2003; 326(10-11): 1075-1078.
Barrett T, Edgar R. Gene Expression Omnibus: microarray data storage, submission, retrie- val, and analysis. Methods in Enzymology. 2006; 411: 352-369.
Wise RP, Caldo RA, Hong L, et al. Barleybase/plexdb. In Plant bioinformatics. Humana Press; 2007. pp. 347-363.
Leinonen R, Sugawara H, Shumway M, et al. The sequence read archive. Nucleic Acids Re- search, 2010; 39(suppl_1): D19-D21.
Harishchander A. A review on application of bioinformatics in medicinal plant research.
Bioinformatics & Proteomics Open Access Journal. 2017; 1(1): 000104.
Kanehisa M. Representation and analysis of molecular networks involving diseases and drugs. Genome Informatics 2009: Genome Informatics Series. 2009; 23: 212-213.
Kaul S, Koo HL, Jenkins J, et al. Analysis of the genome sequence of the flowering plant
Arabidopsis thaliana. Nature. 2000; 408(6814): 796-815.
Matsumoto T, Wu JZ, Kanamori H, et al. The map-based sequence of the rice genome.
Nature. 2005; 436(7052): 793–800.
Skuse GR, Du C. Bioinformatics tools for plant genomics. International Journal of Plant Genomics, 2008; 2008: 910474.
Batley J, Edwards D. The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current Opinion in Plant Biology. 2016; 30: 78-81.
Shafi A. Haq E. Fazili K.M. et al. Impact of Bioinformatics on Plant Science Research and Crop Improvement. Hakeem KR, Shaik NA, Banaganapalli B, et al. (Eds.), Essentials of Bio- informatics, Volume III içinde. Cham: Springer; 2019. p. 29-46.
Henry RJ. Genomics Strategies for Germplasm Characterization and the Development of Climate Resilient Crops. Santosh Kumar (Ed.) Crop breeding: bioinformatics and prepa- ring for climate change içinde. New York: Apple Academic Press; 2016. p. 3-12.
Takeda S, Matsuoka M. Genetic approaches to crop improvement: responding to environ- mental and population changes. Nature Reviews Genetics. 2008; 9(6): 444-457.
Ahmad P, Ashraf, M, Younis M, et al. Role of transgenic plants in agriculture and biophar- ming. Biotechnology advances, 2012; 30(3): 524-540.
Tester M, Langridge P. Breeding technologies to increase crop production in a changing world. Science. 2010; 327(5967): 818-822.
Cogburn LA, Porter TE, Duclos MJ, et al. Functional genomics of the chicken-a model organism. Poultry Science, 2007; 86(10): 2059-2094.
AH. Genomics of Sorghum. International Journal of Plant Genomics. 2008; 2008: 362451.
Malav AK, Chandrawat I, Chandrawat KS. Gene pyramiding: an overview. International Journal of Current Research inBiosciences and Plant Biology. 2016; 3(7): 22-28.
Feltus FA, Wan J, Schulze SR, et al. An SNP resource for rice genetics and breeding ba- sed on subspecies indica and japonica genome alignments. Genome Research. 2004; 14(9): 1812-1819.
Varshney RK, Graner A, Sorrells ME. Genomics-assisted breeding for crop improvement.
Trends in Plant Science. 2005; 10(12): 621-630.
Pandey SP, Somssich IE. The role of WRKY transcription factors in plant immunity. Plant Physiology. 2009; 150(4): 1648-1655.
Schenk PM, Carvalhais LC, Kazan K. Unraveling plant–microbe interactions: can mul- ti-species transcriptomics help? Trends in Biotechnology, 2012; 30(3): 177-184.
Hu H, Scheben A, Edwards D. Advances in integrating genomics and bioinformatics in the plant breeding pipeline. Agriculture. 2008; 8(6): 75.
Jorgensen WL. The many roles of computation in drug discovery. Science. 2004; 303(5665): 1813-1818.
Kavitha K, Venkataraman G, Parida A. An oxidative and salinity stress induced peroxiso- mal ascorbate peroxidase from Avicennia marina: molecular and functional characteriza- tion. Plant Physiology and Biochemistry. 2008; 46(8-9): 794-804.
Cabral A, Stassen JH, Seidl MF, et al. Identification of Hyaloperonospora arabidopsidis transcript sequences expressed during infection reveals isolate-specific effectors. PLoS One, 2011; 6(5): e19328.
Yuan D, Tu L, Zhang X. Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One. 2011; 6(7): e22758.
