Abstract
In the twentieth century, many researchers have started working on bioinformatics for disease biomarker detection using genetic information, i.e., DNA microarray dataset and RNA sequencing dataset with machine learning approaches. The journey of this concept starts with the classification technique on DNA microarray dataset by comparing it with reference genome or by deNovo (without reference genome) technique, and lots of different tools were published in different publications. Later, with the availability and advancement of computational power many researchers started working on large RNA sequencing dataset and some tools are published again with significant features. Nowadays, also this area is like a newborn baby and several challenges are still not solved, but it does not have a proper guideline for new researchers to face those challenges. After analyzing so many tools on DNA as well as RNA, we are able to summarize these works with a common workflow, and in this paper, we have proposed a generalized workflow for detecting epidemic diseases like HIV-AIDS, Cancer using machine learning approaches.
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References
Tomasz P, Szymon W, Jacek B (2016) Computer representations of bioinformatics models. Curr Bioinform 11(5):551–560
Agbachi CPE (2017) Pathways in bioinformatics: A window in computer science. Int J Comput Trends Technol 49(2):83–90
Sardaraz M, Tahir M, Ikram AA (2016) Advances in high throughput DNA sequence data compression. J Bioinf Comput Biol 14(3):18
Ge SX (2017) Exploratory bioinformatics investigation reveals importance of junk DNA in early embryo development. BMC Genom 18(1):200
Chen S, Liu M, Zhou Y (2018) Bioinformatics analysis for cell-free tumor DNA sequencing data. In: Computational Systems Biology. Humana Press, New York, NY, USA, pp 67–95
Zhang J, Huang K (2017) Pan-cancer analysis of frequent DNA come thylation patterns reveals consistent epigenetic landscape changes in multiple cancers. BMC Genom 18:1045
Van Dam S, Craig T, de Magalhaes JP (2015) Gene friends: a human RNA-seq-based gene and transcript co-expression database. Nucl Acids Res 43:1124–1132
Zeisel A, Munoz-Manchado AB, Codeluppi S et al (2015) Brain structure cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. 347:1138–1142
Fiannaca A, La Rosa M, La Paglia L et al (2015) Analysis of miRNA expression profiles in breast cancer using biclustering. BMC Bioinform 16
Xue Z, Huang K, Cai C et al (2013) Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500:593–597
Sanger F (1980) Google Scholar. http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1980/sanger-bio.html
Hutchison C (2007) DNA sequencing: bench to bedside and beyond Nucleic Acids. Nucl Acids Res. 35:6227–6237
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends genet. Trends Genet 24:133–141
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145
Glass K, Huttenhower C, Quackenbush J (2013) Passing messages between biological networks to refine predicted interactions. PLoS One 8
De Smet R, Marchal K (2010) Advantages and limitations of current network inference methods. Nat Rev Microbiol 8:717–729
Yue F, Cheng Y, Breschi A et al (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515:355–364
Amar D, Safer H (2013) Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol 9
Zeisel A, Munoz-Manchado AB, Codeluppi S et al (2015) Brain structure cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347:1138–1142
Bhar A, Haubrock M, Mukhopadhyay A et al (2013) Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell. Algor Mol Biol 8
Fiannaca A, La Rosa M, La Paglia L (2015) Analysis of miRNA expression profiles in breast cancer using biclustering. BMC Bioinform 16
Kakati T, Bhattacharyya DK, Barah P, Kalita JK (2019) Comparison of methods or differential co-expression analysis for disease biomarker prediction. Comput Biol Med 10:100–103
Madeira SC, Oliveira AL (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform 1:24–45
Wang YK, Print CG, Crampin EJ (2013) Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence. BMC Genom 14:102
Oghabian A, Kilpinen S, Hautaniemi S, Czeizler E (2014) Biclustering methods: biological relevance and application in gene expression analysis. PloS One 9
Kakati T, Kashyap H, Bhattacharyya DK (2016) THD-module extractor: an application for CEN module extraction and interesting gene identification for Alzheimer’s disease. Sci Rep 6
Kakati T, Bhattacharyya DK, Barah P, Kalita JK (2019) Comparison of methods for differential co-expression analysis for disease biomarker rediction. Comput Biol Med 10:113
Tan SC, Yiap BC (2009) DNA, RNA, and protein extraction: the past and the present. Hindawi Publ Corp J Biomed Biotechnol Article ID 574398
Zhao Y, Li H, Fang S et al (2016) NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucl Acids Res 44:203–208
Guttman M, Donaghey J, Carey BW et al (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477
Ala U, Piro RM, Grassi E et al (2008) Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput Biol 4
van Someren EP, Vaes BL, Steegenga WT et al (2006) Least absolute regression network analysis of the murine osteoblast differentiation network. Bioinformatics 22:477–484
Friedman N, Linial M, Nachman I et al (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7:601–620
Haeseleer PD (2005) How does gene expression clustering work? Nat Biotechnol 23:1499–1501
Ahmed H, Mahanta P, Bhattacharyya D, Kalita J (2014) Shifting-and-scaling correlation based biclustering algorithm. IEEE/ACM Trans Computat Biol Bioinform 11:1239–1252
Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science 282:699–705
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Baruah, B., Dutta, M.P. (2020). Bioinformatics Advancements for Detecting Epidemic Disease Using Machine Learning Approaches. In: Mallick, P.K., Meher, P., Majumder, A., Das, S.K. (eds) Electronic Systems and Intelligent Computing. Lecture Notes in Electrical Engineering, vol 686. Springer, Singapore. https://doi.org/10.1007/978-981-15-7031-5_100
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