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Up-to-date research in biology, biotechnology, and medicine requires fast genome and transcriptome analysis technologies to investigate cellular state, physiology, and activity. Gene expression is the process of generating messenger RNA copies of a gene. The transcriptome, which contains the mRNA of the cell, reflects the cell's overall gene expression pattern. Understanding the nature and frequency of each RNA molecule in a given cell under certain circumstances is necessary to examine the transcriptome. Microarray and serial analysis of gene expression are two primary techniques researchers use in transcriptome studies. Here, microarray technology and next-generation sequencing of transcripts are states of the art. Since microarray technology is limited to RNA, quantifying transcript levels and sequence information, RNA-Seq provides nearly unlimited possibilities in modern bioanalysis. Sequencing of RNA, or RNA-Seq, is now a standard method to analyze gene expression and uncover novel RNA species. In addition, aspects of RNA biogenesis and metabolism can be interrogated with specialized techniques for cDNA library preparation. The present study will introduce and compare new high-performance methods used in examining the transcriptome. This also presents a detailed description of next-generation sequencing, describes the impact of this technology on transcriptome analysis, and explains its possibilities to explore the modern RNA world.

Mass spectrometry is a method of evaluation used to identify which particles compose an example based on the ions' mass spectrum. Mass spectrometers can perform conventional detection and quantitation of target analytes. However, they can also be used for the rapid discovery of bacteria within a medical setting. Matrix-assisted laser desorption/ionization-time of flight mass spectrometer is one of the most prominent MS tools applied in biology, with its robust and accurate recognition of categories and types of a wide variety of Gram-positive and negative microorganisms. Mass spectrometry detection is based on determining a particular range of each kind and matching it with a comprehensive data source within the tool. Today's study describes the history and sample preparation of the MALDI-TOF MS technique. Moreover, the applications of MALDI-TOF MS microbial recognition in the center and the presence of antimicrobial resistance will be presented. Besides, the present restrictions and future use of MALDI-TOF MS in forthcoming daily scientific practice are reviewed. In this review, microorganisms will also be addressed in future clinical applications, primarily using MALDI-TOF MS in microbiology to identify and analyze antibiotic resistance.

DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.

There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS’s crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.

Ehsaneh Khodadadi,1 Elham Zeinalzadeh,2,3 Sepehr Taghizadeh,1 Bahareh Mehramouz,3 Fadhil S Kamounah,4 Ehsan Khodadadi,5 Khudaverdi Ganbarov,6 Bahman Yousefi,7 Milad Bastami,7 Hossein Samadi Kafil1 1Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; 2Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; 3Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; 4Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark; 5Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran; 6Department of Microbiology, Baku State University, Baku, Azerbaijan; 7Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, IranCorrespondence: Hossein Samadi KafilDrug Applied Research Center, Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht Ave, Tabriz 5166614711, IranTel +98-9127184735Fax +98-4133364661Email Kafilhs@tbzmed.ac.irAbstract: Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.Keywords: bacterial pathogenesis studies, drug resistance, virulence, pathogen, proteomics