ShinUnBeom

Principles of Bioinformatics

 Bioinformatics is a field that invents methods and computer program for understanding biological data. In this days, there are many programs for analyzing gene expression, protein expression, mapping genes and gene annotation. Due to this many biology field can research conveniently and developed more such as genomics and proteomics.

Bioprogramming

 Bioprogrmming is a process for making program of bioinformatics.[1]

Genomics

 Genomics is discipline of genetics for sequencing, assembling and analyzing the function and structure of entire genomes, not single genes.

Genome analysis

DNA sequencing

 First of all, select an organism of interest. Then sequence DNA fragments. There are several ways for sequencing DNA fragments; shotgun sequencing[2], high-throughout sequencing, illumina sequencing[3] and ion torrent[4].

Sequence assembly

 After sequencing DNA fragments, next step is assembling DNA fragments to rebuild original chromosome. There are two ways; de-novo assembly[5] which assemble without any reference sequences, and comparative assembly which use sequences of similar organism for reference.

Annotation

 Genome annotation is giving some biological information to sequences. Main aspects for genome annotation is finding non-protein coding portion, identifying elements on genome and giving information to elements.

Fields of genomics

Functional genomics

 Functional genomics is a field for studying gene function and interactions. They want to find the relationship between the genome and its phenotype.

Structural genomics

 Structural genomics is a field for studying the three dimensional structure of proteins encoded by genome.

Epigenomics

 Epigenomics is a study about the complete set of epigenetic modifications, such as DNA methylation and histone modification, in the cell.

Metagenomics

 Metagenomics is a study of genetic material of environmental samples.

Transcriptomics 

 Transcriptomics is a study on RNAs, such as mRNA, rRNA, tRNA and non-coding RNA. Usually transcriptomics examine the expression level of RNA and study the function of RNA.

Analyzing methods

 There is two analyzing methods; microarrarys and RNA-seq.

Microarrays

 Microarrays is a method which collect RNA fragments on solid surface. On solid surface, DNAs are fragmented and attached. When RNAs are introduced in surface, RNA is attached to its anti-sense DNA fragments. So people can see which part of DNA(gene) is highly expressed and figure out the function.[6]

RNA-seq

 RNA-seq, also known as RNA sequencing, is a recently method to analyze the amount of RNA in a specific time by using next-generation sequencing. Fore details, see here;[7][8]

Proteomics

 Proteomics is a study for proteins in organism, such as studying the structure, function and interaction.

Techniques

Mass-spectrometry

 Mass-spectrometry is a chemical method to identify a molecule by measuring the abundance and mass-charege ratio of molecule.[9] Protein can be also detected by mass-spectrometry, so this technique is used to identify purified proteins, protiein in mixture, the amount of specific protein and the distribution of protein.

Protein-chip

 Protein-chip is uesd to detect the interaction and activity of proteins and define the function. Since large numbers of protein can use, it can define the function in large scale. Detection is done by probe, which are labled with fluoroscent dye. If there is some reaction between probe and protein, fluoroscent signal are emited.

Proteomics and Bioinformatics

 Since there are so many proteins and thier data, people made computer programs of to analyze protein data conveniently. Examples are here[10]

Proteomics and Genomics-Human Genome Project

 Human genome project is a large scale research project. Its aim are defining DNA sequence of human, find genes and mapping genes in gemone. This project is done in 2004 and people found that human has 3 billion nucleotides and 20,500 genes.[11]

Epigenomics and  Phenomics

Epigenomics

 Epigenomics study the epigenetic molecule in a cell, which are DNA methylation, histone modification and RNA interference.

Techniques

ChIp-chip

 ChIp-chip is a combined technique for chromatin immunoprecipitation and DNA microarray. It can detect interactions between proteins and DNA, especially DNA-binding proteins.[12]

ChIp-seq

 ChIp-seq is another method for detecting DNA-binding protein sites, which is combination of chromatin immunoprecipitation and DNA sequencing.[13]

Bisulfite sequencing

 Bisulfite sequencing is a technique for detecting DNA methylation pattern. The idea is coming from that bisulfite can change cytosine to uracil but can't change 5-methylcystosine. So by compairing orginal DNA and bisulfite-treated DNA, people can find DNA methylation pattern.[14]

Phenomics

 Phenomics study the phenomenon of a organism in respond to gene mutation and environment change.

Canceromics and Geromics

 Canceromics is a biological field of studying cancer. And geromics is a biological field of studying aging.

What Is Real?

 In case tangible things, real is the thing that all people can see directly. For example, since 63 building is in Seoul and we can go to Seoul and see it, 63 building real. However, since we can't see alien anywhere, alien is not real. If all the people can see alien directly, then alien changes real. In case of formless thing, such as past people and  event, if so many articles state and explain something, then that is considered real. In other words, reality is not absolute concept. Reality can be change relatively.