Il Young Cho

Principles of Bioinformatics

Bioinformatics is an interdisciplinary field of science which combines computer science, statistics, mathematics and engineering to study and process biological data.

Bioprogramming

2-1 Programming

Programming is a process that leads from an original formulation of a computing problem to executable computer programs. The purpose of programming is to find a sequence of instructions that will automate performing a specific task or solving a given problem.

2-2 Compiler

Compiler is a computer program that transforms source code written in a programming language into another computer language (binary form).

2-3 Language

There is some languages which we can use as a programming languages, such as C, R, Java, Perl and Matlab.

Genomics

3-1 What is Genomics?

Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes

3-2 Origin, history and future of Genomics.

In 1975 Plus and Minus technique was developed. The refinement of the Plus and Minus method resulted in the chain-termination, or Sanger method which formed the basis of the techniques of DNA sequencing, genome mapping, data storage, and bioinformatic analysis most widely used in the following quarter-century of research. In the same year, the Maxam-Gilbert method was developed which is method of DNA sequencing. In the future, there will be more effective method to sequence DNA.

3-3 Relationship with other -omics.

The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics. The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; similarly omics has come to refer generally to the study of large, comprehensive biological data sets. I think Genomics is fundamental study to other –omics such as proteomics or metabolomics, because technique or knowledge related to genomics is used to other studies to do experiment more efficiently.

Transcriptomics

4-1 What is transcriptomics?

Transcriptomics is study to research transcriptome which means the set of all RNA molecules including mRNA, rRNA, tRNA, and other non-coding RNA transcribed in one cell or a population of cells.

4-2 Relationship between genomics and transcriptomics

Transcriptomics is bigdata which is role of transcriptomes and environment to transcript DNA of organisms. Result from DNA sequence which is known by Genomics, we can expect transcriptome. And if we know certain environment which organism transcript DNA, we can know more about DNA. So I think it is complementary relation.

4-3 What are mRNAs?

mRNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Following transcription of primary transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology.

4-4 Relationship between Transcriptome and Proteome.

Transcriptome have information for translation to proteins and have ability to accomplish translation. So Transcriptomics is some kinds of prior task for study of proteomics.

4-5 What is UTR?

In molecular genetics, an untranslated region refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5' side, it is called the 5' UTR (or leader sequence), or if it is found on the 3' side, it is called the 3' UTR (or trailer sequence).

4-6What is ncRNA?

A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. It can be regulation factor.

4-7What is poly A?

Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA for translation. It, therefore, forms part of the larger process of gene expression. The poly(A) tail is important for the nuclear export, translation, and stability of mRNA.

Proteomics

5-1What is Proteomics

The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

5-2 Relationship between Genomics, Transcriptomics and Proteomics.

Protein is the last product of transcription and transcription. But by studying certain environments of translation and interactions among proteins, we can get information about function of genome and transcriptome.Proteomics

Epigenomics

 Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. Epigenetic modifications are reversible modifications on a cell’s DNA or histones that affect gene expression without altering the DNA sequence.

 

Phenomics

What is phenome & phenomics?

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Examples of human phenotypic traits are skin color, eye color, body height, or specific personality characteristics. Although any phenotype of any organism has a basis in its genotype, phenotypic expression may be influenced by environmental influences, mutation, and genetic variation such as single nucleotide polymorphisms (SNPs), or a combination of these factors.

Relationship betwwen phenomics and other -omics.

Phenomics is the study of the phenome and how it is determined, particularly when studied in relation to the set of all genes (genomics) or all proteins (proteomics). Phenomics is intuitive study which is based on genomics and proteomics. So it seems like output of genomics and proteomics.

Cacer & Aging

Telomere in cancer & aging

 Telomere is sequence repeated in end of choromosomes. Telomere becomes short as cell division in somatic cells. Finally, it becomes shape of knot and cell division is stopped. So shortening in telomere is one of cause of aging. In cancer cell or gamete, there is telomerase which synthesize telomere. It can proliferate infinitely, because telomere doesn't be decreased.