Difference between revisions of "Lim Doyeon"

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<p>&nbsp;<strong>Bioinformatics</strong>&nbsp;(from the Greek&nbsp;<em>genno</em>&nbsp;<strong>&gamma;&epsilon;&nu;&nu;&Iuml;Ž</strong>&nbsp;= give birth) is the science of genes, heredity, evolution, and the variation of organisms. The phenomenon of inheritance has been implicitly utilized in breeding of organisms and selection for desired traits, and the scientific field of genetics seeks to understand the mechanisms of inheritance.<a rel="dofollow" href="http://www.miere-bucovina.ro" title="miere de albine"><img hspace="2" border="0" vspace="2" src="http://www.all-auto.ro/img/a%20auto" alt="miere de albine" /></a></p>
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<p>&nbsp;<strong>Bioinformatics</strong>&nbsp;is addition two word, biology and informatics. Bioinformatics deal with biological information(genomic information etc.). Usually this information is analyzed by computer technology(information technology). However, in traditional biology field also deal with biological data and get the information and work with it, expert JongBhak said &quot;Biology is Bioinformatics and Bioinformatics is Biology&quot;.</p>
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<p>The genetic information of organisms is contained within the chemical structure of [[DNA]] (deoxyribonucleic acid) molecules. Individually inherited traits, corresponding to regions in the DNA sequence, are called genes. Genes encode the information necessary for synthesizing RNA and proteins -- complex molecules generally responsible for enzymatic reactions, synthesis, communication and structure within a cell. DNA sequence is transcribed into an intermediate molecule called &quot;messenger RNA&quot;, and ribosomes translate this sequence to form a chain of amino acids to form a protein. This process is known as the central dogma of molecular biology.<a rel="dofollow" href="http://www.auto-my.com/auto-parts" title="auto parts online"><img hspace="2" border="0" vspace="2" src="http://www.all-auto.ro/img/a%20auto" alt="auto parts online" /></a></p>
 
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<p>Although genetics plays a large role in determining the appearance and behavior of organisms, it is the interaction of genetics with the environment that determines the ultimate outcome. Thus, while identical twins have the same DNA and genes, differences in their experiences during development and childhood results in different personalities and fingerprints.</p>
 
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<h2><span class="mw-headline">History</span></h2>
 
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<div class="thumb tright">
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<h2>Principles of Bioinformatics</h2>
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<div class="thumbinner" style="width: 202px;"><img height="183" width="200" class="thumbimage" alt="Morgan's observation of sex-linked inheritance of a mutation causing white eyes in Drosophila led him to the hypothesis that genes are located upon chromosomes." longdesc="http://biopedia.org/wiki/Image:Sexlinked_inheritance_white.jpg" src="http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/Sexlinked_inheritance_white.jpg/200px-Sexlinked_inheritance_white.jpg" />
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<div>
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<div class="thumbcaption">
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<h2>Bioprogramming</h2>
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<div class="magnify" style="float: right;"><img height="11" width="15" alt="" src="http://en.wikipedia.org/skins-1.5/common/images/magnify-clip.png" /></div>
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<div>
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Morgan's observation of sex-linked inheritance of a mutation causing white eyes in Drosophila led him to the hypothesis that genes are located upon chromosomes.</div>
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<h3>Programming</h3>
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<div>&nbsp;Process of making program. It could be the one format of communication. We translate human's language into computer language. picture in bellow shows translation of High-level Language into Low-level language. We can program with different High-level language (C/C++, Perl, Java etc.). Since now, programming is one-way communication because programmer write the language to make programm and computer do what programmer ask.</div>
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<div>&nbsp;</div>
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<div>.<img src="/ckfinder/userfiles/images/machine%20language.gif" width="350" height="189" align="absBottom" alt="" /></div>
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</div>
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<div>
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<h3>Bioprogramming</h3>
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<div>&nbsp;</div>
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<div>
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<div>Process of creating(Programming) the artificial organism(Program). Bioprogramming is part of programming but handle the biological data and make bio-program(alias artificial organism). Difference between real organism and artificial organism is, organism is made of organic materials and artificial organism is composed of 0 and 1. Biological data can be information of existing organism like &nbsp;genomic data, muscle movement data, connectome etc. By modeling existing organism, we can make it live inside cyberspace and also we can even create entirely new organism (homo sapiens&nbsp;with wings). To bio-program, researchers commonly use Perl, and made a library &quot;BioPerl&quot; to make bio-programming easy.</div>
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<h3>Artrificial Organism</h3>
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<h4>Caenorhabditis elegans(C.elegans)</h4>
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<div>&nbsp;<img src="/ckfinder/userfiles/images/CElegans.png" width="300" height="120" align="absBottom" alt="" />&nbsp; &nbsp; &nbsp;&nbsp;<img src="/ckfinder/userfiles/images/CElegans_A.png" width="500" height="97" alt="" /></div>
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<div>▲Caenorhabditis elegans (C. elegans) &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ▲ Caenorhabditis elegans (C. elegans) &nbsp;-Anatomical picture</div>
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<div>&nbsp;</div>
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<div>Caenorhabditis elegnas has ~1000 cells, 302 neurons, 50k synapses, 95 muscles. All the connectome and anatimic structure is opened, so it became first artificial organism.&nbsp;</div>
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<div>&nbsp;</div>
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<h4>Cyber C. elegans</h4>
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</div>
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<div>&nbsp;There are many researches about Cyber C.elegans. I also called as openworm. Openworm is name of project to make C.elegans in robotic, graphic and may other ways and the name of the cyber C.elegans at the same time. It is 'Open'worm because every structure of C.elegans is open to public and the code to make C.elegans is also accessible to everyone.&nbsp;</div>
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<div>&nbsp;</div>
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<div>&nbsp;<img src="/ckfinder/userfiles/images/connectome.png" width="400" height="224" alt="" /><img src="/ckfinder/userfiles/images/cell.png" width="400" height="224" alt="" /></div>
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<div>&nbsp;</div>
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<div>▲ Connectome of the C.elegans &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ▲Cell linkage map</div>
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<div>&nbsp;</div>
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<div>In cyberspace, C.elegans has exactly same informations with real C.elegans like you can see in above(connectome and cells). It moves, thinks, and reproduction as real one</div>
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<div>&nbsp;</div>
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<div>
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<div>https://www.youtube.com/watch?v=Ek49JSAiKjY</div>
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</div>
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<div>&nbsp;</div>
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<div>&nbsp;</div>
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<div>&nbsp;</div>
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<div>Also we can apply neuronal information to robot. Existing artifical intelligence(AI) have a &quot;right answer&quot; to certain stimuli like 'move left when you meet the wall'. Programmer designed the Algorithm to do the task. These days, AI gather the data and learn itself. But It still need some learning algorithm which programmer is made. Contrary to existing Artificial Algrithm, bellow video shows the robot with neuronal information of C.elegans. It THINK to avoid the wall, even though there was no command of programmer.</div>
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<div>&nbsp;</div>
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<div>
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<div>https://www.youtube.com/watch?v=YWQnzylhgHc</div>
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<div>&nbsp;</div>
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<div>&nbsp;&nbsp;</div>
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</div>
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<div>Also, we can create the new spieces using C.elegans information. Below picture, C.elegans have five artificial arms which is made based on existing muscle information.</div>
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<div><img src="/ckfinder/userfiles/images/C_elegans%20with%20arm.png" width="350" height="196" alt="" /></div>
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<div>▲C.elegans with five arms</div>
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<div>&nbsp;</div>
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<div>
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<p class="MsoNormal" align="center" style="text-align:center">&nbsp;</p>
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<p class="MsoNormal">&nbsp;</p>
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<p class="MsoNormal">&nbsp;</p>
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<h3>What is Reality</h3>
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<p class="MsoNormal"><span lang="EN-US">&nbsp;I will see what is &lsquo;virtual&rsquo; which is antonym of &lsquo;Real&rsquo;. Virtual is something that made, done, seen etc. on the Internet or a computer. Due to the appearance of computer, people had to make the word to divide cyber space and non-cyber space. So, the word &ldquo;Real&rdquo; is just matter of classification. Before, people could experience the virtual world by using only visual information. That was big difference between real and virtual. However, these days, people can experience the cyber space by using almost every sensory system. Also can communicate using biological information(e.g. EEG). In this reason the barrier between real and non-real is ambiguous and divide to into different word is useless. In conclusion, &ldquo;real&rdquo; world is the world we can experience and perceive in our sensory and neural system and also give a feedback by neural, motor and other biological system.</span></p>
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</div>
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<div>&nbsp;</div>
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<div>&nbsp;</div>
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<div>&nbsp;</div>
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</div>
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<h2>Genomics</h2>
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<div>
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<h2>Transcriptomics</h2>
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<div>
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<h2>Proteomics</h2>
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<div>
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<h2>Epigenomics and Phenomics</h2>
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<div>
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<h2>Canceromics and Geromics</h2>
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</div>
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<h2>Reference</h2>
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<p>Gregor Johann Mendel, a German-Czech Augustinian monk and scientist, is often called the &quot;father of modern genetics&quot;, a title given to him due to his early work on the heredity of plants. In his paper &quot;Versuche &uuml;ber Pflanzenhybriden&quot; (&quot;Experiments on Plant Hybridization&quot;), presented in 1865 to the Brunn Natural History Society, Gregor Mendel traced the inheritance patterns of certain traits in pea plants and showed that they could be described mathematically.<sup class="reference" id="_ref-mendel_0">[3]</sup>&nbsp;Although not all features show these patterns of Mendelian inheritance, his work suggested the utility of the application of statistics to the study of inheritance.<a rel="dofollow" href="http://www.auto-my.ro/vanzari-auto" title="vanzari auto"><img hspace="2" border="0" vspace="2" src="http://www.all-auto.ro/img/a%20auto" alt="vanzari auto" /></a></p>
 
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<p>The significance of Mendel's observations was not understood until early in the twentieth century, after his death, when his research was re-discovered by other scientists working on similar problems. The word &quot;genetics&quot; itself was coined by William Bateson, a significant proponent of Mendel's work, in a letter to Adam Sedgwick, dated April 18, 1905.<sup class="reference" id="_ref-1">[4]</sup>&nbsp;Bateson promoted the term &quot;genetics&quot; publicly in his inaugural address to the Third International Conference on Plant Hybridization (London, England) in 1906.<sup class="reference" id="_ref-bateson_genetics_0">[5]</sup></p>
 
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<p>In the decades following rediscovery and popularization of Mendel's work, numerous experiments sought to elucidate the molecular basis of DNA. In 1910 Thomas Hunt Morgan argued that genes reside on chromosomes, based observations of a sex-linked white eye mutation in fruit flies. In 1913 his student Alfred Sturtevant used the phenomenon of genetic linkage and the associated recombination rates to demonstrate and map the linear arrangement of genes upon the chromosome.</p>
 
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<div class="thumb tleft">
 
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<div class="thumbinner" style="width: 302px;"><a class="internal" title="The chemical structure of DNA." href="http://en.wikipedia.org/wiki/Image:DNA_chemical_structure.svg"><img height="350" width="300" class="thumbimage" alt="The chemical structure of DNA." longdesc="http://biopedia.org/wiki/Image:DNA_chemical_structure.svg" src="http://upload.wikimedia.org/wikipedia/commons/thumb/e/e4/DNA_chemical_structure.svg/300px-DNA_chemical_structure.svg.png" /></a>
 
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<div class="thumbcaption">
 
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<div class="magnify" style="float: right;"><a class="internal" title="Enlarge" href="http://en.wikipedia.org/wiki/Image:DNA_chemical_structure.svg"><img height="11" width="15" alt="" src="http://en.wikipedia.org/skins-1.5/common/images/magnify-clip.png" /></a></div>
 
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The chemical structure of DNA.</div>
 
 
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<p>Although chromosomes were known to contain genes, chromosomes were composed of both protein and DNA -- it was unknown which was critical for heredity or how the process occurred. In 1928, Frederick Griffith published his discovery of the phenomenon of transformation (see Griffith's experiment); sixteen years later, in 1944, Oswald Theodore Avery, Colin McLeod and Maclyn McCarty used this phenomenon to isolate and identify the molecule responsible for transformation as DNA<sup class="reference" id="_ref-dna_transforming_0">[6]</sup>. The Hershey-Chase experiment in 1952 identified DNA (rather than protein) as the genetic material of viruses, further evidence that DNA was the molecule responsible for inheritance&nbsp;<a rel="dofollow" href="http://www.auto-tip.ro/dezmembrari-auto" title="dezmembrari auto"><img hspace="2" border="0" vspace="2" src="http://www.all-auto.ro/img/a%20auto" alt="dezmembrari auto" /></a>&nbsp;.</p>
 
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<p>James D. Watson and Francis Crick resolved the structure of DNA in 1953, using X-ray crystallography information that indicated the molecule had a helical structure. Their double-helix model paired a sequence of nucleotides with a &quot;complement&quot; on the other strand. This structure not only provided a physical explanation for information, contained within the order of the nucleotides, but also a physical mechanism for duplication through separation of strands and the reconstruction of a partner strand based on the nucleotide pairings. They famously observed this in their paper, stating:&nbsp;<em>&quot;It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.&quot;</em></p>
 
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<p>In the following decades, an explosion of research based on this understanding of the molecular nature of DNA became possible. The development of DNA sequencing in 1977 enabled the determination of nucleotide sequences on DNA,<sup class="reference" id="_ref-sanger_sequencing_0">[7]</sup>&nbsp;and the PCR method developed by Kary Banks Mullis in 1983 allowed the isolation and amplification of arbitrary segments of DNA. These and other techniques, through the pooled efforts of the Human Genome Project and parallel private effort by Celera Genomics, culminated in the sequencing of the human genome in 2001.</p>
 
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<p><a id="Timeline_of_notable_discoveries" name="Timeline_of_notable_discoveries" style="background-image: url(http://biopedia.org/extensions/FckEditor/editor/css/images/fck_anchor.gif);"></a></p>
 
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<h3><span class="mw-headline">Timeline of notable discoveries</span></h3>
 
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<ul>
 
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    <li>1865 Gregor Mendel's paper,&nbsp;<em>Experiments on Plant Hybridization</em><sup class="reference" id="_ref-mendel_1">[3]</sup></li>
 
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    <li>1869 Friedrich Miescher discovers a weak acid in the nuclei of white blood cells that today we call DNA<sup class="reference" id="_ref-Hartl_and_Jones_1">[1]</sup></li>
 
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    <li>1880-1890 Walther Flemming, Eduard Strasburger, and Edouard van Beneden elucidate chromosome distribution during cell division</li>
 
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    <li>1903 Walter Sutton hypothesizes that chromosomes, which segregate in a Mendelian fashion, are hereditary units<sup class="reference" id="_ref-100_Years_Ago:_Walter_Sutton_and_the_Chromosome_Theory_of_Heredity_0">[8]</sup></li>
 
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    <li>1906 The term &quot;genetics&quot; is proposed by the British biologist William Bateson<sup class="reference" id="_ref-bateson_genetics_1">[5]</sup></li>
 
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    <li>1910 Thomas Hunt Morgan shows that genes reside on chromosomes, and discovered linked genes on chromosomes that do not follow Mendel's law of independent allele segregation</li>
 
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    <li>1913 Alfred Sturtevant makes the first genetic map of a chromosome, showing genes are linearly arranged</li>
 
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    <li>1918 Ronald Fisher publishes &quot;The Correlation Between Relatives on the Supposition of Mendelian Inheritance&quot; the modern synthesis starts.</li>
 
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    <li>1928 Frederick Griffith discovers a hereditary molecule that is transmissible between bacteria (see Griffiths experiment)</li>
 
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    <li>1931 Crossing over is the cause of recombination (see Barbara McClintock and cytogenetics)</li>
 
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    <li>1941 Edward Lawrie Tatum and George Wells Beadle show that genes code for proteins<sup class="reference" id="_ref-2">[9]</sup></li>
 
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    <li>1944 Oswald Theodore Avery, Colin McLeod and Maclyn McCarty isolate DNA as the genetic material (at that time called transforming principle)<sup class="reference" id="_ref-dna_transforming_1">[6]</sup></li>
 
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    <li>1950 Erwin Chargaff shows that the four nucleotides are not present in nucleic acids in stable proportions, but that some general rules appear to hold (e.g., the nucleotide bases Adenine-Thymine and Cytosine-Guanine always remain in equal proportions).</li>
 
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    <li>1950 Barbara McClintock discovers transposons in maize</li>
 
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    <li>1952 The Hershey-Chase experiment proves the genetic information of phages (and all other organisms) to be DNA</li>
 
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    <li>1953 DNA structure is resolved to be a double helix by James D. Watson and Francis Crick, with the help of Rosalind Franklin<sup class="reference" id="_ref-3">[10]</sup></li>
 
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    <li>1956 Joe Hin Tjio and Albert Levan established the correct chromosome number in humans to be 46</li>
 
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    <li>1958 The Meselson-Stahl experiment demonstrates that DNA is semiconservatively replicated<sup class="reference" id="_ref-4">[11]</sup></li>
 
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    <li>1961 The genetic code is arranged in triplets</li>
 
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    <li>1964 Howard Temin showed using RNA viruses that Watson's central dogma is not always true</li>
 
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    <li>1970 Restriction enzymes were discovered in studies of a bacterium,&nbsp;<em>Haemophilus influenzae</em>, enabling scientists to cut and paste DNA</li>
 
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    <li>1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein<sup class="reference" id="_ref-5">[12]</sup>.</li>
 
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    <li>1976, Walter Fiers and his team determine the complete nucleotide-sequence of Bacteriophage MS2-RNA<sup class="reference" id="_ref-6">[13]</sup></li>
 
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    <li>1977 DNA is sequenced for the first time by Fred Sanger, Walter Gilbert, and Allan Maxam working independently. Sanger's lab complete the entire genome of sequence of Bacteriophage &Phi;-X174<sup class="reference" id="_ref-sanger_sequencing_1">[7]</sup>.</li>
 
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    <li>1983 Kary Banks Mullis discovers the polymerase chain reaction enabling the easy amplification of DNA</li>
 
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    <li>1985 Alec Jeffreys discovers genetic finger printing.</li>
 
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    <li>1989 The first human gene is sequenced by Francis Collins and Lap-Chee Tsui. It encodes the CFTR protein. Defects in this gene cause cystic fibrosis<a title="asigurari auto ieftine" href="http://www.all-auto.ro/asigurari-auto" rel="dofollow"><img hspace="2" border="0" vspace="2" alt="asigurari auto ieftine" src="http://www.all-auto.ro/images/asigurari auto" /></a></li>
 
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    <li>1995 The genome of&nbsp;<em>Haemophilus influenzae</em>&nbsp;is the first genome of a free living organism to be sequenced.</li>
 
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    <li>1996 Saccharomyces cerevisiae is the first eukaryote genome sequence to be released</li>
 
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    <li>1998 The first genome sequence for a multicellular eukaryote,&nbsp;<em>C. elegans</em>&nbsp;is released.</li>
 
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    <li>2001 First draft sequences of the human genome are released simultaneously by the Human Genome Project and Celera Genomics&nbsp;<a rel="dofollow" href="http://www.auto-tip.ro/piese-auto" title="piese auto"><img hspace="2" border="0" vspace="2" src="http://www.all-auto.ro/img/a%20auto" alt="piese auto" /></a>&nbsp;.</li>
 
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    <li>2003 (14 April) Successful completion of Human Genome Project with 98% of the genome sequenced to a 99.99% accuracy.<sup class="reference" id="_ref-7">[14]</sup></li>
 
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</ul>
 
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<p><a id="Areas_of_genetics" name="Areas_of_genetics" style="background-image: url(http://biopedia.org/extensions/FckEditor/editor/css/images/fck_anchor.gif);"></a></p>
 
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<h2><span class="mw-headline">Areas of genetics</span></h2>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Classical genetics</span></h3>
 
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<dl><dd><br type="_moz" />
 
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<p>Classical genetics consists of the techniques and methodologies of genetics that predate the advent of molecular biology. After the discovery of the genetic code and such tools of cloning as restriction enzymes, the avenues of investigation open to geneticists were greatly broadened. Some classical genetic ideas have been supplanted with the mechanistic understanding brought by molecular discoveries, but many remain intact and in use, such as Mendel's laws and Muller's morphs. Patterns of inheritance still remain a useful tool for the study of genetic diseases.</p>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Behavioral genetics</span></h3>
 
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<dl><dd><br type="_moz" />
 
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<p>Behavioral genetics studies the influence of varying genetics on animal behavior. Behavioral genetics studies the effects of human disorders as well as its causes. Behavioral genetics has yielded some very interesting questions about the evolution of various behaviors, and even some fundamental principles of evolution in general. For example, guppies and meerkats seem to be genetically driven to post a lookout to watch for predators. This lookout stands a significantly slimmer chance of survival than the others, so because of the mechanism of natural selection, it would seem that this trait would be lost after a few generations. However, the gene has remained, leading evolutionary philosopher/scientists such as Richard Dawkins and W. D. Hamilton to propose explanations, including the theories of kin selection and reciprocal altruism. The interactions and behaviors of gregarious creatures is partially genetic in cause and must therefore be approached by evolutionary theory.</p>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Clinical genetics</span></h3>
 
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<div class="noprint">&nbsp;</div>
 
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<p>Physicians who are trained as Geneticists diagnose, treat, and counsel patients with genetic disorders or syndromes. These doctors are typically trained in a genetics residency and/or fellowship.</p>
 
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<p>Clinical genetics is also the study of genetic causes of clinical diseases.</p>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Molecular genetics</span></h3>
 
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<dl><dd>
 
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<div class="noprint">&nbsp;</div>
 
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<p>Molecular genetics builds upon the foundation of classical genetics but focuses on the structure and function of genes at a molecular level. Molecular genetics employs the methods of both classical genetics (such as hybridization) and molecular biology. It is so-called to differentiate it from other sub fields of genetics such as ecological genetics and population genetics. An important area within molecular genetics is the use of molecular information to determine the patterns of descent, and therefore the correct scientific classification of organisms: this is called molecular systematics. The study of inherited features not strictly associated with changes in the DNA sequence is called epigenetics.</p>
 
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<p>Some take the view that life can be defined, in molecular terms, as the set of strategies which RNA polynucleotides have used and continue to use to perpetuate themselves. This definition grows out of work on the origin of life, specifically the RNA world hypothesis.</p>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Population, quantitative and ecological genetics</span></h3>
 
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<dl><dd><br type="_moz" />
 
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<p>Population, quantitative and ecological genetics are all very closely related subfields and also build upon classical genetics (supplemented with modern molecular genetics). They are chiefly distinguished by a common theme of studying populations of organisms drawn from nature but differ somewhat in the choice of which aspect of the organism on which they focus. The foundational discipline is population genetics which studies the distribution of and change in allele frequencies of genes under the influence of the four evolutionary forces: natural selection, genetic drift, mutation and migration. It is the theory that attempts to explain such phenomena as adaptation and speciation.</p>
 
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<p>The related subfield of quantitative genetics, which builds on population genetics, aims to predict the response to selection given data on the phenotype and relationships of individuals. A more recent development of quantitative genetics is the analysis of quantitative trait loci. Traits that are under the influence of a large number of genes are known as quantitative traits, and their mapping to a location on the chromosome requires accurate phenotypic, pedigree and marker data from a large number of related individuals.</p>
 
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<p>Ecological genetics again builds upon the basic principles of population genetics but is more explicitly focused on ecological issues. While molecular genetics studies the structure and function of genes at a molecular level, ecological genetics focuses on wild populations of organisms, and attempts to collect data on the ecological aspects of individuals as well as molecular markers from those individuals.</p>
 
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<p>Population genetics is closely linked with the methods of genetic epidemiology. One method to study gene-disease associations is using the principle of Mendelian randomization.</p>
 
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<p><a id="Genomics" name="Genomics" style="background-image: url(http://biopedia.org/extensions/FckEditor/editor/css/images/fck_anchor.gif);"></a></p>
 
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<h3><span class="mw-headline">Genomics</span></h3>
 
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<dl><dd>
 
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<div class="noprint">&nbsp;</div>
 
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<p>A more recent development is the rise of genomics, which attempts the study of large-scale genetic patterns across the genome for (and in principle, all the DNA in) a given species. The field typically depends on the availability of whole genome sequences, computational tools and Sequence profiling tool using bioinformatics approaches for analysis of large sets of data.</p>
 
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<p>&nbsp;</p>
 
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<h3><span class="mw-headline">Closely-related fields</span></h3>
 
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<p>The science which grew out of the union of biochemistry and genetics is widely known as molecular biology. The term &quot;genetics&quot; is often widely conflated with the notion of genetic engineering, where the DNA of an organism is modified for some kind of practical end, but most research in genetics is aimed at understanding and explaining the effect of genes on phenotypes and in the role of genes in populations (see population genetics and ecological genetics), rather than genetic engineering.</p>
 
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<p>&nbsp;</p>
 
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<h2><span class="mw-headline">References</span></h2>
 
−
<ol class="references">
 
−
    <li id="_note-Hartl_and_Jones">^&nbsp;<sup><em><strong>a</strong></em></sup>&nbsp;<sup><em><strong>b</strong></em></sup>&nbsp;<cite class="book" style="font-style: normal;">Daniel Hartl and Elizabeth Jones (2005).&nbsp;<em>Genetics: Analysis of Genes and Genomes, 6th edition</em>. Jones &amp; Bartlett.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=book&amp;rft.btitle=Genetics%3A+Analysis+of+Genes+and+Genomes%2C+6th+edition&amp;rft.title=Genetics%3A+Analysis+of+Genes+and+Genomes%2C+6th+edition&amp;rft.au=Daniel+Hartl+and+Elizabeth+Jones&amp;rft.date=2005&amp;rft.pub=Jones+%26+Bartlett">&nbsp;</span>&nbsp;854 pages. ISBN 0-7637-1511-5.</li>
 
−
    <li id="_note-0"><strong>^</strong>&nbsp;<cite class="book" style="font-style: normal;">Robert C. King, Willliam D. Stansfield, Pamela K. Mulligan (2006).&nbsp;<em>A Dictionary of Genetics, 7th edition</em>. New York: Oxford University Press.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=book&amp;rft.btitle=A+Dictionary+of+Genetics%2C+7th+edition&amp;rft.title=A+Dictionary+of+Genetics%2C+7th+edition&amp;rft.au=Robert+C.+King%2C+Willliam+D.+Stansfield%2C+Pamela+K.+Mulligan&amp;rft.date=2006&amp;rft.pub=Oxford+University+Press&amp;rft.place=New+York">&nbsp;</span>&nbsp;596 pages. ISBN 0-19-530761-5 (paper).</li>
 
−
    <li id="_note-mendel">^&nbsp;<sup><em><strong>a</strong></em></sup>&nbsp;<sup><em><strong>b</strong></em></sup>&nbsp;<cite style="font-style: normal;">Mendel, G.. &quot;Versuche &uuml;ber Pflanzen-Hybriden&quot;.&nbsp;<em>Verh. Naturforsch. Ver. Br&uuml;nn</em>&nbsp;<strong>4</strong>: 3-47.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Versuche+%C3%BCber+Pflanzen-Hybriden&amp;rft.title=Verh.+Naturforsch.+Ver.+Br%C3%BCnn&amp;rft.jtitle=Verh.+Naturforsch.+Ver.+Br%C3%BCnn&amp;rft.volume=4&amp;rft.au=Mendel%2C+G.&amp;rft.pages=3-47">&nbsp;</span>&nbsp;(in English in 1901, J. R. Hortic. Soc. 26: 1&ndash;32)</li>
 
−
    <li id="_note-1"><strong>^</strong>&nbsp;Online copy of William Bateson's letter to Adam Sedgwick</li>
 
−
    <li id="_note-bateson_genetics">^&nbsp;<sup><em><strong>a</strong></em></sup>&nbsp;<sup><em><strong>b</strong></em></sup>&nbsp;<cite style="font-style: normal;">Bateson, William (1907). &quot;The Progress of Genetic Research&quot;. Wilks, W. (editor)&nbsp;<em>Report of the Third 1906 International Conference on Genetics: Hybridization (the cross-breeding of genera or species), the cross-breeding of varieties, and general plant breeding</em>, London: Royal Horticultural Society.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=conference&amp;rft.btitle=Report+of+the+Third+1906+International+Conference+on+Genetics%3A+Hybridization+%28the+cross-breeding+of+genera+or+species%29%2C+the+cross-breeding+of+varieties%2C+and+general+plant+breeding&amp;rft.atitle=The+Progress+of+Genetic+Research&amp;rft.au=Bateson%2C+William&amp;rft.date=1907&amp;rft.pub=Royal+Horticultural+Society&amp;rft.place=London">&nbsp;</span><dl><dd>Although the conference was titled &quot;International Conference on Hybridisation and Plant Breeding&quot;, Wilks changed the title for publication as a result of Bateson's speech.</dd></dl></li>
 
−
    <li id="_note-dna_transforming">^&nbsp;<sup><em><strong>a</strong></em></sup>&nbsp;<sup><em><strong>b</strong></em></sup>&nbsp;<cite style="font-style: normal;">Avery, MacLeod, and McCarty (1944). &quot;Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III&quot;.&nbsp;<em>Journal of Experimental Medicine</em>&nbsp;<strong>79</strong>&nbsp;(1): 137-58.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Studies+on+the+Chemical+Nature+of+the+Substance+Inducing+Transformation+of+Pneumococcal+Types%3A+Induction+of+Transformation+by+a+Desoxyribonucleic+Acid+Fraction+Isolated+from+Pneumococcus+Type+III&amp;rft.title=Journal+of+Experimental+Medicine&amp;rft.jtitle=Journal+of+Experimental+Medicine&amp;rft.date=1944&amp;rft.volume=79&amp;rft.issue=1&amp;rft.au=Avery%2C+MacLeod%2C+and+McCarty&amp;rft.pages=137-58">&nbsp;</span>35th anniversary reprint available on&nbsp;<a href="http://www.all-auto.ro/piese-auto">piese auto ieftine</a></li>
 
−
    <li id="_note-sanger_sequencing">^&nbsp;<sup><em><strong>a</strong></em></sup>&nbsp;<sup><em><strong>b</strong></em></sup>&nbsp;Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., Nucleotide sequence of bacteriophage phi X174 DNA, Nature. 1977 Feb 24;265(5596):687-94</li>
 
−
    <li id="_note-100_Years_Ago:_Walter_Sutton_and_the_Chromosome_Theory_of_Heredity"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Ernest W. Crow and James F. Crow (2002). &quot;100 Years Ago: Walter Sutton and the Chromosome Theory of Heredity&quot;.&nbsp;<em>Genetics</em>&nbsp;<strong>160</strong>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=100+Years+Ago%3A+Walter+Sutton+and+the+Chromosome+Theory+of+Heredity&amp;rft.title=Genetics&amp;rft.jtitle=Genetics&amp;rft.date=2002&amp;rft.volume=160&amp;rft.au=Ernest+W.+Crow+and+James+F.+Crow&amp;rft_id=http%3A%2F%2Fwww.genetics.org%2Fcgi%2Fcontent%2Ffull%2F160%2F1%2F1">&nbsp;</span></li>
 
−
    <li id="_note-2"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Beadle GW, Tatum EL (1941). &quot;Genetic control of biochemical reactions in neurospora&quot;.&nbsp;<em>PNAS</em>&nbsp;<strong>27</strong>: 499-506.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Genetic+control+of+biochemical+reactions+in+neurospora&amp;rft.title=PNAS&amp;rft.jtitle=PNAS&amp;rft.date=1941&amp;rft.volume=27&amp;rft.au=Beadle+GW%2C+Tatum+EL&amp;rft.pages=499-506">&nbsp;</span></li>
 
−
    <li id="_note-3"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Watson JD and Crick FH (1953). &quot;Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid&quot;.&nbsp;<em>Nature</em>&nbsp;<strong>171</strong>&nbsp;(4356): 737-8.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Molecular+structure+of+nucleic+acids%3B+a+structure+for+deoxyribose+nucleic+acid&amp;rft.title=Nature&amp;rft.jtitle=Nature&amp;rft.date=1953&amp;rft.volume=171&amp;rft.issue=4356&amp;rft.au=Watson+JD+and+Crick+FH&amp;rft.pages=737-8">&nbsp;</span></li>
 
−
    <li id="_note-4"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Meselson, M. and Stahl, F.W. (1958). &quot;The Replication of DNA in Escherichia coli&quot;.&nbsp;<em>PNAS</em>&nbsp;<strong>44</strong>: 671-82.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=The+Replication+of+DNA+in+Escherichia+coli&amp;rft.title=PNAS&amp;rft.jtitle=PNAS&amp;rft.date=1958&amp;rft.volume=44&amp;rft.au=Meselson%2C+M.+and+Stahl%2C+F.W.&amp;rft.pages=671-82">&nbsp;</span></li>
 
−
    <li id="_note-5"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Min Jou W, Haegeman G, Ysebaert M, Fiers W. (1972). &quot;Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein&quot;.&nbsp;<em>Nature</em>&nbsp;<strong>237</strong>&nbsp;(5350): 82-8.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Nucleotide+sequence+of+the+gene+coding+for+the+bacteriophage+MS2+coat+protein&amp;rft.title=Nature&amp;rft.jtitle=Nature&amp;rft.date=1972&amp;rft.volume=237&amp;rft.issue=5350&amp;rft.au=Min+Jou+W%2C+Haegeman+G%2C+Ysebaert+M%2C+Fiers+W.&amp;rft.pages=82-8">&nbsp;</span></li>
 
−
    <li id="_note-6"><strong>^</strong>&nbsp;<cite style="font-style: normal;">Fiers W et al. (1976). &quot;Complete nucleotide-sequence of Bacteriophage MS2-RNA - primary and secondary structure of replicase gene&quot;.&nbsp;<em>Nature</em>&nbsp;<strong>260</strong>: 500-507.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Complete+nucleotide-sequence+of+Bacteriophage+MS2-RNA+-+primary+and+secondary+structure+of+replicase+gene&amp;rft.title=Nature&amp;rft.jtitle=Nature&amp;rft.date=1976&amp;rft.volume=260&amp;rft.au=Fiers+W+et+al.&amp;rft.pages=500-507">&nbsp;</span></li>
 
−
    <li id="_note-7"><strong>^</strong>&nbsp;http://www.genoscope.cns.fr/externe/English/Actualites/Presse/HGP/HGP_press_release-140403.pdf</li>
 
−
</ol>
 
−
<p>&nbsp;</p>
 
−
<h2><span class="mw-headline">See also</span></h2>
 
−
<ul>
 
−
    <li>Epigenetics</li>
 
−
    <li>Evolution</li>
 
−
    <li>List of genetics-related topics</li>
 
−
    <li>List of genetic engineering topics</li>
 
−
    <li>Central dogma of molecular biology</li>
 
−
    <li>Chimerism</li>
 
−
    <li>Gene gun</li>
 
−
    <li>Gene regulatory network</li>
 
−
    <li>Genetic counseling</li>
 
−
    <li>Genetic engineering</li>
 
−
    <li>Genetic screen</li>
 
−
    <li>Genetic testing</li>
 
−
    <li>Important publications in genetics</li>
 
−
    <li>List of genetics research organizations</li>
 
−
    <li>List of geneticists</li>
 
−
    <li>Human mitochondrial genetics</li>
 
−
    <li>[[Population genetics]]</li>
 
−
    <li>Reprogenetics</li>
 
−
    <li>Punnett square</li>
 
−
    <li>Genetically modified food</li>
 
−
    <li>Transgenic plants</li>
 
−
</ul>
 
−
<p>&nbsp;</p>
 
−
<h2><span class="mw-headline">Journals</span></h2>
 
−
<ul>
 
−
    <li><em><a title="American Journal of Human Genetics" href="http://en.wikipedia.org/wiki/American_Journal_of_Human_Genetics">American Journal of Human Genetics</a></em></li>
 
−
    <li><em><a class="new" title="American Journal of Medical Genetics" href="http://en.wikipedia.org/w/index.php?title=American_Journal_of_Medical_Genetics&amp;action=edit">American Journal of Medical Genetics</a></em></li>
 
−
    <li><em><a title="Annals of Human Genetics" href="http://en.wikipedia.org/wiki/Annals_of_Human_Genetics">Annals of Human Genetics</a></em></li>
 
−
    <li><em><a title="European Journal of Human Genetics" href="http://en.wikipedia.org/wiki/European_Journal_of_Human_Genetics">European Journal of Human Genetics</a></em></li>
 
−
    <li><em><a title="Genome Research" href="http://en.wikipedia.org/wiki/Genome_Research">Genome Research</a></em></li>
 
−
    <li><em><a class="new" title="Genomics (journal)" href="http://en.wikipedia.org/w/index.php?title=Genomics_%28journal%29&amp;action=edit">Genomics</a></em></li>
 
−
    <li><em><a title="Genetics (journal)" href="http://en.wikipedia.org/wiki/Genetics_%28journal%29">Genetics</a></em></li>
 
−
    <li><em><a title="Heredity (journal)" href="http://en.wikipedia.org/wiki/Heredity_%28journal%29">Heredity</a></em></li>
 
−
    <li><em><a class="new" title="Human Molecular Genetics" href="http://en.wikipedia.org/w/index.php?title=Human_Molecular_Genetics&amp;action=edit">Human Molecular Genetics</a></em></li>
 
−
    <li><em><a title="Journal of Genetics" href="http://en.wikipedia.org/wiki/Journal_of_Genetics">Journal of Genetics</a></em></li>
 
−
    <li><em><a class="new" title="Journal of Human Genetics" href="http://en.wikipedia.org/w/index.php?title=Journal_of_Human_Genetics&amp;action=edit">Journal of Human Genetics</a></em></li>
 
−
    <li><em><a class="new" title="Journal of Medical Genetics" href="http://en.wikipedia.org/w/index.php?title=Journal_of_Medical_Genetics&amp;action=edit">Journal of Medical Genetics</a></em></li>
 
−
    <li><em><a title="Nature Reviews Genetics" href="http://en.wikipedia.org/wiki/Nature_Reviews_Genetics">Nature Reviews Genetics</a></em></li>
 
−
    <li><em><a title="PLoS Genetics" href="http://en.wikipedia.org/wiki/PLoS_Genetics">PLoS Genetics</a></em></li>
 
−
</ul>
 
−
<p>&nbsp;</p>
 
−
<h2><span class="mw-headline">External link<br />
 
−
<font size="2">[http://populationgenetics.net Populationgenetics]<br />
 
−
[http://populationgenomics.org Populationgenomics.org]<br />
 
−
[http://personalgenome.net Personalgenome.net]<br />
 
−
[http://omics.org Omics.org]<br />
 
−
[http://www.arizona-breast-cancer-specialists.com/brachytherapy/all-about-what-is-brachytherapy.html Breast brachytherapy]</font></span></h2>
 

Latest revision as of 12:44, 15 May 2015

 Bioinformatics is addition two word, biology and informatics. Bioinformatics deal with biological information(genomic information etc.). Usually this information is analyzed by computer technology(information technology). However, in traditional biology field also deal with biological data and get the information and work with it, expert JongBhak said "Biology is Bioinformatics and Bioinformatics is Biology".

 

 

Principles of Bioinformatics

Bioprogramming

Programming

 Process of making program. It could be the one format of communication. We translate human's language into computer language. picture in bellow shows translation of High-level Language into Low-level language. We can program with different High-level language (C/C++, Perl, Java etc.). Since now, programming is one-way communication because programmer write the language to make programm and computer do what programmer ask.
 
.

Bioprogramming

 
Process of creating(Programming) the artificial organism(Program). Bioprogramming is part of programming but handle the biological data and make bio-program(alias artificial organism). Difference between real organism and artificial organism is, organism is made of organic materials and artificial organism is composed of 0 and 1. Biological data can be information of existing organism like  genomic data, muscle movement data, connectome etc. By modeling existing organism, we can make it live inside cyberspace and also we can even create entirely new organism (homo sapiens with wings). To bio-program, researchers commonly use Perl, and made a library "BioPerl" to make bio-programming easy.

Artrificial Organism

Caenorhabditis elegans(C.elegans)

       
▲Caenorhabditis elegans (C. elegans)                                                 ▲ Caenorhabditis elegans (C. elegans)  -Anatomical picture
 
Caenorhabditis elegnas has ~1000 cells, 302 neurons, 50k synapses, 95 muscles. All the connectome and anatimic structure is opened, so it became first artificial organism. 
 

Cyber C. elegans

 There are many researches about Cyber C.elegans. I also called as openworm. Openworm is name of project to make C.elegans in robotic, graphic and may other ways and the name of the cyber C.elegans at the same time. It is 'Open'worm because every structure of C.elegans is open to public and the code to make C.elegans is also accessible to everyone. 
 
 
 
▲ Connectome of the C.elegans                                                                                                                           ▲Cell linkage map
 
In cyberspace, C.elegans has exactly same informations with real C.elegans like you can see in above(connectome and cells). It moves, thinks, and reproduction as real one
 
 
 
 
Also we can apply neuronal information to robot. Existing artifical intelligence(AI) have a "right answer" to certain stimuli like 'move left when you meet the wall'. Programmer designed the Algorithm to do the task. These days, AI gather the data and learn itself. But It still need some learning algorithm which programmer is made. Contrary to existing Artificial Algrithm, bellow video shows the robot with neuronal information of C.elegans. It THINK to avoid the wall, even though there was no command of programmer.
 
Also, we can create the new spieces using C.elegans information. Below picture, C.elegans have five artificial arms which is made based on existing muscle information.
▲C.elegans with five arms
 

 

 

 

What is Reality

 I will see what is ‘virtual’ which is antonym of ‘Real’. Virtual is something that made, done, seen etc. on the Internet or a computer. Due to the appearance of computer, people had to make the word to divide cyber space and non-cyber space. So, the word “Real” is just matter of classification. Before, people could experience the virtual world by using only visual information. That was big difference between real and virtual. However, these days, people can experience the cyber space by using almost every sensory system. Also can communicate using biological information(e.g. EEG). In this reason the barrier between real and non-real is ambiguous and divide to into different word is useless. In conclusion, “real” world is the world we can experience and perceive in our sensory and neural system and also give a feedback by neural, motor and other biological system.

 
 
 

Genomics

Transcriptomics

Proteomics

Epigenomics and Phenomics

Canceromics and Geromics

Reference

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