Changes
From Biolecture.org
no edit summary
Bioinformatics is the key in personal genome projects and variome projects. Bioinformatics is not a set of tools but it is a proper scientific discipline. It regards life as a gigantic information processing phenomenon and tries to map its components and to model the emerging networks of the components. Bioinformatics in 2008 is driving biology into an information science. Most biology researches are now with massive amount of data that cannot be processed by hand. Nearly all the biological research outcomes in the next five years will have some form of high throughput data such as genome sequences, microarray data, proteome analyses, SNPs, epigenome chips, and large scale phenotype mapping. Bioinformatics tools in genomics and variomics can be found from various internet resources. There are various bioinformatics hubs such as NCBI (National Center for Biotechnology Information), EBI (European Bioinformatics Institute), DDBJ (Databank of Japan), and KOBIC. Some others are: Bioinformatics Organization (<a href="http://bioinformatics.org/"><font color="#0000ff">http://Bioinformatics.Org</font></a>), EMBnet (<a href="http://www.embnet.org/"><font color="#0000ff">http://www.embnet.org/</font></a>), and The International Society for Computational Biology (<a href="http://iscb.org/"><font color="#0000ff">http://iscb.org</font></a>). The following are major bioinformatics journals:<br />
<br />
</span> </p>
<ul type="disc">
<li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Algorithms in <span style="FONT-SIZE: 9pt">Molecular Biology (http://www.almob.org/) </span></span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Bioinformatics (http://bioinformatics.oxfordjournals.org/) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">BMC Bioinformatics (http://www.biomedcentral.com/bmcbioinformatics) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Briefings in Bioinformatics (http://bib.oxfordjournals.org/) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Genome Research (http://genome.cshlp.org/) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Genomics and Informatics (<a href="http://www.genominfo.org/"><font color="#0000ff">http://www.genominfo.org</font></a>) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">The International Journal of Biostatistics (http://www.bepress.com/ijb/) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Journal of Computational Biology (http://www.liebertpub.com/Products/Product.aspx?pid=31&AspxAutoDetectCookieSupport=1) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Cancer Informatics (http://www.la-press.com/journal.php?pa=description&journal_id=10) </span></li> <li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">Molecular Systems Biology (http://www.nature.com/msb/index.html </span></li>
<li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">PLoS Computational Biology (<a href="http://www.ploscompbiol.org/home.action">http://www.ploscompbiol.org/home.action</a>)</span> </li>
<li style="TEXT-ALIGN: left"><span style="FONT-SIZE: 9pt">International Journal of Bioinformatics Research and Applications (http://www.inderscience.com/browse/index.php?journalcode=ijbra)</span> </li></ul><br /span><strong><span style="FONT-SIZE: 9pt">Sequencing DNA, Metagenomics, and Ecogenomics</span></strong><span style="FONT-SIZE: 9pt"><br />
Next generation sequencing methods are not only mapping genomes. They can be used to map the environment. It is called ecogenomics. Environment to humans can be various microbial, plant, and animal interactions around us. Especially, microbial interaction is critical to our health. Gut bacteria are natural environment to us. Metagenomics is a methodology that sequences the whole set of microbes in our food tract. Researchers are realizing that human genome is complemented by such environmental genomes. A new term, 'ecogenomics' is now used to describe these concepts. Metagenomics and ecogenomics are for mapping the variation of environmental genetic factors.<br />
<br />
<br />
</span><strong><span style="FONT-SIZE: 9pt">Mapping expression using DNA sequencing</span></strong><span style="FONT-SIZE: 9pt"><br />
DNA sequencing technology used to be for mapping genotypes. However, they are now used to map expression levels in cells. Cells produce various RNAs. mRNA is the most abundant and important. In the past, microarray and DNA chips were used for measuring expression levels. They are not accurate and it takes many bioinformatic adjustments before it becomes reliable expression data. New sequencing technologies can measure expression levels much more accurately. By sequencing the RNAs, we can now quantify the mRNA levels by precisely knowing the RNA sequences. Sequencing technologies will restructure the expression analyses in the future.</span> <p> </p>
<p> </p>
<div><strong><font size="2">Conclusion</font></strong><br />
