410 lines
43 KiB
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410 lines
43 KiB
HTML
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<meta name="title" property="og:title" content="Senior Investigator, Computational Biology Branch">
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<title>NLM Intramural Research Program - Yi-Kuo Yu, PhD</title>
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<meta name="DC.Date.Issued" content="2019-12-16" />
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<meta name="DC.Date.Modified" content="2024-09-20" />
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<h1 class="forstaffpages" style="opacity: 1;">Yi-Kuo Yu, PhD</h1>
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<h2>About</h2>
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<img src="/research/img/Yi-KuoYu.jpg" alt="Picture of Yi-Kuo Yu, PhD"/>
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<h3>Yi-Kuo Yu, PhD</h3>
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Senior Investigator, Computational Biology Branch
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<p>Dr. Yu’s lab investigates various biological problems at multiple levels of detail in order to gain quantitative understanding in biology. They develop solid foundation for quantitative understanding of biomolecular interactions; to better separate information from noise in massive biological data sets, they develop/employ computational approaches with sound statistical foundations. A major goal is to foster a solid connection between medical research and fundamental scientific research.</p>
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<h3>Contact Information</h3>
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<p>Building 38A, 8600 Rockville Pike, Room 6S610, MSC 3829 Bethesda, MD 20894</p>
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<p>Tel: 301-435-5989</p>
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<p><a href="mailto:yyu@ncbi.nlm.nih.gov">yyu@ncbi.nlm.nih.gov</a></p>
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<h2>Research Interests</h2>
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<p><iframe src="https://www.youtube.com/embed/w59XaDFJxNo" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" width="709" height="399" frameborder="0"></iframe><p>
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<p>As a theoretical physicist working in biology,
|
||
I have always been fascinated by the functional
|
||
and organizational complexity achievable
|
||
in a myriad of diverse organisms, all of which
|
||
share a universal set of building blocks (water,
|
||
ions, saccharides, fatty acids, amino acids, nucleotides
|
||
and other small molecules). Despite
|
||
vast amounts of effort invested, our current understanding
|
||
of biology, ranging from a microscopic
|
||
level to a more macroscopic level, is far
|
||
from complete. For example, in terms of molecular
|
||
interactions, phenomenological treatments
|
||
at the intra- and inter-protein level have not yet
|
||
fostered an effective theory capable of predicting
|
||
how proteins fold and how a protein complex organizes
|
||
itself. Namely, a proper coarse-graining
|
||
procedure to bring out only the relevant degrees
|
||
of freedom is lacking. This may be due to our
|
||
insufficient understanding of biology in terms of
|
||
relevant physics and chemistry, or it may be because
|
||
the search for higher organizing principles
|
||
is hindered by our inability to bring out information
|
||
buried in noise and/or by conflicting interpretations
|
||
of data. Developing methods to
|
||
improve information extraction and establishing
|
||
a firm foundation at the microscopic level are
|
||
essential. Our approach to mitigate the issue
|
||
of noise (or conflicting information) is to devise
|
||
data analysis methods that can assign accurate
|
||
statistical significance to signals identified; our
|
||
take on building a firm foundation at the microscopic
|
||
level is via development of calculation
|
||
methods whose accuracy can be controlled. All
|
||
our research efforts center about these two main
|
||
emphases.</p>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<h2>Publications</h2>
|
||
<div class="citation-wrap">
|
||
<div class="citation">
|
||
<div class="align-left">
|
||
<!-- <input id="cit45680355" type="checkbox" name="cit45680355" value="45680355" class="citation-check"
|
||
|
||
>
|
||
<label for="cit45680355">select</label> -->
|
||
</div>
|
||
<div class="ncbi-docsum">
|
||
<span class="authors">
|
||
Alves G, Yu Y.
|
||
</span><span class="title">
|
||
Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry.
|
||
</span><span class="journalname">J Am Soc Mass Spec. </span><span class="displaydate">2020 January</span><span>; </span><span class="volume">31</span><span class="issue">(1)</span><span class="page">:85-102</span><span>. </span><span class="doi">doi: 10.1021/jasms.9b00035.</span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<br/>
|
||
<div class="citation-wrap">
|
||
<div class="citation">
|
||
<div class="align-left">
|
||
<!-- <input id="cit44150863" type="checkbox" name="cit44150863" value="44150863" class="citation-check"
|
||
|
||
pmid="31374103"
|
||
|
||
>
|
||
<label for="cit44150863">select</label> -->
|
||
</div>
|
||
<div class="ncbi-docsum">
|
||
<span class="authors">
|
||
Hamaneh MB, Yu YK.
|
||
</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/31374103/">
|
||
Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network.
|
||
</a><span class="source">PLoS One</span>.
|
||
|
||
|
||
<span class="pubdate">2019;</span><span class="volume">14</span><span class="issue">(8)</span><span class="pages">:e0220742</span><span>. </span><span class="doi">doi: 10.1371/journal.pone.0220742. </span><span class="pubstatus">eCollection 2019. </span><span class="pmid">PubMed PMID:
|
||
31374103</span><span class="pmcid">; PubMed Central PMCID:
|
||
PMC6677386</span><span>. </span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<br/>
|
||
<div class="citation-wrap">
|
||
<div class="citation">
|
||
<div class="align-left">
|
||
<!-- <input id="cit44150862" type="checkbox" name="cit44150862" value="44150862" class="citation-check"
|
||
|
||
pmid="31499794"
|
||
|
||
>
|
||
<label for="cit44150862">select</label> -->
|
||
</div>
|
||
<div class="ncbi-docsum">
|
||
<span class="authors">
|
||
Yu YK.
|
||
</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/31499794/">
|
||
Electrostatics of charged dielectric spheres with application to biological systems. II. A formalism bypassing Wigner rotation matrices.
|
||
</a><span class="source">Phys Rev E</span>.
|
||
|
||
|
||
<span class="pubdate">2019 Jul;</span><span class="volume">100</span><span class="issue">(1-1)</span><span class="pages">:012401</span><span>. </span><span class="doi">doi: 10.1103/PhysRevE.100.012401. </span><span class="pmid">PubMed PMID:
|
||
31499794</span><span>. </span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<br/>
|
||
<div class="citation-wrap">
|
||
<div class="citation">
|
||
<div class="align-left">
|
||
<!-- <input id="cit44150864" type="checkbox" name="cit44150864" value="44150864" class="citation-check"
|
||
|
||
pmid="30908818"
|
||
|
||
>
|
||
<label for="cit44150864">select</label> -->
|
||
</div>
|
||
<div class="ncbi-docsum">
|
||
<span class="authors">
|
||
Ogurtsov AY, Alves G, Yu YK.
|
||
</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/30908818/">
|
||
RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment.
|
||
</a><span class="source">Proteomics</span>.
|
||
|
||
|
||
<span class="pubdate">2019 Jul;</span><span class="volume">19</span><span class="issue">(14)</span><span class="pages">:e1800367</span><span>. </span><span class="doi">doi: 10.1002/pmic.201800367. </span><span class="pmid">PubMed PMID:
|
||
30908818</span><span class="pmcid">; PubMed Central PMCID:
|
||
PMC6635056</span><span>. </span>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<h3><a href="https://www.ncbi.nlm.nih.gov/myncbi/yi-kuo.yu.2/bibliography/public/">More</a></h3>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
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|
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