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index.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>index.utf8</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/bootstrap.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Shankar K. Shakya</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="recent.html">Recent News</a>
</li>
<li>
<a href="projects.html">Projects</a>
</li>
<li>
<a href="teaching.html">Teaching</a>
</li>
<li>
<a href="awards.html">Awards and services</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="http://github.com/shankarkshakya">
<span class="fa fa-github"></span>
</a>
</li>
<li>
<a href="https://twitter.com/shakya">
<span class="fa fa-twitter"></span>
</a>
</li>
<li>
<a href="https://www.linkedin.com/in/shankarshakya/">
<span class="fa fa-linkedin"></span>
</a>
</li>
<li>
<a href="https://scholar.google.com/citations?user=qlUOXgEAAAAJ&hl=en">
<span class="fa fa-google"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
</div>
<hr />
<hr />
<p><img src="Shakya_Shankar.jpg" style="width:20%; border:5px solid; margin-left: 20px" align="right"></p>
<div id="about-me" class="section level1">
<h1><strong>About me</strong></h1>
<p>Hi, I am Shankar K. Shakya. I was born and raised in Nepal. I have an undergraduate degree in plant pathology from Tribhuwan University of Nepal. Follwing my graduation, I started teaching in a small college in Nepal. In 2012, I was awarded a fellowship from <a href="https://plantpath.ifas.ufl.edu/">University of Florida</a> (Go Gators) and <a href="https://cipotato.org/">International Potato Center</a> (CIP) to pursue a masters degree in the field of plant pathology. After comletion of my M.S degree, I moved to <a href="https://bpp.oregonstate.edu/">Oregon State University</a> (Go Beavs) to pursue my Ph.D in plant pathology with focus on population genetics, genomics and bioinformatics. I graduated from Oregon State University in 2019.</p>
<p><strong>Currently, I am an associate bioinformatics scientist with <a href="https://www.ballhort.com/">Ball Horticultural Company</a> in West Chicago.</strong></p>
</div>
<div id="appointments" class="section level1">
<h1><strong>Appointments</strong></h1>
<p>Bioinformatics associate scientist (Mar 2020-present): Ball Horticultural Company, West Chicago, IL, USA <br> Research associate (2019-Feb 2020): USDA, Corvallis, OR, USA <br> Graduate research assistant (2014-2019): Oregon State University, USA <br> Graduate teaching assistant (2017-2018): Oregon State University, USA <br> Visiting scholar (2013): International Potato Center (CIP), Ecuador <br> USAID-CIP fellow (2012-2014): University of Florida, USA <br> Horticulture and Plant Pathology instructor (2011-2012): Tribhuvan University, Nepal <br></p>
</div>
<div id="education" class="section level1">
<h1><strong>Education</strong></h1>
<p><strong>Ph.D. Plant Pathology (2019)</strong> <br> Oregon State University, Corvallis, OR, USA <br> <a href="http://grunwaldlab.cgrb.oregonstate.edu/">Grunwald Lab, USDA, ARS</a> <br> Advisor: <a href="https://www.ars.usda.gov/pacific-west-area/corvallis-or/horticultural-crops-research/people/niklaus-grunwald/">Nik Grunwald</a></p>
<p><strong>M.S. Plant Pathology (2014)</strong> <br> University of Florida, Gainesville, FL, USA <br> Advisor: <a href="http://www.epi.ufl.edu/people/faculty-profiles/ariena-h-c-van-bruggen/">Ariena van Bruggen</a> <br> Co-advisor: <a href="https://plantpath.ifas.ufl.edu/faculty/erica-goss/profile/">Erica Goss</a> <br></p>
<p><strong>B.S. Plant Pathology (2010)</strong> <br> Tribhuwan University, Nepal <br></p>
</div>
<div id="teaching" class="section level1">
<h1><strong>Teaching</strong></h1>
<p>Introductory Plant Pathology (BOT 350/550): Fall 2017 <br> Introductory Plant Pathology (BOT 350/550): Fall 2018 <br> <a href="https://shankarkshakya.github.io/geppopgen/">Population genetics and data analyses in R workshop, 2019, Tribhuvan University, Nepal</a>.</p>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>