-
Notifications
You must be signed in to change notification settings - Fork 9
Expand file tree
/
Copy pathindex.html
More file actions
310 lines (272 loc) · 13.9 KB
/
index.html
File metadata and controls
310 lines (272 loc) · 13.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml"
xmlns:og="http://ogp.me/ns#"
xmlns:fb="https://www.facebook.com/2008/fbml">
<head>
<title>Research - Beatson Microbial Genomics Lab</title>
<!-- Using the latest rendering mode for IE -->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="/images/favicon.png" rel="icon">
<!-- Open Graph tags -->
<meta property="og:site_name" content="Beatson Microbial Genomics Lab" />
<meta property="og:type" content="article"/>
<meta property="og:title" content="Research"/>
<meta property="og:url" content="/"/>
<!-- Bootstrap -->
<link rel="stylesheet" href="/theme/css/bootstrap.yeti.min.css" type="text/css"/>
<link href="/theme/css/font-awesome.min.css" rel="stylesheet">
<link href="/theme/css/pygments/native.css" rel="stylesheet">
<link rel="stylesheet" href="/theme/css/style.css" type="text/css"/>
</head>
<body>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-ex1-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a href="/" class="navbar-brand">
Beatson Microbial Genomics Lab </a>
</div>
<div class="collapse navbar-collapse navbar-ex1-collapse">
<ul class="nav navbar-nav">
<li><a href="/pages/Anne">
</a></li>
<li><a href="/pages/Areej">
</a></li>
<li><a href="/pages/Brian">
</a></li>
<li><a href="/pages/Bryan">
</a></li>
<li><a href="/pages/Kirstin">
</a></li>
<li><a href="/pages/Leah">
</a></li>
<li><a href="/pages/Marisa">
</a></li>
<li><a href="/pages/Melinda">
</a></li>
<li><a href="/pages/MitchS">
</a></li>
<li><a href="/pages/MitchSC">
</a></li>
<li><a href="/pages/Nabil">
</a></li>
<li><a href="/pages/Nhu">
</a></li>
<li><a href="/pages/Nouri">
</a></li>
<li><a href="/pages/Scott">
</a></li>
<li><a href="/pages/data.html">
Data
</a></li>
<li><a href="/pages/people.html">
People
</a></li>
<li><a href="/pages/projects.html">
Projects
</a></li>
<li><a href="/pages/publications.html">
Publications
</a></li>
<li class="active"><a href="/">
Research
</a></li>
<li><a href="/pages/software.html">
Software
</a></li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li><a href="/archives.html"><i class="fa fa-th-list"></i><span class="icon-label">Archives</span></a></li>
</ul>
</div>
<!-- /.navbar-collapse -->
</div>
</div> <!-- /.navbar -->
<div class="container">
<div class="row">
<div class="col-sm-9">
<section id="content" class="body">
<h1 class="entry-title">Research</h1>
<div class="entry-content">
<img alt="Beatson Lab Group logo" src="/images/bl_logo.png" />
<p>The Beatson group aims to better understand the molecular mechanisms of
infectious disease and identify potential therapeutic and diagnostic targets by
exploiting “Next-gen” genomic data. We aim to exploit next-generation DNA sequencing
to better understand how medically important bacteria cause disease, become resistant
to antibiotics and disseminate globally. Our major focus is the role of mobile genetic
elements in the evolution of virulence and antimicrobial resistance amongst pathogens
such as <em>Escherichia coli</em>, <em>Streptococcus pyogenes</em>, and <em>Pseudomonas aeruginosa</em>. Our
group develops new computational approaches for the rapid analysis of bacterial genome
data from the latest sequencing technologies.</p>
<p>Current projects range from researching fundamental questions such as “how has
<em>Escherichia coli</em> pathogenesis evolved?” and "how are genes transferred
between bacteria?" to the identification of potential diagnostic and vaccine
targets and the development of software tools to enable integrated analysis of
100’s or 1000’s of bacterial genomes.</p>
<div class="section" id="recent-research-highlights">
<h2>Recent research highlights</h2>
<p><strong>NHMRC Funding</strong></p>
<p>Congratulations to Dr Scott Beatson on being awarded a Level 2 NHMRC Career
Development Fellowship. The project was titled "Bacterial Pathogenomics:
whole-genome sequencing to investigate infection transmission, pathogenesis
and antibiotic resistance". A total of $455 452 was awarded and will begin
in 2015.</p>
<p><strong>Complete genome of representative ST131 strain</strong></p>
<p>We determined the complete genome sequence of Escherichia coli EC958: a high
quality reference sequence for the globally disseminated multidrug resistant
E. coli O25b:H4-ST131 clone. We used a 3rd generation sequencing technology,
PacBio SMRT sequencing to determine this genome and associated plasmids.
We declare that "Large discrepancies between ST131 genomes are likely due to
misassembly of E. coli NA114". [<a class="reference external" href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0104400">Link</a>]</p>
<p><strong>Escherichia coli ST131</strong></p>
<p>In April 2014 we had a large scale study of <em>E coli</em> ST131 <a class="reference external" href="http://www.pnas.org/content/early/2014/03/28/1322678111.abstract">published</a> in PNAS.
We wrote a <a class="reference external" href="http://beatsonlab.com/PNAS_ST131_2014.html">blog post</a> about the importance of this study. Both <a class="reference external" href="http://www.uq.edu.au/news/article/2014/04/evolving-superbug-threatens-create-infection-tsunami">UQ News</a>
and <a class="reference external" href="https://au.news.yahoo.com/video/watch/22383656/researchers-declare-war-on-superbugs/">7 News</a> presented a news articles about this study. The data is
available on <a class="reference external" href="https://github.com/BeatsonLab-MicrobialGenomics/ST131_99">GitHub</a>.</p>
</div>
<div class="section" id="collaborations">
<h2>Collaborations</h2>
<p><strong>National:</strong> Prof Mark Schembri (UQ), Prof Mark Walker (UQ), A/Prof Andrew
Barnes (UQ), A/Prof Mark Turner (UQ), A/Prof Glen Ulett (Griffith), Dr Kari Gobius
(CSIRO), Prof David Paterson (UQ), Prof Scott Bell (QHealth/QIMRB), A/Prof Claire
Wainwright (QHealth), Prof Elizabeth Hartland (UMel), Prof James Paton (UAdelaide),
Dr Paul Bartley (Wesley Hospital), A/Prof Darren Trott (UAdelaide), Dr Nick West (UQ).</p>
<p><strong>International:</strong> A/Prof Mat Upton (Manchester), Prof David Gally (Edinburgh),
Dr Andrew Roe (Glasgow), Prof Tim Walsh (Cardiff), Dr Kok Gan Chan (Malaysia),
Prof Ian Henderson (Birmingham), Dr Tim Dallman (PHE).</p>
<p><strong>Read more about our research in our</strong> <a class="reference external" href="http://beatsonlab-microbialgenomics.github.io/archives">blog</a>.</p>
<p><strong>Have a look at some</strong> <a class="reference external" href="http://beatsonlab-microbialgenomics.github.io/photos.html">photos</a> <strong>of recent activities</strong>.</p>
</div>
<div class="section" id="available-projects">
<h2>Available projects</h2>
<dl class="docutils">
<dt>Briefly, projects include:</dt>
<dd><ul class="first last simple">
<li>Developing software for Next-Gen bacterial genome and meta-genome
assembly, annotation and analysis</li>
<li>Investigating the role of positive selection in the evolution of
bacterial pathogenesis</li>
<li>Genomic epidemiology: investigating outbreaks using genome sequencing</li>
<li>Reverse vaccinology: identifying candidate bacterial vaccine candidates</li>
<li>Investigating the role of bacteriophage in mobilizing virulence genes</li>
<li>PacBio SMRT genome assembly and methylome analysis</li>
<li>Antibiotic resistance and virulence gene profiling from Illumina sequence data</li>
</ul>
</dd>
<dt>We have ongoing projects to study the the following organisms:</dt>
<dd><ul class="first last simple">
<li><em>Escherichia coli</em> ST131 and other global pandemic E. coli sequence types</li>
<li>Carbapenem Resistant <em>Enterobacteriaceae</em> (CRE)</li>
<li><em>Pseudomonas aeruginosa</em></li>
<li>Group A and Group B <em>Streptococcus</em></li>
<li><em>Mycobacterium tuberculosis</em></li>
</ul>
</dd>
</dl>
<p><cite>More information on projects <|filename|Projects.rst></cite></p>
<p>Please contact Scott directly (scott dot beatson at uq.edu.au) to enquire about specific opportunities
for Undergraduate, Masters, Honours or PHD projects at The University of Queensland.</p>
</div>
</div>
</section>
</div>
<div class="col-sm-3 well well-sm" id="sidebar">
<aside>
<section>
<ul class="list-group list-group-flush">
<li class="list-group-item"><h4><i class="fa fa-github fa-lg"></i><span class="icon-label">Activity @GitHub</span></h4>
<div id="gh_repos">
<p class="list-group-item">Status updating...</p>
</div>
</li>
<li class="list-group-item"><h4><i class="fa fa-external-link-square fa-lg"></i><span class="icon-label">Links</span></h4>
<ul class="list-group" id="links">
<li class="list-group-item">
<a href="https://github.com/organizations/BeatsonLab-MicrobialGenomics" target="_blank">
Code on GitHub
</a>
</li>
<li class="list-group-item">
<a href="http://staff.scmb.uq.edu.au/staff/scott-beatson" target="_blank">
SCMB@UQ
</a>
</li>
<li class="list-group-item">
<a href="http://sourceforge.net/projects/brig/" target="_blank">
BRIG
</a>
</li>
<li class="list-group-item">
<a href="http://easyfig.sourceforge.net" target="_blank">
EasyFig
</a>
</li>
<li class="list-group-item">
<a href="http://github.com/mscook/SeqFindR" target="_blank">
SeqFindR
</a>
</li>
</ul>
</li>
</ul>
</section>
</aside> </div>
</div>
</div>
<footer>
<div class="container">
<hr>
<div class="row">
<div class="col-xs-10">© 2014 Beatson Group
· Powered by <a href="https://github.com/DandyDev/pelican-bootstrap3" target="_blank">pelican-bootstrap3</a>,
<a href="http://docs.getpelican.com/" target="_blank">Pelican</a>,
<a href="http://getbootstrap.com" target="_blank">Bootstrap</a> </div>
<div class="col-xs-2"><p class="pull-right"><i class="fa fa-arrow-up"></i> <a href="#">Back to top</a></p></div>
</div>
</div>
</footer>
<script src="http://code.jquery.com/jquery.js"></script>
<!-- Include all compiled plugins (below), or include individual files as needed -->
<script src="/theme/js/bootstrap.min.js"></script>
<!-- Enable responsive features in IE8 with Respond.js (https://github.com/scottjehl/Respond) -->
<script src="/theme/js/respond.min.js"></script>
<script type="text/javascript">
$(document).ready(function () {
if (!window.jXHR) {
var jxhr = document.createElement('script');
jxhr.type = 'text/javascript';
jxhr.src = '/theme/js/jXHR.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(jxhr, s);
}
github.showRepos({
user: 'BeatsonLab-MicrobialGenomics',
count: 3,
skip_forks: true,
target: '#gh_repos'
});
});
</script>
<script src="/theme/js/github.js" type="text/javascript"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-49094461-1']);
_gaq.push(['_trackPageview']);
(function () {
var ga = document.createElement('script');
ga.type = 'text/javascript';
ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>