-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
325 lines (319 loc) · 26 KB
/
index.html
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
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Computational Biology Department - School of Computer Science - Carnegie Mellon University</title>
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/black.css">
<!-- Theme used for syntax highlighting of code -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h4><b>School of Computer Science</b><br>Computational Biology Department</h4>
<div style="width:45%; float:left;">
<img src="images/about/help.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">For any general questions contact us: </p>
<p style="font-size:25px; text-align:justify; margin:10px 0;">help@cbd.cmu.edu</p>
</div>
</section>
<section>
<h4><b>School of Computer Science</b><br>Computational Biology Department</h4>
<div style="width:45%; float:left;">
<img src="images/about/computing.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">For questions about the available computing resources in our department contact us: </p>
<p style="font-size:25px; text-align:justify; margin:10px 0;">
computing@cbd.cmu.edu
</p>
</div>
</section>
<section>
<h4><b>School of Computer Science</b> Computational Biology Department</h4>
<div style="width:45%; float:left;">
<img src="images/about/info.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:20px; text-align:justify; margin:10px 0;">7725 Gates-Hillman Complex</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">5000 Forbes Avenue </p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">Pittsburgh, PA 15213</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">(412) 268-2474</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">help@cbd.cmu.edu</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">http://cbd.cmu.edu</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">http://www.facebook.com/cmucbd</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">http://twitter.com/cmucompbio</p>
<p style="font-size:20px; text-align:justify; margin:10px 0;">http://www.instagram.com/cmucbd</p>
</div>
</section>
<section>
<h4>Carnegie Mellon Ranked First in publications in highly-selective Computational Biology conferences</h4>
<p style="font-size:20px;">October 18, 2017</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide1.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Based on analysis by csrankings.org, Carnegie Mellon is the front-runner in computational biology. The rankings are based upon accepted proceedings papers at the top computational biology conferences, ISMB and RECOMB. These conferences typically accept only around 15% of submitted papers and the number of accepted papers over many years is a strong indication of Carnegie Mellon’s leadership in framing novel biomedical research questions in computational terms and developing rigorous and scalable solutions. Carnegie Mellon was also ranked first across all of computer science, consistent with many other ranking metrics.</p>
</div>
</section>
<section>
<h4>Computational Biology Guarantees Research Experience for Undergrads</h4>
<p style="font-size:20px;">October 30, 2017</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide2.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Doing undergraduate research for credit has long been an option exercised at Carnegie Mellon and other universities, but the Computational Biology Department has gone a step further and is guaranteeing that all students in its new undergraduate degree program will be able to pursue a semester-long research experience should they wish to.“Our faculty want to make it a central feature of our program,” said Phillip Compeau, assistant department head for education. “We believe this will be a way to attract students,” he added, noting computational biology majors may be particularly interested in research compared to other students in the School of Computer Science.</p>
</div>
</section>
<section>
<h4>CMU Software Assembles RNA Transcripts More Accurately</h4>
<p style="font-size:20px;">November 13, 2017</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide3.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Computational biologists at Carnegie Mellon University have developed a more accurate computational method for reconstructing the full-length nucleotide sequences of the RNA products in cells, called transcripts, that transform information from a gene into proteins or other gene products.
Their software, called Scallop, will help scientists build a more complete library of RNA transcripts and thus help scientists better understand the regulation of gene expression.
A report on Scallop by Carl Kingsford, associate professor of computational biology, and Mingfu Shao, Lane Fellow in the School of Computer Science’s Computational Biology Department, is being published online today by the journal Nature Biotechnology.</p>
</div>
</section>
<section>
<h4>The Computational Biology Department Undergraduate Program Welcomes Two New Students</h4>
<p style="font-size:20px;">November 14, 2017</p>
<table>
<tr style="align-content: center;">
<td style="margin:auto; border:none; text-align: center;"><img src="images/newsitem/slide4a.png" style="width:45%; margin:auto;" /></td>
<td style="margin:auto; border:none; text-align: center;"><img src="images/newsitem/slide4b.png" style="width:45%; margin:auto;" /></td>
</tr>
<tr>
<p style="font-size:18px; text-align:justify; margin:10px 0;">Welcome Doug and Wendy! The Computational Biology Department will be welcoming its first freshman class of School of Computer Science students in the spring.</p>
</tr>
</table>
</section>
<section>
<h4>Natalie Sauerwald awarded Richard King Mellon Foundation Presidential Scholarship in Life Sciences</h4>
<p style="font-size:20px;">December 5, 2017</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide5.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Natalie Sauerwald, a 3rd year Ph.D student, has been awarded the Richard King Mellon Foundation Presidential Scholarship in the Life Sciences. She is a member of Dr. Carl Kingsford’s lab. Congratulations, Natalie!</p>
</div>
</section>
<section>
<h4>Bar-Joseph Appointed to Endowed Chair</h4>
<p style="font-size:20px;">December 8, 2017 </p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide6.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">At a ceremony this week, Professor Ziv Bar-Joseph was appointed FORE Systems Professor of Computational Biology and Machine Learning. Professor Bar-Joseph is a world leader in computational methods for understanding dynamic biological systems, a critical area of research given that our cells and bodies are continuously changing. He joined Carnegie Mellon in 2003 and played an important role in the development of the Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, which he currently directs (with James Faeder from the University of Pittsburgh). He is well known for developing and applying rigorous computational and machine learning methods to biomedical problems. His group has published extensively both in high impact journals and highly competitive conferences. He is also principal investigator (with Gregory Cooper at the University of Pittsburgh) of Big Data for Better Health, a large, multi-investigator project funded by the Pennsylvania Department of Health.</p>
</div>
</section>
<section>
<h4>The Computational Biology Department Sponsored Recent STEM Junction Symposium</h4>
<p style="font-size:20px;">December 12, 2017 </p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide7.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">The Computational Biology Department recently sponsored Fox Chapel Area High School’s STEM Junction Symposium, an all-day bioinformatics event hosting 180 students from the Pittsburgh area. The Symposium was organized by Fox Chapel senior Shania Khatri to introduce high school students with an interest in computer science and biology to the growing field of computational biology. The Symposium is one of the first of its kind for a high school audience, but this did not dissuade Khatri. “I was convinced,’ Khatri says, ‘that there should be opportunities for high school students to explore bioinformatics.”
The students in attendance were able to choose from multiple breakout sessions led by speakers from both Pittsburgh academia and industry. Dr. Robert Murphy, Dr. Carl Kingsford, Dr. Phillip Compeau, and Dr. Hosein Mohimani were among the speakers for these sessions.</p>
</div>
</section>
<section>
<h4>First Year PhD student has first-authored paper accepted</h4>
<p style="font-size:20px;">January 10, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide8.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Xiangrui Zeng, a first year PhD student in the Joint Carnegie Mellon-University of Pittsburgh Ph.D. program (CPCB), has been conducting a research project under the guidance of Dr. Min Xu. His first-authored paper detailing the outcome of this project title “A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation” has been accepted by Journal of Structural Biology.
Congratulations Xiangrui on the outstanding performance!</p>
</div>
</section>
<section>
<h4>Computational Method Speeds Hunt for New Antibiotics</h4>
<p style="font-size:20px;">January 22, 2018 </p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide9.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">A team of American and Russian computer scientists has developed an algorithm that can rapidly search databases to discover novel variants of known antibiotics – a potential boon in fighting antibiotic resistance.
In just a few hours, the algorithm, called VarQuest, was able to identify 10 times more variants of peptidic natural products, or PNPs, than all previous PNP discovery efforts combined, the researchers report in the latest issue of the journal Nature Microbiology. Previously, such a search might have taken hundreds of years of computation, said Hosein Mohimani, assistant professor in Carnegie Mellon University’s Computational Biology Department.
He and Pavel A. Pevzner, professor of computer science at the University of California, San Diego, designed and directed the effort, which included colleagues at St. Petersburg State University in Russia.</p>
</div>
</section>
<section>
<h4>CPCB PhD Student Recognized for Research Progress</h4>
<p style="font-size:20px;">January 25, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide10.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Yang Yang, a third-year PhD student in the Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology (CPCB), joined the Computational Biology Department in January 2016 and has been working on computational genomics. Yang received her B.E. degree in Automation and M.S. degree in Control Science and Engineering both from Tsinghua University in China. In 2015, she joined Dr. Jian Ma’s research group at the University of Illinois at Urbana-Champaign. When Dr. Ma accepted his position with Carnegie Mellon at the beginning of 2016, Yang also transferred to the University.</p>
</div>
</section>
<section>
<h4>New Carnegie Mellon Dynamic Statistical Model Follows Gene Expressions Over Time</h4>
<p style="font-size:20px;">January 29, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide11.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Researchers at Carnegie Mellon University have developed a new dynamic statistical model to visualize changing patterns in networks, including gene expression during developmental periods of the brain.
Published in the Proceedings of the National Academy of Sciences, the model now gives researchers a tool that extends past observing static networks at a single snapshot in time, which is hugely beneficial since network data are usually dynamic. The analysis of network data—or the study of relationships from a large-scale view—is an emerging field of statistics and data science.
Read Full article on CBD website! </p>
</div>
</section>
<section>
<h4>Latest update of MUMmer written by CBD Project Scientist</h4>
<p style="font-size:20px;">January 31, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide12.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Aligning DNA sequences has been and remains one of the fundamental tool in computational biology. It is widely used to compare genomes, to find SNPs and genome variations, and as a step in many other bioinformatics pipelines.
MUMmer, a widely used alignment package in genomics, was originally published in 1999 when the number and the size of available genome sequences was still small. It has been updated a few times since and the third version MUMmer3 remains a very popular genome to genome aligner.<br>
MUMmer4 is the latest update written by Guillaume Marçais, Project Scientist in the Carnegie Mellon Computational Biology Department. It is a backward compatible version with MUMmer3, while being more versatile, being able to handle much larger sequences and faster. MUMmer4 handles genome to genome comparison as well as aligning short and long reads to a reference genome.</p>
</div>
</section>
<section>
<h4>Lane Fellow DeBlasio Publishes Book</h4>
<p style="font-size:20px;">February 5, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide13.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Lane Fellow Dan DeBlasio, along with his PhD advisor John Kececioglu, recently published a book titled “Parameter Advising for Multiple Sequence Alignment”, which details a method to select input-specific parameter choices for the fundamental problem of multiple sequence alignment. Using Parameter Advising can produce higher quality alignments, which leads to improvements in downstream analyses like protein structure prediction, phylogenetic inference, or homology search. The accuracy of multiple sequence alignments can be greatly impacted by choosing non-ideal parameter settings (and in turn the downstream analyses), and while the default parameter settings work well on average, they may produce poor results on some input. The book also describes Facet (short for Feature-based Accuracy Estimator) which when used with Parameter Advising can automatically select improved parameters for any input set of protein sequences.</p>
</div>
</section>
<section>
<h4>Andreas Pfenning Receives Sloan Research Fellowship</h4>
<p style="font-size:20px;">February 15, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/andreas.png" style="height:80%"/>
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Andreas Pfenning, an assistant professor of Computational Biology, develops computational and experimental genomic techniques to study how genetic differences influence complex traits, with a focus on the brain. He applies these techniques across species to study how the genome evolved for speech and language production. His group also studies the genetic mechanisms of Alzheimer’s disease and aging in humans. Pfenning became a faculty member in 2016 after a joint postdoctoral graduate position at MIT and Harvard Medical School. He earned a Ph.D. in computational biology and bioinformatics at Duke University, and a bachelor’s degree in computer science at Carnegie Mellon. He has published a number of high-impact papers in Nature, Science, Cell and the Proceedings of the National Academy of Science.</p>
</div>
</section>
<section>
<h4>Kingsford & Lee publish paper with new method for HLA typing</h4>
<p style="font-size:20px;">March 1, 2018 </p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide14.gif" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Associate Professor Carl Kingsford & Lane Fellow Heewook Lee have published a paper in Genome Biology. The paper discusses the importance of accurate typing of human leukocyte antigen (HLA). HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching approaches and their outputs are inherently limited by the completeness of already known types, making them unsuitable for discovery of novel alleles. Kingsford and Lee have developed a graph-guided assembly technique for classical HLA genes, which can construct allele sequences given high-coverage whole-genome sequencing data. Their method delivers highly accurate HLA typing, comparable to the current state-of-the-art methods.</p>
</div>
</section>
<section>
<h4>Computational Biology Career Directory Launched</h4>
<p style="font-size:20px;">March 20, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide15.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Members of the Computational Biology Department have developed a directory that can be used to search for companies and organizations that provide internships and full-time opportunities to students in computational biology. Students can search for companies of interest by keyword, location, and area of interest. Each company page contains information about the company along with links to Twitter and LinkedIn. A job board will be frequently updated with positions provided by employers, and listing both internal and external opportunities for internships, jobs and summer programs throughout the country.</p>
</div>
</section>
<section>
<h4>Kingsford Group has 2 ISMB 2018 Papers Accepted</h4>
<p style="font-size:20px;">April 3, 2018</p>
<div style="width:45%; float:left;">
<table>
<tr>
<td style="border:none;"><img src="images/newsitem/slide16a.jpg" /></td>
<td style="border:none;"><img src="images/newsitem/slide16b.jpg" /></td>
</tr>
<tr>
<td style="border:none;"><img src="images/newsitem/slide16c.jpg" /></td>
<td style="border:none;"><img src="images/newsitem/slide16d.jpg" /></td>
</tr>
</table>
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Multiple members of Carl Kingsford’s group have had their papers accepted to ISMB 2018.
Natalie Sauerwald and Carl Kingsford’s paper titled Quantifying the similarity of topological domains across normal and cancer human cell types discusses “three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. The second paper, authored by Guillaume Marçais, Dan DeBlasio and Carl Kingsford, is titled Asymptotically optimal minimizers schemes. "From the analysis of the asymptotic behavior of minimizers, forward and local schemes, we show that the previously believed lower bound on minimizers schemes does not hold, and that schemes with density lower than thought possible actually exist."</p>
</div>
</section>
<section>
<h4>Young CMU students succeed in prestigious conference papers</h4>
<p style="font-size:20px;">April 10, 2018</p>
<div style="width:45%; float:left;">
<table>
<tr>
<td style="border:none;"><img src="images/newsitem/slide17a.jpg" /></td>
<td style="border:none;"><img src="images/newsitem/slide17b.jpeg" /></td>
</tr>
<tr>
<td style="border:none;"><img src="images/newsitem/slide17c.png" /></td>
</tr>
</table>
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">Two first year students in our Computational Biology Ph.D. program and one recent graduate of the M.S. in Computational Biology program have had papers accepted for ISMB 2018. Xiangrui Zeng’s paper proposes an integrated method for electron subtomogram averaging and classification called Fast Alignment Maximum Likelihood (FAML). Yixiu Zhao, a third-year undergraduate in Computer Science collaborated on this paper. Both are in Min Xu’s research group. Ruochi Zhang's paper discusses a new machine learning algorithm to demonstrate that sequence-based features can predict if a pair of convergent CTCF motifs would form a chromatin loop. He is in Jian Ma’s group. Jesse Eaton’s paper describes a method to reconstruct the progression of cancers by accumulating genetic variations. Jingyi Wang, a recent graduate of CMU's M.S. Biomedical Engineering program, collaborated on this paper.</p>
</div>
</section>
<section>
<h4>CBD excels again in accepted ISMB papers</h4>
<p style="font-size:20px;">April 11, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide13.png" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">We are very pleased that six papers by members of the Computational Biology Department (CBD) have been accepted for presentation at ISMB 2018, one of the most selective computational biology conferences. ISMB 2018 accepted 65 papers out of a total of 331 submissions. This year’s results continue Carnegie Mellon’s leadership in accepted papers at ISMB that has been ongoing for many years.
The first authors of two of the papers are first-year students in our Computational Biology Ph.D. program and the first author of a third is a recent graduate of our M.S. in Computational Biology program.</p>
</div>
</section>
<section>
<h4>Lane Fellow Mingfu Shao Accepts Faculty Position</h4>
<p style="font-size:20px;">May 17, 2018</p>
<div style="width:45%; float:left;">
<img src="images/newsitem/slide19.jpg" />
</div>
<div style="width:45%; float:right;">
<p style="font-size:18px; text-align:justify; margin:10px 0;">This fall Mingfu Shao, a Lane Fellow in the Computational Biology Department at Carnegie Mellon University, will join Pennsylvania State University as a tenure-track Assistant Professor in the Department of Computer Science and Engineering. He will be co-hired by the Huck Institutes of the Life Sciences, facilitating his interdisciplinary and collaborative research at the interface of computer science and biology. In recognition of his highly impactful work, Mingfu has been awarded the prestigious Charles K. Etner Career Development Professorship in Engineering at Penn State. Mingfu’s recent work as a Lane Fellow with CMU Associate Professor Carl Kingsford has been to design efficient algorithms for high-throughput gene expression analyses. He plans to continue his research on developing new, more efficient algorithms to solve challenging problems in biology in his new position.</p>
</div>
</section>
<section>
<div class="tweet" data-src="https://twitter.com/CMUCompBio/status/997166185031483393"></div>
</section>
</div>
</div>
<script src="lib/js/head.min.js"></script>
<script src="js/reveal.js"></script>
<script>
// More info about config & dependencies:
// - https://github.com/hakimel/reveal.js#configuration
// - https://github.com/hakimel/reveal.js#dependencies
Reveal.initialize({
dependencies: [
{ src: 'plugin/markdown/marked.js' },
{ src: 'plugin/markdown/markdown.js' },
{ src: 'plugin/notes/notes.js', async: true },
{ src: 'plugin/highlight/highlight.js', async: true, callback: function() { hljs.initHighlightingOnLoad(); } },
{ src: 'plugin/embed-tweet/embed-tweet.js' }
]
});
Reveal.configure({
autoSlide: 10000
});
</script>
</body>
</html>