-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathTeam.html
428 lines (393 loc) · 22 KB
/
Team.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
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
<!DOCTYPE HTML>
<!--
Iridium by TEMPLATED
templated.co @templatedco
Released for free under the Creative Commons Attribution 3.0 license (templated.co/license)
-->
<html>
<head>
<title>Danko Lab</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="" />
<meta name="keywords" content="" />
<link href='http://fonts.googleapis.com/css?family=Arimo:400,700' rel='stylesheet' type='text/css'>
<!--[if lte IE 8]><script src="js/html5shiv.js"></script><![endif]-->
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.0/jquery.min.js"></script>
<script src="js/skel.min.js"></script>
<script src="js/skel-panels.min.js"></script>
<script src="js/init.js"></script>
<noscript>
<link rel="stylesheet" href="css/skel-noscript.css" />
<link rel="stylesheet" href="css/style.css" />
<link rel="stylesheet" href="css/style-desktop.css" />
</noscript>
<!--[if lte IE 8]><link rel="stylesheet" href="css/ie/v8.css" /><![endif]-->
<!--[if lte IE 9]><link rel="stylesheet" href="css/ie/v9.css" /><![endif]-->
</head>
<body class="no-sidebar">
<!-- Header -->
<div id="header">
<div class="container">
<!-- Logo -->
<div id="logo">
<h1><a href="#">Danko Lab</a></h1>
<!--<span>Website coming soon!</span>-->
</div>
<!-- Nav -->
<nav id="nav">
<ul>
<li><a href="index.html">Homepage</a></li>
<li><a href="Research.html">Research</a></li>
<li class="active"><a href="Team.html">Team</a></li>
<li><a href="Publications.html">Publications</a></li>
<li><a href="Software.html">Software</a></li>
<li><a href="Contact.html">Find Us</a></li>
</ul>
</nav>
</div>
</div>
<!-- Main -->
<div id="main">
<div class="container">
<div class="row">
<!-- Content -->
<div id="content" class="12u skel-cell-important">
<div class="container">
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Charles.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Charles Danko</h2>
<p>Associate Professor</p>
<p>Charles is an assistant professor at the Baker Institute and the College of Veterinary Medicine, Cornell University. His research is focused on understanding gene regulation using methods from molecular biology and genetics, computer science, statistics, and machine learning. Learn about active research projects in the <a href="Research.html">Research page</a>.</p>
<div class="row">
<a href="https://bsky.app/profile/charlesdanko.bsky.social" class="bluesky-follow-button"><img src="images/Bluesky.png"/>@charlesdanko.bsky.social</a>
<a href="files/Danko-CV.pdf">CV</a>
</div>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Ed.jpg" alt="" /></a>
<BR>
</div>
<div class="8u">
<h2>Ed Rice</h2>
<p>Laboratory Manager</p>
<p>Ed is a professional laboratory manager, with over 20 years of molecular biology experience. As the lead bench scientist, Ed has his hands in virtually every project in the Danko lab. He has a particular scientific interest in understanding the molecular pathways underlying autoimmune disorders.</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/AdamHe.png" alt="" /></a>
</div>
<div class="8u">
<h2>Adam He</h2>
<p>Computational Biology Graduate Student</p>
<p>Adam is a graduate student in the Computational Biology program at Cornell. He is interested in both the application of machine learning methods to understanding transcriptional regulation and, more broadly, the role that transcriptional regulators play in development and evolution. </p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Brent.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Brent Basso</h2>
<p>Computational Biology Graduate Student</p>
<p>Brent received his bachelor's degree from the University of Rhode Island and then spent two years teaching middle school science at the Bay View Academy in Riverside, RI. After my time as a teacher, I received a master's degree from the University of Connecticut where I worked in the labs of Dr. Sarah Hird and Dr. Charlie Giardina before moving to the Boston area for a job. There I developed sequencing based quality control methods for Sarepta, a gene therapy company.<BR>
My project in the Lis and Danko labs combines new sequencing methods and novel analytical techniques to examine the evolution of divergent noncoding transcription and the behavior of RNA Polymerase II at divergent promoters.<BR>
Outside of the lab, I am active in the local rowing community and love spending time on the water or hiking with my partner Ally and our dogs Marty and Lucy</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Banseok.png" alt="" /></a>
</div>
<div class="8u">
<h2>Banseok Lee</h2>
<p>GG&D Graduate Student</p>
<p>Banseok is a graduate student in the Genetics, Genomics, and Development program at Cornell. His research interest lies in the dynamics of transcriptional regulation during spermatogenesis and how it is associated with the phenotypic differences between species. He is trying to tackle these intriguing questions using wet lab techniques and computational tools.</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Nating.JPG" alt="" /></a>
</div>
<div class="8u">
<h2>Nating Wang</h2>
<p>Computational Biology Graduate Student</p>
<p>Nating Wang received an M.S. in Statistics from Yale University. She is developing BayesPrism as a deconvolution tool for spatial and multiomic data, with extensions that enable integration of bulk and single-cell datasets across different modalities.</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Anita.JPG" alt="" /></a>
</div>
<div class="8u">
<h2>Anita Rogic</h2>
<p>GG&D Graduate Student</p>
<p>Anita is a graduate student in the Genetics, Genomics, and Development program. She worked at the Ichan School of Medicine at Mount Sinai (NYC) studying the mechanisms of inflammatory breast cancer and its treatment in mouse xenograft models. She is currently interested in applying machine learning methods to uncover the regulatory syntax that governs gene expression and identifying causal SNPs associated with autoimmunity.</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Saloni.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Saloni Dhopte</h2>
<p>GG&D Graduate Student</p>
<p>Saloni is a graduate student in Genetics, Genomics and Development. She completed her undergraduate education at the University of California, Davis where she studied R-loops and their role in causing genome instability. Now at Cornell, she is co-advised by Dr. Paula Cohen, and is interested in the mechanisms of transcriptional regulation throughout spermatogenesis.</p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/anon.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Ameen Haj Yahia</h2>
<p>GG&D Graduate Student</p>
<p>Ameen is a new graduate student working jointly in the Danko and Lammerding labs to study how cell compression alters gene expression through changes in chromatin and nuclear packaging.</p>
</div>
</div>
<BR><BR>
<header><span class="subsectit">Lab Alumni</span></header>
<BR><BR>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Gilad_IMG-20190401-WA0003.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Gilad Barshad</h2>
<p>Postdoctroal Associate, 2019-2024</p>
<p>Gilad received his PhD from Ben Gurion University, Beer-Sheva, Israel in 2019. During his PhD Gilad studied the mitochondrial-nuclear co-regulation of gene expression. Looking through an evolutionary lens, Gilad now hopes to shed new light on the relationship between genomic architecture and transcriptional regulation.<BR><BR>
Current position: <a title="[Barshad Lab]" href=https://barshadlab.net.technion.ac.il/>Assistant Professor, Technion</a><BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Barshad+G%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/BlaineHarlan.png" alt="" /></a>
</div>
<div class="8u">
<h2>Blaine Harlan</h2>
<p>Postdoctroal Associate, 2021-2023</p>
<p>Blaine earned her PhD from Cornell University performing scATAC-seq data collection, analysis, and technology development. Blaine's interest is currently in tech development of single cell genomic assays and applications in cancer and germ cell development.<BR><BR>
Current position: Postdoctoral Associate, Yale University<BR> </p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/jlama.jpeg" alt="" /></a>
</div>
<div class="8u">
<h2>Jyoti Lama</h2>
<p>Postdoctroal Associate, 2021-2023</p>
<p>Jyoti completed her PhD from University of Houston studying host tolerance to transposable elements. Jyoti's focus in the Danko and Cohen labs is to understand how changes in transcription and chromatin influence germ cell development.<BR><BR>
Current position: Bioinformatics Scientist at Mass. Eye and Ear, Harvard medical school<BR> </p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/A.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Alexandra Chivu</h2>
<p>GG&D Graduate Student, 2019-2023</p>
<p>Alex worked at the Genome Institute of Singapore (GIS) & Medical Research Council (MRC), London studying transcription bursts and epigenetic regulation in cancer and immunity. Currently Alex is interested in understanding the impact of chromatin architecture on transcriptional regulation, as well as developing new RNA-based technologies.<BR><BR>
Current position: Associate, Flagship Pioneering<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Chivu+AG%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Jon.DSC_0443.JPG" alt="" /></a>
</div>
<div class="8u">
<h2>Jon Villanueva</h2>
<p>Biomedical and Biological Sciences Graduate Student, 2018-2023</p>
<p>Jonathan Villanueva is a graduate student in the Biomedical and Biological Sciences program at Cornell. He is interested in utilizing dry and wet lab techniques to identify how specific mutational combinations alter the gene regulatory mechanisms (enhancers and miRNAs) that drive colon cancer development.<BR><BR>
Current position: Postdoctoral Scholar, Spence lab, University of Michigan<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Villanueva+JW%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/JJL-IMG.png" alt="" /></a>
</div>
<div class="8u">
<h2>James Lewis</h2>
<p>Postdoctroal Associate, 2016-2021</p>
<p>James received his postdoc from Bob Reed at Cornell. James is interested in understanding the molecular basis of evolutionary adaptation, especially for traits driven by cis-regulatory changes. </p>
Current position: <a title="[Lewis Lab]" href=https://jameslewislab.com/>Assistant Professor, Clemson University</a><BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Lewis+JJ%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Shao-Pei_Chou.JPG" alt="" /></a>
</div>
<div class="8u">
<h2>Shao-Pei Chou</h2>
<p>GG&D Graduate Student, 2016-2021</p>
<p>Shao-Pei is a graduate student in the Genetics, Genomics, and Development program at Cornell. She likes to develop new computational methods that can better tackle the problems and provide a different perspectives to examine the biological data. Here is a method she developed recently: <a href=": https://www.biorxiv.org/content/early/2018/08/10/389262">AlleleHMM</a>. Her current project is to identify genomic factors that play a role in transcription regulation using allele-specific analysis.</p>
Current position: Computational Biologist, Ginkgo Bioworks<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Chou+SP%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Adriana-Wide.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Adriana Alexander</h2>
<p>Biomedical and Biological Sciences Graduate Student, 2017-2021</p>
<p>Adriana is a graduate student in the Biological and Biomedical Sciences Program at Cornell. She is interested in understanding the mechanisms controlling transcriptional inactivation during spermatogenesis using a combination of wet lab and computational tools.</p>
Current position: Consumer Safety Officer, FDA<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Alexander+AK%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Mridu.JPG" alt="" /></a>
</div>
<div class="8u">
<h2>Mridusmita Saikia</h2>
<p>Postdoctroal Associate, 2016-2020</p>
<p>A biochemist by training, Mridu received her PhD from University of Chicago in 2009, where she studied the role of posttranscriptional modifications present in cellular RNA. During her postdoctoral training she continued to study the non-coding RNAs, and their function in gene expression control, especially in the context of human diseases. Mridu is now making her debut into single cell genomics, her goal is to establish a single cell RNA sequencing technology, and adapt that technology to study canine immune cells. </p>
Current position: Lecturer, Biomedical Engineering, Cornell University<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Saikia+M%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Lauren.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Lauren Choate</h2>
<p>GG&D Graduate Student, 2015-2020</p>
<p>Lauren is a graduate student in the Genetics, Genomics, and Development program at Cornell. She is interested in understanding the role of disease risk alleles on transcriptional regulation in autoimmunity using computational and wet lab techniques.</p>
Current position: Cytogeneticist, Brigham and Women's Hospital<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Choate+LA%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Paul.Munn.roto_tiller.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Paul Munn</h2>
<p>Computational Biology Graduate Student, 2016-2020</p>
<p>Paul is a graduate student in the Computational Biology program at Cornell. He is interested in both developing machine learning techniques to aid in the identification of transcription unit boundaries, and in improving our understanding of chromatin structure and how it affects gene regulation.</p>
Current position: Computational Biologist, TREx core, Cornell University<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Munn+PR%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/zhongwang_2014.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Zhong Wang</h2>
<p>Programer, Research Associate, 2015-2019</p>
<p>Zhong Wang arrived at Cornell University with 6 years of experience in Statistical Genetics and Biostatistics. He conducted postdoctoral training at Penn State College of Medicine and Yale School of Public Health, where he worked in the areas of statistical modeling and software development. <BR><BR>
Current position: Professor, Dalian University of Technology, China<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Wang+Z%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
<div class="row">
<div class="4u">
<a href="#" class="image team"><img src="images/Tinyi.jpg" alt="" /></a>
</div>
<div class="8u">
<h2>Tinyi Chu</h2>
<p>Croucher Foundation Graduate Fellow, 2014-2019</p>
<p>Tinyi is a graduate student in the Computational Biology program at Cornell and a scholar of the <a href="http://scholars.croucher.org.hk/scholars/tinyi-chu">Croucher Foundation</a>. He is actively working on developing bioinformatic tools for analyzing PRO-seq data, and is broadly interested in understanding how the rewiring of transcriptional regulatory networks plays a role in oncogenesis.<BR><BR>
Current position: Postdoc (Dana Pe'er), Memorial Sloan Kettering Cancer Center, New York<BR>
<a title="[PubMed]" href=https://pubmed.ncbi.nlm.nih.gov/?term=%22danko+cg%22%5Bau%5D+%22Chu+T%22%5Bau%5D&sort=date>Danko lab publications.</a></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Footer -->
<div id="footer">
<div class="container">
<div class="row">
<div class="4u">
<section>
<h2>Danko Lab</h2>
<ul class="contact">
<li>
<span class="mail">E-Mail</span>
<span>
<script type="text/javascript" language="Javascript">// <![CDATA[Hide script from non-javascript-enabled browsers
var username="dankoc";
var at="@";
var domain="gmail.com";
document.write("<a href='mailto:" +username+""+at+""+domain+ "'>" + username+""+at+""+domain + "</a>");
</script>
</span>
</li>
<li>
<span class="mail">Social</span>
<a href="https://bsky.app/profile/charlesdanko.bsky.social"><img src="images/Bluesky.png" alt="" /></a>
<a href="https://github.com/danko-lab"><img src="images/github.png" alt="" /></a>
<img src="images/Fist.png" alt="" />
</li>
<li>
<span class="address">Address</span>
<span>
The Baker Institute for Animal Health<br />
College of Veterinary Medicine <br />
Cornell University <br />
Hungerford Hill Road<br />
Ithaca, NY 14853
</span>
</li>
</ul>
</section>
</div>
<div class="4u">
<section>
<h2>Cornell University</h2>
<ul class="default">
<li><a href="https://www2.vet.cornell.edu/departments-centers-and-institutes/baker-institute">The Baker Institute</a></li>
<li><a href="http://www.vet.cornell.edu/biosci/">Department of Biomedical Sciences</a></li>
<li><a href="http://www.vet.cornell.edu/">College of Veterinary Medicine</a></li>
<li><a href="http://www.cb.cornell.edu/">Computational Biology Graduate Program</a></li>
<li><a href="http://www.cornell.edu">Cornell University</a></li>
</ul>
</section>
</div>
<div class="4u">
<section>
<h2>Join the lab!</h2>
<ul class="contact">
<li>
<span>We welcome exceptionally talented scientists from any country or ethnicity.</span>
</li>
<li>
<span class="mail">Postdocs:</span>
<span>E-mail a 1 page cover letter, a curriculum vitae, and 3 letters of reference to Charles Danko.</span>
</li>
<li>
<span class="mail">Students:</span>
<span>Apply through the graduate fields of <a href="http://www.cb.cornell.edu/">Computational Biology</a> or <a href="http://www.gendev.cornell.edu/">Genetics, Genomics & Development</a>.</span>
</li>
</ul>
</section>
</div>
</div>
</div>
</div>
<!-- Copyright -->
<div id="copyright">
<div class="container">
Design: <a href="http://templated.co">TEMPLATED</a>
</div>
</div>
</body>
</html>