-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathpublications.html
More file actions
738 lines (629 loc) · 35.1 KB
/
publications.html
File metadata and controls
738 lines (629 loc) · 35.1 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
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
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
<!DOCTYPE html>
<html lang="en"><head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1"><!-- Begin Jekyll SEO tag v2.8.0 -->
<title>Publications | Terhorst lab</title>
<meta name="generator" content="Jekyll v3.9.2" />
<meta property="og:title" content="Publications" />
<meta property="og:locale" content="en_US" />
<link rel="canonical" href="https://jthlab.github.io/publications.html" />
<meta property="og:url" content="https://jthlab.github.io/publications.html" />
<meta property="og:site_name" content="Terhorst lab" />
<meta property="og:type" content="website" />
<meta name="twitter:card" content="summary" />
<meta property="twitter:title" content="Publications" />
<script type="application/ld+json">
{"@context":"https://schema.org","@type":"WebPage","headline":"Publications","url":"https://jthlab.github.io/publications.html"}</script>
<!-- End Jekyll SEO tag -->
<link rel="stylesheet" href="/assets/main.css"><link type="application/atom+xml" rel="alternate" href="https://jthlab.github.io/feed.xml" title="Terhorst lab" /><script type="text/javascript">
function toggle(id) {
var x = document.getElementById(id);
if (x.style.display === "none") {
x.style.display = "block";
} else {
x.style.display = "none";
}
}
</script>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/katex.min.css" integrity="sha384-AfEj0r4/OFrOo5t7NnNe46zW/tFgW6x/bCJG8FqQCEo3+Aro6EYUG4+cU+KJWu/X" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/katex.min.js" integrity="sha384-g7c+Jr9ZivxKLnZTDUhnkOnsh30B4H0rpLUpJ4jAIKs4fnJI+sEnkvrMWph2EDg4" crossorigin="anonymous"></script>
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.12.0/dist/contrib/auto-render.min.js" integrity="sha384-mll67QQFJfxn0IYznZYonOWZ644AWYC+Pt2cHqMaRhXVrursRwvLnLaebdGIlYNa" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
<body><header class="site-header" role="banner">
<div class="wrapper"><a class="site-title" rel="author" href="/">Terhorst lab</a><nav class="site-nav">
<input type="checkbox" id="nav-trigger" class="nav-trigger" />
<label for="nav-trigger">
<span class="menu-icon">
<svg viewBox="0 0 18 15" width="18px" height="15px">
<path d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.032C17.335,0,18,0.665,18,1.484L18,1.484z M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.032C17.335,6.031,18,6.696,18,7.516L18,7.516z M18,13.516C18,14.335,17.335,15,16.516,15H1.484 C0.665,15,0,14.335,0,13.516l0,0c0-0.82,0.665-1.483,1.484-1.483h15.032C17.335,12.031,18,12.695,18,13.516L18,13.516z"/>
</svg>
</span>
</label>
<div class="trigger"><a class="page-link" href="/group.html">Group members</a><a class="page-link" href="/news.html">News</a><a class="page-link" href="/publications.html">Publications</a><a class="page-link" href="/teaching.html">Teaching</a></div>
</nav></div>
</header>
<main class="page-content" aria-label="Content">
<div class="wrapper">
<article class="post">
<header class="post-header">
<h1 class="post-title">Publications</h1>
</header>
<div class="post-content">
<p>The most up-to-date listing of our papers can be found on <a href="https://scholar.google.com/citations?user=wmo0gh0AAAAJ&hl=en">Jonathan’s Google Scholar page</a>.</p>
<h3 id="preprints">Preprints</h3>
<p>In various stages of revision:</p>
<ol class="bibliography"><li><span id="jin2023the-solution">Jin Y, Terhorst J. The solution surface of the Li-Stephens haplotype copying model. Algorithms for Molecular Biology. 2023;18: 12. doi:10.1186/s13015-023-00237-z</span>
[<a href="https://dx.doi.org/10.1186/s13015-023-00237-z">link</a>]
[<a href="#" onclick="toggle('jin2023the-solutionbibtex'); return false;">bibtex</a>]<pre id="jin2023the-solutionbibtex" style="display:none">@article{jin2023the-solution,
author = {Jin, Yifan and Terhorst, Jonathan},
author+an = {1=bold},
date = {2023-08-09},
date-added = {2023-08-09 11:07:39 -0400},
date-modified = {2023-10-05 12:52:00 -0400},
doi = {10.1186/s13015-023-00237-z},
journal = {Algorithms for Molecular Biology},
keywords = {submitted},
number = {1},
pages = {12},
title = {The solution surface of the {Li-Stephens} haplotype copying model},
volume = {18},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1186/s13015-023-00237-z}
}
</pre>
</li>
<li><span id="dilber2023accelerated">Dilber E, Terhorst J. Accelerated inference of complex demographic models from large allele frequency spectra. 2023;: in preparation. </span>
[<a href="#" onclick="toggle('dilber2023acceleratedbibtex'); return false;">bibtex</a>]<pre id="dilber2023acceleratedbibtex" style="display:none">@article{dilber2023accelerated,
author = {Dilber, Enes and Terhorst, Jonathan},
author+an = {1=bold},
keywords = {submitted},
month = jun,
pages = {in preparation},
title = {Accelerated inference of complex demographic models from large allele frequency spectra},
year = {2023}
}
</pre>
</li>
<li><span id="https://doi.org/10.48550/arxiv.2008.06664">Erdmann-Pham DD, Terhorst J, Song YS. Exact and arbitrarily accurate non-parametric two-sample tests based on rank spacings. 2020. doi:10.48550/ARXIV.2008.06664</span>
[<a href="https://dx.doi.org/10.48550/ARXIV.2008.06664">link</a>]
[<a href="#" onclick="toggle('https://doi.org/10.48550/arxiv.2008.06664bibtex'); return false;">bibtex</a>]<pre id="https://doi.org/10.48550/arxiv.2008.06664bibtex" style="display:none">@article{https://doi.org/10.48550/arxiv.2008.06664,
author = {Erdmann-Pham, Dan D. and Terhorst, Jonathan and Song, Yun S.},
doi = {10.48550/ARXIV.2008.06664},
keywords = {submitted},
month = jun,
publisher = {arXiv},
title = {Exact and arbitrarily accurate non-parametric two-sample tests based on rank spacings},
year = {2020},
bdsk-url-1 = {https://doi.org/10.48550/ARXIV.2008.06664}
}
</pre>
</li></ol>
<h3 id="published">Published</h3>
<ol class="bibliography"><li><span id="ki2023exact">Ki C, Terhorst J. Exact Decoding of a Sequentially Markov Coalescent Model in Genetics. Journal of the American Statistical Association. 2022;: in press. doi:10.1080/01621459.2023.2252570</span>
[<a href="https://dx.doi.org/10.1080/01621459.2023.2252570">link</a>]
[<a href="#" onclick="toggle('ki2023exactbibtex'); return false;">bibtex</a>]<pre id="ki2023exactbibtex" style="display:none">@article{ki2023exact,
author = {Ki, Caleb and Terhorst, Jonathan},
author+an = {1=bold},
date-added = {2023-09-14 11:24:46 -0400},
date-modified = {2023-10-05 12:58:52 -0400},
doi = {10.1080/01621459.2023.2252570},
journal = {Journal of the American Statistical Association},
keywords = {published},
pages = {in press},
publisher = {Taylor \& Francis},
title = {Exact Decoding of a Sequentially {Markov} Coalescent Model in Genetics},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1080/01621459.2023.2252570}
}
</pre>
</li>
<li><span id="legried2022rates">Legried B, Terhorst J. Rates of convergence in the two-island and isolation-with-migration models. Theoretical Population Biology. 2022;147: 16–27. doi:10.1016/j.tpb.2022.08.001</span>
[<a href="https://dx.doi.org/10.1016/j.tpb.2022.08.001">link</a>]
[<a href="#" onclick="toggle('legried2022ratesbibtex'); return false;">bibtex</a>]<pre id="legried2022ratesbibtex" style="display:none">@article{legried2022rates,
author = {Legried, Brandon and Terhorst, Jonathan},
author+an = {1=bold},
date-added = {2023-05-04 17:06:57 -0400},
date-modified = {2023-05-04 17:07:17 -0400},
doi = {10.1016/j.tpb.2022.08.001},
issn = {0040-5809},
journal = {Theoretical Population Biology},
keywords = {published},
pages = {16-27},
title = {Rates of convergence in the two-island and isolation-with-migration models},
volume = {147},
year = {2022},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S004058092200051X},
bdsk-url-2 = {https://doi.org/10.1016/j.tpb.2022.08.001}
}
</pre>
</li>
<li><span id="fan2023whole-genome">Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, et al. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell. 2023;186: 923–939.e14. doi:10.1016/j.cell.2023.01.042</span>
[<a href="https://dx.doi.org/10.1016/j.cell.2023.01.042">link</a>]
[<a href="#" onclick="toggle('fan2023whole-genomebibtex'); return false;">bibtex</a>]<pre id="fan2023whole-genomebibtex" style="display:none">@article{fan2023whole-genome,
author = {Fan, Shaohua and Spence, Jeffrey P. and Feng, Yuanqing and Hansen, Matthew E.B. and Terhorst, Jonathan and Beltrame, Marcia H. and Ranciaro, Alessia and Hirbo, Jibril and Beggs, William and Thomas, Neil and Nyambo, Thomas and Mpoloka, Sununguko Wata and Mokone, Gaonyadiwe George and Njamnshi, Alfred K. and Fokunang, Charles and Meskel, Dawit Wolde and Belay, Gurja and Song, Yun S. and Tishkoff, Sarah A.},
date-added = {2023-05-04 17:05:54 -0400},
date-modified = {2023-05-04 17:06:11 -0400},
doi = {10.1016/j.cell.2023.01.042},
journal = {Cell},
keywords = {published},
month = mar,
number = {5},
pages = {923-939.e14},
title = {Whole-genome sequencing reveals a complex {African} population demographic history and signatures of local adaptation},
volume = {186},
year = {2023},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0092867423001010},
bdsk-url-2 = {https://doi.org/10.1016/j.cell.2023.01.042}
}
</pre>
</li>
<li><span id="mathieson2022direct">Mathieson I, Terhorst J. Direct detection of natural selection in Bronze Age Britain. Genome Research. 2022;32: 2057–2067. doi:10.1101/gr.276862.122</span>
[<a href="https://dx.doi.org/10.1101/gr.276862.122">link</a>]
[<a href="#" onclick="toggle('mathieson2022directbibtex'); return false;">bibtex</a>]<pre id="mathieson2022directbibtex" style="display:none">@article{mathieson2022direct,
author = {Mathieson, Iain and Terhorst, Jonathan},
author+an = {1=star, 2=star},
date-added = {2023-04-03 11:57:38 -0400},
date-modified = {2023-04-03 12:00:00 -0400},
doi = {10.1101/gr.276862.122},
journal = {Genome Research},
keywords = {published},
month = nov,
number = {11-12},
pages = {2057-2067},
title = {Direct detection of natural selection in {Bronze Age Britain}},
volume = {32},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1101/gr.276862.122}
}
</pre>
</li>
<li><span id="10.1093/molbev/msac154">Ki C, Terhorst J. Variational phylodynamic inference using pandemic-scale data. Molecular Biology and Evolution. 2022;39. doi:10.1093/molbev/msac154</span>
[<a href="https://dx.doi.org/10.1093/molbev/msac154">link</a>]
[<a href="#" onclick="toggle('10.1093/molbev/msac154bibtex'); return false;">bibtex</a>]<pre id="10.1093/molbev/msac154bibtex" style="display:none">@article{10.1093/molbev/msac154,
author = {Ki, Caleb and Terhorst, Jonathan},
author+an = {1=bold},
doi = {10.1093/molbev/msac154},
issn = {1537-1719},
journal = {Molecular Biology and Evolution},
keywords = {published},
month = jul,
number = {8},
title = {Variational phylodynamic inference using pandemic-scale data},
volume = {39},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1093/molbev/msac154}
}
</pre>
</li>
<li><span id="10.1093/biomet/asad029">Maity S, Dutta D, Terhorst J, Sun Y, Banerjee M. A linear adjustment based approach to posterior drift in transfer learning. Biometrika. 2023. doi:10.1093/biomet/asad029</span>
[<a href="https://dx.doi.org/10.1093/biomet/asad029">link</a>]
[<a href="#" onclick="toggle('10.1093/biomet/asad029bibtex'); return false;">bibtex</a>]<pre id="10.1093/biomet/asad029bibtex" style="display:none">@article{10.1093/biomet/asad029,
author = {Maity, Subha and Dutta, Diptavo and Terhorst, Jonathan and Sun, Yuekai and Banerjee, Moulinath},
author+an = {1=bold,2=bold},
doi = {10.1093/biomet/asad029},
issn = {1464-3510},
journal = {Biometrika},
keywords = {published},
month = may,
title = {{A linear adjustment based approach to posterior drift in transfer learning}},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1093/biomet/asad029}
}
</pre>
</li>
<li><span id="dilber2022robust">Dilber E, Terhorst J. Robust detection of natural selection using a probabilistic model of tree imbalance. Genetics. 2022;220. doi:10.1093/genetics/iyac009</span>
[<a href="https://dx.doi.org/10.1093/genetics/iyac009">link</a>]
[<a href="#" onclick="toggle('dilber2022robustbibtex'); return false;">bibtex</a>]<pre id="dilber2022robustbibtex" style="display:none">@article{dilber2022robust,
author = {Dilber, Enes and Terhorst, Jonathan},
author+an = {1=bold},
date-added = {2022-05-04 17:18:04 -0400},
date-modified = {2022-05-04 17:18:04 -0400},
doi = {10.1093/genetics/iyac009},
journal = {Genetics},
keywords = {published},
month = mar,
number = {3},
publisher = {Oxford University Press},
title = {Robust detection of natural selection using a probabilistic model of tree imbalance},
volume = {220},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1093/genetics/iyac009}
}
</pre>
</li>
<li><span id="legried2023identifiability">Legried B, Terhorst J. Identifiability and inference of phylogenetic birth–death models. Journal of Theoretical Biology. 2023;568: 111520. doi:10.1016/j.jtbi.2023.111520</span>
[<a href="https://dx.doi.org/10.1016/j.jtbi.2023.111520">link</a>]
[<a href="#" onclick="toggle('legried2023identifiabilitybibtex'); return false;">bibtex</a>]<pre id="legried2023identifiabilitybibtex" style="display:none">@article{legried2023identifiability,
author = {Legried, Brandon and Terhorst, Jonathan},
author+an = {1=bold},
doi = {10.1016/j.jtbi.2023.111520},
issn = {0022-5193},
journal = {Journal of Theoretical Biology},
keywords = {published},
month = jul,
pages = {111520},
title = {Identifiability and inference of phylogenetic birth--death models},
volume = {568},
year = {2023},
bdsk-url-1 = {https://doi.org/10.1016/j.jtbi.2023.111520}
}
</pre>
</li>
<li><span id="legried2022class">Legried B, Terhorst J. A class of identifiable phylogenetic birth–death models. Proceedings of the National Academy of Sciences. 2022;119: e2119513119. doi:10.1073/pnas.2119513119</span>
[<a href="https://dx.doi.org/10.1073/pnas.2119513119">link</a>]
[<a href="#" onclick="toggle('legried2022classbibtex'); return false;">bibtex</a>]<pre id="legried2022classbibtex" style="display:none">@article{legried2022class,
author = {Legried, Brandon and Terhorst, Jonathan},
author+an = {1=bold},
doi = {10.1073/pnas.2119513119},
journal = {Proceedings of the National Academy of Sciences},
keywords = {published},
month = aug,
number = {35},
pages = {e2119513119},
publisher = {National Acad Sciences},
title = {A class of identifiable phylogenetic birth--death models},
volume = {119},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1073/pnas.2119513119}
}
</pre>
</li>
<li><span id="kamm2020efficiently">Kamm J, Terhorst J, Durbin R, Song YS. Efficiently Inferring the Demographic History of Many Populations With Allele Count Data. Journal of the American Statistical Association. 2020;115: 1472–1487. doi:10.1080/01621459.2019.1635482</span>
[<a href="https://dx.doi.org/10.1080/01621459.2019.1635482">link</a>]
[<a href="#" onclick="toggle('kamm2020efficientlybibtex'); return false;">bibtex</a>]<pre id="kamm2020efficientlybibtex" style="display:none">@article{kamm2020efficiently,
author = {Kamm, Jack and Terhorst, Jonathan and Durbin, Richard and Song, Yun S.},
date-added = {2020-10-26 15:40:21 -0400},
date-modified = {2020-10-26 15:51:46 -0400},
doi = {10.1080/01621459.2019.1635482},
journal = {Journal of the American Statistical Association},
keywords = {published},
month = jul,
number = {531},
pages = {1472-1487},
publisher = {Taylor \& Francis},
title = {Efficiently Inferring the Demographic History of Many Populations With Allele Count Data},
volume = {115},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1080/01621459.2019.1635482}
}
</pre>
</li>
<li><span id="pmlr-v119-plumb20a">Plumb G, Terhorst J, Sankararaman S, Talwalkar A. Explaining Groups of Points in Low-Dimensional Representations. In: III HD, Singh A, editors. Proceedings of the 37th International Conference on Machine Learning. PMLR; 2020. pp. 7762–7771. Retrieved: https://proceedings.mlr.press/v119/plumb20a.html</span>
[<a href="https://proceedings.mlr.press/v119/plumb20a.html">link</a>]
[<a href="#" onclick="toggle('pmlr-v119-plumb20abibtex'); return false;">bibtex</a>]<pre id="pmlr-v119-plumb20abibtex" style="display:none">@inproceedings{pmlr-v119-plumb20a,
author = {Plumb, Gregory and Terhorst, Jonathan and Sankararaman, Sriram and Talwalkar, Ameet},
author+an = {1=bold},
booktitle = {Proceedings of the 37th International Conference on Machine Learning},
editor = {III, Hal Daum{\'e} and Singh, Aarti},
keywords = {published},
month = jul,
pages = {7762--7771},
pdf = {http://proceedings.mlr.press/v119/plumb20a/plumb20a.pdf},
publisher = {PMLR},
series = {Proceedings of Machine Learning Research},
title = {Explaining Groups of Points in Low-Dimensional Representations},
url = {https://proceedings.mlr.press/v119/plumb20a.html},
volume = {119},
year = {2020},
bdsk-url-1 = {https://proceedings.mlr.press/v119/plumb20a.html}
}
</pre>
</li>
<li><span id="gao2019u-pass:">Gao Z, Terhorst J, Van Hout CV, Stoev S. U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies. Bioinformatics. 2019;36: 974–975. doi:10.1093/bioinformatics/btz637</span>
[<a href="https://dx.doi.org/10.1093/bioinformatics/btz637">link</a>]
[<a href="#" onclick="toggle('gao2019u-pass:bibtex'); return false;">bibtex</a>]<pre id="gao2019u-pass:bibtex" style="display:none">@article{gao2019u-pass:,
author = {Gao, Zheng and Terhorst, Jonathan and Van Hout, Cristopher V. and Stoev, Stilian},
author+an = {1=bold},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1093/bioinformatics/btz637},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {published},
month = aug,
number = {3},
pages = {974-975},
title = {{U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies}},
volume = {36},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btz637}
}
</pre>
</li>
<li><span id="spence2018inference">Spence JP, Steinrücken M, Terhorst J, Song YS. Inference of population history using coalescent HMMs: review and outlook. Current Opinion in Genetics & Development. 2018;53: 70–76. doi:10.1016/j.gde.2018.07.002</span>
[<a href="https://dx.doi.org/10.1016/j.gde.2018.07.002">link</a>]
[<a href="#" onclick="toggle('spence2018inferencebibtex'); return false;">bibtex</a>]<pre id="spence2018inferencebibtex" style="display:none">@article{spence2018inference,
author = {Spence, Jeffrey P. and Steinr{\"u}cken, Matthias and Terhorst, Jonathan and Song, Yun S.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1016/j.gde.2018.07.002},
issn = {0959-437X},
journal = {Current Opinion in Genetics \& Development},
keywords = {published},
month = dec,
note = {Genetics of Human Origins},
pages = {70 - 76},
title = {Inference of population history using coalescent {HMMs}: review and outlook},
volume = {53},
year = {2018},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0959437X18300765},
bdsk-url-2 = {https://doi.org/10.1016/j.gde.2018.07.002}
}
</pre>
</li>
<li><span id="palamara2018high-throughput">Palamara P, Terhorst J, Song YS, Price AL. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nature Genetics. 2018;50: 1311. doi:10.1038/s41588-018-0177-x</span>
[<a href="https://dx.doi.org/10.1038/s41588-018-0177-x">link</a>]
[<a href="#" onclick="toggle('palamara2018high-throughputbibtex'); return false;">bibtex</a>]<pre id="palamara2018high-throughputbibtex" style="display:none">@article{palamara2018high-throughput,
author = {Palamara, Pier and Terhorst, Jonathan and Song, Yun S. and Price, Alkes L.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1038/s41588-018-0177-x},
journal = {Nature Genetics},
keywords = {published},
month = aug,
number = {9},
pages = {1311},
title = {High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.},
volume = {50},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1038/s41588-018-0177-x}
}
</pre>
</li>
<li><span id="moreno-mayar2018terminal">Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature. 2018. doi:10.1038/nature25173</span>
[<a href="https://dx.doi.org/10.1038/nature25173">link</a>]
[<a href="#" onclick="toggle('moreno-mayar2018terminalbibtex'); return false;">bibtex</a>]<pre id="moreno-mayar2018terminalbibtex" style="display:none">@article{moreno-mayar2018terminal,
author = {Moreno-Mayar, J. V\'ictor and Potter, Ben A. and Vinner, Lasse and Steinr{\"u}cken, Matthias and Rasmussen, Simon and Terhorst, Jonathan and Kamm, John A. and Albrechtsen, Anders and Malaspinas, Anna-Sapfo and Sikora, Martin and Reuther, Joshua D. and Irish, Joel D. and Malhi, Ripan S. and Orlando, Ludovic and Song, Yun S. and Nielsen, Rasmus and Meltzer, David J. and Willerslev, Eske},
date-modified = {2021-11-24 11:29:53 -0500},
day = {03},
doi = {10.1038/nature25173},
journal = {Nature},
keywords = {published},
month = jan,
title = {Terminal {Pleistocene Alaskan} genome reveals first founding population of {Native Americans}},
year = {2018},
bdsk-url-1 = {https://doi.org/10.1038/nature25173}
}
</pre>
</li>
<li><span id="terhorst2017robust">Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics. 2017;49: 303–309. doi:10.1038/ng.3748</span>
[<a href="https://dx.doi.org/10.1038/ng.3748">link</a>]
[<a href="#" onclick="toggle('terhorst2017robustbibtex'); return false;">bibtex</a>]<pre id="terhorst2017robustbibtex" style="display:none">@article{terhorst2017robust,
author = {Terhorst, Jonathan and Kamm, John A. and Song, Yun S.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1038/ng.3748},
journal = {Nature Genetics},
keywords = {published},
month = jan,
number = {2},
pages = {303--309},
title = {Robust and scalable inference of population history from hundreds of unphased whole genomes},
volume = {49},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1038/ng.3748}
}
</pre>
</li>
<li><span id="kamm2017efficient">Kamm JA, Terhorst J, Song YS. Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations. Journal of Computational and Graphical Statistics. 2017;26: 182–194. doi:10.1080/10618600.2016.1159212</span>
[<a href="https://dx.doi.org/10.1080/10618600.2016.1159212">link</a>]
[<a href="#" onclick="toggle('kamm2017efficientbibtex'); return false;">bibtex</a>]<pre id="kamm2017efficientbibtex" style="display:none">@article{kamm2017efficient,
author = {Kamm, John A. and Terhorst, Jonathan and Song, Yun S.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1080/10618600.2016.1159212},
journal = {Journal of Computational and Graphical Statistics},
keywords = {published},
month = feb,
number = {1},
pages = {182-194},
title = {Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations},
volume = {26},
year = {2017},
bdsk-url-1 = {https://doi.org/10.1080/10618600.2016.1159212}
}
</pre>
</li>
<li><span id="liu2016riches">Liu T-Y, Dodson AE, Terhorst J, Song YS, Rine J. Riches of phenotype computationally extracted from microbial colonies. Proceedings of the National Academy of Sciences. 2016;113: E2822–E2831. doi:10.1073/pnas.1523295113</span>
[<a href="https://dx.doi.org/10.1073/pnas.1523295113">link</a>]
[<a href="#" onclick="toggle('liu2016richesbibtex'); return false;">bibtex</a>]<pre id="liu2016richesbibtex" style="display:none">@article{liu2016riches,
author = {Liu, Tzu-Yu and Dodson, Anne E. and Terhorst, Jonathan and Song, Yun S. and Rine, Jasper},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1073/pnas.1523295113},
journal = {Proceedings of the National Academy of Sciences},
keywords = {published},
month = may,
number = {20},
pages = {E2822-E2831},
title = {Riches of phenotype computationally extracted from microbial colonies},
volume = {113},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1073/pnas.1523295113}
}
</pre>
</li>
<li><span id="terhorst2015multi-locus">Terhorst J, Schlötterer C, Song YS. Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution. PLoS Genetics. 2015;11: 1–29. doi:10.1371/journal.pgen.1005069</span>
[<a href="https://dx.doi.org/10.1371/journal.pgen.1005069">link</a>]
[<a href="#" onclick="toggle('terhorst2015multi-locusbibtex'); return false;">bibtex</a>]<pre id="terhorst2015multi-locusbibtex" style="display:none">@article{terhorst2015multi-locus,
author = {Terhorst, Jonathan and Schl{\"o}tterer, Christian and Song, Yun S.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1371/journal.pgen.1005069},
journal = {PLoS Genetics},
keywords = {published},
month = apr,
number = {4},
pages = {1-29},
title = {Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution},
volume = {11},
year = {2015},
bdsk-url-1 = {https://doi.org/10.1371/journal.pgen.1005069}
}
</pre>
</li>
<li><span id="terhorst2015fundamental">Terhorst J, Song YS. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proceedings of the National Academy of Sciences. 2015;112: 7677–7682. doi:10.1073/pnas.1503717112</span>
[<a href="https://dx.doi.org/10.1073/pnas.1503717112">link</a>]
[<a href="#" onclick="toggle('terhorst2015fundamentalbibtex'); return false;">bibtex</a>]<pre id="terhorst2015fundamentalbibtex" style="display:none">@article{terhorst2015fundamental,
author = {Terhorst, Jonathan and Song, Yun S.},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1073/pnas.1503717112},
journal = {Proceedings of the National Academy of Sciences},
keywords = {published},
month = jun,
number = {25},
pages = {7677-7682},
title = {Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum},
volume = {112},
year = {2015},
bdsk-url-1 = {https://doi.org/10.1073/pnas.1503717112}
}
</pre>
</li>
<li><span id="talwalkar2014smash:">Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, et al. SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics. 2014;30: 2787–2795. doi:10.1093/bioinformatics/btu345</span>
[<a href="https://dx.doi.org/10.1093/bioinformatics/btu345">link</a>]
[<a href="#" onclick="toggle('talwalkar2014smash:bibtex'); return false;">bibtex</a>]<pre id="talwalkar2014smash:bibtex" style="display:none">@article{talwalkar2014smash:,
author = {Talwalkar, Ameet and Liptrap, Jesse and Newcomb, Julie and Hartl, Christopher and Terhorst, Jonathan and Curtis, Kristal and Bresler, Ma'ayan and Song, Yun S. and Jordan, Michael I. and Patterson, David},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1093/bioinformatics/btu345},
journal = {Bioinformatics},
keywords = {published},
month = jun,
number = {19},
pages = {2787-2795},
title = {{{SMaSH}}: a benchmarking toolkit for human genome variant calling},
volume = {30},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btu345}
}
</pre>
</li>
<li><span id="jaggi2014communication-efficient">Jaggi M, Smith V, Takac M, Terhorst J, Krishnan S, Hofmann T, et al. Communication-Efficient Distributed Dual Coordinate Ascent. In: Ghahramani Z, Welling M, Cortes C, Lawrence ND, Weinberger KQ, editors. Advances in Neural Information Processing Systems 27. 2014. pp. 3068–3076. </span>
[<a href="#" onclick="toggle('jaggi2014communication-efficientbibtex'); return false;">bibtex</a>]<pre id="jaggi2014communication-efficientbibtex" style="display:none">@incollection{jaggi2014communication-efficient,
author = {Jaggi, Martin and Smith, Virginia and Takac, Martin and Terhorst, Jonathan and Krishnan, Sanjay and Hofmann, Thomas and Jordan, Michael I},
booktitle = {Advances in Neural Information Processing Systems 27},
date-modified = {2020-10-26 15:51:49 -0400},
editor = {Ghahramani, Z. and Welling, M. and Cortes, C. and Lawrence, N. D. and Weinberger, K. Q.},
keywords = {published},
month = nov,
pages = {3068--3076},
title = {Communication-Efficient Distributed Dual Coordinate Ascent},
year = {2014},
bdsk-url-1 = {http://papers.nips.cc/paper/5599-communication-efficient-distributed-dual-coordinate-ascent.pdf}
}
</pre>
</li>
<li><span id="bloniarz2014changepoint">Bloniarz A, Talwalkar A, Terhorst J, Jordan MI, Patterson D, Yu B, et al. Changepoint Analysis for Efficient Variant Calling. In: Sharan R, editor. RECOMB 2014. Cham; 2014. pp. 20–34. doi:10.1007/978-3-319-05269-4_3</span>
[<a href="https://dx.doi.org/10.1007/978-3-319-05269-4_3">link</a>]
[<a href="#" onclick="toggle('bloniarz2014changepointbibtex'); return false;">bibtex</a>]<pre id="bloniarz2014changepointbibtex" style="display:none">@incollection{bloniarz2014changepoint,
address = {Cham},
author = {Bloniarz, Adam and Talwalkar, Ameet and Terhorst, Jonathan and Jordan, Michael I. and Patterson, David and Yu, Bin and Song, Yun S.},
booktitle = {RECOMB 2014},
date-modified = {2020-10-26 15:51:49 -0400},
doi = {10.1007/978-3-319-05269-4_3},
editor = {Sharan, Roded},
isbn = {978-3-319-05269-4},
keywords = {published},
month = apr,
pages = {20--34},
title = {Changepoint Analysis for Efficient Variant Calling},
year = {2014},
bdsk-url-1 = {https://doi.org/10.1007/978-3-319-05269-4_3}
}
</pre>
</li>
<li><span id="xia2012distributed">Xia R, Sheehan S, Zhang Y, Talwalkar A, Zaharia M, Terhorst J, et al. Distributed Pipeline for Genomic Variant Calling. NIPS Workshop on BIG Learning. 2012. </span>
[<a href="#" onclick="toggle('xia2012distributedbibtex'); return false;">bibtex</a>]<pre id="xia2012distributedbibtex" style="display:none">@inproceedings{xia2012distributed,
author = {Xia, Richard and Sheehan, Sara and Zhang, Yuchen and Talwalkar, Ameet and Zaharia, Matei and Terhorst, Jonathan and Jordan, Michael and Song, Yun S and Fox, Armando and Patterson, David},
booktitle = {NIPS Workshop on BIG Learning},
date-modified = {2022-05-04 17:23:47 -0400},
keywords = {published},
month = nov,
title = {Distributed Pipeline for Genomic Variant Calling},
year = {2012}
}
</pre>
</li></ol>
<h3 id="unpublished">Unpublished</h3>
<ol class="bibliography"><li><span id="terhorst2011the-kalmanson">Terhorst J. The Kalmanson Complex. Master's thesis, San Francisco State University. 2011. Retrieved: https://arxiv.org/abs/1102.3177</span>
[<a href="https://arxiv.org/abs/1102.3177">link</a>]
[<a href="#" onclick="toggle('terhorst2011the-kalmansonbibtex'); return false;">bibtex</a>]<pre id="terhorst2011the-kalmansonbibtex" style="display:none">@mastersthesis{terhorst2011the-kalmanson,
address = {San Francisco, CA},
author = {Terhorst, Jonathan},
date-modified = {2020-10-26 15:52:07 -0400},
keywords = {unpublished},
month = may,
school = {San Francisco State University},
title = {{The Kalmanson Complex}},
url = {https://arxiv.org/abs/1102.3177},
year = {2011},
bdsk-url-1 = {https://arxiv.org/abs/1102.3177}
}
</pre>
</li></ol>
<h3 id="pre-history">Pre-history</h3>
<ol class="bibliography"><li><span id="sunding2014conserving">Sunding D, Terhorst J. Conserving endangered species through regulation of urban development: the case of California vernal pools. Land Economics. 2014;90: 290–305. doi:10.3368/le.90.2.290</span>
[<a href="https://dx.doi.org/10.3368/le.90.2.290">link</a>]
[<a href="#" onclick="toggle('sunding2014conservingbibtex'); return false;">bibtex</a>]<pre id="sunding2014conservingbibtex" style="display:none">@article{sunding2014conserving,
author = {Sunding, David and Terhorst, Jonathan},
date-modified = {2021-05-19 12:16:13 -0400},
doi = {10.3368/le.90.2.290},
journal = {Land Economics},
keywords = {old},
number = {2},
pages = {290--305},
title = {Conserving endangered species through regulation of urban development: the case of California vernal pools},
volume = {90},
year = {2014},
bdsk-url-1 = {https://doi.org/10.3368/le.90.2.290}
}
</pre>
</li>
<li><span id="terhorst2010effect">Terhorst J, Berkman M. Effect of coal-fired power generation on visibility in a nearby national park. Atmospheric Environment. 2010;44: 2524–2531. doi:10.1016/j.atmosenv.2010.04.022</span>
[<a href="https://dx.doi.org/10.1016/j.atmosenv.2010.04.022">link</a>]
[<a href="#" onclick="toggle('terhorst2010effectbibtex'); return false;">bibtex</a>]<pre id="terhorst2010effectbibtex" style="display:none">@article{terhorst2010effect,
author = {Terhorst, Jonathan and Berkman, Mark},
date-modified = {2021-05-19 12:15:29 -0400},
doi = {10.1016/j.atmosenv.2010.04.022},
issn = {1352-2310},
journal = {Atmospheric Environment},
keywords = {old},
number = {21--22},
pages = {2524 - 2531},
title = {Effect of coal-fired power generation on visibility in a nearby national park},
volume = {44},
year = {2010},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.atmosenv.2010.04.022}
}
</pre>
</li>
<li><span id="sunding2007federal">Sunding D, Swoboda A, Terhorst J. Federal Land Use Controls and the Planning Anticommons. UC Berkeley, Department of Agricultural and Resource Economics; 2007. Retrieved: https://are.berkeley.edu/ sunding/FederalLandUse.pdf</span>
[<a href="https://are.berkeley.edu/ sunding/FederalLandUse.pdf">link</a>]
[<a href="#" onclick="toggle('sunding2007federalbibtex'); return false;">bibtex</a>]<pre id="sunding2007federalbibtex" style="display:none">@techreport{sunding2007federal,
author = {Sunding, David and Swoboda, Aaron and Terhorst, Jonathan},
date-modified = {2021-05-19 12:15:37 -0400},
institution = {UC Berkeley, Department of Agricultural and Resource Economics},
keywords = {old},
title = {Federal Land Use Controls and the Planning Anticommons},
url = {https://are.berkeley.edu/~sunding/FederalLandUse.pdf},
year = {2007},
bdsk-url-1 = {https://are.berkeley.edu/~sunding/FederalLandUse.pdf}
}
</pre>
</li></ol>
</div>
</article>
</div>
</main><footer class="site-footer h-card">
<data class="u-url" href="/"></data>
<div class="wrapper">
<h2 class="footer-heading">Terhorst lab</h2>
<div class="footer-col-wrapper">
<div class="footer-col footer-col-1">
<ul class="contact-list">
<li class="p-name"></li><li><a class="u-email" href="mailto:jonth@umich.edu">jonth@umich.edu</a></li></ul>
</div>
<div class="footer-col footer-col-2"><ul class="social-media-list"><li><a href="https://github.com/terhorst"><svg class="svg-icon"><use xlink:href="/assets/minima-social-icons.svg#github"></use></svg> <span class="username">terhorst</span></a></li></ul>
</div>
<div class="footer-col footer-col-3">
<p></p>
</div>
</div>
</div>
</footer>
</body>
</html>