-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathreferences.bib
More file actions
767 lines (681 loc) · 22.9 KB
/
references.bib
File metadata and controls
767 lines (681 loc) · 22.9 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
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
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
@article{Julia-2017,
title={Julia: A fresh approach to numerical computing},
author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
journal={SIAM {R}eview},
volume={59},
number={1},
pages={65--98},
year={2017},
publisher={SIAM},
doi={10.1137/141000671},
url={https://epubs.siam.org/doi/10.1137/141000671}
}
@article{rackauckas2017differentialequations,
title={Differentialequations.jl--a performant and feature-rich ecosystem for solving differential equations in julia},
author={Rackauckas, Christopher and Nie, Qing},
journal={Journal of Open Research Software},
volume={5},
number={1},
pages={15},
year={2017},
publisher={Ubiquity Press}
}
@article{mogensen2018optim,
title={Optim: A mathematical optimization package for Julia},
author={Mogensen, P and Riseth, A},
journal={Journal of Open Source Software},
volume={3},
number={24},
year={2018},
publisher={Open Journals}
}
@misc{Margolskee2020_xGx,
author = {Margolskee, A. and Khanshan, F. and Stein, A. M. and Ho, Y.-Y. and Looby, M.},
title = {Exploratory Graphics (xGx): An open-source pharmacometrician’s workflow in R – from exploration (xGx) to model building (nlmixr) and diagnostics (ggPMX)},
howpublished = {Tutorial at ACoP11 2020 Annual Meeting (virtual)},
year = {2020},
note = {Open-source materials available at https://opensource.nibr.com/xgx/}
}
@misc{pumas_datatypes,
title = {{Pumas Tutorials: Data Wrangling and Visualization}},
author = {{Pumas Developers}},
howpublished = {\url{https://tutorials.pumas.ai/html/LearningPaths/01-LP/02-Module/mod2-data-wrangling-visualization.html#reading-and-writing-data}},
year = {2023},
note = {Accessed: [Dec 1, 2025]}
}
@misc{SummaryTables,
title = {{SummaryTables.jl}: Publication-quality tables in Julia},
author = {{PumasAI}},
howpublished = {\url{https://pumasai.github.io/SummaryTables.jl/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{ReadStatTables,
title = {{ReadStatTables.jl}},
author = {{ReadStatTables Developers}},
howpublished = {\url{https://junyuan-chen.github.io/ReadStatTables.jl/stable/}},
year = {2023},
note = {Accessed: Dec 2025}
}
@misc{XLSX,
title = {{XLSX.jl}},
author = {{XLSX Developers}},
howpublished = {\url{https://felipenoris.github.io/XLSX.jl/stable/}},
year = {2023},
note = {Accessed: Dec 2025}
}
@misc{AlgebraOfGraphics,
title = {{AlgebraOfGraphics.jl}: A grammar of graphics for Julia},
author = {{PumasAI}},
howpublished = {\url{https://aog.makie.org/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{Makie,
title = {{Makie.jl}},
author = {{Makie.jl Developers}},
howpublished = {\url{https://docs.makie.org/stable/}},
year = {2023},
note = {Accessed: Dec 2025}
}
% ============================================
% SOFTWARE AND TOOLS
% ============================================
@book{beal2013nonmem,
title={NONMEM 7.3.0 Users Guides},
author={Beal, S and Sheiner, LB and Boeckmann, A and Bauer, RJ},
year={2013},
publisher={ICON plc, Gaithersburg, MD}
}
@manual{monolix2024,
title={Monolix version 2024R1},
author={{Lixoft}},
year={2024},
url={http://lixoft.com/products/monolix/}
}
@manual{R2024,
title={R: A Language and Environment for Statistical Computing},
author={{R Core Team}},
organization={R Foundation for Statistical Computing},
address={Vienna, Austria},
year={2024},
url={https://www.R-project.org/}
}
@manual{SAS2024,
title={{SAS/STAT} Software, Version 9.4},
author={{SAS Institute Inc.}},
address={Cary, NC},
year={2024},
url={https://www.sas.com/}
}
@manual{Phoenix2024,
title={Phoenix WinNonlin, Version 8.4},
author={{Certara USA, Inc.}},
address={Princeton, NJ},
year={2024},
url={https://www.certara.com/software/phoenix-winnonlin/}
}
@book{Python2009,
title={Python 3 Reference Manual},
author={Van Rossum, Guido and Drake, Fred L.},
year={2009},
publisher={CreateSpace},
address={Scotts Valley, CA}
}
@manual{MATLAB2024,
title={{MATLAB} version 24.2 (R2024b)},
author={{The MathWorks Inc.}},
address={Natick, Massachusetts},
year={2024},
url={https://www.mathworks.com}
}
@book{wickham2016ggplot2,
title={ggplot2: elegant graphics for data analysis},
author={Wickham, Hadley},
year={2016},
publisher={Springer}
}
@manual{wickham2023dplyr,
title={dplyr: A Grammar of Data Manipulation},
author={Wickham, Hadley and Fran{\c{c}}ois, Romain and Henry, Lionel and M{\"u}ller, Kirill and Vaughan, Davis},
year={2023},
note={R package version 1.1.2},
url={https://CRAN.R-project.org/package=dplyr}
}
@article{danisch2021makie,
title={Makie.jl: Flexible high-performance data visualization for Julia},
author={Danisch, Simon and Krumbiegel, Julius},
journal={Journal of Open Source Software},
volume={6},
number={65},
pages={3349},
year={2021}
}
% ============================================
% PHARMACOMETRIC METHODS AND ALGORITHMS
% ============================================
@article{lindstrom1990nonlinear,
title={Nonlinear mixed effects models for repeated measures data},
author={Lindstrom, Mary J and Bates, Douglas M},
journal={Biometrics},
volume={46},
number={3},
pages={673--687},
year={1990},
publisher={JSTOR}
}
@article{kuhn2005maximum,
title={Maximum likelihood estimation in nonlinear mixed effects models},
author={Kuhn, Estelle and Lavielle, Marc},
journal={Computational Statistics \& Data Analysis},
volume={49},
number={4},
pages={1020--1038},
year={2005},
publisher={Elsevier}
}
@article{Wei1990,
title = {A Monte Carlo Implementation of the EM Algorithm and the Poor Man's Data Augmentation Algorithms},
volume = {85},
ISSN = {1537-274X},
url = {http://dx.doi.org/10.1080/01621459.1990.10474930},
DOI = {10.1080/01621459.1990.10474930},
number = {411},
journal = {Journal of the American Statistical Association},
publisher = {Informa UK Limited},
author = {Wei, Greg C. G. and Tanner, Martin A.},
year = {1990},
month = sep,
pages = {699–704}
}
@article{hoffman2014nuts,
title={The No-U-Turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo},
author={Hoffman, Matthew D and Gelman, Andrew},
journal={Journal of Machine Learning Research},
volume={15},
number={1},
pages={1593--1623},
year={2014}
}
@article{hooker2007cwres,
title={Conditional weighted residuals (CWRES): a model diagnostic for the FOCE method},
author={Hooker, Andrew C and Staatz, Christine E and Karlsson, Mats O},
journal={Pharmaceutical Research},
volume={24},
number={12},
pages={2187--2197},
year={2007},
publisher={Springer}
}
@article{savic2009shrinkage,
title={Importance of shrinkage in empirical Bayes estimates for diagnostics: problems and solutions},
author={Savic, Radojka M and Karlsson, Mats O},
journal={The AAPS Journal},
volume={11},
number={3},
pages={558--569},
year={2009},
publisher={Springer}
}
@article{karlsson2007error,
title={The importance of modeling interoccasion variability in population pharmacokinetic analyses},
author={Karlsson, Mats O and Savic, Radojka M},
journal={Journal of Pharmacokinetics and Pharmacodynamics},
volume={34},
number={6},
pages={735--750},
year={2007},
publisher={Springer}
}
% ============================================
% STATISTICAL METHODS
% ============================================
@book{efron1994bootstrap,
title={An introduction to the bootstrap},
author={Efron, Bradley and Tibshirani, Robert J},
year={1994},
publisher={CRC press}
}
@article{akaike1974aic,
title={A new look at the statistical model identification},
author={Akaike, Hirotugu},
journal={IEEE Transactions on Automatic Control},
volume={19},
number={6},
pages={716--723},
year={1974},
publisher={IEEE}
}
@article{schwarz1978bic,
title={Estimating the dimension of a model},
author={Schwarz, Gideon},
journal={The Annals of Statistics},
volume={6},
number={2},
pages={461--464},
year={1978},
publisher={Institute of Mathematical Statistics}
}
@article{white1980sandwich,
title={A heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity},
author={White, Halbert},
journal={Econometrica},
volume={48},
number={4},
pages={817--838},
year={1980},
publisher={JSTOR}
}
% ============================================
% MODEL DIAGNOSTICS AND VALIDATION
% ============================================
@article{holford2005vpc,
title={The visual predictive check--superiority to standard diagnostic (Rorschach) plots},
author={Holford, Nicholas},
journal={PAGE},
volume={14},
pages={738},
year={2005}
}
@article{bergstrand2011vpc,
title={Prediction-corrected visual predictive checks for diagnosing nonlinear mixed-effects models},
author={Bergstrand, Martin and Hooker, Andrew C and Wallin, Joakim E and Karlsson, Mats O},
journal={The AAPS Journal},
volume={13},
number={2},
pages={143--151},
year={2011},
publisher={Springer}
}
% ============================================
% PK-PD MODELING
% ============================================
@article{dayneka1993indirect,
title={Comparison of four basic models of indirect pharmacodynamic responses},
author={Dayneka, Nicholas L and Garg, Vinod and Jusko, William J},
journal={Journal of Pharmacokinetics and Biopharmaceutics},
volume={21},
number={4},
pages={457--478},
year={1993},
publisher={Springer}
}
@article{jusko1994indirect,
title={Physiologic indirect response models characterize diverse types of pharmacodynamic effects},
author={Jusko, William J and Ko, Hocheol C},
journal={Clinical Pharmacology \& Therapeutics},
volume={56},
number={4},
pages={406--419},
year={1994},
publisher={Wiley Online Library}
}
@article{holford1981pkpd,
title={Understanding the dose-effect relationship},
author={Holford, NHG and Sheiner, LB},
journal={Clinical Pharmacokinetics},
volume={6},
number={6},
pages={429--453},
year={1981},
publisher={Springer}
}
@article{sharma1998indirect,
title={Characteristics of indirect pharmacodynamic models and applications to clinical drug responses},
author={Sharma, Ayyappa and Jusko, William J},
journal={British Journal of Clinical Pharmacology},
volume={45},
number={3},
pages={229--239},
year={1998},
publisher={Wiley Online Library}
}
% ============================================
% ALLOMETRIC SCALING AND COVARIATES
% ============================================
@article{anderson2008allometric,
title={Mechanistic basis of using body size and maturation to predict clearance in humans},
author={Anderson, Brian J and Holford, Nick HG},
journal={Drug Metabolism and Pharmacokinetics},
volume={23},
number={1},
pages={13--25},
year={2008},
publisher={Japanese Society for the Study of Xenobiotics}
}
@article{west1997allometric,
title={A general model for the origin of allometric scaling laws in biology},
author={West, Geoffrey B and Brown, James H and Enquist, Brian J},
journal={Science},
volume={276},
number={5309},
pages={122--126},
year={1997},
publisher={American Association for the Advancement of Science}
}
% ============================================
% SENSITIVITY ANALYSIS AND IDENTIFIABILITY
% ============================================
@article{sobol2001sensitivity,
title={Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates},
author={Sobol, Ilya M},
journal={Mathematics and Computers in Simulation},
volume={55},
number={1-3},
pages={271--280},
year={2001},
publisher={Elsevier}
}
@article{morris1991factorial,
title={Factorial sampling plans for preliminary computational experiments},
author={Morris, Max D},
journal={Technometrics},
volume={33},
number={2},
pages={161--174},
year={1991},
publisher={Taylor \& Francis}
}
@article{saltelli1999efast,
title={A quantitative model-independent method for global sensitivity analysis of model output},
author={Saltelli, Andrea and Tarantola, Stefano and Chan, Karen PS},
journal={Technometrics},
volume={41},
number={1},
pages={39--56},
year={1999},
publisher={Taylor \& Francis}
}
@article{raue2009identifiability,
title={Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood},
author={Raue, Andreas and Kreutz, Clemens and Maiwald, Thomas and Bachmann, Julie and Schilling, Marcel and Klingm{\"u}ller, Ursula and Timmer, Jens},
journal={Bioinformatics},
volume={25},
number={15},
pages={1923--1929},
year={2009},
publisher={Oxford University Press}
}
@article{bellman1970structural,
title={On structural identifiability},
author={Bellman, Richard and {\AA}str{\"o}m, Karl J},
journal={Mathematical Biosciences},
volume={7},
number={3-4},
pages={329--339},
year={1970},
publisher={Elsevier}
}
% ============================================
% OPTIMAL DESIGN
% ============================================
@book{atkinson2007optimal,
title={Optimum experimental designs, with SAS},
author={Atkinson, Anthony and Donev, Alexander and Tobias, Randy},
year={2007},
publisher={Oxford University Press}
}
@article{mentre1997optimal,
title={Optimal design in random-effects regression models},
author={Mentr{\'e}, France and Mallet, Aur{\'e}lie and Baccar, Djalil},
journal={Biometrika},
volume={84},
number={2},
pages={429--442},
year={1997},
publisher={Oxford University Press}
}
@article{nyberg2012methods,
title={Methods and software tools for design evaluation in population pharmacokinetics--pharmacodynamics studies},
author={Nyberg, Joakim and Karlsson, Mats O and Hooker, Andrew C},
journal={British Journal of Clinical Pharmacology},
volume={74},
number={6},
pages={909--923},
year={2012},
publisher={Wiley Online Library}
}
% ============================================
% MACHINE LEARNING IN PKPD
% ============================================
@article{rackauckas2020universal,
title={Universal differential equations for scientific machine learning},
author={Rackauckas, Christopher and Ma, Yingbo and Martensen, Julius and Warner, Collin and Zubov, Kirill and Supekar, Rohit and Skinner, Dominic and Ramadhan, Ali and Edelman, Alan},
journal={arXiv preprint arXiv:2001.04385},
year={2020}
}
@article{raissi2019pinn,
title={Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations},
author={Raissi, Maziar and Perdikaris, Paris and Karniadakis, George E},
journal={Journal of Computational Physics},
volume={378},
pages={686--707},
year={2019},
publisher={Elsevier}
}
% ============================================
% REGULATORY GUIDANCE AND MIDD
% ============================================
@misc{fda2022popPK,
title={Population Pharmacokinetics: Guidance for Industry},
author={{FDA}},
year={2022},
howpublished={U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER)},
url={https://www.fda.gov/regulatory-information/search-fda-guidance-documents/population-pharmacokinetics}
}
@misc{fda2014bioequivalence,
title={Bioavailability and Bioequivalence Studies Submitted in NDAs or INDs--General Considerations},
author={{FDA}},
year={2014},
howpublished={U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER)},
url={https://www.fda.gov/regulatory-information/search-fda-guidance-documents/bioavailability-and-bioequivalence-studies-submitted-ndas-or-inds-general-considerations}
}
@misc{ema2010bioequivalence,
title={Guideline on the Investigation of Bioequivalence},
author={{EMA}},
year={2010},
howpublished={European Medicines Agency, Committee for Medicinal Products for Human Use (CHMP)},
url={https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-investigation-bioequivalence-rev1_en.pdf}
}
@article{marshall2016midd,
title={Good practices in model-informed drug discovery and development: practice, application, and documentation},
author={Marshall, Stuart F and Burghaus, Rolf and Cosson, Vincent and Cheung, Siew Yee and Chenel, Marylore and DellaPasqua, Oscar and Frey, Nicolas and Hamr{\'e}n, Bengt and Harnisch, Loew and Ivanow, Fran{\c{c}}ois and others},
journal={CPT: Pharmacometrics \& Systems Pharmacology},
volume={5},
number={3},
pages={93--122},
year={2016},
publisher={Wiley Online Library}
}
@article{barrett2022midd,
title={Model-informed drug discovery and development: current industry good practice and regulatory expectations},
author={Barrett, Jeffrey S and Narayan, Murali and Patel, Kinjal and Zutshi, Abhishek and Cheung, Siew Yee and Dodds, Michael G and Ene, Ivelina and Gopalakrishnan, Mathangi and Fossler, Michael J and Holloway, Christopher W and others},
journal={CPT: Pharmacometrics \& Systems Pharmacology},
volume={11},
number={12},
pages={1583--1608},
year={2022},
publisher={Wiley Online Library}
}
% ============================================
% PHARMACOMETRIC TEXTBOOKS AND TUTORIALS
% ============================================
@book{gabrielsson2006pharmacokinetic,
title={Pharmacokinetic and pharmacodynamic data analysis: concepts and applications},
author={Gabrielsson, Johan and Weiner, Daniel},
year={2006},
publisher={Swedish Pharmaceutical Press},
edition={4th}
}
@book{bonate2011pharmacokinetic,
title={Pharmacokinetic-pharmacodynamic modeling and simulation},
author={Bonate, Peter L},
year={2011},
publisher={Springer},
edition={2nd}
}
@article{bauer2019nonmem,
title={NONMEM tutorial part II: estimation methods and advanced examples},
author={Bauer, Robert J},
journal={CPT: Pharmacometrics \& Systems Pharmacology},
volume={8},
number={8},
pages={538--556},
year={2019},
publisher={Wiley Online Library}
}
@article{upton2014nonmem,
title={Basic concepts in population modeling, simulation, and model-based drug development: part 3--introduction to pharmacokinetic modeling methods},
author={Upton, Richard N and Mould, Diane R},
journal={CPT: Pharmacometrics \& Systems Pharmacology},
volume={3},
number={1},
pages={e88},
year={2014},
publisher={Wiley Online Library}
}
% ============================================
% PHARMACOKINETIC FUNDAMENTALS
% ============================================
@book{rowland2011clinical,
title={Clinical pharmacokinetics and pharmacodynamics: concepts and applications},
author={Rowland, Malcolm and Tozer, Thomas N},
year={2011},
publisher={Lippincott Williams \& Wilkins},
edition={4th}
}
% ============================================
% CDISC STANDARDS
% ============================================
@misc{cdisc2023,
title={Clinical Data Interchange Standards Consortium (CDISC) Standards},
author={{CDISC}},
year={2023},
howpublished={CDISC},
url={https://www.cdisc.org/standards}
}
% ============================================
% QUARTO AND REPRODUCIBLE RESEARCH
% ============================================
@misc{allaire2023quarto,
title={Quarto: An open-source scientific and technical publishing system},
author={Allaire, JJ and Teague, Charles and Xie, Yihui and Dervieux, Christophe},
year={2023},
howpublished={Posit Software, PBC},
url={https://quarto.org}
}
@article{sandve2013reproducible,
title={Ten simple rules for reproducible computational research},
author={Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
journal={PLoS Computational Biology},
volume={9},
number={10},
pages={e1003285},
year={2013},
publisher={Public Library of Science}
}
% ============================================
% PUMASAI OPEN-SOURCE PACKAGES
% ============================================
@misc{WriteDocx,
title = {{WriteDocx.jl}: Programmatic generation of Word documents in Julia},
author = {{PumasAI}},
howpublished = {\url{https://pumasai.github.io/WriteDocx.jl/dev/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{QuartoNotebookRunner,
title = {{QuartoNotebookRunner.jl}: Backend for executing Quarto notebooks with Julia},
author = {{PumasAI}},
howpublished = {\url{https://github.com/PumasAI/QuartoNotebookRunner.jl}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{QuartoTools,
title = {{QuartoTools.jl}: Integration utilities for Quarto document rendering},
author = {{PumasAI}},
howpublished = {\url{https://pumasai.github.io/QuartoTools.jl/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{SimpleChains,
title = {{SimpleChains.jl}: High-performance neural networks for small models},
author = {{PumasAI}},
howpublished = {\url{https://pumasai.github.io/SimpleChains.jl/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
% ============================================
% JULIA ECOSYSTEM PACKAGES
% ============================================
@misc{DataFrames,
title = {{DataFrames.jl}: Flexible data manipulation in Julia},
author = {{JuliaData}},
howpublished = {\url{https://dataframes.juliadata.org/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{DataFramesMeta,
title = {{DataFramesMeta.jl}: Metaprogramming tools for DataFrames.jl},
author = {{JuliaData}},
howpublished = {\url{https://juliadata.github.io/DataFramesMeta.jl/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{CSV,
title = {{CSV.jl}: Fast and flexible CSV reading and writing in Julia},
author = {{JuliaData}},
howpublished = {\url{https://csv.juliadata.org/stable/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@inproceedings{AdvancedHMC,
title={AdvancedHMC. jl: A robust, modular and efficient implementation of advanced HMC algorithms},
author={Xu, Kai and Ge, Hong and Tebbutt, Will and Tarek, Mohamed and Trapp, Martin and Ghahramani, Zoubin},
booktitle={Symposium on Advances in Approximate Bayesian Inference},
pages={1--10},
year={2020},
organization={PMLR}
}
@misc{StableRNGs,
title = {{StableRNGs.jl}: Stable random number generators for reproducible results},
author = {{JuliaRandom}},
howpublished = {\url{https://github.com/JuliaRandom/StableRNGs.jl}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{pumas2024docs,
title = {{Pumas Documentation}},
author = {{PumasAI}},
howpublished = {\url{https://docs.pumas.ai/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{askpumas2024,
title = {{AskPumas}: AI-powered learning assistant for pharmacometrics in Pumas},
author = {{PumasAI}},
howpublished = {\url{https://ask.pumas.ai/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{pumasdiscourse,
title = {{Pumas Discourse Forum}},
author = {{PumasAI}},
howpublished = {\url{https://discourse.pumas.ai/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{juliadocs,
title = {{Julia Documentation}},
author = {{JuliaLang}},
howpublished = {\url{https://docs.julialang.org/}},
year = {2024},
note = {Accessed: Dec 2025}
}
@misc{pumastutorials,
title = {{Pumas Tutorials}},
author = {{PumasAI}},
howpublished = {\url{https://tutorials.pumas.ai/}},
year = {2024},
note = {Accessed: Dec 2025}
}