generated from alshedivat/al-folio
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpapers.bib
1318 lines (1317 loc) · 62.1 KB
/
papers.bib
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
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@article{wolken2024prek,
title={PreK-12 school and citywide wastewater monitoring of the enteric viruses astrovirus, rotavirus, and sapovirus},
author={Wolken, Madeline and Wang, Michael and Schedler, Julia and Campos Jr, Roberto H and Ensor, Katherine and Hopkins, Loren and Treangen, Todd and Stadler, Lauren B},
journal={Science of The Total Environment},
volume={931},
pages={172683},
year={2024},
publisher={Elsevier}
}
@article{wu2024rapid,
title={Rapid Genomic Characterization of High-Risk, Antibiotic Resistant Pathogens Using Long-Read Sequencing to Identify Nosocomial},
author={Wu, Chin-Ting and Spallone, Amy and Cantu, Sherry and Treangen, Todd and Shropshire, William and Bhatti, Micah and Glover, Israel and Liu, Xiaojun and Shelburne, Samuel and Kalia, Awdhesh},
journal={Antimicrobial Stewardship \& Healthcare Epidemiology},
volume={4},
number={S1},
pages={s106--s106},
year={2024},
publisher={Cambridge University Press}
}
@article{adenaiye2022infectious,
bibtex_show={true},
title = {Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled aerosols and efficacy of masks during early mild infection},
author = {Adenaiye, Oluwasanmi O and Lai, Jianyu and Bueno de Mesquita, P Jacob and Hong, Filbert and Youssefi, Somayeh and German, Jennifer and Tai, SH Sheldon and Albert, Barbara and Schanz, Maria and Weston, Stuart and others},
year = 2022,
journal = {Clinical Infectious Diseases},
publisher = {Oxford University Press US},
volume = 75,
number = 1,
pages = {e241--e248}
}
@article{agustinho2024unveiling,
bibtex_show = {true},
scholar_paper_id={BwyfMAYsbu0C},
title = {Unveiling microbial diversity: harnessing long-read sequencing technology},
author = {Agustinho, Daniel P and Fu, Yilei and Menon, Vipin K and Metcalf, Ginger A and Treangen, Todd J and Sedlazeck, Fritz J},
year = 2024,
journal = {Nature Methods},
publisher = {Nature Publishing Group US New York},
pages = {1--13}
}
@inproceedings{albin2019seqscreen,
bibtex_show={true},
title = {SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest},
author = {Albin, Dreycey and Nasko, Dan and Elworth, RA Leo and Lu, Jacob and Balaji, Advait and Diaz, Christian and Shah, Nidhi and Selengut, Jeremy and Hulme-Lowe, Chris and Muthu, Pravin and others},
year = 2019,
booktitle = {2019 IEEE international conference on bioinformatics and biomedicine (BIBM)},
pages = {1729--1736},
organization = {IEEE}
}
@article{amaral2024probiotic,
title = {Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury},
author = {Amaral, Wellington Z and Kokroko, Natalie and Treangen, Todd J and Villapol, Sonia and Gomez-Pinilla, Fernando},
year = 2024,
journal = {Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease},
publisher = {Elsevier},
pages = 167483
}
@article{azizpour2024graph,
bibtex_show={true},
title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly},
author = {Azizpour, Ali and Balaji, Advait and Treangen, Todd J and Segarra, Santiago},
year = 2024,
journal = {Genome Research},
publisher = {Cold Spring Harbor Lab},
pages = {gr--279136}
}
@inproceedings{azizpour2024grassrep,
bibtex_show={true},
title = {GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly},
author = {Azizpour, Ali and Balaji, Advait and Treangen, Todd J and Segarra, Santiago},
year = 2024,
booktitle = {International Conference on Research in Computational Molecular Biology},
pages = {372--376},
organization = {Springer Nature Switzerland Cham}
}
@article{balaji2020komb,
bibtex_show={true},
title = {KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities},
author = {Balaji, Advait and Sapoval, Nicolae and Seto, Charlie and Elworth, RA Leo and Nute, Michael G and Savidge, Tor and Segarra, Santiago and Treangen, Todd J},
year = 2020,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2020--05}
}
@article{balaji2022komb,
bibtex_show={true},
title = {KOMB: K-core based de novo characterization of copy number variation in microbiomes},
author = {Balaji, Advait and Sapoval, Nicolae and Seto, Charlie and Elworth, RA Leo and Fu, Yilei and Nute, Michael G and Savidge, Tor and Segarra, Santiago and Treangen, Todd J},
year = 2022,
journal = {Computational and Structural Biotechnology Journal},
publisher = {Elsevier},
volume = 20,
pages = {3208--3222}
}
@article{balaji2022seqscreen,
bibtex_show={true},
selected={true},
altmetric={130006025},
scholar_paper_id={CHSYGLWDkRkC},
title = {SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning},
author = {Balaji, Advait and Kille, Bryce and Kappell, Anthony D and Godbold, Gene D and Diep, Madeline and Elworth, RA Leo and Qian, Zhiqin and Albin, Dreycey and Nasko, Daniel J and Shah, Nidhi and others},
year = 2022,
journal = {Genome biology},
publisher = {BioMed Central London},
volume = 23,
number = 1,
pages = 133
}
@inproceedings{balaji2023seqscreen,
bibtex_show={true},
title = {SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens},
author = {Balaji, Advait and Liu, Yunxi and Nute, Michael G and Hu, Bingbing and D. Kappell, Anthony and S. Lesassier, Danielle and D. Godbold, Gene and Ternus, Krista and Treangen, Todd},
year = 2023,
booktitle = {Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
pages = {1--10}
}
@inproceedings{bateman2016limitations,
bibtex_show={true},
title = {Limitations of current approaches for reference-free, graph-based variant detection},
author = {Bateman, Amelia and Treangen, Todd J and Pop, Mihai},
year = 2016,
booktitle = {Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
pages = {499--500}
}
@article{benjamin2019diversified,
bibtex_show={true},
title = {Diversified race sampling on data streams applied to metagenomic sequence analysis. bioRxiv},
author = {Benjamin Coleman, Benito Geordie and Chou, Li and Elworth, RA Leo and Treangen, Todd J and Shrivastava, Anshumali},
year = 2019
}
@article{berry2021high,
bibtex_show={true},
title = {High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings},
author = {Berry, Irina Maljkovic and Treangen, Todd and Fung, Christian and Tai, Sheldon and Pollett, Simon and Hong, Filbert and Li, Tao and Pireku, Papa and Thomanna, Ashley and German, Jennifer and others},
year = 2021,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2021--07}
}
@article{cepeda2017metacompass,
bibtex_show={true},
title = {MetaCompass: reference-guided assembly of metagenomes},
author = {Cepeda, Victoria and Liu, Bo and Almeida, Mathieu and Hill, Christopher M and Koren, Sergey and Treangen, Todd J and Pop, Mihai},
year = 2017,
journal = {BioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = 212506
}
@article{chopyk2020comparative,
bibtex_show={true},
title = {Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications},
author = {Chopyk, Jessica and Nasko, Daniel J and Allard, Sarah and Bui, Anthony and Treangen, Todd and Pop, Mihai and Mongodin, Emmanuel F and Sapkota, Amy R},
year = 2020,
journal = {Water Research},
publisher = {Pergamon},
volume = 169,
pages = 115250
}
@article{coleman2019diversified,
bibtex_show={true},
title = {Diversified RACE sampling on data streams applied to metagenomic sequence analysis},
author = {Coleman, Benjamin and Geordie, Benito and Chou, Li and Elworth, RA Leo and Treangen, Todd J and Shrivastava, Anshumali},
year = 2019,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = 852889
}
@inproceedings{coleman2022one,
bibtex_show={true},
title = {One-pass diversified sampling with application to terabyte-scale genomic sequence streams},
author = {Coleman, Benjamin and Geordie, Benito and Chou, Li and Elworth, RA Leo and Treangen, Todd and Shrivastava, Anshumali},
year = 2022,
booktitle = {International Conference on Machine Learning},
pages = {4202--4218},
organization = {PMLR}
}
@article{curry2021takes,
bibtex_show={true},
title = {It takes guts to learn: machine learning techniques for disease detection from the gut microbiome},
author = {Curry, Kristen D and Nute, Michael G and Treangen, Todd J},
year = 2021,
journal = {Emerging Topics in Life Sciences},
publisher = {Portland Press Ltd.},
volume = 5,
number = 6,
pages = {815--827}
}
@article{curry2022emu,
bibtex_show={true},
scholar_paper_id={1sJd4Hv_s6UC},
selected={true},
altmetric={130469175},
title = {Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data},
author = {Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others},
year = 2022,
journal = {Nature methods},
publisher = {Nature Publishing Group US New York},
volume = 19,
number = 7,
pages = {845--853}
}
@article{curry2024microbial,
bibtex_show={true},
title = {Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu},
author = {Curry, Kristen D and Soriano, Sirena and Nute, Michael G and Villapol, Sonia and Dilthey, Alexander and Treangen, Todd J},
year = 2024,
journal = {Current Protocols},
volume = 4,
number = 3,
pages = {e978}
}
@article{curry2024reference,
bibtex_show={true},
title = {Reference-free structural variant detection in microbiomes via long-read coassembly graphs},
author = {Curry, Kristen D and Yu, Feiqiao Brian and Vance, Summer E and Segarra, Santiago and Bhaya, Devaki and Chikhi, Rayan and Rocha, Eduardo PC and Treangen, Todd J},
year = 2024,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory Preprints}
}
@article{curtis2012structure,
bibtex_show={true},
title = {Structure, function and diversity of the healthy human microbiome},
author = {Curtis, Huttenhower and Blaser, Martin J and Dirk, Gevers and Kota, Karthik C and Rob, Knight and Liu, Bo and Wang, Lu and Sahar, Abubucker and White, James R and Badger, Jonathan H and others},
year = 2012,
journal = {Nature (London)},
volume = 486,
number = 7402,
pages = {207--214}
}
@article{da2020comprehensive,
bibtex_show={true},
title = {Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact},
author = {da Silveira, Willian A and Fazelinia, Hossein and Rosenthal, Sara Brin and Laiakis, Evagelia C and Kim, Man S and Meydan, Cem and Kidane, Yared and Rathi, Komal S and Smith, Scott M and Stear, Benjamin and others},
year = 2020,
journal = {Cell},
publisher = {Elsevier},
volume = 183,
number = 5,
pages = {1185--1201}
}
@inproceedings{darling2006procrastination,
bibtex_show={true},
title = {Procrastination leads to efficient filtration for local multiple alignment},
author = {Darling, Aaron E and Treangen, Todd J and Zhang, Louxin and Kuiken, Carla and Messeguer, Xavier and Perna, Nicole T},
year = 2006,
booktitle = {International Workshop on Algorithms in Bioinformatics},
pages = {126--137},
organization = {Springer Berlin Heidelberg Berlin, Heidelberg}
}
@article{darling2007analyzing,
bibtex_show={true},
title = {Analyzing patterns of microbial evolution using the mauve genome alignment system},
author = {Darling, Aaron E and Treangen, Todd J and Messeguer, Xavier and Perna, Nicole T},
year = 2007,
journal = {Comparative genomics},
publisher = {Humana Press},
pages = {135--152}
}
@article{davison2016diversity,
bibtex_show={true},
title = {Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers},
author = {Davison, Michelle and Treangen, Todd J and Koren, Sergey and Pop, Mihai and Bhaya, Devaki},
year = 2016,
journal = {PloS one},
publisher = {Public Library of Science San Francisco, CA USA},
volume = 11,
number = 9,
pages = {e0160574}
}
@article{elworth2020petabytes,
bibtex_show={true},
title = {To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics},
author = {Elworth, RA Leo and Wang, Qi and Kota, Pavan K and Barberan, CJ and Coleman, Benjamin and Balaji, Advait and Gupta, Gaurav and Baraniuk, Richard G and Shrivastava, Anshumali and Treangen, Todd J},
year = 2020,
journal = {Nucleic acids research},
publisher = {Oxford University Press},
volume = 48,
number = 10,
pages = {5217--5234}
}
@article{elworth2020synthetic,
bibtex_show={true},
title = {Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides},
author = {Elworth, RA Leo and Diaz, Christian and Yang, Jing and de Figueiredo, Paul and Ternus, Krista and Treangen, Todd},
year = 2020,
journal = {PLoS Pathogens},
publisher = {Public Library of Science San Francisco, CA USA},
volume = 16,
number = 8,
pages = {e1008649}
}
@article{enk2011complete,
bibtex_show={true},
title = {Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths},
author = {Enk, Jacob and Devault, Alison and Debruyne, Regis and King, Christine E and Treangen, Todd and O'Rourke, Dennis and Salzberg, Steven L and Fisher, Daniel and MacPhee, Ross and Poinar, Hendrik},
year = 2011,
journal = {Genome biology},
publisher = {BioMed Central},
volume = 12,
pages = {1--8}
}
@inproceedings{eubank20232164,
bibtex_show={true},
title = {2164. Resistome patterns associated with vancomycin non-susceptibility in clinical Clostridioides difficile isolates},
author = {Eubank, Taryn A and Gonzales-Luna, Anne J and Hanson, Blake M and Treangen, Todd and Earl, Ashlee and Garey, Kevin W},
year = 2023,
booktitle = {Open Forum Infectious Diseases},
volume = 10,
number = {Supplement\_2},
pages = {ofad500--1787},
organization = {Oxford University Press US}
}
@article{fedarko2018hierarchically,
bibtex_show={true},
title = {Hierarchically visualizing metagenome assembly graphs with metagenomescope},
author = {Fedarko, Marcus and Ghurye, Jay and Treangen, Todd and Pop, Mihai},
year = 2018
}
@article{flinn2024antibiotic,
bibtex_show={true},
scholar_user_id={XBOSZ7YAAAAJ},
scholar_paper_id={9yKSN-GCB0IC},
title = {Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice.},
author = {Flinn, Hannah and Marshall, Austin and Holcomb, Morgan and Cruz-Pineda, Leonardo and Soriano, Sirena and Treangen, Todd and Villapol, Sonia},
year = 2024,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2024--05}
}
@article{fu2021vulcan,
bibtex_show={true},
title = {Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment},
author = {Fu, Yilei and Mahmoud, Medhat and Muraliraman, Viginesh Vaibhav and Sedlazeck, Fritz J and Treangen, Todd J},
year = 2021,
journal = {GigaScience},
publisher = {Oxford University Press},
volume = 10,
number = 9,
pages = {giab063}
}
@article{fu2023methphaser,
bibtex_show={true},
title = {MethPhaser: methylation-based haplotype phasing of human genomes},
author = {Fu, Yilei and Aganezov, Sergey and Mahmoud, Medhat and Beaulaurier, John and Juul, Sissel and Treangen, Todd J and Sedlazeck, Fritz J},
year = 2023,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2023--05}
}
@article{fu2024methphaser,
bibtex_show={true},
title = {MethPhaser: methylation-based long-read haplotype phasing of human genomes},
author = {Fu, Yilei and Aganezov, Sergey and Mahmoud, Medhat and Beaulaurier, John and Juul, Sissel and Treangen, Todd J and Sedlazeck, Fritz J},
year = 2024,
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
volume = 15,
number = 1,
pages = 5327
}
@article{gallego2022limited,
bibtex_show={true},
title = {Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters},
author = {Gallego-Garc{\'\i}a, Pilar and Varela, Nair and Est{\'e}vez-G{\'o}mez, Nuria and De Chiara, Loretta and Fern{\'a}ndez-Silva, Iria and Valverde, Diana and Sapoval, Nicolae and Treangen, Todd J and Regueiro, Benito and Cabrera-Alvargonz{\'a}lez, Jorge Julio and others},
year = 2022,
journal = {Virus Evolution},
publisher = {Oxford University Press UK},
volume = 8,
number = 1,
pages = {veac008}
}
@article{ghurye2019metacarvel,
bibtex_show={true},
title = {MetaCarvel: linking assembly graph motifs to biological variants},
author = {Ghurye, Jay and Treangen, Todd and Fedarko, Marcus and Hervey, W Judson and Pop, Mihai},
year = 2019,
journal = {Genome biology},
publisher = {BioMed Central},
volume = 20,
pages = {1--14}
}
@article{godbold2022categorizing,
bibtex_show={true},
title = {Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis},
author = {Godbold, Gene D and Kappell, Anthony D and LeSassier, Danielle S and Treangen, Todd J and Ternus, Krista L},
year = 2022,
journal = {Infection and immunity},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
volume = 90,
number = 5,
pages = {e00334--21}
}
@article{godbold2023improved,
bibtex_show={true},
title = {Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern},
author = {Godbold, Gene D and Hewitt, F Curtis and Kappell, Anthony D and Scholz, Matthew B and Agar, Stacy L and Treangen, Todd J and Ternus, Krista L and Sandbrink, Jonas B and Koblentz, Gregory D},
year = 2023,
journal = {Frontiers in Bioengineering and Biotechnology},
publisher = {Frontiers Media SA},
volume = 11,
pages = 1124100
}
@article{gupta2017gaurav,
bibtex_show={true},
title = {Gaurav Gupta},
author = {Gupta, Gaurav},
year = 2017
}
@article{gupta2019rambo,
bibtex_show={true},
title = {RAMBO: Repeated And Merged BloOm filter for ultra-fast Multiple Set Membership Testing (MSMT) on large-scale data},
author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Elworth, RA and Medini, Tharun and Treangen, Todd and Shrivastava, Anshumali},
year = 2019,
journal = {arXiv preprint arXiv:1910.02611}
}
@article{gupta2019sub,
bibtex_show={true},
title = {Sub-linear sequence search via a Repeated And Merged Bloom Filter (RAMBO): indexing 170 TB data in 14 hours},
author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Elworth, RA Leo and Treangen, Todd and Shrivastava, Anshumali},
year = 2019,
journal = {arXiv preprint arXiv:1910.04358}
}
@inproceedings{gupta2021fast,
bibtex_show={true},
title = {Fast processing and querying of 170tb of genomics data via a repeated and merged bloom filter (rambo)},
author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Kille, Bryce and Elworth, RA Leo and Medini, Tharun and Treangen, Todd and Shrivastava, Anshumali},
year = 2021,
booktitle = {Proceedings of the 2021 International Conference on Management of Data},
pages = {2226--2234}
}
@article{harrington2013genome,
bibtex_show={true},
title = {Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis},
author = {Harrington, Robin and Ondov, Brian D and Radune, Diana and Friss, Mary Beth and Klubnik, Joy and Diviak, Lynn and Hnath, Jonathan and Cendrowski, Stephen R and Blank, Thomas E and Karaolis, David and others},
year = 2013,
journal = {Genome announcements},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
volume = 1,
number = 1,
pages = {10--1128}
}
@inproceedings{hill2013novo,
bibtex_show={true},
title = {De novo likelihood-based measures for comparing metagenomic assemblies},
author = {Hill, Christopher M and Astrovskaya, Irina and Huang, Howard and Koren, Sergey and Memon, Atif and Treangen, Todd J and Pop, Mihai},
year = 2013,
booktitle = {2013 IEEE International Conference on Bioinformatics and Biomedicine},
pages = {94--98},
organization = {IEEE}
}
@article{holcomb2024probiotic,
bibtex_show={true},
scholar_user_id={XBOSZ7YAAAAJ},
scholar_paper_id={d1gkVwhDpl0C},
title = {Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice},
author = {Holcomb, Morgan and Marshall, Austin and Flinn, Hannah and Lozano, Mariana and Soriano, Sirena and Gomez-Pinilla, Fernando and Treangen, Todd J and Villapol, Sonia},
year = 2024,
journal = {Research Square},
publisher = {American Journal Experts}
}
@article{huang2023giab,
bibtex_show={true},
scholar_user_id={80dI_x8AAAAJ},
scholar_paper_id={u5HHmVD_uO8C},
title = {The GIAB genomic stratifications resource for human reference genomes},
author = {Dwarshuis, Nathan and Kalra, Divya and McDaniel, Jennifer and Sanio, Philippe and Soriano, Jerez and Pilar A, Jadhav and Huang, Wenyu and Mondal, Rajarshi and Busby, Ben and Olson, Nathanael D and Sedlazeck, Fritz J and Wagner, Justin and Majidian, Sina and Zook, Justin M},
year = 2023,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory}
}
@article{jochum2022analysis,
bibtex_show={true},
title = {Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease},
author = {Jochum, Michael and Lee, Michael D and Curry, Kristen and Zaksas, Victoria and Vitalis, Elizabeth and Treangen, Todd and Aagaard, Kjersti and Ternus, Krista L},
year = 2022,
journal = {Scientific Reports},
publisher = {Nature Publishing Group UK London},
volume = 12,
number = 1,
pages = 21125
}
@article{kasthuri2017draft,
bibtex_show={true},
title = {Draft Genome Sequences from a Novel Clade of Bacillus cereus{\'a}Sensu Lato Strains, Isolated from the International Space Station},
author = {Kasthuri, Venkateswaran and Aleksandra, Checinska Sielaff and Shashikala, Ratnayake and Pope, Robert K and Blank, Thomas E and Stepanov, Victor G and Fox, George E and van Tongeren Sandra, P and Torres, Clinton and Allen, Jonathan and others},
year = 2017,
journal = {Microbiology Resource Announcements},
publisher = {American Society for Microbiology},
number = 32
}
@article{schwalen2018bioinformatic,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={TFP_iSt0sucC},
title={Bioinformatic expansion and discovery of thiopeptide antibiotics},
author={Schwalen, Christopher J and Hudson, Graham A and Kille, Bryce and Mitchell, Douglas A},
journal={Journal of the American Chemical Society},
volume={140},
number={30},
pages={9494--9501},
year={2018},
publisher={ACS Publications}
}
@article{hudson2019bioinformatic,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={zA6iFVUQeVQC},
title={Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new C{$\alpha$}, C{$\beta$}, and C{$\gamma$}-linked thioether-containing peptides},
author={Hudson, Graham A and Burkhart, Brandon J and DiCaprio, Adam J and Schwalen, Christopher J and Kille, Bryce and Pogorelov, Taras V and Mitchell, Douglas A},
journal={Journal of the American Chemical Society},
volume={141},
number={20},
pages={8228--8238},
year={2019},
publisher={ACS Publications}
}
@inproceedings{kille2021accelerating,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={_xSYboBqXhAC},
title = {Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets},
author = {Kille, Bryce and Liu, Yunxi and Sapoval, Nicolae and Nute, Michael and Rauchwerger, Lawrence and Amato, Nancy and Treangen, Todd J},
year = 2021,
booktitle = {2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
pages = {204--208},
organization = {IEEE}
}
@article{kille2022multiple,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={nb7KW1ujOQ8C},
title = {Multiple genome alignment in the telomere-to-telomere assembly era},
author = {Kille, Bryce and Balaji, Advait and Sedlazeck, Fritz J and Nute, Michael and Treangen, Todd J},
year = 2022,
journal = {Genome Biology},
publisher = {BioMed Central London},
volume = 23,
number = 1,
pages = 182
}
@article{kille2023minmers,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={p2g8aNsByqUC},
title = {Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation},
author = {Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M},
year = 2023,
journal = {Bioinformatics},
publisher = {Oxford University Press},
volume = 39,
number = 9,
pages = {btad512}
}
@article{kille2024parsnp,
bibtex_show={true},
scholar_user_id={EUtkB0sAAAAJ},
scholar_paper_id={K3LRdlH-MEoC},
title = {Parsnp 2.0: scalable core-genome alignment for massive microbial datasets},
author = {Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J},
year = 2024,
journal = {Bioinformatics},
publisher = {Oxford University Press},
volume = 40,
number = 5,
pages = {btae311}
}
@article{kirby2022notes,
bibtex_show={true},
title = {Notes from the field: early evidence of the SARS-CoV-2 B. 1.1. 529 (Omicron) variant in community wastewater—United States, November--December 2021},
author = {Kirby, Amy E},
year = 2022,
journal = {MMWR. Morbidity and Mortality Weekly Report},
volume = 71
}
@article{koren2011bambus,
bibtex_show={true},
title = {Bambus 2: scaffolding metagenomes},
author = {Koren, Sergey and Treangen, Todd J and Pop, Mihai},
year = 2011,
journal = {Bioinformatics},
publisher = {Oxford University Press},
volume = 27,
number = 21,
pages = {2964--2971}
}
@article{koren2011scaffviz,
bibtex_show={true},
title = {ScaffViz: visualizing metagenome assemblies},
author = {Koren, Sergey and Treangen, Todd and Pop, Mihai},
year = 2011,
journal = {Genome Biology},
publisher = {Springer},
volume = 12,
pages = {1--27}
}
@article{koren2014automated,
bibtex_show={true},
title = {Automated ensemble assembly and validation of microbial genomes},
author = {Koren, Sergey and Treangen, Todd J and Hill, Christopher M and Pop, Mihai and Phillippy, Adam M},
year = 2014,
journal = {BMC bioinformatics},
publisher = {BioMed Central},
volume = 15,
pages = {1--9}
}
@article{liu2011accurate,
bibtex_show={true},
title = {Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences},
author = {Liu, Bo and Gibbons, Theodore and Ghodsi, Mohammad and Treangen, Todd and Pop, Mihai},
year = 2011,
journal = {BMC Genomics},
publisher = {BioMed Central Ltd},
volume = 12,
number = {Suppl 2},
pages = {S4}
}
@article{liu2012deep,
bibtex_show={true},
title = {Deep sequencing of the oral microbiome reveals signatures of periodontal disease},
author = {Liu, Bo and Faller, Lina L and Klitgord, Niels and Mazumdar, Varun and Ghodsi, Mohammad and Sommer, Daniel D and Gibbons, Theodore R and Treangen, Todd J and Chang, Yi-Chien and Li, Shan and others},
year = 2012,
journal = {PloS one},
publisher = {Public Library of Science San Francisco, USA},
volume = 7,
number = 6,
pages = {e37919}
}
@article{liu2022novo,
bibtex_show={true},
title = {De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee},
author = {Liu, Yunxi and Elworth, RA Leo and Jochum, Michael D and Aagaard, Kjersti M and Treangen, Todd J},
year = 2022,
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
volume = 13,
number = 1,
pages = 6799
}
@article{liu2022rescuing,
bibtex_show={true},
title = {Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data},
author = {Liu, Yunxi and Kearney, Joshua and Mahmoud, Medhat and Kille, Bryce and Sedlazeck, Fritz J and Treangen, Todd J},
year = 2022,
journal = {Nature communications},
publisher = {Nature Publishing Group UK London},
volume = 13,
number = 1,
pages = 1321
}
@article{liu2024crykey,
bibtex_show={true},
title = {Crykey: rapid identification of SARS-CoV-2 cryptic mutations in wastewater},
author = {Liu, Yunxi and Sapoval, Nicolae and Gallego-Garc{\'\i}a, Pilar and Tom{\'a}s, Laura and Posada, David and Treangen, Todd J and Stadler, Lauren B},
year = 2024,
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
volume = 15,
number = 1,
pages = 4545
}
@article{lou2022direct,
bibtex_show={true},
title = {Direct Comparison of Rt-Ddpcr and Targeted Amplicon Sequencing for Sars-Cov-2 Mutation Monitoring in Wastewater},
author = {Lou, Esther and Sapoval, Nicolae and McCall, Camille and Bauhs, Lauren and Carlson-Stadler, Russell and Kalvapalle, Prashant and Lai, Yanlai and Palmer, Kyle and Penn, Ryker and Rich, Whitney and others},
year = 2022,
journal = {SSRN Preprint},
publisher = {https://ssrn.com/abstract=4022373},
volume = 4022373
}
@article{lou2024sensitivity,
bibtex_show={true},
title = {Sensitivity and consistency of long-and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater},
author = {Lou, Esther G and Fu, Yilei and Wang, Qi and Treangen, Todd J and Stadler, Lauren B},
year = 2024,
journal = {Journal of Hazardous Materials},
publisher = {Elsevier},
volume = 469,
pages = 133939
}
@article{luan2024metacompass,
bibtex_show={true},
title = {MetaCompass: Reference-guided Assembly of Metagenomes},
author = {Luan, Tu and Cepeda, Victoria and Liu, Bo and Bowen, Zac and Ayyangar, Ujjwal and Almeida, Mathieu and Hill, Christopher M and Koren, Sergey and Treangen, Todd J and Porter, Adam and others},
year = 2024,
journal = {arXiv preprint arXiv:2403.01578}
}
@article{mahmoud2020methods,
bibtex_show={true},
title = {Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine},
author = {Mahmoud, Medhat and Gener, Alejandro Rafael and Khayat, Michael M and English, Adam C and Balaji, Advait and Zhou, Anbo and Hehn, Andreas and Fungtammasan, Arkarachai and Chrisman, Brianna Sierra and Chin, Chen-Shan and others},
year = 2020,
journal = {F1000Research},
publisher = {F1000 Research Limited},
volume = 9,
number = 1141,
pages = 1141
}
@article{marshall2024aerobiome,
bibtex_show={true},
scholar_user_id={XBOSZ7YAAAAJ},
scholar_paper_id={2osOgNQ5qMEC},
title = {Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies},
author = {Marshall, Austin and Fuller, Daniel T. and Dougall, Paul and Kumaragama, Kavindra and Dhaniyala, Suresh and Sur, Shantanu},
year = 2024,
journal = {Environ. Sci.: Atmos.},
publisher = {RSC},
volume = 4,
pages = {754--766},
}
@article{mc2021international,
bibtex_show={true},
title = {An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates},
author = {Mc Cartney, Ann M and Mahmoud, Medhat and Jochum, Michael and Agustinho, Daniel Paiva and Zorman, Barry and Al Khleifat, Ahmad and Dabbaghie, Fawaz and Kesharwani, Rupesh K and Smolka, Moritz and Dawood, Moez and others},
year = 2021,
journal = {F1000Research},
publisher = {Faculty of 1000 Ltd},
volume = 10
}
@article{mccall2023targeted,
bibtex_show={true},
scholar_user_id={pg2cWi8AAAAJ},
scholar_paper_id={u5HHmVD_uO8C},
title = {Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance},
author = {McCall, Camille and Leo Elworth, Ryan A and Wylie, Kristine M and Wylie, Todd N and Dyson, Katherine and Doughty, Ryan and Treangen, Todd J and Hopkins, Loren and Ensor, Katherine and Stadler, Lauren B},
year = 2023,
journal = {ACS ES\&T Water},
publisher = {American Chemical Society},
volume = 3,
number = 9,
pages = {2955--2965}
}
@article{mcdonald2021role,
bibtex_show={true},
title = {Role of miR-2392 in driving SARS-CoV-2 infection},
author = {McDonald, J Tyson and Enguita, Francisco J and Taylor, Deanne and Griffin, Robert J and Priebe, Waldemar and Emmett, Mark R and Sajadi, Mohammad M and Harris, Anthony D and Clement, Jean and Dybas, Joseph M and others},
year = 2021,
journal = {Cell reports},
publisher = {Elsevier},
volume = 37,
number = 3
}
@article{meisel2018current,
bibtex_show={true},
title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018},
author = {Meisel, Jacquelyn S and Nasko, Daniel J and Brubach, Brian and Cepeda-Espinoza, Victoria and Chopyk, Jessica and Corrada-Bravo, H{\'e}ctor and Fedarko, Marcus and Ghurye, Jay and Javkar, Kiran and Olson, Nathan D and others},
year = 2018,
journal = {Microbiome},
publisher = {BioMed Central},
volume = 6,
pages = {1--10}
}
@article{molino2021natural,
bibtex_show={true},
title = {Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial},
author = {Molino, Silvia and Pisarevsky, Andrea and Mingorance, Fabiana Lopez and Vega, Patricia and Stefanolo, Juan Pablo and Repetti, Julieta and Ludue{\~n}a, Guillermina and Pepa, Pablo and Olmos, Juan Ignacio and Fermepin, Marcelo Rodriguez and others},
year = 2021,
journal = {Trials},
publisher = {BioMed Central London},
volume = 22,
number = 1,
pages = 310
}
@article{muralidharan2024graph,
bibtex_show={true},
title = {Graph-based variant discovery reveals novel dynamics in the human microbiome},
author = {Muralidharan, Harihara Subrahmaniam and Michaelis, Jacquelyn S and Ghurye, Jay and Treangen, Todd and Koren, Sergey and Fedarko, Marcus and Pop, Mihai},
year = 2024,
journal = {arXiv preprint arXiv:2403.01610}
}
@article{nasko2018refseq,
bibtex_show={true},
title = {RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification},
author = {Nasko, Daniel J and Koren, Sergey and Phillippy, Adam M and Treangen, Todd J},
year = 2018,
journal = {Genome biology},
publisher = {BioMed Central},
volume = 19,
pages = {1--10}
}
@article{o2023ultra,
bibtex_show={true},
title = {Ultra-high throughput mapping of genetic design space},
author = {O’Connell, Ronan W and Rai, Kshitij and Piepergerdes, Trenton C and Wang, Yiduo and Samra, Kian D and Wilson, Jack A and Lin, Shujian and Zhang, Thomas H and Ramos, Eduardo M and Sun, Andrew and others},
year = 2023,
journal = {BioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2023--03}
}
@article{olson2017metagenomic,
bibtex_show={true},
title = {Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.},
author = {Olson, Nathanael D and Hill, Chris M and Cepeda-Espinoza, Vistoria and Ghurye, Jay and Koren, Sergey and Treangen, Todd J and Pop, Mihai},
year = 2017,
publisher = {Nathanael D. Olson, Chris M. Hill, Vistoria Cepeda-Espinoza, Jay Ghurye~…}
}
@article{olson2019metagenomic,
bibtex_show={true},
title = {Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes},
author = {Olson, Nathan D and Treangen, Todd J and Hill, Christopher M and Cepeda-Espinoza, Victoria and Ghurye, Jay and Koren, Sergey and Pop, Mihai},
year = 2019,
journal = {Briefings in bioinformatics},
publisher = {Oxford University Press},
volume = 20,
number = 4,
pages = {1140--1150}
}
@article{ondov2016mash,
bibtex_show={true},
title = {Mash: fast genome and metagenome distance estimation using MinHash},
author = {Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
year = 2016,
journal = {Genome biology},
publisher = {BioMed Central},
volume = 17,
pages = {1--14}
}
@article{park2022comprehensive,
bibtex_show={true},
title = {Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing},
author = {Park, So Hyun and Cao, Mingming and Pan, Yidan and Davis, Timothy H and Saxena, Lavanya and Deshmukh, Harshavardhan and Fu, Yilei and Treangen, Todd and Sheehan, Vivien A and Bao, Gang},
year = 2022,
journal = {Science Advances},
publisher = {American Association for the Advancement of Science},
volume = 8,
number = 42,
pages = {eabo7676}
}
@article{phillippy2012irreconcilable,
bibtex_show={true},
title = {Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone},
author = {Phillippy, Adam and Treangen, Todd},
year = 2012,
journal = {Genome Biology},
publisher = {BMC},
volume = 13,
number = 181
}
@article{pisarevsky2021fr578,
bibtex_show={true},
title = {Fr578 ORAL TANNINS REDUCE PROINFLAMMATORY CYTOKINES ASSOCIATED WITH DIARRHEA AND PNEUMONIA IN HOSPITALIZED COVID-19 PATIENTS.},
author = {Pisarevsky, Ana A and Mingorance, Fabiana Lopez and Vega, Patrica and Stefanolo, Juan P and Repetti, Julieta A and Ludue{\~n}a, Guillermina and Pepa, Pablo D and Olmos, Juan I and Fermepin, Marcelo Rodr{\'\i}guez and Molino, Silvia and others},
year = 2021,
journal = {Gastroenterology},
publisher = {Elsevier},
volume = 160,
number = 6,
pages = {S--371}
}
@article{pope2017draft,
bibtex_show={true},
title = {Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station},
author = {Pope, Robert K and Blank, Thomas E and Stepanov, Victor G and Fox, George E and van Tongeren, Sandra P and Torres, Clinton and Allen, Jonathan and Jaing, Crystal and Pierson, Duane and Perry, Jay and others},
year = 2017
}
@inproceedings{quintana2023leveraging,
bibtex_show={true},
title = {Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence},
author = {Quintana, Felix and Treangen, Todd and Kavraki, Lydia},
year = 2023,
booktitle = {Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
pages = {1--6}
}
@article{salzberg2012gage,
bibtex_show={true},
title = {GAGE: A critical evaluation of genome assemblies and assembly algorithms},
author = {Salzberg, Steven L and Phillippy, Adam M and Zimin, Aleksey and Puiu, Daniela and Magoc, Tanja and Koren, Sergey and Treangen, Todd J and Schatz, Michael C and Delcher, Arthur L and Roberts, Michael and others},
year = 2012,
journal = {Genome research},
publisher = {Cold Spring Harbor Lab},
volume = 22,
number = 3,
pages = {557--567}
}
@article{sapoval2021enhanced,
bibtex_show={true},
title = {Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater},
author = {Sapoval, Nicolae and Lou, Esther and Hopkins, Loren and Ensor, Katherine B and Schneider, Rebecca and Treangen, Todd J and Stadler, Lauren B},
year = 2021,
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
pages = {2021--09}
}
@article{sapoval2021intrahost,
bibtex_show={true},
title = {Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community},
author = {Sapoval, Nicolae and de Mesquita, P Jacob Bueno and Liu, Yunxi and Wang, Roger and Liu, Tian Rui and Garza, Josie and Williams, Torrey and Cadiz, Carmelli and Tan, Gene S and Van Bakel, Harm and others},
year = 2021,
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
pages = {2021--10}
}
@article{sapoval2021sars,
bibtex_show={true},
title = {SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission},
author = {Sapoval, Nicolae and Mahmoud, Medhat and Jochum, Michael D and Liu, Yunxi and Elworth, RA Leo and Wang, Qi and Albin, Dreycey and Ogilvie, Huw A and Lee, Michael D and Villapol, Sonia and others},
year = 2021,
journal = {Genome research},
publisher = {Cold Spring Harbor Lab},
volume = 31,
number = 4,
pages = {635--644}
}
@article{sapoval2022current,
bibtex_show={true},
title = {Current progress and open challenges for applying deep learning across the biosciences},
selected={true},
scholar_paper_id={1qzjygNMrQYC},
altmetric={125736934},
author = {Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others},
year = 2022,
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
volume = 13,
number = 1,
pages = 1728
}
@article{sapoval2023enabling,
bibtex_show={true},
title = {Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater},
author = {Sapoval, Nicolae and Liu, Yunxi and Lou, Esther G and Hopkins, Loren and Ensor, Katherine B and Schneider, Rebecca and Stadler, Lauren B and Treangen, Todd J},
year = 2023,
journal = {Nature Communications},
publisher = {Nature Publishing Group UK London},
volume = 14,
number = 1,
pages = 2834
}
@inproceedings{sapoval2023kombover,
bibtex_show={true},
title = {KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome},
author = {Sapoval, Nicolae and Tanevski, Marko and Treangen, Todd J},
year = 2023,
booktitle = {Pacific Symposium on Biocomputing 2024},
pages = {506--520}
}
@article{sapoval2024lightweight,
bibtex_show={true},
scholar_paper_id={ILKRHgRFtOwC},
title = {Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet},
author = {Sapoval, Nicolae and Liu, Yunxi and Curry, Kristen and Kille, Bryce and Huang, Wenyu and Kokroko, Natalie and Nute, Michael G and Tyshaieva, Alona and Dilthey, Alexander T and Molloy, Erin and others},
year = 2024,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2024--06}
}
@article{selvaraj2024identification,
bibtex_show={true},
title = {Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA},
author = {Selvaraj Anand, Selvalakshmi and Wu, Chin-Ting and Bremer, Jordan and Bhatti, Micah and Treangen, Todd J and Kalia, Awdhesh and Shelburne, Samuel A and Shropshire, William C},
year = 2024,
journal = {Microbial genomics},
publisher = {Microbiology Society},
volume = 10,
number = 2,
pages = {001201}
}
@article{shropshire2022systematic,
bibtex_show={true},
title = {Systematic analysis of mobile genetic elements mediating $\beta$-lactamase gene amplification in noncarbapenemase-producing carbapenem-resistant Enterobacterales bloodstream infections},
author = {Shropshire, WC and Konovalova, A and McDaneld, P and Gohel, M and Strope, B and Sahasrabhojane, P and Tran, CN and Greenberg, D and Kim, J and Zhan, X and others},
year = 2022,
journal = {Msystems},
publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
volume = 7,
number = 5,
pages = {e00476--22}
}
@article{soriano2021fecal,
bibtex_show={true},
title = {Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in young C57BL/6 mice},
author = {Soriano, Sirena and Curry, Kristen and Wang, Qi and Chow, Elsbeth and Treangen, Todd and Villapol, Sonia},
year = 2021,
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
pages = {2021--11}
}
@article{soriano2022alterations,
bibtex_show={true},
title = {Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study},
author = {Soriano, Sirena and Curry, Kristen and Sadrameli, Saeed S and Wang, Qi and Nute, Michael and Reeves, Elizabeth and Kabir, Rasadul and Wiese, Jonathan and Criswell, Amber and Schodrof, Sarah and others},
year = 2022,
journal = {Brain, Behavior, \& Immunity-Health},
publisher = {Elsevier},
volume = 21,
pages = 100438
}
@article{soriano2022fecal,
bibtex_show={true},
title = {Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls},
author = {Soriano, Sirena and Curry, Kristen and Wang, Qi and Chow, Elsbeth and Treangen, Todd J and Villapol, Sonia},
year = 2022,
journal = {International Journal of Molecular Sciences},
publisher = {MDPI},
volume = 23,
number = 9,
pages = 4476
}
@article{subrahmaniam2024graph,
bibtex_show={true},