All Publications
10.7554/eLife.63332
10.1016/j.eururo.2022.06.015
Nat Methods. 2022 Jun;19(6):770. doi: 10.1038/s41592-022-01538-8. Erratum for: Nat Methods. 2022 Apr;19(4):445-448. PMID: 35618956; PMCID: PMC9184272.

Blood. 2022 Apr 27:blood.2021015132. doi: 10.1182/blood.2021015132. Epub ahead of print. PMID: 35476648.
Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Yandell M, Tristani-Firouzi M, Etheridge SP, Webster G, George AL, McNally EM, MacLeod H, Burns KM. Family Screening After Sudden Death in a Population-Based Study of Children. Pediatrics. 2022 Apr 1;149(4):e2021054432. doi: 10.1542/peds.2021-054432. PMID: 35284934; PMCID: PMC9153292.
10.1542/peds.2021-054432

Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK. Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency. J Clin Endocrinol Metab. 2022 Feb 17;107(3):685-714. doi: 10.1210/clinem/dgab775. PMID: 34718612; PMCID: PMC9006976.
10.1210/clinem/dgab775

Nicholas TJ, Al-Sweel N, Farrell A, Mao R, Bayrak-Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren MA, Bonkowsky JL, Tristani-Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir RM, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med. 2022 Apr;10(4):e1888. doi: 10.1002/mgg3.1888. Epub 2022 Feb 4. PMID: 35119225; PMCID: PMC9000945.
10.1002/mgg3.1888
Wesołowski S, Lemmon G, Hernandez EJ, Henrie A, Miller TA, Weyhrauch D, Puchalski MD, Bray BE, Shah RU, Deshmukh VG, Delaney R, Yostl HJ, Eilbeck K, Tristani-Firouzi M, Yandell M. An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records. PLOS Digit Health. 2022;1(1):e0000004. doi: 10.1371/journal.pdig.0000004. Epub 2022 Jan 18. PMID: 35373216; PMCID: PMC8975108.
10.1371/journal.pdig.0000004
Current Biology. 2021. Nov 22. 31:1–8. https://doi.org/10.1016/j.cub.2021.08.068
PMC8612976
Nat Commun. 2021; 12: 6442. Published online 2021 Nov 8. doi: 10.1038/s41467-021-26741-7
PMC8575962
J Clin Transl Sci. 2021. Oct 28. 5(1):e177. doi: https://doi.org/10.1017/cts.2021.833
PMC8596074

Lemmon G, Wesolowski S, Henrie A, Tristani-Firouzi M, Yandell M. A Poisson binomial-based statistical testing framework for comorbidity discovery across electronic health record datasets. Nat Comput Sci. 2021 Oct;1(10):694-702. doi: 10.1038/s43588-021-00141-9. Epub 2021 Oct 21. PMID: 35252879; PMCID: PMC8896515.
De La Vega FM, Chowdhury S, Moore B, Frise E, McCarthy J, Hernandez EJ, Wong T, James K, Guidugli L, Agrawal PB, Genetti CA, Brownstein CA, Beggs AH, Löscher BS, Franke A, Boone B, Levy SE, Õunap K, Pajusalu S, Huentelman M, Ramsey K, Naymik M, Narayanan V, Veeraraghavan N, Billings P, Reese MG, Yandell M, Kingsmore SF. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med. 2021 Oct 14;13(1):153. doi: 10.1186/s13073-021-00965-0. PMID: 34645491; PMCID: PMC8515723.

Fertil Steril. 2021 Sept. 16(3):e207-e208. doi:10.1016/j.fertnstert.2021.07.568
bioRxiv . 2021 Jun 28;2021.02.03.429646. doi: 10.1101/2021.02.03.429646
PMID: 33564759
Sci Rep. 2021. Jun 22;11(1):13020. doi: 10.1038/s41598-021-92444-0
PMID: 34158539
Nature Comp Sci. 2021. June 21;1:441–447. https://doi.org/10.1038/s43588-021-00085-0
Bioinformatics. 2021. Jun 19:btab454. doi: 10.1093/bioinformatics/btab454
Oncologist. 2021. Jun 22. doi: 10.1002/onco.13869
PMID: 34157173

Human Mutation. 2021. June 13;1–15. Human Mutation. 2021;1–15
PMID: 34153142

Raquel Reisinger, Victor Sacristan Santos, Roberto Nussenzveig, Sergiusz Wesolowski, Edgar Javier Hernandez, Alexander Ryan Henrie, Benjamin L. Maughan, Umang Swami, Mark Yandell, Petros Grivas, and Neeraj Agarwal Journal of Clinical Oncology 2021 39:15_suppl, 4542-4542
10.1200/JCO.2021.39.15_suppl.4542 Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021) 4542-4542.
Genome Biol. 2021. May 25;22(1):161. doi: 10.1186/s13059-021-02380-5.
PMID: 34034781

Genome Res. 2021. May 4;31(7):1203-1215. doi: 10.1101/gr.272310.120
PMID: 33947700
Mol Biol Evol. 2021. May 3;msab127. doi: 10.1093/molbev/msab127.
PMID: 33944920

Genes (Basel). 2021. Apr 27;12(5):655. doi: 10.3390/genes12050655
PMID: 33925651
Nat Commun . 2021 Apr 12;12(1):2151. doi: 10.1038/s41467-021-22381-z
PMID: 33846313

PLoS One . 2021 Apr 8;16(4):e0241253. doi: 10.1371/journal.pone.0241253. eCollection 2021
PMID: 33830997 PMCID: PMC8031414

Am J Hum Genet . 2021 Apr 1;108(4):597-607. doi: 10.1016/j.ajhg.2021.02.012. Epub 2021 Mar 5
PMID: 33675682

Genome Med . 2021 Mar 26;13(1):46. doi: 10.1186/s13073-021-00854-6
PMID: 33771218 PMCID: PMC7995589

bioRxiv . 2021 Feb 4;2021.02.03.429646. doi: 10.1101/2021.02.03.429646. Preprint
PMID: 33564759 PMCID: PMC7872347
Hum Genet. 2021. Jan;140(1):217-227. doi: 10.1007/s00439-020-02236-1. Epub 2020 Nov 19. PMID: 33211200
PMID: 33211200

BMC Bioinformatics. 2020 Dec 9;21(1):569. doi: 10.1186/s12859-020-03917-4.
PMID: 33297934

medRxiv. 2020 Nov 6:2020.11.05.20224865. doi: 10.1101/2020.11.05.20224865. Preprint.
PMID: 33173897

HGG Adv. 2020 Oct 22;1(1):100008. doi: 10.1016/j.xhgg.2020.100008. Epub 2020 Aug 25.
PMID: 33263113
Circulation: Cardiovascular Quality and Outcomes, 13(10) October 2020, e006516

PLoSONE 15(9):e0238991

Nat Genet. 2020 Aug;52(8):769-777. doi: 10.1038/s41588-020-0652-z. Epub 2020 Jun 29.
PMID: 32601476
Biomedicines . 2020 Jul 22;8(8):E235. doi: 10.3390/biomedicines8080235.
PMID: 32708023
Genome Med. 2020; 12: 62. Published online 2020 Jul 14. doi: 10.1186/s13073-020-00761-2
PMC7362544

Cancer Cell . 2020 Jul 13;38(1):60-78.e12. doi: 10.1016/j.ccell.2020.05.001. Epub 2020 May 30.
PMID: 32473656
Nucleic Acids Res. 2020 Jul 9;48(12):6597-6610. doi: 10.1093/nar/gkaa454
PMID: 32479598
Am J Pathol . 2020 Jul;190(7):1438-1448. doi: 10.1016/j.ajpath.2020.03.005. Epub 2020 Apr 3.
PMID: 32251643
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305191/
PMID: 32561805

PLoS Genet . 2020 May 20;16(5):e1008274. doi: 10.1371/journal.pgen.1008274. eCollection 2020 May.
PMID: 32433666
Genome Biol Evol . 2020 May 1;12(5):684-700. doi: 10.1093/gbe/evaa083.
PMID: 32333764

Oncologist . 2020 Apr;25(4):327-333. doi: 10.1634/theoncologist.2019-0115. Epub 2019 Nov 11.
PMID: 32297439
PLoS One. 2020 Feb 21;15(2):e0229063. doi: 10.1371/journal.pone.0229063. eCollection 2020.
PMID: 32084206

PLoS Comput Biol . 2020 Jan 31;16(1):e1007625. doi: 10.1371/journal.pcbi.1007625. eCollection 2020 Jan.
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BMC Medical Genomics 12:190
PMID: 31829207

Nat Commun. 2019 Oct 17;10(1):4722. doi: 10.1038/s41467-019-12582-y.
PMID: 31624253

Elife. 2019 Sep 24;8. pii: e46922. doi: 10.7554/eLife.46922.
PMID: 31549960

Hepatology. 2019 Sep;70(3):899-910. doi: 10.1002/hep.30515. Epub 2019 Mar 21
PMID: 30664273

Clinical Imaging 58:108-113

BioRxiv doi: https://doi.org/10.1101/688671
J Clin Oncol 37 suppl 15:4548
J Clin Oncol 37 suppl 15:5043
J Clin Oncol 37 suppl 15:5032
Proc Natl Acad Sci U S A. 2019 May 7; 116(19): 9491–9500
PMCID: PMC6511033

Gigascience. 2019 Apr; 8(4): giz040. doi: 10.1093/gigascience/giz040
PMCID: PMC6479422

Genome Res. 2019 Apr;29(4):532-542. doi: 10.1101/gr.239442.118. Epub 2019 Mar 1
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Nat Commun. 2019; 10: 1784. Published online 2019 Apr 16. doi: 10.1038/s41467-018-08148-z
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J Clin Oncol 37 suppl 7:226
Science. 2018 Dec 14;362(6420). pii: eaat6576. doi: 10.1126/science.aat6576.
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Nat Genet. 2018 Dec 10. doi: 10.1038/s41588-018-0294-6. [Epub ahead of print]
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Toxins (Basel). 2018 Dec 1;10(12). pii: E503. doi: 10.3390/toxins10120503
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J Med Genet. 2018 Dec;55(12):824-830. doi: 10.1136/jmedgenet-2018-105561. Epub 2018 Sep 2
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Nat Genet. 2018 Oct;50(10):1366-1374. doi: 10.1038/s41588-018-0216-7. Epub 2018 Sep 17
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Elife. 2018 Aug 29;7. pii: e35453. doi: 10.7554/eLife.35453
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NPJ Genom Med. 2018 Aug 13;3:22. doi: 10.1038/s41525-018-0061-8. eCollection 2018
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PLoS One. 2018 Jul 25;13(7):e0197333. doi: 10.1371/journal.pone.0197333. eCollection 201
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Elife. 2018 Jul 17;7. pii: e34803. doi: 10.7554/eLife.34803
PMCID: PMC6050045

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474
PMCID: PMC6030976

Aliment Pharmacol Ther. 2018 Jul;48(2):219-225. doi: 10.1111/apt.14825. Epub 2018 Jun 4
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Gigascience. 2018 May 31. doi: 10.1093/gigascience/giy064. [Epub ahead of print]
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Plant Cell. 2018 May 9. pii: tpc.00194.2018. doi: 10.1105/tpc.18.00194. [Epub ahead of print]
PMID: 29743197
Bioinformatics. 2018 Apr 30. doi: 10.1093/bioinformatics/bty358. [Epub ahead of print]
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Nat Genet. 2018 Apr 26. doi: 10.1038/s41588-018-0107-y. [Epub ahead of print]
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Bioinformatics. 2018 Apr 25. doi: 10.1093/bioinformatics/bty324. [Epub ahead of print]
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Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O’Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.
Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29

Leukemia. 2018 Mar 27. doi: 10.1038/s41375-018-0050-z. [Epub ahead of print]
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G3 (Bethesda). 2018 Mar 8. pii: g3.300443.2017. doi: 10.1534/g3.117.300443. [Epub ahead of print]
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Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699
PMID: 29096012

BMC Bioinformatics. 2018 Feb 20;19(1):57. doi: 10.1186/s12859-018-2056-y.
PMID: 29463208

J Clin Endocrinol Metab. 2018 Feb 1;103(2):555-563. doi: 10.1210/jc.2017-01966
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BJOG. 2018 Feb;125(3):343-350. doi: 10.1111/1471-0528.14485. Epub 2017 Jan 31
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Nat Genet. 2018 Jan 22. doi: 10.1038/s41588-017-0036-1. [Epub ahead of print]
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Nat Methods. 2018 Jan 8. doi: 10.1038/nmeth.4556. [Epub ahead of print]
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Int J Radiat Oncol Biol Phys. 2018 Jan 1;100(1):162-173. doi: 10.1016/j.ijrobp.2017.08.033. Epub 2017 Sep 21
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Nucleic Acids Res. 2017 Dec 23. doi: 10.1093/nar/gkx1280. [Epub ahead of print]
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J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.
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Nat Genet. 2017 Nov;49(11):1593-1601. doi: 10.1038/ng.3970. Epub 2017 Oct 9
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Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3
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Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090
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Nat Rev Genet. 2017 Oct;18(10):599-612. doi: 10.1038/nrg.2017.52. Epub 2017 Aug 14.
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J Infect Dis. 2017 Sep 15;216(6):688-696. doi: 10.1093/infdis/jix352.
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Genome Biol Evol. 2017 Sep 1;9(9):2211-2225. doi: 10.1093/gbe/evx157
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G3 (Bethesda). 2017 Jul 27. pii: g3.300078.2017. doi: 10.1534/g3.117.300078. [Epub ahead of print]
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Neurology. 2017 Jul 18;89(3):226-233. doi: 10.1212/WNL.0000000000004109. Epub 2017 Jun 22
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J Mol Diagn. 2017 May;19(3):417-426. doi: 10.1016/j.jmoldx.2016.12.001. Epub 2017 Mar 18.
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BMC Genomics. 2017 May 22;18(1):396. doi: 10.1186/s12864-017-3767-6
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Mar Drugs. 2017 May 20;15(5). pii: E145
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PLoS Genet. 2017 Apr 27;13(4):e1006675. doi: 10.1371/journal.pgen.1006675. eCollection 2017 Apr
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J. Endocr. Soc. (2017) 1 (3): 162-173

Bioinformatics. 2017 Feb 6. doi: 10.1093/bioinformatics/btx057
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Am J Hum Genet. 2017 Jan 30. pii: S0002-9297(17)30017-4. doi: 10.1016/j.ajhg.2017.01.017. [Epub ahead of print]
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Bioinformatics. 2016 Dec 23. pii: btw799. doi: 10.1093/bioinformatics/btw799. [Epub ahead of print]
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J Virol. 2016 Dec 7. pii: JVI.01428-16. [Epub ahead of print]
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Genome Med. 2016 Aug 25;8(1):91. doi: 10.1186/s13073-016-0341-9
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Leukemia. 2016 Aug 2. doi: 10.1038/leu.2016.218.
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JAMA Otolaryngol Head Neck Surg. 2016 Jun 16. doi: 10.1001/jamaoto.2016.1444
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Curr Protoc Bioinformatics. 2015 Dec 17;52:4.1.1-4.1.17. doi: 10.1002/0471250953.bi0401s52
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Trends Genet. 2015 Nov;31(11):613-26. doi: 10.1016/j.tig.2015.09.002. Epub 2015 Oct 8
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Nucleic Acids Res. 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575. Epub 2015 Jun 1
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Nature 526, 68–74 (01 October 2015) doi:10.1038/nature15393
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J Cell Biol. 2014 Dec 22;207(6):705-15. doi: 10.1083/jcb.201409123.
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AMIA Annu Symp Proc. 2014 Nov 14;2014:496-505. eCollection 2014
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Gigascience. 2014 Oct 20;3:22. doi: 10.1186/2047-217X-3-22. eCollection 2014.
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Cancer Inform. 2014 Oct 15;13(Suppl 4):45-52. doi: 10.4137/CIN.S13979. eCollection 2014.
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BMC Genomics. 2014 Sep 16;15:795. doi: 10.1186/1471-2164-15-795.
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Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.
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Stem Cell Reports. 2014 Sep 9;3(3):475-88. doi: 10.1016/j.stemcr.2014.06.019. Epub 2014 Jul 31.
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Curr Protoc Bioinformatics. 2014 Sep 8;47:11.12.1-11.12.34. doi: 10.1002/0471250953.bi1112s47.
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Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.
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PLoS One. 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014
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