Publications – Yandell Lab

2. Juarez EF, Peterson B, Sanford Kobayashi E, Gilmer S, Tobin LE, Schultz B, Lenberg J, Carroll J, Bai-Tong S, Sweeney NM, Beebe C, Stewart L, Olsen L, Reinke J, Kiernan EA, Reimers R, Wigby K, Tackaberry C, Yandell M, Hobbs C, Bainbridge MN (2025).

A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit.

NPJ Digit Med, 8(1), 72

3. Zimmerman RM, Hernandez EJ, Yandell M, Tristani-Firouzi M, Silver RM, Grobman W, Haas D, Saade G, Steller J, Blue NR (2024).

AI-based analysis of fetal growth restriction in a prospective obstetric cohort quantifies compound risks for perinatal morbidity and mortality and identifies previously unrecognized high risk clinical scenarios

Res Sq.

Kingsmore SF, Wright M, Smith LD, Liang Y, Mowrey WR, Protopsaltis L, Bainbridge M, Baker M, Batalov S, Blincow E, Cao B, Caylor S, Chambers C, Ellsworth K, Feigenbaum A, Frise E, Guidugli L, Hall KP, Hansen C, Kiel M, Van Der Kraan L, Krilow C, Kwon H, Madhavrao L, Lefebvre S, Leipzig J, Mardach R, Moore B, Oh D, Olsen L, Ontiveros E, Owen MJ, Reimers R, Scharer G, Schleit J, Shelnutt S, Mehtalia SS, Oriol A, Sanford E, Schwartz S, Wigby K, Willis MJ, Yandell M, Kunard CM, Defay T (2024).

Prequalification of genome-based newborn screening for severe childhood genetic diseases through federated training based on purifying hyperselection.

Am J Hum Genet, 111(12), 2618-2642.

Espino S, Watkins M, Probst R, Koch TL, Chase K, Imperial J, Robinson SD, Flrez Salcedo P, Taylor D, Gajewiak J, Yandell M, Safavi-Hemami H, Olivera BM (2024).

χ-Conotoxins are an Evolutionary Innovation of Mollusk-Hunting Cone Snails as a Counter-Adaptation to Prey Defense.

Mol Biol Evol, 41(11).

Koch TL, Robinson SD, Salcedo PF, Chase K, Biggs J, Fedosov AE, Yandell M, Olivera BM, Safavi-Hemami H (2024).

Prey Shifts Drive Venom Evolution in Cone Snails.

Mol Biol Evol, 41(8).

Allen-Brady K, Moore B, Verrilli LE, Alvord MA, Kern M, Camp N, Kelley K, Letourneau J, Cannon-Albright L, Yandell M, Johnstone EB, Welt CK (2024).

Breast Cancer is Increased in Women with Primary Ovarian Insufficiency

J Clin Endocrinol Metab.

Kiser AC, Schliep KC, Hernandez EJ, Peterson CM, Yandell M, Eilbeck K (2024).

An artificial intelligence approach for investigating multifactorial pain-related features of endometriosis.

PLoS One, 19(2), e0297998

Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Karthik F, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Faulkner M, MacLeod HM, Burns KM, Yandell M, Tristani-Firouzi M, George AL Jr, McNally EM (2024).

The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young.

Genome Med, 16(1), 13.

Maclary ET, Holt C, Concepcion GT, Sovi I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD (2023).

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F(1) hybrid

bioRxiv.

Miller TA, Hernandez EJ, Gaynor JW, Russell MW, Newburger JW, Chung W, Goldmuntz E, Cnota JF, Zyblewski SC, Mahle WT, Zak V, Ravishankar C, Kaltman JR, McCrindle BW, Clarke S, Votava-Smith JK, Graham EM, Seed M, Rudd N, Bernstein D, Lee TM, Yandell M, Tristani-Firouzi M (2023).

Genetic and clinical variables act synergistically to impact neurodevelopmental outcomes in children with single ventricle heart disease.

Commun Med (Lond), 3(1), 127.

McMahon KL, OBrien H, Schroeder CI, Deuis JR, Venkatachalam D, Huang D, Green BR, Bandyopadhyay PK, Li Q, Yandell M, Safavi-Hemami H, Olivera BM, Vetter I, Robinson SD (2023).

Identification of sodium channel toxins from marine cone snails of the subgenera Textilia and Afonsoconus.

Cell Mol Life Sci, 80(10), 287

Johnstone EB, Gorsi B, Coelho E, Moore B, Farr AM, Cooper AR, Mardis ER, Rajkovic A, Chow CY, Yandell M, Welt CK (2022).

DIS3 Variants are Associated With Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis

J Clin Endocrinol Metab, 108(9), 2330-2335.

Zimmerman RM, Hernandez EJ, Watkins WS, Blue N, Tristani-Firouzi M, Yandell M, Steinberg BA (2023).

An Explainable Artificial Intelligence Approach for Discovering Social Determinants of Health and Risk Interactions for Stroke in Patients With Atrial Fibrillation

Am J Cardiol, 201, 224-226

Yang G, Ullah HMA, Parker E, Gorsi B, Libowitz M, Maguire C, King JB, Coon H, Lopez-Larson M, Anderson JS, Yandell M, Shcheglovitov A (2023).

Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder

Mol Psychiatry, 28(6), 2525-2539

Timoshevskaya N, Ekut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, Mountcastle J, Haase B, Balacco JR, Formenti G, Pelan S, Sims Y, Howe K, Fedrigo O, Jarvis ED, Smith JJ (2023).

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

Cell Rep, 42(3), 112263.

Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL (2023).

The status of the human gene catalogue.

ArXiv.

Peterson B, Hernandez EJ, Hobbs C, Malone Jenkins S, Moore B, Rosales E, Zoucha S, Sanford E, Bainbridge MN, Frise E, Oriol A, Brunelli L, Kingsmore SF, Yandell M (2023).

Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning.

Genome Med, 15(1), 18.

Maclary ET, Holt C, Concepcion GT, Sovi I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD (2023).

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid.

G3 (Bethesda).

Zimmerman R, Bilen MA, Heath EI, Nandagopal L, Swami U, Kessel A, Jaeger E, Wesolowski S, Hernanadez EJ, Chipman J, Mack A, Ravindranathan D, Maughan BL, Nussenzveig R, Yandell M, Kohli M, Lilly MB, Sartor AO, Agarwal N, Barata PC (2022).

Comprehensive Genomic Profiling of Cell-Free DNA in Men With Advanced Prostate Cancer: Differences in Genomic Landscape Based on Race.

Oncologist, 27(10), e815-e818.

Swami U, Zimmerman RM, Nussenzveig RH, Hernandez EJ, Jo Y, Sayegh N, Wesolowski S, Kiedrowski LA, Barata PC, Lemmon GH, Bilen MA, Heath EI, Nandagopal L, Babiker HM, Pal SK, Lilly M, Maughan BL, Haaland B, Yandell M, Sartor O, Agarwal N (2022).

Genomic landscape of advanced prostate cancer patients with BRCA1 versus BRCA2 mutations as detected by comprehensive genomic profiling of cell-free DNA.

Front Oncol, 12, 966534.

Simeone CA, Wilkerson JL, Poss AM, Banks JA, Varre JV, Guevara JL, Hernandez EJ, Gorsi B, Atkinson DL, Turapov T, Frodsham SG, Morales JCF, ONeil K, Moore B, Yandell M, Summers SA, Krolewski AS, Holland WL, Pezzolesi MG (2022).

A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia.

NPJ Genom Med, 7(1), 43.

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 (2021).

Family Screening After Sudden Death in a Population-Based Study of Children.

Pediatrics, 149(4).

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 (2022).

Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia.

Mol Genet Genomic Med, 10(4), e1888.

Wesoowski 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 (2022).

An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records.

PLOS Digit Health, 1(1).