2025 ​​​​​​​

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• Kreienkamp RJ, Deutsch AJ, Huerta-Chagoya A, et al. Type 1 Diabetes Polygenic Scores Improve Diagnostic Accuracy in Pediatric Diabetes Care. Preprint. medRxiv. 2025;2025.03.06.25323229. Published 2025 Mar 13. doi:10.1101/2025.03.06.25323229

 

• Samad A, Avillach P, Kong SW, et al. The high prevalence of rare pulmonary diseases among patients with severe asthma. Preprint. American Thoracic Society (ATS) International Conference Proceedings. 2025.  

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• Kennedy JC, Vargas SO, Fishman MP, et al. A progranulin variant causing childhood interstitial lung disease responsive to anti-TNF-α biologic therapy. Med. Published online February 25, 2025. doi:10.1016/j.medj.2025.100607

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• Kong SW, Lee IH, Collen LV, et al. Discordance between a deep learning model and clinical-grade variant pathogenicity classification in a rare disease cohort. NPJ Genom Med. 2025;10(1):17. Published 2025 Feb 28. doi:10.1038/s41525-025-00480-w

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2024

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• Li M, Li X, Pan K, et al. Multisource representation learning for pediatric knowledge extraction from electronic health records. NPJ Digit Med. 2024;7(1):319. Published 2024 Nov 13. doi:10.1038/s41746-024-01320-4

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• Mandl KD, Gottlieb D, Mandel JC. Integration of AI in healthcare requires an interoperable digital data ecosystem. Nat Med. 2024;30(3):631-634. doi:10.1038/s41591-024-0210-8.

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• Mannix R, Borglund E, Monashefsky A, et al. Age-dependent differences in blood levels of glial fibrillary acidic protein but not ubiquitin carboxy-terminal hydrolase L1 in children. Neurology. 2024;103(3). doi:10.1212/wnl.0000000000209651.​​​

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• Jones JR, Gottlieb D, McMurry AJ, Atreja A, Desai PM, Dixon BE, Payne PRO, Saldanha AJ, Shankar P, Solad Y, Wilcox AB, Ali MS, Kang E, Martin AM, Sprouse E, Taylor DE, Terry M, Ignatov V, Mandl KD. Real world performance of the 21st Century Cures Act population-level application programming interface. J Am Med Inform Assoc. 2024;31(5):1144-1150. doi:10.1093/jamia/ocab022.

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• McMurry AJ, Gottlieb DI, Miller TA, et al. Cumulus: a federated electronic health record-based learning system powered by Fast Healthcare Interoperability Resources and artificial intelligence. J Am Med Inform Assoc. 2024;31(8):1638-1647. doi:10.1093/jamia/ocae130. PMID: 38860521; PMCID: PMC11258401.

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• Phelan D, Gottlieb D, Mandel JC, Ignatov V, Jones J, Marquard B, Ellis A, Mandl KD. Beyond compliance with the 21st Century Cures Act Rule: a patient controlled electronic health information export application programming interface. J Am Med Inform Assoc. 2024;31(4):901-909. doi:10.1093/jamia/ocab014.

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• Voorhies K, Mohammed A, Chinthala L, Kong SW, Lee IH, Kho AT, McGeachie M, Mandl KD, Raby B, Hayes M, Davis RL, Wu AC, Lutz SM. GSDMB/ORMDL3 Rare/Common Variants Are Associated with Inhaled Corticosteroid Response among Children with Asthma. Genes (Basel). 2024;15(4). doi:10.3390/genes15040313.

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• Xu R, Bode L, Geva A, Mandl KD, McMurry AJ. Accuracy of ICD-10 Codes for Suicidal Ideation and Action in Pediatric Emergency Department Encounters. Pediatr Emerg Care. Published online December 30, 2024. doi:10.1097/PEC.0000000000003328

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• Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell. 2024;84(2):261-276 e218. doi:10.1016/j.molcel.2023.11.032.

 

2023

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• Alecu JE, Saffari A, Ziegler M, Jordan C, Tam A, Kim S, Leung E, Szczaluba K, Mierzewska H, King SD, Santorelli FM, Yoon G, Trombetta B, Kivisakk P, Zhang B, Sahin M, Ebrahimi-Fakhari D. Plasma Neurofilament Light Chain Is Elevated in Adaptor Protein Complex 4-Related Hereditary Spastic Paraplegia. Mov Disord. 2023;38(9):1742-1750. doi:10.1002/mds.28992.

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• Babcock SJ, Flores-Marin D, Thiagarajah JR. The genetics of monogenic intestinal epithelial disorders. Hum Genet. 2023;142(5):613-654. doi:10.1007/s00439-023-02473-w.

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• Lee IH, Kong SW. ADGR: Admixture-Informed Differential Gene Regulation. Genes (Basel). 2023;14(1). doi:10.3390/genes14010059.

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• Lee IH, Walker DI, Lin Y, Smith MR, Mandl KD, Jones DP, Kong SW. Association between Neuroligin-1 polymorphism and plasma glutamine levels in individuals with autism spectrum disorder. EBioMedicine. 2023;95:104746. doi:10.1016/j.ebiom.2023.104746.

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• Miller TA, McMurry AJ, Jones J, Gottlieb D, Mandl KD. The SMART Text2FHIR Pipeline. AMIA Annu Symp Proc. 2023;2023:514-520. doi:10.1002/mds.28992.

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• Monashefsky A, Alon D, Baranowski T, Barreira TV, Chiu KA, Fleischman A, Green MC, Huang S, Samuels RC, Sousa CV, Thompson D, Lu AS. How much did it cost to develop and implement an eHealth intervention for a minority children population that overlapped with the COVID-19 pandemic? Contemp Clin Trials. 2023;125:107044. doi:10.1016/j.cct.2023.107044.

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• Perry J, Redfield S, Oza A, Rouse S, Stewart C, Khela H, Srinivasan T, Albano V, Shearer E, Kenna M. Exome Sequencing Expands the Genetic Diagnostic Spectrum for Pediatric Hearing Loss. Laryngoscope. 2023;133(9):2417-2424. doi:10.1002/lary.29883.

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• Saffari A, Kellner M, Jordan C, Rosengarten H, Mo A, Zhang B, Strelko O, Neuser S, Davis MY, Yoshikura N, Futamura N, Takeuchi T, Nabatame S, Ishiura H, Tsuji S, Aldeen HS, Cali E, Rocca C, Houlden H, Efthymiou S, Assmann B, Yoon G, Trombetta BA, Kivisakk P, Eichler F, Nan H, Takiyama Y, Tessa A, Santorelli FM, Sahin M, Blackstone C, Yang E, Schule R, Ebrahimi-Fakhari D. The clinical and molecular spectrum of ZFYVE26-associated hereditary spastic paraplegia: SPG15. Brain. 2023;146(5):2003-2015. doi:10.1093/brain/awab155.

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• Wang L, Zipursky AR, Geva A, McMurry AJ, Mandl KD, Miller TA. A computable case definition for patients with SARS-CoV2 testing that occurred outside the hospital. JAMIA Open. 2023;6(3):ooad047. doi:10.1093/jamiaopen/ooad047.

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2022 

 

• Abbasi W, French CE, Rockowitz S, Kenna MA, Eliot Shearer A. Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet. 2022;141(3-4):387-400. doi:10.1007/s00439-022-02475-3.

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• Al-Musa A, LaBere B, Habiballah S, Nguyen AA, Chou J. Advances in clinical outcomes: What we have learned during the COVID-19 pandemic. J Allergy Clin Immunol. 2022;149(2):569-578. doi:10.1016/j.jaci.2021.12.1289.

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• Alecu JE, Saffari A, Jumo H, Ziegler M, Strelko O, Brownstein CA, Gonzalez-Heydrich J, Rodan LH, Gorman MP, Sahin M, Ebrahimi-Fakhari D. Novel CAPN1 missense variants in complex hereditary spastic paraplegia with early-onset psychosis. Ann Clin Transl Neurol. 2022;9(4):570-576. doi:10.1002/acn3.51680.

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• Berger K, Arafat D, Chandrakasan S, Snapper SB, Gibson G. Targeted RNAseq Improves Clinical Diagnosis of Very Early-Onset Pediatric Immune Dysregulation. J Pers Med. 2022;12(6). doi:10.3390/jpm12060661.

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• Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M, Cho J, Shouval DS, Kammermeier J, Koletzko S, Bagalopal K, Capitani M, Cavounidis A, Pires E, Weidinger C, McCullagh J, Arkwright PD, Haller W, Siegmund B, Peters L, Jostins L, Travis SPL, Anderson CA, Snapper S, Klein C, Schadt E, Zilbauer M, Xavier R, Teichmann S, Muise AM, Regev A, Uhlig HH. An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease. Gastroenterology. 2022;162(3):859-876. doi:10.1053/j.gastro.2021.10.045.

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• Brownstein C, Douard E, Mollon J, Smith R, Hojlo M, Garvey E, Cabral K, Bowen J, Deaso E, Rao A, Genetti C, Carroll D, Knowles E, Agrawal P, Beggs A, D’Angelo E, Almasy L, Saci Z, Moreau C, Huguet G, Jacquemont S, Glahn D, Gonzalez-Heydrich J. Prevalence of Rate of Deleterious Copy Number Variants Similar in Early Onset Psychosis and Autism Spectrum Disorders: Implications for Clinical Practice. Biological Psychiatry. 2022;91(9):S56-S57. doi:10.1016/j.biopsych.2022.02.162.

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• Brownstein CA, Douard E, Mollon J, Smith R, Hojlo MA, Das A, Goldman M, Garvey E, Cabral K, Li J, Bowen J, Rao AS, Genetti C, Carroll D, Knowles EEM, Deaso E, Agrawal PB, Beggs AH, D'Angelo E, Almasy L, Alexander-Bloch A, Saci Z, Moreau CA, Huguet G, Deo AJ, Jacquemont S, Glahn DC, Gonzalez-Heydrich J. Similar Rates of Deleterious Copy Number Variants in Early-Onset Psychosis and Autism Spectrum Disorder. Am J Psychiatry. 2022;179(11):853-861. doi:10.1176/appi.ajp.2022.21101167.

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• Chopra M, Gable DL, Love-Nichols J, Tsao A, Rockowitz S, Sliz P, Barkoudah E, Bastianelli L, Coulter D, Davidson E, DeGusmao C, Fogelman D, Huth K, Marshall P, Nimec D, Sanders JS, Shore BJ, Snyder B, Stone SSD, Ubeda A, Watkins C, Berde C, Bolton J, Brownstein C, Costigan M, Ebrahimi-Fakhari D, Lai A, O'Donnell-Luria A, Paciorkowski AR, Pinto A, Pugh J, Rodan L, Roe E, Swanson L, Zhang B, Kruer MC, Sahin M, Poduri A, Srivastava S. Mendelian etiologies identified with whole exome sequencing in cerebral palsy. Ann Clin Transl Neurol. 2022;9(2):193-205. doi:10.1002/acn3.51670.

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• Chou J, Thomas PG, Randolph AG. Immunology of SARS-CoV-2 infection in children. Nat Immunol. 2022;23(2):177-185. doi:10.1038/s41590-022-01138-x.

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• Collen LV, Kim DY, Field M, Okoroafor I, Saccocia G, Whitcomb SD, Green J, Dong MD, Barends J, Carey B, Weatherly ME, Regeneron Genetics c, Rockowitz S, Sliz P, Liu E, Eran A, Grushkin-Lerner L, Bousvaros A, Muise AM, Klein C, Mitsialis V, Ouahed J, Snapper SB. Clinical Phenotypes and Outcomes in Monogenic Versus Non-monogenic Very Early Onset Inflammatory Bowel Disease. J Crohns Colitis. 2022;16(9):1380-1396. doi:10.1093/ecco-jcc/jjab096.

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• Collen LV, Salgado CA, Bao B, Janssen E, Weir D, Goldsmith J, Leichtner A, Sabery Khavari N, Gernez Y, Snapper SB. Cytotoxic T Lymphocyte Antigen 4 Haploinsufficiency Presenting As Refractory Celiac-Like Disease: Case Report. Front Immunol. 2022;13:894648. doi:10.3389/fimmu.2022.894648.

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• Dannheim K, Ouahed J, Field M, Snapper S, Raphael BP, Glover SC, Bishop PR, Bhesania N, Kamin D, Thiagarajah J, Goldsmith JD. Pediatric Gastrointestinal Histopathology in Patients With Tetratricopeptide Repeat Domain 7A (TTC7A) Germline Mutations: A Rare Condition Leading to Multiple Intestinal Atresias, Severe Combined Immunodeficiency, and Congenital Enteropathy. Am J Surg Pathol. 2022;46(6):846-853. doi:10.1097/PAS.0000000000001865.

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• Dohrn MF, Rebelo AP, Srivastava S, Cappuccio G, Smigiel R, Malhotra A, Basel D, van de Laar I, Neuteboom RF, Aarts-Tesselaar C, Mahida S, Brunetti-Pierri N, Taft RJ, Zuchner S. De Novo ATP1A1 Variants in an Early-Onset Complex Neurodevelopmental Syndrome. Neurology. 2022;98(11):440-445. doi:10.1212/WNL.0000000000012880.

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• Ghalandary M, Li Y, Frohlich T, Magg T, Liu Y, Rohlfs M, Hollizeck S, Conca R, Schwerd T, Uhlig HH, Bufler P, Koletzko S, Muise AM, Snapper SB, Hauck F, Klein C, Kotlarz D. Valosin-containing protein-regulated endoplasmic reticulum stress causes NOD2-dependent inflammatory responses. Sci Rep. 2022;12(1):3906. doi:10.1038/s41598-022-08547-w.

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• Gordon RJ, Pappa HM, Vajapeyam S, Mulkern R, Ecklund K, Snapper SB, Gordon CM. Bone marrow adiposity in pediatric Crohn's disease. Bone. 2022;162:116453. doi:10.1016/j.bone.2022.116453.

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• Gordon RJ, Wells R, Johansen C, Liu S, Dahlberg SE, Snapper SB, Rufo PA. Efficacy and Safety of High-dose Cholecalciferol in Patients With Inflammatory Bowel Disease Receiving Infliximab. J Pediatr Gastroenterol Nutr. 2022;74(4):476-483. doi:10.1097/MPG.0000000000003339.

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• Gutierrez-Sacristan A, Saez C, De Niz C, Jalali N, DeSain TN, Kumar R, Zachariasse JM, Fox KP, Palmer N, Kohane I, Avillach P. Multi-PheWAS intersection approach to identify sex differences across comorbidities in 59 140 pediatric patients with autism spectrum disorder. J Am Med Inform Assoc. 2022;29(2):230-238. doi:10.1093/jamia/ocab144.

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• Kan M, Diwadkar AR, Shuai H, Joo J, Wang AL, Ong MS, Sordillo JE, Iribarren C, Lu MX, Hernandez-Pacheco N, Perez-Garcia J, Gorenjak M, Potocnik U, Burchard EG, Pino-Yanes M, Wu AC, Himes BE. Multiomics analysis identifies BIRC3 as a novel glucocorticoid response-associated gene. J Allergy Clin Immunol. 2022;149(6):1981-1991. doi:10.1016/j.jaci.2022.02.005.

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• Kerur B, Fiedler K, Stahl M, Hyams J, Stephens M, Lu Y, Pfefferkorn M, Alkhouri R, Strople J, Kelsen J, Siebold L, Goyal A, Rosh JR, LeLeiko N, Van Limbergen J, Guerrerio AL, Maltz RM, Karam L, Crowley E, Griffiths AM, Heyman MB, Deneau M, Benkov K, Noe J, Moulton D, Pappa H, Galanko J, Snapper S, Muise AM, Kappelman MD, Benchimol EI. Utilization of Antitumor Necrosis Factor Biologics in Very Early Onset Inflammatory Bowel Disease: A Multicenter Retrospective Cohort Study From North America. J Pediatr Gastroenterol Nutr. 2022;75(1):64-69. doi:10.1097/MPG.0000000000003289.

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• Lee IH, Smith MR, Yazdani A, Sandhu S, Walker DI, Mandl KD, Jones DP, Kong SW. Comprehensive characterization of putative genetic influences on plasma metabolome in a pediatric cohort. Hum Genomics. 2022;16(1):67. doi:10.1186/s40246-022-00386-9.

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• Ouahed JD, Broggi A, Glick A, Haring RT, Field M, Chinnapen D, Grey MJ, Lencer W, Steiner SJ, Dennis-Heyward E, Shroyer N, Criss Z, Lin S-C, Zeng X-L, Crawford SE, Estes MK, Thiagarajah JR, Capilla A, Scoon W, Mostoslavsky G, Spence J, Klein C, Muise AM, Horwitz B, Zanoni I, Snapper SB. Variants in Interferon Lambda are Associated with Very Early Onset Inflammatory Bowel Disease. medRxiv. 2022:2022.2003.2017.22271929. doi:10.1101/2022.03.17.22271929.

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• Renella R, Gagne K, Beauchamp E, Fogel J, Perlov A, Sola M, Schlaeger T, Hofmann I, Shimamura A, Ebert BL, Schmitz-Abe K, Markianos K, Murphy K, Sun L, Rockowitz S, Sliz P, Campagna DR, Springer TA, Bahl C, Agarwal S, Fleming MD, Williams DA. Congenital X-linked neutropenia with myelodysplasia and somatic tetraploidy due to a germline mutation in SEPT6. Am J Hematol. 2022;97(1):18-29. doi:10.1002/ajh.26351.

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• Sigal GB, Novak T, Mathew A, Chou J, Zhang Y, Manjula N, Bathala P, Joe J, Padmanabhan N, Romero D, Allegri-Machado G, Joerger J, Loftis LL, Schwartz SP, Walker TC, Fitzgerald JC, Tarquinio KM, Zinter MS, Schuster JE, Halasa NB, Cullimore ML, Maddux AB, Staat MA, Irby K, Flori HR, Coates BM, Crandall H, Gertz SJ, Randolph AG, Pollock NR, Overcoming C-I. Measurement of Severe Acute Respiratory Syndrome Coronavirus 2 Antigens in Plasma of Pediatric Patients With Acute Coronavirus Disease 2019 or Multisystem Inflammatory Syndrome in Children Using an Ultrasensitive and Quantitative Immunoassay. Clin Infect Dis. 2022;75(8):1351-1358. doi:10.1093/cid/ciab101.

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• Tang J, Novak T, Hecker J, Grubbs G, Zahra FT, Bellusci L, Pourhashemi S, Chou J, Moffitt K, Halasa NB, Schwartz SP, Walker TC, Tarquinio KM, Zinter MS, Staat MA, Gertz SJ, Cvijanovich NZ, Schuster JE, Loftis LL, Coates BM, Mack EH, Irby K, Fitzgerald JC, Rowan CM, Kong M, Flori HR, Maddux AB, Shein SL, Crandall H, Hume JR, Hobbs CV, Tremoulet AH, Shimizu C, Burns JC, Chen SR, Moon HK, Lange C, Randolph AG, Khurana S. Cross-reactive immunity against the SARS-CoV-2 Omicron variant is low in pediatric patients with prior COVID-19 or MIS-C. Nat Commun. 2022;13(1):2979. doi:10.1038/s41467-022-24511-3.

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• Terek S, Del Rosario MC, Hain HS, Connolly JJ, Behr MA, Harr M, Hakonarson H, Holm IA. Attitudes among Parents towards Return of Disease-Related Polygenic Risk Scores (PRS) for Their Children. J Pers Med. 2022;12(12). doi:10.3390/jpm12121433.

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• Whitney JE, Lee IH, Lee JW, Kong SW. Evolution of multiple omics approaches to define pathophysiology of pediatric acute respiratory distress syndrome. Elife. 2022;11:e83444. doi:10.7554/eLife.83444.

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• Wobma H, Perkins R, Bartnikas L, Dedeoglu F, Chou J, Vleugels RA, Lo MS, Janssen E, Henderson LA, Whangbo J, Vargas SO, Fishman M, Krone KA, Casey A. Genetic diagnosis of immune dysregulation can lead to targeted therapy for interstitial lung disease: A case series and single center approach. Pediatr Pulmonol. 2022;57(7):1577-1587. doi:10.1002/ppul.25889.

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• Yao Y, Kim G, Shafer S, Chen Z, Kubo S, Ji Y, Luo J, Yang W, Perner SP, Kanellopoulou C, Park AY, Jiang P, Li J, Baris S, Aydiner EK, Ertem D, Mulder DJ, Warner N, Griffiths AM, Topf-Olivestone C, Kori M, Werner L, Ouahed J, Field M, Liu C, Schwarz B, Bosio CM, Ganesan S, Song J, Urlaub H, Oellerich T, Malaker SA, Zheng L, Bertozzi CR, Zhang Y, Matthews H, Montgomery W, Shih HY, Jiang J, Jones M, Baras A, Shuldiner A, Gonzaga-Jauregui C, Snapper SB, Muise AM, Shouval DS, Ozen A, Zhang Y, Stittrich A, Snapper SB, Chen K, Zhang K. Loss of function mutations in LRBA leads to Interferon (IFN)- and Tumor Necrosis Factor (TNF)-dominant Immune Dysregulation Syndrome. J Allergy Clin Immunol. 2022;149(2):582-595. doi:10.1016/j.jaci.2021.12.1291.

2021 

• Brownstein CA, Smith RS, Rodan LH, Gorman MP, Hojlo MA, Garvey EA, Li J, Cabral K, Bowen JJ, Rao AS, Genetti CA, Carroll D, Deaso EA, Agrawal PB, Rosenfeld JA, Bi W, Howe J, Stavropoulos DJ, Hansen AW, Hamoda HM, Pinard F, Caracansi A, Walsh CA, D'Angelo EJ, Beggs AH, Zarrei M, Gibbs RA, Scherer SW, Glahn DC, Gonzalez-Heydrich J. RCL1 copy number variants are associated with a range of neuropsychiatric phenotypes. Mol Psychiatry. 2021;26(5):1706-1718. doi:10.1038/s41380-021-01094-7.

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• Chou J, Platt CD, Habiballah S, Nguyen AA, Elkins M, Weeks S, Peters Z, Day-Lewis M, Novak T, Armant M, Williams L, Rockowitz S, Sliz P, Williams DA, Randolph AG, Geha RS, Taking on C-TSI. Mechanisms underlying genetic susceptibility to multisystem inflammatory syndrome in children (MIS-C). J Allergy Clin Immunol. 2021;148(3):732-738 e731. doi:10.1016/j.jaci.2021.05.038.

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• Chung MK, Smith MR, Lin Y, Walker DI, Jones D, Patel CJ, Kong SW. Plasma metabolomics of autism spectrum disorder and influence of shared components in proband families. Exposome. 2021;1(1):osab004. doi:10.1093/ioxopen/osab004.

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• Geva A, Liu M, Panickan VA, Avillach P, Cai T, Mandl KD. A high-throughput phenotyping algorithm is portable from adult to pediatric populations. J Am Med Inform Assoc. 2021;28(6):1265-1269. doi:10.1093/jamia/ocaa178.

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•  Gutierrez-Sacristan A, De Niz C, Kothari C, Kong SW, Mandl KD, Avillach P. GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. Brief Bioinform. 2021;22(1):55-65. doi:10.1093/bib/bbaa108. 

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• Johnson CL, Jazan E, Kong SW, Pennell KD. A two-step gas chromatography-tandem mass spectrometry method for measurement of multiple environmental pollutants in human plasma. Environ Sci Pollut Res Int. 2021;28(3):3266-3279. doi:10.1007/s11356-020-11162-0.

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• Klann JG, Estiri H, Weber GM, Moal B, Avillach P, Hong C, Tan ALM, Beaulieu-Jones BK, Castro V, Maulhardt T, Geva A, Malovini A, South AM, Visweswaran S, Morris M, Samayamuthu MJ, Omenn GS, Ngiam KY, Mandl KD, Boeker M, Olson KL, Mowery DL, Follett RW, Hanauer DA, Bellazzi R, Moore JH, Loh NW, Bell DS, Wagholikar KB, Chiovato L, Tibollo V, Rieg S, Li A, Jouhet V, Schriver E, Xia Z, Hutch M, Luo Y, Kohane IS, Brat GA, Murphy SN. Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. J Am Med Inform Assoc. 2021;28(7):1411-1420. doi:10.1093/jamia/ocaa255.

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• Lee IH, Lin Y, Alvarez WJ, Hernandez-Ferrer C, Mandl KD, Kong SW. WEScover: selection between clinical whole exome sequencing and gene panel testing. BMC Bioinformatics. 2021;22(1):259. doi:10.1186/s12859-021-04284-4.

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• Lee JW, Lee IH, Iimura T, Kong SW. Two macrophages, osteoclasts and microglia: from development to pleiotropy. Bone Res. 2021;9(1):11. doi:10.1038/s41413-021-00136-5.

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• Lee JW, Lee IH, Sato T, Kong SW, Iimura T. Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution. Dev Growth Differ. 2021;63(3):219-227. doi:10.1111/dgd.12767.

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•  Li Q, Dibus M, Casey A, et al. A homozygous stop-gain variant in ARHGAP42 is associated with childhood interstitial lung disease, systemic hypertension, and immunological findings. PLoS Genet. 2021;17(7):e1009639. doi:10.1371/journal.pgen.1009639.

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• Liu D, Olson KL, Manzi SF, Mandl KD. Patients dispensed medications with actionable pharmacogenomic biomarkers: rates and characteristics. Genet Med. 2021;23(4):782-786. doi:10.1038/s41436-020-01052-5.

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• McGraw D, Mandl KD. Privacy protections to encourage use of health-relevant digital data in a learning health system. NPJ Digit Med. 2021;4(1):2. doi:10.1038/s41746-020-00377-2.

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• Millington K, Chan YM. Lipoprotein subtypes after testosterone therapy in transmasculine adolescents. J Clin Lipidol. 2021;15(6):840-844. doi:10.1016/j.jacl.2021.09.022.

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• Platt CD, Zaman F, Bainter W, et al. Efficacy and economics of targeted panel versus whole-exome sequencing in 878 patients with suspected primary immunodeficiency. J Allergy Clin Immunol. 2021;147(2):723-726. doi:10.1016/j.jaci.2020.08.043.

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• Poussaint TY, LaRovere KL, Newburger JW, et al. Multisystem Inflammatory-like Syndrome in a Child Following COVID-19 mRNA Vaccination. Vaccines (Basel). 2021;10(1):41. doi:10.3390/vaccines10010041. 

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• Santoro JD, Kerr LM, Codden R, et al. Increased Prevalence of Familial Autoimmune Disease in Children With Opsoclonus-Myoclonus Syndrome. Neurol Neuroimmunol Neuroinflamm. 2021;8(6):e1119. doi:10.1212/NXI.0000000000001119.

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• Shubina-Oleinik O, Nist-Lund C, French C, et al. Dual-vector gene therapy restores cochlear amplification and auditory sensitivity in a mouse model of DFNB16 hearing loss. Sci Adv. 2021;7(51):eabi7629. doi:10.1126/sciadv.abi7629.

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• Zhang YJ, Jimenez L, Azova S, et al. Novel variants in the stem cell niche factor WNT2B define the disease phenotype as a congenital enteropathy with ocular dysgenesis. Eur J Hum Genet. 2021;29(6):998-1007. doi:10.1038/s41431-021-00896-8.

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2020

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• Alterovitz G, Heale B, Jones J, et al. FHIR Genomics: enabling standardization for precision medicine use cases. NPJ Genom Med. 2020;5:13. doi:10.1038/s41525-020-0129-0.

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• Geva A, Abman SH, Manzi SF, et al. Adverse drug event rates in pediatric pulmonary hypertension: a comparison of real-world data sources. J Am Med Inform Assoc. 2020;27(2):294-300. doi:10.1093/jamia/ocz224.

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• Geva A, Stedman JP, Manzi SF, et al. Adverse drug event presentation and tracking (ADEPT): semiautomated, high throughput pharmacovigilance using real-world data. JAMIA Open. 2020;3(3):413-421. doi:10.1093/jamiaopen/ooaa036.

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• Kong SW, Hernandez-Ferrer C. Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. PMID 31797630.

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• Lee IH, Lee JW, Kong SW. A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations. Infect Genet Evol. 2020;85:104507. doi:10.1016/j.meegid.2020.104507.

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• Lee IH, Negron JA, Hernandez-Ferrer C, et al. The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Hum Mutat. 2020;41(2):387-396. doi:10.1002/humu.23941.

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• Lee PY, Kellner ES, Huang Y, et al. Genotype and functional correlates of disease phenotype in deficiency of adenosine deaminase 2 (DADA2). J Allergy Clin Immunol. 2020;145(6):1664-1672.e1610. doi:10.1016/j.jaci.2019.12.915.

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• Lee PY, Platt CD, Weeks S, et al. Immune dysregulation and multisystem inflammatory syndrome in children (MIS-C) in individuals with haploinsufficiency of SOCS1. J Allergy Clin Immunol. 2020;146(5):1194-1200.e1191. doi:10.1016/j.jaci.2020.08.031.

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• Lin KJ, Rosenthal GE, Murphy SN, et al. External Validation of an Algorithm to Identify Patients with High Data-Completeness in Electronic Health Records for Comparative Effectiveness Research. Clin Epidemiol. 2020;12:133-141. doi:10.2147/CLEP.S236178.

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• Lorenzini T, Fliegauf M, Klammer N, et al. Characterization of the clinical and immunologic phenotype and management of 157 individuals with 56 distinct heterozygous NFKB1 mutations. J Allergy Clin Immunol. 2020;146(4):901-911. doi:10.1016/j.jaci.2020.08.011.

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• Luo Y, Eran A, Palmer N, et al. A multidimensional precision medicine approach identifies an autism subtype characterized by dyslipidemia. Nat Med. 2020;26(9):1375-1379. doi:10.1038/s41591-020-1006-6.

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• Mandl KD, Glauser T, Krantz ID, et al. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genet Med. 2020;22(2):371-380. doi:10.1038/s41436-019-0650-0.

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• Mengel D, Liu W, Glynn RJ, et al. Dynamics of plasma biomarkers in Down syndrome: the relative levels of Abeta42 decrease with age, whereas NT1 tau and NfL increase. Alzheimers Res Ther. 2020;12(1):27. doi:10.1186/s13195-020-00607-x.

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• Miller TA, Avillach P, Mandl KD. Experiences implementing scalable, containerized, cloud-based NLP for extracting biobank participant phenotypes at scale. JAMIA Open. 2020;3(2):185-189. doi:10.1093/jamiaopen/ooaa008.

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• Rockowitz S, LeCompte N, Carmack M, et al. Children's rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genom Med. 2020;5:29. doi:10.1038/s41525-020-0123-6.

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• Sayeed R, Gottlieb D, Mandl KD. SMART Markers: collecting patient-generated health data as a standardized property of health information technology. NPJ Digit Med. 2020;3:9. doi:10.1038/s41746-020-0247-1.

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• Serra EG, Schwerd T, Moutsianas L, et al. Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease. Nat Commun. 2020;11(1):995. doi:10.1038/s41467-020-14618-z.

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• Slyper M, Porter CBM, Ashenberg O, et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020;26(5):792-802. doi:10.1038/s41591-020-0844-1.

 

2019 

 

• Coravos A, Khozin S, Mandl KD. Developing and adopting safe and effective digital biomarkers to improve patient outcomes. NPJ Digit Med. 2019;2(1):14. doi:10.1038/s41746-019-0090-7.

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• Epi25 Collaborative. Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 Individuals. Am J Hum Genet. 2019;105(2):267-282. doi:10.1016/j.ajhg.2019.06.020.

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• Helbig I, Lopez-Hernandez T, Shor O, et al. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. Am J Hum Genet. 2019;104(6):1060-1072. doi:10.1016/j.ajhg.2019.04.009.

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• Hwang KB, Lee IH, Li H, et al. Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings. Sci Rep. 2019;9(1):3219. doi:10.1038/s41598-019-39984-7.

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2018 

 

• Helbig I, Riggs ER, Barry CA, et al. The ClinGen Epilepsy Gene Curation Expert Panel-Bridging the divide between clinical domain knowledge and formal gene curation criteria. Hum Mutat. 2018;39(11):1476-1484. doi:10.1002/humu.23627.

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• Helbig KL, Lauerer RJ, Bahr JC, et al. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet. 2018;103(5):666-678. doi:10.1016/j.ajhg.2018.09.016.

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•  International League Against Epilepsy Consortium on Complex Epilepsies. Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies. Nat Commun. 2018;9(1):5269. doi:10.1038/s41467-018-07524-z.

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• Keszei M, Record J, Kritikou JS, et al. Constitutive activation of WASp in X-linked neutropenia renders neutrophils hyperactive. J Clin Invest. 2018;128(9):4115-4131. doi:10.1172/JCI96764.

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•  Kong SW, Lee IH, Liu X, Hirschhorn JN, Mandl KD. Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genet Med. 2018;20(12):1617-1626. doi:10.1038/gim.2018.38.

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• Zaman T, Helbig I, Božović IB, et al. Mutations in SCN3A cause early infantile epileptic encephalopathy. Ann Neurol. 2018;83(4):703-717. doi:10.1002/ana.25191.

2017 

• Bourgeois FT, Avillach P, Kong SW, et al. Development of the Precision Link Biobank at Boston Children's Hospital: Challenges and Opportunities. J Pers Med. 2017;7(4):. doi:10.3390/jpm7040022.

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•  Helbig I, Lindhout D. Advancing the phenome alongside the genome in epilepsy studies. Neurology. 2017;89(1):14-15. doi:10.1212/WNL.0000000000004053.

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• Mandl KD, Bourgeois FT. The Evolution of Patient Diagnosis: From Art to Digital Data-Driven Science. JAMA. 2017;318(19):1859-1860. doi:10.1001/jama.2017.12894.

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• Shen D, Hernandez CC, Shen W, et al. De novo GABRG2 mutations associated with epileptic encephalopathies. Brain. 2017;140(1):49-67. doi:10.1093/brain/aww274.

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• Smith LA, Ullmann JF, Olson HE, et al. A Model Program for Translational Medicine in Epilepsy Genetics. J Child Neurol. 2017;32(4):429-436. doi:10.1177/0883073816686706.

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