Tomoki Nomakuchi, MD, PhD
Areas of expertise: Rare genetic neurodevelopmental disorders, Innovative molecular therapies
Locations: Main Building, Buerger Center for Advanced Pediatric Care
About Tomoki Nomakuchi, MD, PhD
Tomoki Nomakuchi, MD, PhD, is an attending physician-scientist in Pediatrics and Medical Genetics at Children’s Hospital of Philadelphia (CHOP), where he also serves as a research fellow. His work focuses on rare genetic neurodevelopmental disorders and innovative molecular therapies. Dr. Nomakuchi earned his MD/PhD in Molecular Genetics from Stony Brook University and completed his residency and fellowship at CHOP, where he served as Chief Resident in Genetics. He is an expert in the design and use of antisense oligonucleotide technology to treat rare diseases, and received additional specialized training in cell and gene therapy at CHOP. His ongoing research integrates iPSC models and biobank-driven analyses to uncover novel gene-phenotype associations and guide precision therapeutic strategies.
Titles
Attending Physician
Certifications
Pediatrics – American Board of Pediatrics
General Genetics and Molecular Genetics – American College of Genetics and Genomics
Awards and Honors
2015-2017, NIH (NINDS) F31 Predoctoral Ruth L. Kirschstein National Research Service Award (NRSA)
2015, Travel Award, 11th Annual Meeting of the Oligonucleotide Therapeutics Society, in Leiden, the Netherlands
2009, Summer Undergraduate Fellowship, Feinstein Institute at Northwell Health, NY
2008, Summer Undergraduate Fellowship, Hofstra University, NY
Leadership and Memberships
2022-present, American College of Medical Genetics and Genomics
2018-present, American Academy of Pediatrics
Editorial and Academic Positions
Editorial Positions
2024-present, Ad Hoc Reviewer, BMC Pediatrics
Academic and Institutional Committees
2022-present, Genetics Residency Candidate Selection Committee
Education & training
Graduate Degree
PhD in Molecular Genetics and Microbiology - Stony Brook University School of Medicine, New York, NY
Medical Degree
MD - Stony Brook University School of Medicine, New York, NY
Residency
Pediatrics and Medical Genetics - Children's Hospital of Philadelphia, Philadelphia, PA (Chief Resident)
Fellowship
Postdoctoral Fellowship - Children’s Hospital of Philadelphia, Philadelphia, PA
Publications
Publications
2025
Safonov A*, Nomakuchi T*, Chao E, Horton C, Dolinsky JS, Yussuf A, Richardson M, Speare V, Li S, Bogus ZC, Bonanni M, Raper A, Odia T, Wubbenhorst BS, Faulders E, Schuth EM, Loranger K, Zhang J, Scalise CB, ElNaggar A, Sha Y, Felker SA, Weitzel J, Kallish S, Ritchie MD, Regeneron Genetics Center, Penn Medicine BioBank, Nathanson KL, Drivas TG. "A genotype-first approach identifies high incidence of NF1 pathogenic variants with distinct disease associations". In press, Nature Communications (accepted Feb 2025).
*co-first authors
2024
Nomakuchi TT, Teferedegn EY, Li D, Muirhead KJ, Dubbs H, Leonard J, Muraresku C, Sergio E, Arnold K, Pizzino A, Skraban CM, Zackai EH, Wang K, Ganetzky RD, Vanderver AL, Ahrens-Nicklas RC, Bhoj EJK. Utility of genome sequencing in exome-negative pediatric patients with neurodevelopmental phenotypes. American Journal of Medical Genetics Part A. 2024;n/a(n/a):e63817.
Nomakuchi TT, Alves CAP, Beslow LA, Zarnow D, Goyal N, Zackai EH, Reynoso Santos FJ. Subdural Hemorrhage as an Early Presentation in a Case of Sotos Syndrome. Neuropediatrics. 2024 Feb;55(1):71–4.
2023
Kumar N, Nomakuchi T, Vossough A, Leonard JMM, Dubbs H, Agarwal S. A Case of INPP5E-Related Joubert Syndrome: Connecting Evolving Phenotype With Novel Genotype. Pediatr Neurol. 2023 Aug;145:112–4.
Nomakuchi TT, Danowitz M, Stewart B, Leonard J, Izumi K, Krantz I, Kolon TF, Langdon D, Skraban C, Van Batavia J, Zackai E, Jiao K, Linn R, Alexander C, Zaontz M, Vogiatzi MG, Pyle LC. Expanding the reproductive organ phenotype of CHD7-spectrum disorder. Am J Med Genet A. 2023 May;191(5):1418–24.
O’Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM. Neurodevelopmental disorder mutations in the purine biosynthetic enzyme IMPDH2 disrupt its allosteric regulation. J Biol Chem. 2023 Aug;299(8):105012.
2022
Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun. 2022 May 27;13(1):2978.
Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell. 2022 Jun 9;185(12):2057-2070.e15.
2021
Wild KT, Nomakuchi TT, Sheppard SE, Leavens KF, De León DD, Zackai EH. Hyperinsulinism in an individual with an EP300 variant of Rubinstein-Taybi syndrome. Am J Med Genet A. 2021 Apr;185(4):1251–5.
2018
Aznarez I, Nomakuchi TT, Tetenbaum-Novatt J, Rahman MA, Fregoso O, Rees H, Krainer AR. Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Rep. 2018 May 15;23(7):2186–98.
Sinha R, Kim YJ, Nomakuchi T, Sahashi K, Hua Y, Rigo F, Bennett CF, Krainer AR. Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice. Nucleic Acids Res. 2018 Jun 1;46(10):4833–44.
2016
Nomakuchi TT, Rigo F, Aznarez I, Krainer AR. Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay. Nat Biotechnol. 2016 Feb;34(2):164–6.
2013
Sahashi K, Ling KKY, Hua Y, Wilkinson JE, Nomakuchi T, Rigo F, Hung G, Xu D, Jiang YP, Lin RZ, Ko CP, Bennett CF, Krainer AR. Pathological impact of SMN2 mis-splicing in adult SMA mice. EMBO Mol Med. 2013 Oct;5(10):1586–601.
Lectures by Invitation
2023
Nomakuchi TT. “Biobank-based investigation of the phenotypic effects of rare variants within disease-associated genes”. Invited Research Seminar Speaker, Hofstra University, Hempstead, NY. Apr 2023.
2022
Nomakuchi TT. “Cutting Edge Cases Presented at David Smith Dysmorphology Workshop” CHOP Genetics Grand Rounds. Sept 2022.
Nomakuchi TT. “Common Diagnosis With An Unexpected Complication”. CHOP Genetics Grand Rounds. Apr 2022.