Hongying Shen, PhD
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Cellular & Molecular Physiology
ISTC building Rm120, 850 West Campus Drive , Yale West Campus
West Haven, CT 06516
United States
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Associate Professor Term
Biography
Hongying (Hoy) Shen is an assistant professor at Cellular & Molecular Physiology at Yale School of Medicine and Systems Biology Institute at Yale West Campus from Jan 2020. Dr. Shen is interested to use multidisciplinary approaches ranging from biochemistry, cell biology, genetics, molecular evolution, and metabolomics to study cellular metabolism underlying human health and diseases, which would ultimately offer new directions for diagnostics and therapeutics. Specifically, we will focus on the “deorphanization” of hundreds of enzymes and transporters of unknown functions that are encoded in the human genome and are important to cellular and organismal physiology.
Dr. Shen received her B.S. in chemistry from Nanjing University in China in 2006 and her Ph.D. in Molecular Biophysics and Biochemistry (MB&B) at Yale University in 2013, where she studied membrane curvature formation and lipid metabolism in endocytic trafficking in the laboratory of Dr. Pietro De Camilli at the cell biology department. She then completed her postdoctoral training with Dr. Vamsi Mootha at Massachusetts General Hospital and Harvard Medical School to develop integrated metabolomics and CRISPR screen approaches to study mitochondrial metabolism.
Last Updated on May 29, 2025.
Appointments
Cellular & Molecular Physiology
Associate Professor on TermPrimary
Other Departments & Organizations
- Cellular & Molecular Physiology
- Diabetes Research Center
- Interdepartmental Neuroscience Program
- Janeway Society
- Molecular Cell Biology, Genetics and Development
- Molecular Medicine, Pharmacology, and Physiology
- Neuroscience Track
- Wu Tsai Institute
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
Education & Training
- PhD
- Yale University, Molecular Biophysics and Biochemistry (2013)
- BS
- Nanjing University, China, Chemistry (2006)
Research
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Overview
Medical Research Interests
Cell Biology; Mass Spectrometry; Metabolism
ORCID
0000-0002-2115-7037- View Lab Website
Shen lab
Research at a Glance
Yale Co-Authors
Frequent collaborators of Hongying Shen's published research.
Publications Timeline
A big-picture view of Hongying Shen's research output by year.
Pietro De Camilli, MD
James Duncan, PhD
Kariona Grabinska, PhD
Shawn Ferguson, PhD
TuKiet Lam, PhD, BS
Xiaojian Shi
Former YSM
28Publications
2,667Citations
Publications
Featured Publications
Systems biochemistry to “deorphanize” human mitochondrial proteome
Miros F, Liu R, Shen H. Systems biochemistry to “deorphanize” human mitochondrial proteome. Molecular Cell 2022, 82: 2735-2737. PMID: 35931038, DOI: 10.1016/j.molcel.2022.07.005.Peer-Reviewed Original ResearchAltmetricCombinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS
Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nature Communications 2022, 13: 2483. PMID: 35513392, PMCID: PMC9072411, DOI: 10.1038/s41467-022-30126-9.Peer-Reviewed Original ResearchCitationsAltmetricThe Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
Shen H, Campanello GC, Flicker D, Grabarek Z, Hu J, Luo C, Banerjee R, Mootha VK. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell 2017, 171: 771-782.e11. PMID: 29056341, PMCID: PMC5827971, DOI: 10.1016/j.cell.2017.09.051.Peer-Reviewed Original ResearchCitationsAltmetricPhylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.
Byrne, K.L.; Szeligowski, R.V.; Shen, H. Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters. Biomolecules 2023, 13, 1314.Peer-Reviewed Original Research
2026
Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo
Fernandez Garcia M, Retallick-Townsley K, Pruitt A, Davidson E, Balafkan N, Warrell J, Huang T, Kibowen A, Chu Z, Dai Y, Fitzpatrick S, Meng R, Sen A, Cohen S, Livoti O, Khan S, Becker C, Luiz Teles e Silva A, Liu J, Dossou G, Cheung J, Liu S, Ghorbani S, Deans P, DeCiucis M, Emani P, Gao H, Shen H, Gerstein M, Wang Z, Huckins L, Hoffman E, Brennand K. Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo. Nature Neuroscience 2026, 29: 1079-1094. PMID: 42032432, PMCID: PMC13156037, DOI: 10.1038/s41593-026-02247-7.Peer-Reviewed Original ResearchCitationsAltmetric
2025
Cellular pan-chain acyl-CoA profiling reveals SLC25A42/SLC25A16 in mitochondrial CoA import and metabolism
Liu R, Zhang Z, Kyaw A, Grabińska K, Shah H, Shen H. Cellular pan-chain acyl-CoA profiling reveals SLC25A42/SLC25A16 in mitochondrial CoA import and metabolism. Nature Metabolism 2025, 7: 1871-1888. PMID: 40925986, PMCID: PMC12460162, DOI: 10.1038/s42255-025-01358-y.Peer-Reviewed Original ResearchCitationsAltmetricAn in vivo screen identifies NAT10 as a master regulator of brain metastasis
Chen J, Xu P, Cai W, Chen H, Wingrove E, Shi X, Li W, Biancon G, Zhang M, Balabaki A, Krop E, Asare E, Zhang Y, Yin M, Tebaldi T, Meier J, Westbrook T, Halene S, Liu Y, Shen H, Nguyen D, Yan Q. An in vivo screen identifies NAT10 as a master regulator of brain metastasis. Science Advances 2025, 11: eads6021. PMID: 40138393, PMCID: PMC11939035, DOI: 10.1126/sciadv.ads6021.Peer-Reviewed Original ResearchCitationsAltmetric
2023
Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis
Shi X, DeCiucis M, Grabinska K, Kanyo J, Liu A, Lam T, Shen H. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Molecular Cell 2023, 84: 802-810.e6. PMID: 38157846, PMCID: PMC10922821, DOI: 10.1016/j.molcel.2023.12.008.Peer-Reviewed Original ResearchCitationsAltmetricSalvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions
Skinner O, Blanco-Fernández J, Goodman R, Kawakami A, Shen H, Kemény L, Joesch-Cohen L, Rees M, Roth J, Fisher D, Mootha V, Jourdain A. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nature Metabolism 2023, 5: 765-776. PMID: 37198474, PMCID: PMC10229423, DOI: 10.1038/s42255-023-00774-2.Commentaries, Editorials and LettersCitationsAltmetricThe C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion
Onuchic L, Padovano V, Schena G, Rajendran V, Dong K, Shi X, Pandya R, Rai V, Gresko N, Ahmed O, Lam T, Wang W, Shen H, Somlo S, Caplan M. The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion. Nature Communications 2023, 14: 1790. PMID: 36997516, PMCID: PMC10063565, DOI: 10.1038/s41467-023-37449-1.Peer-Reviewed Original ResearchCitationsAltmetric
Academic Achievements & Community Involvement
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Honors
honor Rita Allen Foundation Scholar
09/01/2023National AwardRita Allen Foundationhonor 1907 Foundation Trailblazer Award in mental health
01/01/2022National Award1907 FoundationDetailsUnited Stateshonor Klingenstein-Simons Fellowship Award in Neurosciences
07/01/2021National AwardKlingenstein-Simons FoundationDetailsUnited Stateshonor Lois E. and Franklin H. Top, Jr., Yale Scholar Award
04/16/2021Yale School of Medicine AwardYale School of MedicineDetailsUnited Stateshonor Chan Zuckerberg Initiative Neurodegeneration Challenge Network Collaborative Pairs Pilot Project Awards
12/01/2020International AwardChan Zuckerberg InitiativeDetailsUnited States
News
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News
- May 25, 2026
Back to School: What Mitochondria Really Do
- September 15, 2025
How an Essential Vitamin B-Derived Nutrient Concentrates in Mitochondria
- March 26, 2025
A Genetic Screen Identifies a New Master Regulator of Brain Metastasis
- September 19, 2023
Investigators Launch Study Aimed at Accelerating Understanding of Bipolar Disorder
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Cellular & Molecular Physiology
ISTC building Rm120, 850 West Campus Drive , Yale West Campus
West Haven, CT 06516
United States