Publications

  1. Young RE, Qiao L, Hernan R, Sweetser DA, Waxler JL, Scott DA, Scott TM, Lalani SR, Azamian MS, Rosenfeld JA, Bostwick B, Burrage LC, Rodan LH, Russell BE, Dutra-Clarke M, Kruer M, Bakhtiarim S, Darvish H, Amor DJ, Rahman S, Stals K, Bradley L, Byrne S, Tolusso LK, Wong B, Benedict L, Wallis K, Micke K, Colson C, Smol T, Southwick SV, Miller KA, Kush ML, Chorin O, Rothschild A, Wang W, Shen Y, Chung WK, Undiagnosed Diseases Network. LONP1 Variants Are Associated With Clinically Diverse Phenotypes. Clin Genet. 2026 Mar; 109 (3):437-457 Epub 2025 Sept 10
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  2. Gilbert RM, Jones DL, Wellmerling J, Caporarello N, Meridew JA, Choi KM, Haak AJ, Link PA, Tan Q, Lee JH, Ordog T, Ligresti G, Tschumperlin DJ. RUNX1 is a mediator of fibrotic activation and epigenetic memory in lung fibroblasts. Am J Respir Cell Mol Biol. 2026 Feb 11 [Epub ahead of print]
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  3. Keehan LA, Ono-Minagi H, Hadhud M, Rips J, Hinds DM, Fischer AJ, Bartlett JA, McCray PB, Qawasmi N, Nathan N, Louvrier C, Desroziers T, Damme M, Griese M, Wegner DJ, Cole FS, Wambach JA, Wheeler MT, Burbelo PD, Bonner DE, Bernstein JA, Chiorini JA, Breuer O, Milla C, Undiagnosed Diseases Network. Biallelic LAMP3 variants in 5 families with interstitial lung disease: Evidence of a disease-gene association. Genet Med. 2026 Feb 3; 28 (4):102531 Epub 2026 Feb 03
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  4. Stewart R, Ezell KM, Bell DS, Corner B, McMinn A, Cogan JD, Hamid R, Rives L, Phillips JA 3rd, Paddu N, Srivastava G, Marom R, Ladha FA, Soler-Alfonso C, Franciskovich R, Koziura M, Pruthi S, Richard G, Sheedy CB, Cassini T, Undiagnosed Diseases Network. Case Series of Nizon-Isidor Syndrome by Heterozygous Variants in MED12L With Further Evidence of Mitotic Instability in One Case With Diploid-Triploid Mosaicism. Am J Med Genet A. 2026 Jan; 200 (1):205-214 Epub 2025 Aug 21
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  5. Furuta Y, Ezell KM, Hamid R, Cogan JD, Cassini TA, Rives L, McMinn A, Shah S, Peltier AC, Layfield S, Fletcher RS, Tedder ML, Louie RJ, Lee JA, Kerkhof J, Rzasa J, Sadikovic B, Al Mamun A, Sheehan JH, Moth CW, Meiler J, Vawter-Lee M, Mendoza-Sengco PM, Holzen JB, Pruthi S, Phillips JA 3rd, Tinker RJ, Undiagnosed Diseases Network. Phenotypic Variability and Paternal Inheritance of a CHD8 Variant Causing Intellectual Developmental Disorder With Autism and Macrocephaly Confirmed by Epigenetic and Structural Analyses. Mol Genet Genomic Med. 2025 Dec; 13 (12):e70165
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  6. Cooperstein IB, Marwaha S, Ward A, Kobren SN, Carter JN, Wheeler MT, Undiagnosed Diseases Network, Marth GT. An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser. Genome Med. 2025 Oct 21; 17 (1):127
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  7. Dore R, Chang CT, Decleve A, Brunori G, Ludlam WG, Huang A, Movahedinia M, Damseh NS, Anwar I, Vahidi Mehrjardi MY, Ny A, Khorrami M, Kheirollahi M, Frederiksen H, Eghbal F, Mirjalili MR, Dehghani M, Karimiani EG, Oreshkov S, Alves C, Striano P, Suri M, Martinez-Agosto J, Ansar M, Zahid M, Akram S, Ansar M, Nelson SF, Antonarakis SE, Houlden H, Copmans D, Martemyanov KA, Maroofian R, Undiagnosed Diseases Network. ELFN1 deficiency: The mechanistic basis and phenotypic spectrum of a neurodevelopmental disorder with epilepsy. Genet Med. 2025 Sep; 27 (9):101506 Epub 2025 June 23
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  8. Kobren SN, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Corona RI, Carvalho Neto GV, Willett J, Berselli M, Ronchetti W, Nelson SF, Martinez-Agosto JA, Sherwood R, Krier J, Kohane IS, Sunyaev SR, Undiagnosed Diseases Network. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. Nat Commun. 2025 Aug 7; 16 (1):7267 Epub 2025 Aug 07
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  9. Fazal S, Dashnow H, Dohrn MF, Raposo J, Hiatt L, Danzi MC, Xu IRL, Toro C, Adams DR, Usdin K, Hayward B, Kobren SN, Sunyaev SR, Spillmann RC, Shashi V, Rebelo A, Bademci G, Tekin M, Quinlan AR, Zuchner S, Undiagnosed Diseases Network. A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort. Genet Med. 2025 Aug; 27 (8):101462 Epub 2025 May 22
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  10. Weisz-Hubshman M, Burrage LC, Jangam SV, Rosenfeld JA, von Hardenberg S, Bergmann A, Richter MF, Rydzanicz M, Ploski R, Stembalska A, Chung WK, Hernan RR, Lim FY, Brunet T, Syrbe S, Keren B, Heide S, Murdock DR, Dai H, Xia F, Ketkar S, Dawson B, Narayanan V, Graves HK, Wangler MF, Bacino C, Lee B, Undiagnosed Diseases Network. De novo variants in RYBP are associated with a severe neurodevelopmental disorder and congenital anomalies. Genet Med. 2025 Apr; 27 (4):101369 Epub 2025 Jan 28
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  11. Borja NA, Tinker RJ, Bivona SA, Smith CA, Locker TK, Fernandes S, Phillips JA 3rd, Stoler J, Taylor H, Zuchner S, Tekin M. Advancing Equity in Rare Disease Research: Insights From the Undiagnosed Disease Network. Am J Med Genet A. 2025 Feb; 197 (2):e63904 Epub 2024 Oct 14
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  12. Borja NA, Zafeer MF, Bivona S, Peart L, Gultekin SH, Bademci G, Tekin M, Undiagnosed Diseases Network NIH. KIF21A-associated peripheral neuropathy defined by impaired binding with TUBB3. J Med Genet. 2025 Jan 27; 62 (2):117-122
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  13. Fitzsimmons L, Beaulieu-Jones B, Kobren SN, Undiagnosed Diseases Network. Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. BioData Min. 2025 Jan 17; 18 (1):6
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  14. Tan J, Yu Y, He Y, Zheng J, Tan Q, Zhang X, Wan C, Zhang Z, Wu X, Tan R. Data Mining and Analysis for Iodinated Contrast Media Adverse Event Signals Based on the Food and Drug Administration Adverse Event Reporting System Database. Clin Ther. 2025 Jan; 47 (1):82-90 Epub 2024 Dec 02
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  15. McNamee L, Schoch K, Huang A, Lee H, Wang LK, Smith EC, Lark RK, Buckley AF, Jobanputra V, Nelson SF, Shashi V. Reanalysis of RNA sequencing data ends diagnostic odyssey and expands the phenotypic spectrum of congenital titinopathy. Am J Med Genet A. 2024 Nov; 194 (11):e63798 Epub 2024 June 24
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  16. Stellacci E, Carter JN, Pannone L, Stevenson D, Moslehi D, Venanzi S, Bernstein JA, Tartaglia M, Martinelli S. Immunological and hematological findings as major features in a patient with a new germline pathogenic CBL variant. Am J Med Genet A. 2024 Aug; 194 (8):e63627 Epub 2024 Apr 12
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  17. Tan Q, Wellmerling JH, Song S, Dresler SR, Meridew JA, Choi KM, Li Y, Prakash YS, Tschumperlin DJ. Targeting CEBPA to restore cellular identity and tissue homeostasis in pulmonary fibrosis. JCI Insight. 2024 Jul 16; 9 (16) Epub 2024 July 16
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  18. Ezell KM, Tinker RJ, Furuta Y, Gulsevin A, Bastarache L, Hamid R, Cogan JD, Rives L, Neumann S, Corner B, Kozuria M, Phillips JA 3rd. Undiagnosed Disease Network collaborative approach in diagnosing rare disease in a patient with a mosaic CACNA1D variant. Am J Med Genet A. 2024 Jul; 194 (7):e63597 Epub 2024 Mar 21
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  19. Wellmerling JH, Dresler SR, Meridew JA, Choi KM, Tschumperlin DJ, Tan Q. RNA-sequencing reveals differential fibroblast responses to bleomycin and pneumonectomy. Physiol Rep. 2024 Jul; 12 (13):e16148
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  20. Li Y, Prakash YS, Tan Q, Tschumperlin D. Defining signals that promote human alveolar type I differentiation. Am J Physiol Lung Cell Mol Physiol. 2024 Apr 1; 326 (4):L409-L418 Epub 2024 Feb 13
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  21. Park H, Bekaii-Saab T, Kim SS, Pishvaian MJ, Sunakawa Y, Kamath SD, Kawazoe A, Muro K, Zhen DB, Hirano H, Maestas E, Grierson P, Sugimoto N, Yamaguchi K, Ubowski M, Tan Q, Adelberg DE, Strickler JH. Results from the phase 1b/2 sgntuc-024 study: assessment of tucatinib, trastuzumab, and folfox for her2+ gi cancers. Journal of Clinical Oncology. 2024; 42 (3 Suppl):100
  22. Pham TX, Lee J, Guan J, Caporarello N, Meridew JA, Jones DL, Tan Q, Huang SK, Tschumperlin DJ, Ligresti G. Transcriptional analysis of lung fibroblasts identifies PIM1 signaling as a driver of aging-associated persistent fibrosis. JCI Insight. 2022 Mar 22; 7 (6)
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  23. Jones DL, Meridew JA, Link PA, Ducharme MT, Lydon KL, Choi KM, Caporarello N, Tan Q, Diaz Espinosa AM, Xiong Y, Lee JH, Ye Z, Yan H, Ordog T, Ligresti G, Varelas X, Tschumperlin DJ. ZNF416 is a pivotal transcriptional regulator of fibroblast mechanoactivation. J Cell Biol. 2021 May 3; 220 (5)
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  24. Tan Q, Link PA, Meridew JA, Pham TX, Caporarello N, Ligresti G, Tschumperlin DJ. Spontaneous Lung Fibrosis Resolution Reveals Novel Antifibrotic Regulators. Am J Respir Cell Mol Biol. 2021 Apr; 64 (4):453-464
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  25. Caporarello N, Meridew JA, Aravamudhan A, Jones DL, Austin SA, Pham TX, Haak AJ, Moo Choi K, Tan Q, Haresi A, Huang SK, Katusic ZS, Tschumperlin DJ, Ligresti G. Vascular dysfunction in aged mice contributes to persistent lung fibrosis. Aging Cell. 2020 Aug; 19 (8):e13196 Epub 2020 July 21
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  26. Aravamudhan A, Haak AJ, Choi KM, Meridew JA, Caporarello N, Jones DL, Tan Q, Ligresti G, Tschumperlin DJ. TBK1 regulates YAP/TAZ and fibrogenic fibroblast activation. Am J Physiol Lung Cell Mol Physiol. 2020 May 1; 318 (5):L852-L863 Epub 2020 Mar 11
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  27. Purdy MP, Ducharme M, Haak AJ, Ravix J, Tan Q, Sicard D, Prakash YS, Tschumperlin DJ, Stewart EA. YAP/TAZ are Activated by Mechanical and Hormonal Stimuli in Myometrium and Exhibit Increased Baseline Activation in Uterine Fibroids. Reprod Sci. 2020 Apr; 27 (4):1074-1085 Epub 2020 Feb 13
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  28. Liu W, Meridew JA, Aravamudhan A, Ligresti G, Tschumperlin DJ, Tan Q. Targeted regulation of fibroblast state by CRISPR-mediated CEBPA expression. Respir Res. 2019 Dec 11; 20 (1):281
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  29. Tan Q, Ma XY, Liu W, Meridew JA, Jones DL, Haak AJ, Sicard D, Ligresti G, Tschumperlin DJ. Nascent Lung Organoids Reveal Epithelium- and Bone Morphogenetic Protein-mediated Suppression of Fibroblast Activation. Am J Respir Cell Mol Biol. 2019 Nov; 61 (5):607-619
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  30. Haak AJ, Kostallari E, Sicard D, Ligresti G, Choi KM, Caporarello N, Jones DL, Tan Q, Meridew J, Diaz Espinosa AM, Aravamudhan A, Maiers JL, Britt RD Jr, Roden AC, Pabelick CM, Prakash YS, Nouraie SM, Li X, Zhang Y, Kass DJ, Lagares D, Tager AM, Varelas X, Shah VH, Tschumperlin DJ. Selective YAP/TAZ inhibition in fibroblasts via dopamine receptor D1 agonism reverses fibrosis. Sci Transl Med. 2019 Oct 30; 11 (516)
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  31. Caporarello N, Meridew JA, Jones DL, Tan Q, Haak AJ, Choi KM, Manlove LJ, Prakash YS, Tschumperlin DJ, Ligresti G. PGC1alpha repression in IPF fibroblasts drives a pathologic metabolic, secretory and fibrogenic state. Thorax. 2019 Aug; 74 (8):749-760 Epub 2019 June 10
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  32. Ligresti G, Caporarello N, Meridew JA, Jones DL, Tan Q, Choi KM, Haak AJ, Aravamudhan A, Roden AC, Prakash YS, Lomberk G, Urrutia RA, Tschumperlin DJ. CBX5/G9a/H3K9me-mediated gene repression is essential to fibroblast activation during lung fibrosis. JCI Insight. 2019 May 16; 5
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  33. Haak AJ, Tan Q, Tschumperlin DJ. Matrix biomechanics and dynamics in pulmonary fibrosis. Matrix Biol. 2018 Nov; 73:64-76 Epub 2017 Dec 21
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  34. Tan Q, Tschumperlin DJ. Epigenome Editing Enters the Arena. A New Tool to Reveal (and Reverse?) Pathologic Gene Regulation. Am J Respir Crit Care Med 2018 Sep 1; 198 (5):549-551
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  35. Tan Q, Choi KM, Sicard D, Tschumperlin DJ. Human airway organoid engineering as a step toward lung regeneration and disease modeling. Biomaterials. 2017 Jan; 113:118-132 Epub 2016 Oct 28
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  36. Tan Q, Lui PP, Lee YW. In vivo identity of tendon stem cells and the roles of stem cells in tendon healing. Stem Cells Dev. 2013 Dec 1; 22 (23):3128-40 Epub 2013 Aug 03
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  37. Rui YF, Lui PP, Wong YM, Tan Q, Chan KM. BMP-2 stimulated non-tenogenic differentiation and promoted proteoglycan deposition of tendon-derived stem cells (TDSCs) in vitro. J Orthop Res. 2013 May; 31 (5):746-53 Epub 2012 Dec 13
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  38. Rui YF, Lui PP, Wong YM, Tan Q, Chan KM. Altered fate of tendon-derived stem cells isolated from a failed tendon-healing animal model of tendinopathy. Stem Cells Dev. 2013 Apr 1; 22 (7):1076-85 Epub 2012 Dec 16
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  39. Ni M, Rui YF, Tan Q, Liu Y, Xu LL, Chan KM, Wang Y, Li G. Engineered scaffold-free tendon tissue produced by tendon-derived stem cells. Biomaterials. 2013 Mar; 34 (8):2024-37 Epub 2012 Dec 14
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  40. Wang SZ, Rui YF, Tan Q, Wang C. Enhancing intervertebral disc repair and regeneration through biology: platelet-rich plasma as an alternative strategy. Arthritis Res Ther. 2013; 15 (5):220
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  41. Tan Q, Lui PP, Rui YF, Wong YM. Comparison of potentials of stem cells isolated from tendon and bone marrow for musculoskeletal tissue engineering. Tissue Eng Part A. 2012 Apr; 18 (7-8):840-51 Epub 2011 Dec 13
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  42. Ni M, Lui PP, Rui YF, Lee YW, Lee YW, Tan Q, Wong YM, Kong SK, Lau PM, Li G, Chan KM. Tendon-derived stem cells (TDSCs) promote tendon repair in a rat patellar tendon window defect model. J Orthop Res. 2012 Apr; 30 (4):613-9 Epub 2011 Sept 16
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  43. Tan Q, Lui PP, Rui YF. Effect of in vitro passaging on the stem cell-related properties of tendon-derived stem cells-implications in tissue engineering. Stem Cells Dev. 2012 Mar 20; 21 (5):790-800 Epub 2011 Aug 08
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