Publications

Joynt AT, Kavanagh EW, Newby GA, Mitchell S, Eastman AC, Paul KC, Bowling AD, Osorio DL, Merlo CA, Patel SU, Raraigh KS, Liu DR, Sharma N, Cutting GR. Protospacer modification improves base editing of a canonical splice site variant and recovery of CFTR function in human airway epithelial cells. Mol Ther Nucleic Acids. 2023 Jun 29;33:335-350. doi: 10.1016/j.omtn.2023.06.020. PMID: 37547293; PMCID: PMC10400809.

Shinder, I., Hu, R., Ji, H.J. et al. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes. Nat Commun 14, 7223 (2023). https://doi.org/10.1038/s41467-023-43017-4
https://rdcu.be/dtq27

Yeung-Luk BH, Wally A, Swaby C, Jauregui S, Lee E, Zhang R, Chen D, Luk SH, Upadya N, Tieng E, Wilmsen K, Sherman E, Sudhakar D, Luk M, Shrivastav AK, Cao S, Ghosh B, Christenson SA, Huang YJ, Ortega VE, Biswal S, Tang WY, Sidhaye VK. Epigenetic Reprogramming Drives Epithelial Disruption in COPD. Am J Respir Cell Mol Biol. 2023 Nov 17. doi: 10.1165/rcmb.2023-0147OC. Epub ahead of print. PMID: 37976469.
https://www.atsjournals.org/doi/10.1165/rcmb.2023-0147OC

Swaby C, Yeung-Luk B, Thapa S, Nishida K, Wally A, Ghosh B, Niederkofler A, Luk S, Girgis M, Keller A, Cortez C, Ramaswamy S, Wilmsen K, Bouché L, Dell A, Drummond MB, Putcha N, Haslam SM, Mathias R, Hansel NN, Sheng J, Sidhaye V. Decreased fucosylation impacts epithelial integrity and increases risk for COPD. bioRxiv [Preprint]. 2023 Nov 2:2023.10.31.564805. doi: 10.1101/2023.10.31.564805. PMID: 37961411; PMCID: PMC10635007.
https://www.biorxiv.org/content/10.1101/2023.10.31.564805v1

Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K. H., Park, S., Hein, J., Pockrand, C., Shumate, A., Rincon, N., Puiu, S., Steinegger, M., Salzberg, S. L., & Pertea, M. (2023). CHESS 3: An improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. Genome Biology, 24, 249.
https://doi.org/10.1186/s13059-023-03088-4

Lagowala DA, Wally A, Wilmsen K, Kim B, Yeung-Luk B, Choi J, Swaby C, Luk M, Feller L, Ghosh B, Niedrkofler A, Tieng E, Sherman E, Chen D, Upadya N, Zhang R, Kim DH, Sidhaye V. Microphysiological Models of Lung Epithelium-Alveolar Macrophage Co-Cultures to Study Chronic Lung Disease. Adv Biol (Weinh). 2023 Oct 15:e2300165. doi: 10.1002/adbi.202300165. Epub ahead of print. PMID: 37840439.
https://onlinelibrary.wiley.com/doi/10.1002/adbi.202300165

Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O’Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23. PMID: 37612512; PMCID: PMC10752217.
https://www.nature.com/articles/s41586-023-06457-y

Ghosh B, Loube J, Thapa S, Ryan H, Capodanno E, Chen D, Swaby C, Chen S, Mahmud S, Girgis M, Nishida K, Ying L, Chengala PP, Tieng E, Burnim M, Wally A, Bhowmik D, Zaykaner M, Yeung-Luk B, Mitzner W, Biswal S, Sidhaye VK. Loss of E-cadherin is causal to pathologic changes in chronic lung disease. Commun Biol. 2022 Oct 29;5(1):1149. doi: 10.1038/s42003-022-04150-w. PMID: 36309587; PMCID: PMC9617938.
https://www.nature.com/articles/s42003-022-04150-w#citeas

Ghosh B, Nishida K, Chandrala L, Mahmud S, Thapa S, Swaby C, Chen S, Khosla AA, Katz J, Sidhaye VK. Epithelial plasticity in COPD results in cellular unjamming due to an increase in polymerized actin. J Cell Sci. 2022 Feb 15;135(4):jcs258513. doi: 10.1242/jcs.258513. Epub 2022 Feb 24. PMID: 35118497; PMCID: PMC8919336.

Kavanagh EW, Green JJ. Toward Gene Transfer Nanoparticles as Therapeutics. Adv Healthc Mater. 2022 Apr;11(7):e2102145. doi: 10.1002/adhm.202102145. Epub 2022 Jan 17. PMID: 35006646.

Avigdor, B. E., Yang, K., Shinder, I., Orsburn, B. C., Rais, R., Kano, S. I., Sawa, A., & Pevsner, J. (2021). Characterization of antipsychotic medications, amino acid signatures, and platelet-activating factor in first-episode psychosis. Biomarkers in Neuropsychiatry, 5, 100045.
https://doi.org/10.1016/j.bionps.2021.100045

Zimin, A. V., Shumate, A., Shinder, I., Heinz, J., Puiu, D., Pertea, M., & Salzberg, S. L. (2022). A reference-quality, fully annotated genome from a Puerto Rican individual. Genetics, 220(2), iyab227.
https://doi.org/10.1093/genetics/iyab227