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Borot, F., Humbert, O., Ehmsen, J. T., Fields, E., Kohli, S., Radtke, S., Swing, K., Pande, D., Enstrom, M. R., Laszlo, G. S., Mayuranathan, T., Ali, A. M., Weiss, M. J., Yen, J. S., Newby, G. A., Walter, R. B., Liu, D. R., Mukherjee, S., & Kiem, H.-P. (2025). Multiplex base editing to protect from CD33 directed drugs for immune and gene therapy. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-59713-2
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Barua, S., Murty, V. V., Iglesias, A., & Liao, J. (2025). A Novel EP300 Variant in an African American Girl With Global Developmental Delay and Leukemia. Molecular Genetics & Genomic Medicine, 13(6). Portico. https://doi.org/10.1002/mgg3.70102
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Li, B. I., Alvarez, M. J., Zhao, H., Chirathivat, N., Califano, A., & Shen, M. M. (2025). The regulatory architecture of the primed pluripotent cell state. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57894-4
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Department of Systems Biology; Vagelos College of Physicians and Surgeons; Department of Biochemistry and Molecular Biophysics; Department of Biomedical Informatics; Department of Medicine; Division of Hematology/Oncology; Herbert Irving Comprehensive Cancer Center; Department of Genetics and Development
Vann, K. R., Sharma, R., Hsu, C.-C., Devoucoux, M., Tencer, A. H., Zeng, L., Lin, K., Zhu, L., Li, Q., Lachance, C., Ospina, R. R., Tong, Q., Cheung, K. L., Yang, S., Biswas, S., Xuan, H., Gatchalian, J., Alamillo, L., Wang, J., … Kutateladze, T. G. (2025). Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57556-5
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Hong, S. J., Resnick, S. J., Iketani, S., Cha, J. W., Albert, B. A., Fazekas, C. T., Chang, C.-W., Liu, H., Dagan, S., Abagyan, M. R., Fajtová, P., Culbertson, B., Brace, B., Reddem, E. R., Forouhar, F., Glickman, J. F., Balkovec, J. M., Stockwell, B. R., Shapiro, L., … Chavez, A. (2025). A multiplex method for rapidly identifying viral protease inhibitors. Molecular Systems Biology, 21(2), 158–172. https://doi.org/10.1038/s44320-024-00082-1
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Vagelos College of Physicians and Surgeons; Department of Medicine; Division of Infectious Diseases; Aaron Diamond AIDS Research Center; Herbert Irving Comprehensive Cancer Center; Department of Pathology and Cell Biology; Department of Biochemistry and Molecular Biophysics; Zuckerman Mind, Brain, and Behavior Institute; Department of Microbiology and Immunology
Oas, H., Cook, L., Schwantes-An, T.-H., Walsh, L. E., Wills, A.-M., Mata, I. F., Nance, M. A., Beck, J. C., Naito, A., Marder, K., Alcalay, R. N., & Verbrugge, J. (2024). Participant-reported personal utility of genetic testing for Parkinson’s disease and interest in clinical trial participation. Npj Parkinson’s Disease, 10(1). https://doi.org/10.1038/s41531-024-00805-z
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Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., Jankovic, K., Parker-Burns, L., Jin, Y., Zhang, J. Y., Hong, J., Niu, X., Costa, J. A., Pezet, M. G., Chou, J., … Gaublomme, J. T. (2024). Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02386-x
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Vagelos College of Physicians and Surgeons; Department of Genetics and Development; Herbert Irving Comprehensive Cancer Center; Department of Pathology and Cell Biology; Department of Medicine; Division of Pulmonary, Allergy, and Critical Care Medicine; Division of Hematology/Oncology; Institute for Cancer Genetics; Department of Microbiology and Immunology; Irving Institute for Cancer Dynamics; Center for Stem Cell Therapies
Liguori, F., Pellicciotta, N., Milanetti, E., Xi Windemuth, S., Ruocco, G., Di Leonardo, R., & Danino, T. (2024). Dynamic Gene Expression Mitigates Mutational Escape in Lysis-Driven Bacteria Cancer Therapy. BioDesign Research, 6. https://doi.org/10.34133/bdr.0049
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Jeon, Y., Lu, Y., Ferrari, M. M., Channagiri, T., Xu, P., Meers, C., Zhang, Y., Balachander, S., Park, V. S., Marsili, S., Pursell, Z. F., Jonoska, N., & Storici, F. (2024). RNA-mediated double-strand break repair by end-joining mechanisms. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51457-9
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Cai, P., & Korem, T. (2024). Microsynteny is a powerful front for microbial strain tracking. Cell Reports Methods, 4(9), 100862. https://doi.org/10.1016/j.crmeth.2024.100862
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Cook, L., Verbrugge, J., Schwantes-An, T.-H., Schulze, J., Foroud, T., Hall, A., Marder, K. S., Mata, I. F., Mencacci, N. E., Nance, M. A., Schwarzschild, M. A., Simuni, T., Bressman, S., Wills, A.-M., Fernandez, H. H., Litvan, I., Lyons, K. E., Shill, H. A., Singer, C., … Alcalay, R. N. (2024). Parkinson’s disease variant detection and disclosure: PD GENEration, a North American study. Brain, 147(8), 2668–2679. https://doi.org/10.1093/brain/awae142
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Li, Y., Yang, R. R., Li, Y. S., Hsu, C. W., Jenny, L. A., Kong, Y., Ruan, M. Z., Sparrow, J. R., & Tsang, S. H. (2024). Evaluating precision medicine approaches for gene therapy in patient-specific cellular models of Bietti crystalline dystrophy. JCI insight, 9(16), e177231. https://doi.org/10.1172/jci.insight.177231
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Tai, Y., Chow, A., Han, S., Coker, C., Ma, W., Gu, Y., Estrada Navarro, V., Kandpal, M., Hibshoosh, H., Kalinsky, K., Manova-Todorova, K., Safonov, A., Walsh, E. M., Robson, M., Norton, L., Baer, R., Merghoub, T., Biswas, A. K., & Acharyya, S. (2024). FLT1 activation in cancer cells promotes PARP-inhibitor resistance in breast cancer. EMBO Molecular Medicine, 16(8), 1957–1980. https://doi.org/10.1038/s44321-024-00094-2
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Bravo, J. I., Mizrahi, C. R., Kim, S., Zhang, L., Suh, Y., & Benayoun, B. A. (2024). An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells. PLOS Genetics, 20(6), e1011311. https://doi.org/10.1371/journal.pgen.1011311
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Teles, D., & Fine, B. M. (2024). Using induced pluripotent stem cells for drug discovery in arrhythmias. Expert Opinion on Drug Discovery, 19(7), 827–840. https://doi.org/10.1080/17460441.2024.2360420
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Kim, J., Kratz, A. F., Chen, S., Sheng, J., Kim, H. K., Zhang, L., Singh, B. K., & Chavez, A. (2024). High-throughput tagging of endogenous loci for rapid characterization of protein function. Science Advances, 10(18). https://doi.org/10.1126/sciadv.adg8771
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Georgieva, D., Wang, N., Taglialatela, A., Jerabek, S., Reczek, C. R., Lim, P. X., Sung, J., Du, Q., Horiguchi, M., Jasin, M., Ciccia, A., Baer, R., & Egli, D. (2024). BRCA1 and 53BP1 regulate reprogramming efficiency by mediating DNA repair pathway choice at replication-associated double-strand breaks. Cell Reports, 43(4), 114006. https://doi.org/10.1016/j.celrep.2024.114006
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Vagelos College of Physicians and Surgeons; Department of Genetics and Development; Department of Pediatrics; Division of Molecular Genetics; Department of Dermatology; Herbert Irving Comprehensive Cancer Center; Department of Pathology and Cell Biology; Institute for Cancer Genetics; Department of Obstetrics and Gynecology; Naomi Berrie Diabetes Center
Nolan, N. D., Cui, X., Robbings, B. M., Demirkol, A., Pandey, K., Wu, W.-H., Hu, H. F., Jenny, L. A., Lin, C.-S., Hass, D. T., Du, J., Hurley, J. B., & Tsang, S. H. (2024). CRISPR editing of anti-anemia drug target rescues independent preclinical models of retinitis pigmentosa. Cell Reports Medicine, 5(4), 101459. https://doi.org/10.1016/j.xcrm.2024.101459
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Abela, L., Gianfrancesco, L., Tagliatti, E., Rossignoli, G., Barwick, K., Zourray, C., Reid, K. M., Budinger, D., Ng, J., Counsell, J., Simpson, A., Pearson, T. S., Edvardson, S., Elpeleg, O., Brodsky, F. M., Lignani, G., Barral, S., & Kurian, M. A. (2024). Neurodevelopmental and synaptic defects in DNAJC6 parkinsonism, amenable to gene therapy. Brain, 147(6), 2023–2037. https://doi.org/10.1093/brain/awae020
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Shi, P., & Wu, X. (2024). Programmable RNA targeting with CRISPR-Cas13. RNA Biology, 21(1), 1–9. https://doi.org/10.1080/15476286.2024.2351657
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Qian, J., & Liu, X. (2024). CRISPR/dCas9-Tet1-Mediated DNA Methylation Editing. BIO-PROTOCOL, 14(1343). https://doi.org/10.21769/bioprotoc.4976
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MacCarthy, C. M., Wu, G., Malik, V., Menuchin-Lasowski, Y., Velychko, T., Keshet, G., Fan, R., Bedzhov, I., Church, G. M., Jauch, R., Cojocaru, V., Schöler, H. R., & Velychko, S. (2024). Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell, 31(1), 127-147.e9. https://doi.org/10.1016/j.stem.2023.11.010
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Heilmann, R., Pfalzer, A., Bichell, T. J., Terala, A., Campbell, A., Taatjes, D., Ghoumid, J., Grueter, C., Bain, J., Strich, R., Dias, V., Sokorai, K., Seaver, N., Sexton, K., & Boychuck, K. (2024). The MED13L Foundation strategic research plan: a roadmap to the future. Therapeutic Advances in Rare Disease, 5. https://doi.org/10.1177/26330040241290252
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Blomquist, V. G., Niu, J., Choudhury, P., Al Saneh, A., Colecraft, H. M., & Ahern, C. A. (2023). Transfer RNA-mediated restoration of potassium current and electrical correction in premature termination long-QT syndrome hERG mutants. Molecular Therapy - Nucleic Acids, 34, 102032. https://doi.org/10.1016/j.omtn.2023.102032
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Wang, N.-K., Liu, P.-K., Kong, Y., Tseng, Y.-J., Jenny, L. A., Nolan, N. D., Chen, N., Wang, H.-H., Hsu, C. W., Huang, W.-C., Sparrow, J. R., Lin, C.-S., & Tsang, S. H. (2023). Spatiotemporal control of genome engineering in cone photoreceptors. Cell & Bioscience, 13(1). https://doi.org/10.1186/s13578-023-01033-3
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Shi, P., Murphy, M. R., Aparicio, A. O., Kesner, J. S., Fang, Z., Chen, Z., Trehan, A., Guo, Y., & Wu, X. (2023). Collateral activity of the CRISPR/RfxCas13d system in human cells. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-04708-2
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Papaioannou, V. E., & Behringer, R. R. (2023). Strategies for the Production and Phenotypic Analysis of Mutations in the Mouse. Cold Spring Harbor Protocols, 2023(12), pdb.over107955. https://doi.org/10.1101/pdb.over107955
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DiPersio, J., Cooper, B. W., Suh, H. C., Koura, D., Bernard, L., Shah, N. N., Walter, R. B., Perales, M.-A., Mapara, M., Tamari, R., Loken, M. R., Breitschwerdt, K., Nath, S., Raffel, G. D., & Koehne, G. (2023). Trem-Cel, a CRISPR/Cas9 Gene-Edited Allograft Lacking CD33, Shows Rapid Primary Engraftment with CD33-Negative Hematopoiesis in Patients with High-Risk Acute Myeloid Leukemia (AML) and Avoids Hematopoietic Toxicity during Gemtuzumab Ozogamicin (GO) Maintenance Post-Hematopoietic Cell Transplant (HCT). Blood, 142(Supplement 1), 483–483. https://doi.org/10.1182/blood-2023-190037
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Camargo, J. A., Viana, N. I., Pimenta, R., Guimarães, V. R., dos Santos, G. A., Candido, P., Ghazarian, V., Romão, P., Silva, I. A., Birbrair, A., Srougi, M., Nahas, W. C., Leite, K. R., Trarbach, E. B., & Reis, S. T. (2023). The Effect of Gene Editing by CRISPR-Cas9 of miR-21 and the Indirect Target MMP9 in Metastatic Prostate Cancer. International Journal of Molecular Sciences, 24(19), 14847. https://doi.org/10.3390/ijms241914847
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Dugger, S. A., Dhindsa, R. S., Sampaio, G. D. A., Ressler, A. K., Rafikian, E. E., Petri, S., Letts, V. A., Teoh, J., Ye, J., Colombo, S., Peng, Y., Yang, M., Boland, M. J., Frankel, W. N., & Goldstein, D. B. (2023). Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency. PLOS Genetics, 19(10), e1010952. https://doi.org/10.1371/journal.pgen.1010952
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Vagelos College of Physicians and Surgeons; Department of Pathology and Cell Biology; Zuckerman Mind, Brain, and Behavior Institute; Department of Neurology; Department of Psychiatry; Department of Genetics and Development; Institute for Genomic Medicine; Department of Biochemistry and Molecular Biophysics
Lao, Y.-H., Ji, R., Zhou, J. K., Snow, K. J., Kwon, N., Saville, E., He, S., Chauhan, S., Chi, C.-W., Datta, M. S., Zhang, H., Quek, C. H., Cai, S. S., Li, M., Gaitan, Y., Bechtel, L., Wu, S.-Y., Lutz, C. M., Tomer, R., … Leong, K. W. (2023). Focused ultrasound–mediated brain genome editing. Proceedings of the National Academy of Sciences, 120(34). https://doi.org/10.1073/pnas.2302910120
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Mauro, M., Wei, S., Breborowicz, A., Li, X., Bognanni, C., Fuller, Z., Philipp, T., McDonald, T., Lattin, M. T., & Williams, Z. (2023). Endogenous retrotransposons cause catastrophic deoxyribonucleic acid damage in human trophoblasts. F&S Science, 4(3), 200–210. https://doi.org/10.1016/j.xfss.2023.05.005
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Pal, G., Cook, L., Schulze, J., Verbrugge, J., Alcalay, R. N., Merello, M., Sue, C. M., Bardien, S., Bonifati, V., Chung, S. J., Foroud, T., Gatto, E., Hall, A., Hattori, N., Lynch, T., Marder, K., Mascalzoni, D., Novaković, I., Thaler, A., … Klein, C. (2023). Genetic Testing in Parkinson’s Disease. Movement Disorders, 38(8), 1384–1396. Portico. https://doi.org/10.1002/mds.29500
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Calame, D. G., Guo, T., Wang, C., Garrett, L., Jolly, A., Dawood, M., Kurolap, A., Henig, N. Z., Fatih, J. M., Herman, I., Du, H., Mitani, T., Becker, L., Rathkolb, B., Gerlini, R., Seisenberger, C., Marschall, S., Hunter, J. V., Gerard, A., … Lupski, J. R. (2023). Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. The American Journal of Human Genetics, 110(8), 1394–1413. https://doi.org/10.1016/j.ajhg.2023.06.013
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Kimble, M. T., Johnson, M. J., Nester, M. R., & Symington, L. S. (2023). Long-range DNA end resection supports homologous recombination by checkpoint activation rather than extensive homology generation. ELife, 12. CLOCKSS. https://doi.org/10.7554/elife.84322
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Eigenhuis, K. N., Somsen, H. B., van der Kroeg, M., Smeenk, H., Korporaal, A. L., Kushner, S. A., de Vrij, F. M. S., & van den Berg, D. L. C. (2023). A simplified protocol for the generation of cortical brain organoids. Frontiers in Cellular Neuroscience, 17. https://doi.org/10.3389/fncel.2023.1114420
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Gnügge, R., Reginato, G., Cejka, P., & Symington, L. S. (2023). Sequence and chromatin features guide DNA double-strand break resection initiation. Molecular Cell, 83(8), 1237-1250.e15. https://doi.org/10.1016/j.molcel.2023.02.010
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Wang, B. Z., Nash, T. R., Zhang, X., Rao, J., Abriola, L., Kim, Y., Zakharov, S., Kim, M., Luo, L. J., Morsink, M., Liu, B., Lock, R. I., Fleischer, S., Tamargo, M. A., Bohnen, M., Welch, C. L., Chung, W. K., Marx, S. O., Surovtseva, Y. V., … Fine, B. M. (2023). Engineered cardiac tissue model of restrictive cardiomyopathy for drug discovery. Cell Reports Medicine, 4(3), 100976. https://doi.org/10.1016/j.xcrm.2023.100976
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Schimmel, J., Muñoz-Subirana, N., Kool, H., van Schendel, R., van der Vlies, S., Kamp, J. A., de Vrij, F. M. S., Kushner, S. A., Smith, G. C. M., Boulton, S. J., & Tijsterman, M. (2023). Modulating mutational outcomes and improving precise gene editing at CRISPR-Cas9-induced breaks by chemical inhibition of end-joining pathways. Cell Reports, 42(2), 112019. https://doi.org/10.1016/j.celrep.2023.112019
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Limone, F., Guerra San Juan, I., Mitchell, J. M., Smith, J. L. M., Raghunathan, K., Meyer, D., Ghosh, S. D., Couto, A., Klim, J. R., Joseph, B. J., Gold, J., Mello, C. J., Nemesh, J., Smith, B. M., Verhage, M., McCarroll, S. A., Pietiläinen, O., Nehme, R., & Eggan, K. (2023). Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues. Cell Reports, 42(1), 111896. https://doi.org/10.1016/j.celrep.2022.111896
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Ganapathi, M., Thomas-Wilson, A., Buchovecky, C., Dharmadhikari, A., Barua, S., Lee, W., Ruan, M. Z. C., Soucy, M., Ragi, S., Tanaka, J., Clark, L. N., Naini, A. B., Liao, J., Mansukhani, M., Tsang, S., & Jobanputra, V. (2022). Clinical exome sequencing for inherited retinal degenerations at a tertiary care center. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-13026-2
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Pandit, K., Petrescu, J., Cuevas, M., Stephenson, W., Smibert, P., Phatnani, H., & Maniatis, S. (2022). An open source toolkit for repurposing Illumina sequencing systems as versatile fluidics and imaging platforms. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-08740-w
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Laise, P., Stanifer, M. L., Bosker, G., Sun, X., Triana, S., Doldan, P., La Manna, F., De Menna, M., Realubit, R. B., Pampou, S., Karan, C., Alexandrov, T., Kruithof-de Julio, M., Califano, A., Boulant, S., & Alvarez, M. J. (2022). A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03663-8
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Cook, L., Schulze, J., Uhlmann, W. R., Verbrugge, J., Marder, K., Lee, A. J., Wang, Y., Alcalay, R. N., Nance, M., & Beck, J. C. (2022). Tools for communicating risk for Parkinson’s disease. Npj Parkinson’s Disease, 8(1). https://doi.org/10.1038/s41531-022-00432-6
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Cheng, F., Zheng, W., Liu, C., Barbuti, P. A., Yu-Taeger, L., Casadei, N., Huebener-Schmid, J., Admard, J., Boldt, K., Junger, K., Ueffing, M., Houlden, H., Sharma, M., Kruger, R., Grundmann-Hauser, K., Ott, T., & Riess, O. (2022). Intronic enhancers of the human SNCA gene predominantly regulate its expression in brain in vivo. Science Advances, 8(47). https://doi.org/10.1126/sciadv.abq6324
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Li, D., Yang, J., Malik, V., Huang, Y., Huang, X., Zhou, H., & Wang, J. (2022). An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Research, 50(21), 12462–12479. https://doi.org/10.1093/nar/gkac1084
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Walters, M. C., Thompson, A. A., Kwiatkowski, J. L., Parikh, S., Mapara, M. Y., Rifkin-Zenenberg, S., Aygun, B., Kasow, K. A., Miller, A., Zhang, L., Chawla, A., Macari, E. R., Pierciey, F. J., Tisdale, J. F., & Kanter, J. (2022). Lovo-cel (bb1111) Gene Therapy for Sickle Cell Disease: Updated Clinical Results and Investigations into Two Cases of Anemia from Group C of the Phase 1/2 HGB-206 Study. Blood, 140(Supplement 1), 26–28. https://doi.org/10.1182/blood-2022-162288
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Malik, V., Zang, R., Fuentes-Iglesias, A., Huang, X., Li, D., Fidalgo, M., Zhou, H., & Wang, J. (2022). Comparative functional genomics identifies unique molecular features of EPSCs. Life Science Alliance, 5(11), e202201608. https://doi.org/10.26508/lsa.202201608
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Wang, S.-H., Hao, J., Zhang, C., Duan, F.-F., Chiu, Y.-T., Shi, M., Huang, X., Yang, J., Cao, H., & Wang, Y. (2022). KLF17 promotes human naive pluripotency through repressing MAPK3 and ZIC2. Science China Life Sciences, 65(10), 1985–1997. https://doi.org/10.1007/s11427-021-2076-x
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