Publicaciones estudiantiles

Zhang, L., Lee, M., Hao, X., Ehlert, J., Chi, Z., Jin, B., Cutler, R., Maslov, A., Barabási, A., Hoeijmakers, J.,  Edelmann, W., Vijg, J., Dong, X. “Divergent Accumulation Patterns of SNVs and INDELs Reveal Negative Selection in Noncancerous Cells” In review at The Innovation (Cell). bioRxiv 2024.05.04.592535; doi: https://doi.org/10.1101/2024.05.04.592535

Stransky, S., Cutler, R., Aguilan, J. DeAngelo, JD., Schechter, D., Sidoli, S., “Histone H3 tails co-modified with the silencing mark H3K9me3 and acetylations serve as surveillance from spurious non-coding RNA transcription mediated by the protein EXOSC4” (2024) bioRxiv 2024.08.05.606680; doi: https://doi.org/10.1101/2024.08.05.606680

Cutler, R.,* Corvelyn, L.,* Ctortecka, C.,* Cantlon, J., Alvaro Jacome Vaca, S., Deforce, D., Vijg, J., Dhaenens, M., Papanastasiou, M., Carr, SA., Sidoli, S., (2024) “Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity”. In review at Nature Communications. bioRxiv 2024.07.05.602213; doi: https://doi.org/10.1101/2024.07.05.602213
*Indicates equal contributions to the manuscript.

Heid, J.,* Cutler, R.,* Sun, S., Lee, M., Maslov, A., Dong, X., Sidoli, S., Vijg, J. (2024) “Evidence for negative selection in human primary fibroblasts to tolerate high somatic mutation loads upon treatment with multiple low doses of N-ethyl-N-nitrosourea”  In review at Cell Genomics. bioRxiv 2024.04.07.588286; doi: https://doi.org/10.1101/2024.04.07.588286
*Indicates equal contributions to the manuscript.

Heid, J., Cutler, R., Lee, M., Vijg J., Maslov A. (2024) “Concurrent analysis of genome and transcriptome in one single cell” BMC Res Notes 17, 267 (2024). https://doi.org/10.1186/s13104-024-06927-0

Cutler, R., Vijg, J. (2023) Genetic wrinkles in time. Nat Rev Mol Cell Biol. 10.1038/s41580-023-00652-5

Luo, R., Yan, J., Oh, J. W., Xi, W., Shigaki, D., Wong, W., Cho, H., Murphy, D., Cutler, R., Rosen, B. P., Pulecio, J., Yang, D., Glenn, R., Chen, T., Li, Q. V., Vierbuchen, T., Sidoli, S., Apostolou, E., Huangfu, D., Beer, M. A. (2023) “Dynamic-network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer-gene regulatory activity during cell state transitions” Nature Genetics. 10.1038/s41588-023-01450-7

Cutler, R. & Vijg, J. (2022) “A mechanism for inheriting radiation-induced DNA damage.” Naturaleza. 10.1038/d41586-022-04449-y

Sidoli, S., Stransky, S., Cutler, R., Graff, S., Aguilan, J. (2022) “MODELING REACTIVATED HETEROCHROMATIN USING AN AGING 3D CELL MODEL.” Innovation in Aging. 10.1093/geroni/igac059.103

Stransky, S., Cutler, R., Aguilan, J., Nieves, E., Sidoli S. (2022) “Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model.” Epigenetics & Chromatin. 10.1186/s13072-022-00470-7

Ulahannan, N.*, Cutler, R.*, Doña-Termine, R.*, Simões-Pires, C., Wijetunga, N.A., McKnight Croken, M., Johnston, A., Kong, Y., Maqbool, S., Suzuki, M., Greally, J. (2022) “Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii” PLOS ONE. 10.1371/journal.pone.0275226. *Indicates equal contributions to the manuscript.

Joseph-Chowdhury, J., Stransky, S., Graff, S., Cutler, R., Young, D., Kim, J., Madrid-Aliste, C., Aguilan, J., Nieves, E., Sun, Y., Yoo, E., Sidoli, S. (2022) “Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue” JoVE. 10.3791/63606

Shun-Mei Liu, Bruno Ifebi, Fred Johnson, Alison Xu, Jacquelin Ho, Yunlei Yang, Gary Schwartz, Young Hwan Jo, Streamson Chua. The gut signals to AGRP-expressing cells of the pituitary to control glucose homeostasis. Revista de investigación clínica, 2023; 133(7). https://doi.org/10.1172/JCI164185

Leo Tsz-Ho Tang, Garrett A Lee, Steven J Cook, Jacquelin W Ho, Cassandra C Potter, Hannes E Bülow. Anatomical restructuring of a lateralized neural circuit during associative learning by asymmetric insulin signaling. Current Biology, 2023; 33(18), 3835-3850.e6. https://doi.org/10.1016/j.cub.2023.07.041

Shakila Behzadi, Jacquelin Ho, Zainab Tanvir, Gal Haspel, Limor Freifeld, Kristen E. Severi. Expansion microscopy reveals neural circuit organization in genetic animal models. Neurophotonics, Dec 2024, DOI: 10.1117/1.nph.12.1.010601

scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.NAR Genomics & Bioinformatics, Sep 2024. Ferrena A, Zheng XY, Jackson K, Hoang B, Morrow B, and Zheng D.

Ian MacArthur, Liyang Ma, Cheng-Yen Huang, Hrutvik Bhavsar, Masako Suzuki, and Meelad M. Dawlaty.  Developmental DNA demethylation is a determinant of neural stem cell identity and gliogenic competence.  Avances científicos Vol 10, Issue 35, DOI:  1126/sciadv.ado5424 (2024)

Kevin O’Leary and Deyou Zheng.  Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19j patient pBMCs.  Npj | Systems Biology and Applications 10, Article \number:  36 (2024)

H2AK119ub dynamics controls hair follicle stem cell quiescence. BioRxiv, Oct 2024.Flora P, Li MY, Zhou Y, Mercédes M, Zheng XY, Galbo P, Zheng D, Ezhkova E.

scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.NAR Genomics & Bioinformatics, Sep 2024. Ferrena A, Zheng XY, Jackson K, Hoang B, Morrow B, and Zheng D.

Deletion of Mgat2 in Spermatogonia Blocks Spermatogenesis. Frontiers in Cell and Developmental Biology, Sep 2024. Asmat MS, Zheng XY, Nauman M, Zheng D, and Stanley P.

Comprehensive single cell transcriptomics analysis of murine osteosarcoma uncovers Skp2 function in metastasis, genomic instability and immune activation and reveals additional target pathways.BioRxiv, Jun 2024. Ferrena A, Zhang R, Wang J, Zheng XY, Zhao H, Schwartz E, Loeb D, Goker B, Borjihan H, Chae S, Yang R, Geller D, Zheng D, and Hoang B.

TOP CAR with TMIGD2 as a safe and effective costimulatory domain in CAR cells treating human solid tumors.Science Advances, May 2024. Nishimura C, Corrigan D, Zheng XY, Galbo P, Wang S, Liu Y, Wei Y, Suo L, Cui W, Mercado N, Zheng D, Zhang C, and Zang X.

KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Research, Apr 2024. Yheskel M, Hatch H, Pedrosa E, Terry B, Siebels A, Zheng XY, Blok L, Fenckova M, Sidoli S, Schenck A, Zheng D, Lachman H, and Secombe J.

Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages. Science Advances, Jan 2024. Nguyen M, Flora P, Branch M, Weber M, Zheng XY, Sivan U, Joost S, Annusver K, Zheng D, Kasper M, and Ezhkova E.