Genomic Analysis
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Temporal recording of mammalian development and precancer
Islam, M.; Yang, Y.; Simmons, A.J.; Shah, V.M.; Musale, K.P.; Xu, Y.; Tasneem, N.; Chen, Z.; Trinh, L.T.; Molina, P.; Ramirez-Solano, M.A.; Sadien, I.D.; Dou, J.; Rolong, A.; Chen, K.; Magnuson, M.A.; Rathmell, J.C.; Macara, I.G.; Winton, D.J.; Liu, Q.; Zafar, H.; Kalhor, R.; Church, G.M.; Shrubsole, M.J.; Coffey,… Read MoreNovember 21, 2024
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Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM)
Kaur, H.; Heiser, C.N.; McKinley, E.T.; Ventura-Antunes, L.; Harris, C.R.; Roland, J.T.; Farrow, M.A.; Selden, H.J.; Pingry, E.L.; Moore, J.F.; Ehrlich, L.I.R.; Shrubsole, M.J.; Spraggins, J.M.; Coffey, R.J.; Lau, K.S.; Vandekar, S.N. “Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology… Read MoreNovember 21, 2024
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Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn鈥檚 disease
Li, Jia, Simmons, Alan J., Hawkins, Caroline V., Chiron, Sophie, Ramirez-Solano, Marisol A., Tasneem, Naila, Kaur, Harsimran, Xu, Yanwen, Revetta, Frank, Vega, Paige N., Bao, Shunxing, Cui, Can, Tyree, Regina N., Raber, Larry W., Conner, Anna N., Pilat, Jennifer M., Jacobse, Justin, McNamara, Kara M., Allaman, Margaret M., Raffa, Gabriella… Read MoreSeptember 22, 2024
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Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale
Hoang, Nhung, Sardaripour, Neda, Ramey, Grace D., Schilling, Kurt, Liao, Emily, Chen, Yiting, Park, Jee Hyun, Bledsoe, Xavier, Landman, Bennett A., Gamazon, Eric R., Benton, Mary Lauren, & Capra, John A., Rubinov, Mikail.聽(2024). Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank… Read MoreSeptember 22, 2024
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Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
Hu, Yunfei; Xie, Manfei; Li, Yikang; Rao, Mingxing; Shen, Wenjun; Luo, Can; Qin, Haoran; Baek, Jihoon; Zhou, Xin Maizie. “Benchmarking clustering, alignment, and integration methods for spatial transcriptomics.” Genome Biology, volume 25, Article number: 212 (2024). https://doi.org/10.1186/s13059-024-02665-w. Published: 09 August 2024. Understanding the complexities… Read MoreAugust 22, 2024
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Parallel signatures of cognitive maturation in primate antisaccade performance and prefrontal activity
Zhu, Junda; Zhou, Xin Maizie; Constantinidis, Christos; Salinas, Emilio; Stanford, Terrence R. “Parallel signatures of cognitive maturation in primate antisaccade performance and prefrontal activity.” iScience, Volume 27, Issue 8, 16 August 2024, 110488, https://doi.org/10.1016/j.isci.2024.110488. In this study, researchers examined how our ability to control… Read MoreAugust 22, 2024
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SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data
Zhang, Liting; Zhou, Xin Maizie; Mallory, Xian. “SCCNAInfer: a robust and accurate… Read MoreAugust 22, 2024
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Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data
Liu YH, Luo C, Golding SG, Ioffe JB, Zhou XM. Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data. Nat Commun. 2024 Mar 19;15(1):2447. doi: 10.1038/s41467-024-46614-z. PMID: 38503752; PMCID: PMC10951360. Researchers have systematically evaluated a range of tools designed to detect structural variants (SVs)… Read MoreApril 16, 2024