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Trey Ideker

As seen in: Nature, Wiley Online Library, PLOS, Biomed Central (BMC), Flipboard, Genome Medicine, BioRxiv, Cell Press
UC, Cytoscape, Cell Mapping, Data4Cure
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Articles

A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells

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By Sami Nourreddine, Yesh Doctor, Amir Dailamy, Jan N. Hansen, Antoine Forget, Benjamin J. Polacco, Monita Muralidharan, Alina Sigaeva, Emily Pan, Jiahao Gao, Jake Chen, Timothy D. Clark, Jillian Parker, Kirsten Obernier, Christian M. Metallo, Trey Ideker, Emma Lundberg, Nevan J. Krogan, Prashant Mali, Yi-Hung Lee, Rebecca Chinn, Sushant Sunder
| Nature Verified
Abstract Comprehensively mapping the relationship between genotype and phenotype offers essential insights into how a cell’s state arises from its genetic components. Toward this goal, we generated an expressed genome-scale CRISPRi perturbation cell atlas in KOLF2.1J human induced pluripotent stem cells, mapping transcriptional phenotypes associated with 11,692 perturbed genes across >2.5 million single cells.
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scLong: a billion-parameter foundation model for capturing long-range gene context in single-cell transcriptomics - Nature Communications

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By Ding Bai, Yingtao Luo, Hamidreza Rahmani, Danielle A. Grotjahn, Nathan Lewis, Wei Wang, Trey Ideker, Pengtao XiePengtao Xie
| Nature Verified
Abstract Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity by providing gene expression data at single-cell resolution, uncovering insights into rare cell populations, cell-cell interactions, and gene regulation.
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Pan‐Epigenetic Age Prediction in Mammals

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By Zane Koch, Adam Li, Trey Ideker
| Wiley Online Library Verified
1 Introduction Among the hallmarks of aging, considerable attention has been devoted to the study of epigenetic alterations, particularly changes in DNA methylation patterns (Gonzalo 2010). Across the human lifespan, thousands of cytosine-guanine dinucleotides (CpGs) undergo systematic gains or losses of methylation (Christensen et al. 2009; Fraga et al. 2005; Hannum et al. 2013; Li et al. 2022).
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