Unbiased single-cell morphology with self-supervised vision transformers Publication: Unpublished Doron, Michael, Théo Moutakanni, Zitong S. Chen, Nikita Moshkov, Mathilde Caron, Hugo Touvron, Piotr Bojanowski, Wolfgang M. Pernice, and Juan C. Caicedo. 2023. “Unbiased Single-Cell Morphology With Self-Supervised Vision Transformers.”
Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. Publication: Journal Article Hu, Yan, Sai Ma, Vinay K Kartha, Fabiana M Duarte, Max Horlbeck, Ruochi Zhang, Rojesh Shrestha, et al. 2023. “Single-Cell Multi-Scale Footprinting Reveals the Modular Organization of DNA Regulatory Elements.”. BioRxiv : The Preprint Server for Biology.
Massively parallel base editing to map variant effects in human hematopoiesis. Publication: Journal Article Martin-Rufino, Jorge D, Nicole Castano, Michael Pang, Emanuelle I Grody, Samantha Joubran, Alexis Caulier, Lara Wahlster, et al. 2023. “Massively Parallel Base Editing to Map Variant Effects in Human Hematopoiesis.”. Cell 186 (11): 2456-2474.e24.
Functional inference of gene regulation using single-cell multi-omics. Publication: Journal Article Kartha, Vinay K, Fabiana M Duarte, Yan Hu, Sai Ma, Jennifer G Chew, Caleb A Lareau, Andrew Earl, et al. 2022. “Functional Inference of Gene Regulation Using Single-Cell Multi-Omics.”. Cell Genomics 2 (9).
Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma. Publication: Journal Article Kwok, Hui Si, Allyson M Freedy, Allison P Siegenfeld, Julia W Morriss, Amanda L Waterbury, Stephen M Kissler, and Brian B Liau. 2023. “Drug Addiction Unveils a Repressive Methylation Ceiling in EZH2-Mutant Lymphoma.”. Nature Chemical Biology.
Epigenetic clocks, aging, and cancer. Publication: Journal Article Johnstone, Sarah E, Vadim N Gladyshev, Martin J Aryee, and Bradley E Bernstein. 2022. “Epigenetic Clocks, Aging, and Cancer.”. Science (New York, N.Y.) 378 (6626): 1276-77.
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Publication: Journal Article Zhao, Tongtong, Zachary D Chiang, Julia W Morriss, Lindsay M LaFave, Evan M Murray, Isabella Del Priore, Kevin Meli, et al. 2022. “Spatial Genomics Enables Multi-Modal Study of Clonal Heterogeneity in Tissues.”. Nature 601 (7891): 85-91.
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Publication: Journal Article Gabriele, Michele, Hugo B Brandão, Simon Grosse-Holz, Asmita Jha, Gina M Dailey, Claudia Cattoglio, Tsung-Han S Hsieh, Leonid Mirny, Christoph Zechner, and Anders S Hansen. 2022. “Dynamics of CTCF- and Cohesin-Mediated Chromatin Looping Revealed by Live-Cell Imaging.”. Science (New York, N.Y.) 376 (6592): 496-501.