Bolondi, Adriano, Benjamin K Law, Helene Kretzmer, Seher Ipek Gassaloglu, René Buschow, Christina Riemenschneider, Dian Yang, et al. (2024) 2024. “Reconstructing Axial Progenitor Field Dynamics in Mouse Stem Cell-Derived Embryoids.”. Developmental Cell 59 (12): 1489-1505.e14. doi:10.1016/j.devcel.2024.03.024.

Sashittal, Palash, Richard Y Zhang, Benjamin K Law, Alexander Strzalkowski, Henri Schmidt, Adriano Bolondi, Michelle M Chan, and Benjamin J Raphael. (2024) 2024. “Inferring Cell Differentiation Maps from Lineage Tracing Data.”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2024.09.09.611835.

Yan, Jun, Paul Oyler-Castrillo, Purnima Ravisankar, Carl C Ward, Sébastien Levesque, Yangwode Jing, Danny Simpson, et al. (2024) 2024. “Improving Prime Editing With an Endogenous Small RNA-Binding Protein.”. Nature 628 (8008): 639-47. doi:10.1038/s41586-024-07259-6.

McNamara, Harold M, Sabrina C Solley, Britt Adamson, Michelle M Chan, and Jared E Toettcher. (2023) 2023. “Recording Morphogen Signals Reveals Origins of Gastruloid Symmetry Breaking.”. BioRxiv : The Preprint Server for Biology. doi:10.1101/2023.06.02.543474.

Sashittal, Palash, Henri Schmidt, Michelle Chan, and Benjamin J Raphael. (2023) 2023. “Startle: A Star Homoplasy Approach for CRISPR-Cas9 Lineage Tracing.”. Cell Systems 14 (12): 1113-1121.e9. doi:10.1016/j.cels.2023.11.005.

Yang, Dian, Matthew G Jones, Santiago Naranjo, William M Rideout, Kyung Hoi Joseph Min, Raymond Ho, Wei Wu, et al. (2022) 2022. “Lineage Tracing Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution.”. Cell 185 (11): 1905-1923.e25. doi:10.1016/j.cell.2022.04.015.

Quinn, Jeffrey J, Matthew G Jones, Ross A Okimoto, Shigeki Nanjo, Michelle M Chan, Nir Yosef, Trever G Bivona, and Jonathan S Weissman. (2021) 2021. “Single-Cell Lineages Reveal the Rates, Routes, and Drivers of Metastasis in Cancer Xenografts.”. Science (New York, N.Y.) 371 (6532). doi:10.1126/science.abc1944.

Jones, Matthew G, Alex Khodaverdian, Jeffrey J Quinn, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, and Nir Yosef. (2020) 2020. “Inference of Single-Cell Phylogenies from Lineage Tracing Data Using Cassiopeia.”. Genome Biology 21 (1): 92. doi:10.1186/s13059-020-02000-8.

Chan, Michelle M, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, et al. (2019) 2019. “Molecular Recording of Mammalian Embryogenesis.”. Nature 570 (7759): 77-82. doi:10.1038/s41586-019-1184-5.

Smith, Zachary D, Michelle M Chan, Kathryn C Humm, Rahul Karnik, Shila Mekhoubad, Aviv Regev, Kevin Eggan, and Alexander Meissner. (2014) 2014. “DNA Methylation Dynamics of the Human Preimplantation Embryo.”. Nature 511 (7511): 611-5. doi:10.1038/nature13581.

Thompson, Dawn A, Sushmita Roy, Michelle Chan, Mark P Styczynsky, Jenna Pfiffner, Courtney French, Amanda Socha, et al. (2013) 2013. “Evolutionary Principles of Modular Gene Regulation in Yeasts.”. ELife 2: e00603. doi:10.7554/eLife.00603.

Akopian, Veronika, Michelle M Chan, Kendell Clement, Christina Galonska, Casey A Gifford, Elizabeth Lehtola, Jing Liao, et al. (2012) 2012. “Epigenomics and Chromatin Dynamics.”. Genome Biology 13 (2): 313. doi:10.1186/gb-2012-13-2-313.

Chan, Michelle M, Zachary D Smith, Dieter Egli, Aviv Regev, and Alexander Meissner. (2012) 2012. “Mouse Ooplasm Confers Context-Specific Reprogramming Capacity.”. Nature Genetics 44 (9): 978-80. doi:10.1038/ng.2382.

Mende, Daniel R, Alison S Waller, Shinichi Sunagawa, Aino I Järvelin, Michelle M Chan, Manimozhiyan Arumugam, Jeroen Raes, and Peer Bork. (2012) 2012. “Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data.”. PloS One 7 (2): e31386. doi:10.1371/journal.pone.0031386.

Smith, Zachary D, Michelle M Chan, Tarjei S Mikkelsen, Hongcang Gu, Andreas Gnirke, Aviv Regev, and Alexander Meissner. (2012) 2012. “A Unique Regulatory Phase of DNA Methylation in the Early Mammalian Embryo.”. Nature 484 (7394): 339-44. doi:10.1038/nature10960.