pyNVR: investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction

by Chen, Bob, Herring, Charles A, Lau, Ken S
Published in Bioinformatics (2019)

Single-Cell Computational Strategies for Lineage Reconstruction in Tissue Systems

by Herring, Charles A., Chen, Bob, McKinley, Eliot T., Lau, Ken S.
Published in Cell Mol Gastroenterol Hepatol (2018)

Multiscale analysis of the murine intestine for modeling human diseases

by Lyons, Jesse, Herring, Charles A., Banerjee, Amrita, Simmons, Alan J., Lau, Ken S.
Published in Integr Biol (Camb) (2015)

Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks

by Simmons, Alan J., Scurrah, Cherie’ R., McKinley, Eliot T., Herring, Charles A., Irish, Jonathan M., Washington, Mary K., Coffey, Robert J., Lau, Ken S.
Published in Sci Signal (2016)

Quantitative assessment of cell population diversity in single-cell landscapes

by Liu, Qi, Herring, Charles A., Sheng, Quanhu, Ping, Jie, Simmons, Alan J., Chen, Bob, Banerjee, Amrita, Li, Wei, Gu, Guoqiang, Coffey, Robert J., Shyr, Yu, Lau, Ken S.
Published in PLoS Biol (2018)

Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternate tuft cell origins in the gut

by Herring, Charles A., Banerjee, Amrita, McKinley, Eliot T., Simmons, Alan J., Ping, Jie, Roland, Joseph T., Franklin, Jeffrey L., Liu, Qi, Gerdes, Michael J., Coffey, Robert J., Lau, Ken S.
Published in Cell Syst (2017)

Neurog3-independent methylation is the earliest detectable mark distinguishing pancreatic progenitor identity

by Liu, Jing, Banerjee, Amrita, Herring, Charles A., Attalla, Jonathan, Hu, Ruiying, Xu, Yanwen, Shao, Qiujia, Simmons, Alan J., Dadi, Prasanna K., Wang, Sui, Jacobson, David A., Liu, Bindong, Hodges, Emily, Lau, Ken S., Gu, Guoqiang
Published in Dev Cell (2019)

Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo

by Simmons, Alan J, Banerjee, Amrita, McKinley, Eliot T, Scurrah, Cherie' R, Herring, Charles A, Gewin, Leslie S, Masuzaki, Ryota, Karp, Seth J, Franklin, Jeffrey L, Gerdes, Michael J, Irish, Jonathan M, Coffey, Robert J, Lau, Ken S
Published in Mol Syst Biol (2015)

Cytometry‐based single‐cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF‐α‐induced apoptosis in vivo

by Simmons, Alan J, Banerjee, Amrita, McKinley, Eliot T, Scurrah, Cherie’ R, Herring, Charles A, Gewin, Leslie S, Masuzaki, Ryota, Karp, Seth J, Franklin, Jeffrey L, Gerdes, Michael J, Irish, Jonathan M, Coffey, Robert J, Lau, Ken S
Published in Mol Syst Biol (2016)

Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation

by Banerjee, Amrita, Herring, Charles A., Chen, Bob, Kim, Hyeyon, Simmons, Alan J., Southard-Smith, Austin N., Allaman, Margaret M., White, James R., Macedonia, Mary C., Mckinley, Eliot T., Solano, Marisol A. Ramirez, Scoville, Elizabeth A., Liu, Qi, Wilson, Keith T., Coffey, Robert J., Washington, M. Kay, Goettel, Jeremy A., Lau, Ken S.
Published in Gastroenterology (2020)