Combinatorial mapping of E3 ubiquitin ligases to their target substrates

Authors: Suiter, Chase C. ^{1, 2, 3, 8, ∗}, Calderon, Diego ^{2, 8}, Lee, David S. ², Chiu, Melodie ², Jain, Shruti ², Chardon, Florence M. ^{2, 3}, Lee, Choli ², Daza, Riza M. ^{2, 3}, Trapnell, Cole ^{2, 3, 4, 5}, Zheng, Ning ^{6, 7}, Shendure, Jay ^{1, 2, 3, 4, 5, 7, 9, ∗∗}

Source: In Molecular Cell 20 February 2025 85(4):829-842

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

Authors: Li, Xiaoyi, Chen, Wei, Martin, Beth K., Calderon, Diego, Lee, Choli, Choi, Junhong, Chardon, Florence M., McDiarmid, Troy A., Daza, Riza M., Kim, Haedong, Lalanne, Jean-Benoît, Nathans, Jenny F., Lee, David S., Shendure, Jay

Source: In Cell 9 May 2024 187(10):2411-2427

Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells

Authors: Ramani, Vijay, Deng, Xinxian, Qiu, Ruolan, Lee, Choli, Disteche, Christine M., Noble, William S., Shendure, Jay, Duan, Zhijun

Source: In Methods 1 January 2020 170:61-68

Retinoic acid induces human gastruloids with posterior embryo-like structures

Authors: Hamazaki, Nobuhiko, Yang, Wei, Kubo, Connor A., Qiu, Chengxiang, Martin, Beth K., Garge, Riddhiman K., Regalado, Samuel G., Nichols, Eva K., Pendyala, Sriram, Bradley, Nicholas, Fowler, Douglas M., Lee, Choli, Daza, Riza M., Srivatsan, Sanjay, Shendure, Jay

Source: Nature Cell Biology; October 2024, Vol. 26 Issue: 10 p1790-1803, 14p

Symbolic recording of signalling and cis-regulatory element activity to DNA.

Authors: Chen, Wei, Choi, Junhong, Li, Xiaoyi, Nathans, Jenny F., Martin, Beth, Yang, Wei, Hamazaki, Nobuhiko, Qiu, Chengxiang, Lalanne, Jean-Benoît, Regalado, Samuel, Kim, Haedong, Agarwal, Vikram, Nichols, Eva, Leith, Anh, Lee, Choli, Shendure, Jay

Source: Nature; Aug2024, Vol. 632 Issue 8027, p1073-1081, 9p

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Authors: Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan, Christiansen, Lena, DeWitt, William S., Lee, Choli, Regalado, Samuel G., Read, David F., Steemers, Frank J., Disteche, Christine M., Trapnell, Cole, Shendure, Jay

Source: In Cell 23 August 2018 174(5):1309-1324

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

Authors: Ma, Wenxiu, Ay, Ferhat, Lee, Choli, Gulsoy, Gunhan, Deng, Xinxian, Cook, Savannah, Hesson, Jennifer, Cavanaugh, Christopher, Ware, Carol B., Krumm, Anton, Shendure, Jay, Blau, C. Anthony, Disteche, Christine M., Noble, William S., Duan, ZhiJun

Source: In Methods 1 June 2018 142:59-73

Comprehensive single-cell transcriptional profiling of a multicellular organism

Authors: Cao, Junyue, Packer, Jonathan S., Ramani, Vijay, Cusanovich, Darren A., Huynh, Chau, Daza, Riza, Qiu, Xiaojie, Lee, Choli, Furlan, Scott N., Steemers, Frank J., Adey, Andrew, Waterston, Robert H., Trapnell, Cole, Shendure, Jay

Source: Science, 2017 Aug . 357(6352), 661-667.

Access URL: https://www.jstor.org/stable/26399645

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions

Authors: Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay

Source: In The American Journal of Human Genetics 3 August 2017 101(2):192-205

Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters

Authors: Lalanne, Jean-Benoît, Regalado, Samuel G., Domcke, Silvia, Calderon, Diego, Martin, Beth K., Li, Xiaoyi, Li, Tony, Suiter, Chase C., Lee, Choli, Trapnell, Cole, Shendure, Jay

Source: Nature Methods; 20240101, Issue: Preprints p1-11, 11p

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

Authors: Duan, Zhijun, Andronescu, Mirela, Schutz, Kevin, Lee, Choli, Shendure, Jay, Fields, Stanley, Noble, William S., Anthony Blau, C.

Source: In Methods November 2012 58(3):277-288

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Authors: O'Roak, Brian J., Vives, Laura, Fu, Wenqing, Egertson, Jarrett D., Stanaway, Ian B., Phelps, Ian G., Carvill, Gemma, Kumar, Akash, Lee, Choli, Ankenman, Katy, Munson, Jeff, Hiatt, Joseph B., Turner, Emily H., Levy, Roie, O'Day, Diana R., Krumm, Niklas, Coe, Bradley P., Martin, Beth K., Borenstein, Elhanan, Nickerson, Deborah A., Mefford, Heather C., Doherty, Dan, Akey, Joshua M., Bernier, Raphael, Eichler, Evan E., Shendure, Jay

Source: Science, 2012 Dec . 338(6114), 1619-1622.

Access URL: http://dx.doi.org/10.1126/science.1227764

Capturing native long-range contiguity by in situ library construction and optical sequencing

Authors: Schwartz, Jerrod J., Lee, Choli, Hiatt, Joseph B., Adey, Andrew, Shendure, Jay

Source: Proceedings of the National Academy of Sciences of the United States of America, 2012 Nov . 109(46), 18749-18754.

Access URL: https://www.jstor.org/stable/41830097

Resolving the Breakpoints of the 17q21.31 Microdeletion Syndrome with Next-Generation Sequencing

Authors: Itsara, Andy, Vissers, Lisenka E.L.M., Steinberg, Karyn Meltz, Meyer, Kevin J., Zody, Michael C., Koolen, David A., de Ligt, Joep, Cuppen, Edwin, Baker, Carl, Lee, Choli, Graves, Tina A., Wilson, Richard K., Jenkins, Robert B., Veltman, Joris A., Eichler, Evan E.

Source: In The American Journal of Human Genetics 6 April 2012 90(4):599-613

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

Authors: Kumar, Akash, White, Thomas A., MacKenzie, Alexandra P., Clegg, Nigel, Lee, Choli, Dumpit, Ruth F., Coleman, Ilsa, Ng, Sarah B., Salipante, Stephen J., Rieder, Mark J., Nickerson, Deborah A., Corey, Eva, Lange, Paul H., Morrissey, Colm, Vessella, Robert L., Nelson, Peter S., Shendure, Jay

Source: Proceedings of the National Academy of Sciences of the United States of America, 2011 Oct 01. 108(41), 17087-17092.

Access URL: https://www.jstor.org/stable/41321837

A time-resolved, multi-symbol molecular recorder via sequential genome editing.

Authors: Choi, Junhong, Chen, Wei, Minkina, Anna, Chardon, Florence M., Suiter, Chase C., Regalado, Samuel G., Domcke, Silvia, Hamazaki, Nobuhiko, Lee, Choli, Martin, Beth, Daza, Riza M., Shendure, Jay

Source: Nature; Aug2022, Vol. 608 Issue 7921, p98-107, 10p

Precise genomic deletions using paired prime editing.

Authors: Choi, Junhong, Chen, Wei, Suiter, Chase C., Lee, Choli, Chardon, Florence M., Yang, Wei, Leith, Anh, Daza, Riza M., Martin, Beth, Shendure, Jay

Source: Nature Biotechnology; Feb2022, Vol. 40 Issue 2, p218-226, 9p

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.

Authors: Bonora, Giancarlo, Ramani, Vijay, Singh, Ritambhara, Fang, He, Jackson, Dana L., Srivatsan, Sanjay, Qiu, Ruolan, Lee, Choli, Trapnell, Cole, Shendure, Jay, Duan, Zhijun, Deng, Xinxian, Noble, William S., Disteche, Christine M.

Source: Genome Biology; 9/27/2021, Vol. 22 Issue 1, p1-36, 36p

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.

Authors: Kim, Hyeon-Jin, Yardımcı, Galip Gurkan, Bonora, Giancarlo, Ramani, Vijay, Liu, Jie, Qiu, Ruolan, Lee, Choli, Hesson, Jennifer, Ware, Carol B., Shendure, Jay, Duan, Zhijun, Noble, William Stafford

Source: PLoS Computational Biology; 9/18/2020, Vol. 16 Issue 9, p1-19, 19p, 2 Diagrams, 1 Chart, 4 Graphs

Subject Terms: NATURAL language processing, CELL cycle, CELLS

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

Authors: O'Roak, Brian J., Deriziotis, Pelagia, Lee, Choli

Source: Nature Genetics; June 2011, Vol. 43 Issue 6, p585-589, 5p