Browse by CSHL Author

Paper

Werner, Jonathan M, Gillis, Jesse (December 2024) Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue. PLoS Biology, 22 (12). e3002912. ISSN 1544-9173

Colonna, Marco, Konopka, Genevieve, Liddelow, Shane A, Nowakowski, Tomasz, Awatramani, Rajeshwar, Bateup, Helen S, Cadwell, Cathryn R, Caglayan, Emre, Chen, Jerry L, Gillis, Jesse, Kampmann, Martin, Krienen, Fenna, Marsh, Samuel E, Monje, Michelle, O'Dea, Michael R, Patani, Rickie, Pollen, Alex A, Quintana, Francisco J, Scavuzzo, Marissa, Schmitz, Matthew, Sloan, Steven A, Tesar, Paul J, Tollkuhn, Jessica, Tosches, Maria Antonietta, Urbanek, Madeleine E, Werner, Jonathan M, Bayraktar, Omer A, Gokce, Ozgun, Habib, Naomi (December 2024) Implementation and validation of single-cell genomics experiments in neuroscience. Nature Neuroscience, 27 (12). pp. 2310-2325. ISSN 1097-6256

Werner, Jonathan M, Hover, John, Gillis, Jesse (October 2024) Population variability in X-chromosome inactivation across 10 mammalian species. Nature Communications, 15 (1). p. 8991. ISSN 2041-1723 (Public Dataset)

Werner, Jonathan M, Hover, John, Gillis, Jesse (October 2023) Population variability in X-chromosome inactivation across 9 mammalian species. (Submitted)

Werner, Jonathan M, Gillis, Jesse (October 2023) Preservation of co-expression defines the primary tissue fidelity of human neural organoids. bioRxiv. (Submitted)

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S, Wright, James, Chang, Justin, Cameron, Christopher JF, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B, Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A, Farid, Daniel, Farrell, Nina P, Gabdank, Idan, Gofin, Yoel, Gorkin, David U, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R, Gerstein, Mark (March 2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186 (7). 1493-1511.e40. ISSN 0092-8674

Werner, Jonathan M, Ballouz, Sara, Hover, John, Gillis, Jesse (July 2022) Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Developmental Cell, 57 (16). S1534-5807(22)00496. ISSN 1534-5807

Werner, Jonathan, Ballouz, Sara, Hover, John, Gillis, Jesse (September 2021) Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development. BioRxiv. (Unpublished)

Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark (April 2021) Multi-tissue integrative analysis of personal epigenomes. bioRxiv. (Unpublished)

Thesis

Werner, Jonathan M (December 2023) Transcriptomic approaches for investigating developmental lineage: exploiting the X-chromosome as a marker for lineage specification and quantifying the lineage fidelity of neural organoid systems. PhD thesis, Cold Spring Harbor Laboratory.