Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data von Pliner, Hannah A., Packer, Jonathan S., McFaline-Figueroa, José L., Cusanovich, Darren A., Daza, Riza M., Aghamirzaie, Delasa, Srivatsan, Sanjay, Qiu, Xiaojie, Jackson, Dana, Minkina, Anna, Adey, Andrew C., Steemers, Frank J., Shendure, Jay, Trapnell, Cole

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Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation von Packer, Jonathan, Trapnell, Cole

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Comprehensive single-cell transcriptional profiling of a multicellular organism von 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

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Joint profiling of chromatin accessibility and gene expression in thousands of single cells von Cao, Junyue, Cusanovich, Darren A, Ramani, Vijay, Aghamirzaie, Delasa, Pliner, Hannah A, Hill, Andrew J, Daza, Riza M, McFaline-Figueroa, Jose L, Packer, Jonathan S, Christiansen, Lena, Steemers, Frank J, Adey, Andrew C, Trapnell, Cole, Shendure, Jay

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A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution von Packer, Jonathan S, Zhu, Qin, Huynh, Chau, Sivaramakrishnan, Priya, Preston, Elicia, Dueck, Hannah, Stefanik, Derek, Tan, Kai, Trapnell, Cole, Kim, Junhyong, Waterston, Robert H, Murray, John I

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Embryo-scale, single-cell spatial transcriptomics von Srivatsan, Sanjay R, Regier, Mary C, Barkan, Eliza, Franks, Jennifer M, Packer, Jonathan S, Grosjean, Parker, Duran, Madeleine, Saxton, Sarah, Ladd, Jon J, Spielmann, Malte, Lois, Carlos, Lampe, Paul D, Shendure, Jay, Stevens, Kelly R, Trapnell, Cole

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3D printed biofunctionalized scaffolds for microfracture repair of cartilage defects von Guo, Ting, Noshin, Maeesha, Baker, Hannah B., Taskoy, Evin, Meredith, Sean J., Tang, Qinggong, Ringel, Julia P., Lerman, Max J., Chen, Yu, Packer, Jonathan D., Fisher, John P.

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A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease von Abul-Husn, Noura S, Cheng, Xiping, Li, Alexander H, Xin, Yurong, Schurmann, Claudia, Stevis, Panayiotis, Liu, Yashu, Kozlitina, Julia, Stender, Stefan, Wood, G. Craig, Stepanchick, Ann N, Still, Matthew D, McCarthy, Shane, O’Dushlaine, Colm, Packer, Jonathan S, Balasubramanian, Suganthi, Gosalia, Nehal, Esopi, David, Kim, Sun Y, Mukherjee, Semanti, Lopez, Alexander E, Fuller, Erin D, Penn, John, Chu, Xin, Luo, Jonathan Z, Mirshahi, Uyenlinh L, Carey, David J, Still, Christopher D, Feldman, Michael D, Small, Aeron, Damrauer, Scott M, Rader, Daniel J, Zambrowicz, Brian, Olson, William, Murphy, Andrew J, Borecki, Ingrid B, Shuldiner, Alan R, Reid, Jeffrey G, Overton, John D, Yancopoulos, George D, Hobbs, Helen H, Cohen, Jonathan C, Gottesman, Omri, Teslovich, Tanya M, Baras, Aris, Mirshahi, Tooraj, Gromada, Jesper, Dewey, Frederick E

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Massively multiplex chemical transcriptomics at single-cell resolution von Srivatsan, Sanjay R, McFaline-Figueroa, José L, Ramani, Vijay, Saunders, Lauren, Cao, Junyue, Packer, Jonathan, Pliner, Hannah A, Jackson, Dana L, Daza, Riza M, Christiansen, Lena, Zhang, Fan, Steemers, Frank, Shendure, Jay, Trapnell, Cole

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Bone Marrow–Derived Mesenchymal Stem Cells Transduced With Scleraxis Improve Rotator Cuff Healing in a Rat Model von Gulotta, Lawrence V., Kovacevic, David, Packer, Jonathan D., Deng, Xiang Hua, Rodeo, Scott A.

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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages von Saunders, Lauren M, Mishra, Abhishek K, Aman, Andrew J, Lewis, Victor M, Toomey, Matthew B, Packer, Jonathan S, Qiu, Xiaojie, McFaline-Figueroa, Jose L, Corbo, Joseph C, Trapnell, Cole, Parichy, David M

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On the design of CRISPR-based single-cell molecular screens von Hill, Andrew J, McFaline-Figueroa, José L, Starita, Lea M, Gasperini, Molly J, Matreyek, Kenneth A, Packer, Jonathan, Jackson, Dana, Shendure, Jay, Trapnell, Cole

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Amplified Gliosis and Interferon-Associated Inflammation in the Aging Brain following Diffuse Traumatic Brain Injury von Wangler, Lynde M, Bray, Chelsea E, Packer, Jonathan M, Tapp, Zoe M, Davis, Amara C, O'Neil, Shane M, Baetz, Kara, Ouviña, Michelle, Witzel, Mollie, Godbout, Jonathan P

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Application of Bone Marrow-Derived Mesenchymal Stem Cells in a Rotator Cuff Repair Model von Gulotta, Lawrence V., Kovacevic, David, Ehteshami, John R., Dagher, Elias, Packer, Jonathan D., Rodeo, Scott A.

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Biomechanical Aspects of Osteochondral Regeneration: Implications and Strategies for Three-Dimensional Bioprinting von Choe, Robert, Devoy, Eoin, Jabari, Erfan, Packer, Jonathan D, Fisher, John P

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Impaired cortical neuronal homeostasis and cognition after diffuse traumatic brain injury are dependent on microglia and type I interferon responses von Packer, Jonathan M., Bray, Chelsea E., Beckman, Nicolas B., Wangler, Lynde M., Davis, Amara C., Goodman, Ethan J., Klingele, Nathaniel E., Godbout, Jonathan P.

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Enhanced fear memory after social defeat in mice is dependent on interleukin-1 receptor signaling in glutamatergic neurons von Goodman, Ethan J., Biltz, Rebecca G., Packer, Jonathan M., DiSabato, Damon J., Swanson, Samuel P., Oliver, Braeden, Quan, Ning, Sheridan, John F., Godbout, Jonathan P.

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How Should We Secure Our Transplanted Meniscus? A Meta-analysis von Jauregui, Julio J., Wu, Zhan Dong, Meredith, Sean, Griffith, Cullen, Packer, Jonathan D., Henn, R. Frank

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Computational investigation of interface printing patterns within 3D printed multilayered scaffolds for osteochondral tissue engineering von Choe, Robert, Devoy, Eoin, Kuzemchak, Blake, Sherry, Mary, Jabari, Erfan, Packer, Jonathan D, Fisher, John P

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Patient Perception of Being “Completely Better” After Anterior Cruciate Ligament Reconstruction von Schneider, Matheus B., Kung, Justin E., Zhang, Tina, Rocca, Michael S., Foster, Michael J., Meredith, Sean J., Leong, Natalie L., Packer, Jonathan D., Henn, R. Frank

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