Search Results - "Packer, Jonathan"

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

“…Cells in a multicellular organism fulfill specific functions by enacting cell-type-specific programs of gene regulation. Single-cell RNA sequencing…”
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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data by 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

“…Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an…”
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Comprehensive single-cell transcriptional profiling of a multicellular organism by 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

“…To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq…”
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Joint profiling of chromatin accessibility and gene expression in thousands of single cells by 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

“…Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays…”
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A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution by 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

“…is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the…”
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Embryo-scale, single-cell spatial transcriptomics by 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

“…Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However,…”
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3D printed biofunctionalized scaffolds for microfracture repair of cartilage defects by 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.

“…While articular cartilage defects affect millions of people worldwide from adolescents to adults, the repair of articular cartilage defects still remains…”
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Massively multiplex chemical transcriptomics at single-cell resolution by 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

“…High-throughput chemical screens typically use coarse assays such as cell survival, limiting what can be learned about mechanisms of action, off-target…”
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A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease by 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

“…A genetic variant conferring a loss of function on the enzyme hydroxysteroid 17-beta dehydrogenase 13, expressed in the membrane surrounding the hepatic lipid…”
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Bone Marrow–Derived Mesenchymal Stem Cells Transduced With Scleraxis Improve Rotator Cuff Healing in a Rat Model by Gulotta, Lawrence V., Kovacevic, David, Packer, Jonathan D., Deng, Xiang Hua, Rodeo, Scott A.

“…Background: Rotator cuffs heal through a scar tissue interface after repair that makes them prone to failure. Scleraxis (Scx) is a basic helix-loop-helix…”
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On the design of CRISPR-based single-cell molecular screens by Hill, Andrew J, McFaline-Figueroa, José L, Starita, Lea M, Gasperini, Molly J, Matreyek, Kenneth A, Packer, Jonathan, Jackson, Dana, Shendure, Jay, Trapnell, Cole

“…CRISPR-based single-cell pooled screens that use linked barcodes suffer from lost sensitivity due to lentiviral template switching. The barcode-free CROP-seq…”
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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages by 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

“…Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest…”
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Biomechanical Aspects of Osteochondral Regeneration: Implications and Strategies for Three-Dimensional Bioprinting by Choe, Robert, Devoy, Eoin, Jabari, Erfan, Packer, Jonathan D, Fisher, John P

“…Osteoarthritis is among the most prevalent of musculoskeletal disorders in the world that causes joint pain, deformity, and limited range of movement. The…”
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Application of Bone Marrow-Derived Mesenchymal Stem Cells in a Rotator Cuff Repair Model by Gulotta, Lawrence V., Kovacevic, David, Ehteshami, John R., Dagher, Elias, Packer, Jonathan D., Rodeo, Scott A.

“…Background Rotator cuff tendons heal to bone with interposed scar tissue, which makes repairs prone to failure. The purpose of this study was to determine if…”
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Amplified Gliosis and Interferon-Associated Inflammation in the Aging Brain following Diffuse Traumatic Brain Injury by 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

“…Traumatic brain injury (TBI) is associated with chronic psychiatric complications and increased risk for development of neurodegenerative pathology. Aged…”
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How Should We Secure Our Transplanted Meniscus? A Meta-analysis by Jauregui, Julio J., Wu, Zhan Dong, Meredith, Sean, Griffith, Cullen, Packer, Jonathan D., Henn, R. Frank

“…Background: Meniscal allograft transplant (MAT) is a salvage procedure for young patients with symptomatic meniscal deficiency. Although many studies report…”
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Enhanced fear memory after social defeat in mice is dependent on interleukin-1 receptor signaling in glutamatergic neurons by 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.

“…Chronic stress is associated with increased anxiety, cognitive deficits, and post-traumatic stress disorder. Repeated social defeat (RSD) in mice causes…”
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Impaired cortical neuronal homeostasis and cognition after diffuse traumatic brain injury are dependent on microglia and type I interferon responses by Packer, Jonathan M., Bray, Chelsea E., Beckman, Nicolas B., Wangler, Lynde M., Davis, Amara C., Goodman, Ethan J., Klingele, Nathaniel E., Godbout, Jonathan P.

“…Neuropsychiatric complications including depression and cognitive decline develop in the years after traumatic brain injury (TBI), negatively affecting quality…”
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Computational investigation of interface printing patterns within 3D printed multilayered scaffolds for osteochondral tissue engineering by Choe, Robert, Devoy, Eoin, Kuzemchak, Blake, Sherry, Mary, Jabari, Erfan, Packer, Jonathan D, Fisher, John P

“…Osteoarthritis is a highly prevalent rheumatic musculoskeletal disorder that commonly affects many joints. Repetitive joint overloading perpetuates the damage…”
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Outcomes of Anterior Cruciate Ligament Reconstruction in Obese and Overweight Patients: A Systematic Review by DiSilvestro, Kevin J, Jauregui, Julio J, Glazier, Elizabeth, Cherkalin, Denis, Bennett, Craig H, Packer, Jonathan D, Henn, Ralph Frank

“…OBJECTIVE:To evaluate the mechanism of injury, outcomes, and complications of anterior cruciate ligament (ACL) reconstruction in overweight and obese patients…”
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