Search Results - "Cahan, Patrick"

A conversation with ChatGPT on the role of computational systems biology in stem cell research by Cahan, Patrick, Treutlein, Barbara

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Origins and implications of pluripotent stem cell variability and heterogeneity by Cahan, Patrick, Daley, George Q.

“…Key Points There are marked differences in the in vitro differentiation capacity of pluripotent stem cell lines, including embryonic stem (ES) cells and…”
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Hippo pathway activity influences liver cell fate by Yimlamai, Dean, Christodoulou, Constantina, Galli, Giorgio G, Yanger, Kilangsungla, Pepe-Mooney, Brian, Gurung, Basanta, Shrestha, Kriti, Cahan, Patrick, Stanger, Ben Z, Camargo, Fernando D

“…The Hippo-signaling pathway is an important regulator of cellular proliferation and organ size. However, little is known about the role of this cascade in the…”
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Poly(A)-specific ribonuclease (PARN) mediates 3′-end maturation of the telomerase RNA component by Moon, Diane H, Segal, Matthew, Boyraz, Baris, Guinan, Eva, Hofmann, Inga, Cahan, Patrick, Tai, Albert K, Agarwal, Suneet

“…Suneet Agarwal and colleagues use somatic cells and induced pluripotent stem cells from patients with PARN mutations to show that PARN is required for the…”
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Deconstructing transcriptional heterogeneity in pluripotent stem cells by Kumar, Roshan M., Cahan, Patrick, Shalek, Alex K., Satija, Rahul, Jay DaleyKeyser, A., Li, Hu, Zhang, Jin, Pardee, Keith, Gennert, David, Trombetta, John J., Ferrante, Thomas C., Regev, Aviv, Daley, George Q., Collins, James J.

“…Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and…”
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Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM by Shachaf, Lior I, Roberts, Elijah, Cahan, Patrick, Xiao, Jie

“…A cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene…”
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Chromatin-modifying enzymes as modulators of reprogramming by Onder, Tamer T., Kara, Nergis, Cherry, Anne, Sinha, Amit U., Zhu, Nan, Bernt, Kathrin M., Cahan, Patrick, Mancarci, B. Ogan, Unternaehrer, Juli, Gupta, Piyush B., Lander, Eric S., Armstrong, Scott A., Daley, George Q.

“…Inhibition of DOT1L, the H3K79 histone methyltransferase, increases cell reprogramming and substituted for KLF4 and c-Myc, showing that chromatin-modifying…”
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Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma by Powers, John T., Tsanov, Kaloyan M., Pearson, Daniel S., Roels, Frederik, Spina, Catherine S., Ebright, Richard, Seligson, Marc, de Soysa, Yvanka, Cahan, Patrick, Theißen, Jessica, Tu, Ho-Chou, Han, Areum, Kurek, Kyle C., LaPier, Grace S., Osborne, Jihan K., Ross, Samantha J., Cesana, Marcella, Collins, James J., Berthold, Frank, Daley, George Q.

“…Poor prognosis in neuroblastoma is associated with genetic amplification of MYCN . MYCN is itself a target of let-7 , a tumour suppressor family of microRNAs…”
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Transcriptional Landscape of Cardiomyocyte Maturation by Uosaki, Hideki, Cahan, Patrick, Lee, Dong I., Wang, Songnan, Miyamoto, Matthew, Fernandez, Laviel, Kass, David A., Kwon, Chulan

“…Decades of progress in developmental cardiology has advanced our understanding of the early aspects of heart development, including cardiomyocyte (CM)…”
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Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells by Kim, Kitai, Zhao, Rui, Doi, Akiko, Ng, Kitwa, Unternaehrer, Juli, Cahan, Patrick, Hongguang, Huo, Loh, Yuin-Han, Aryee, Martin J, Lensch, M William, Li, Hu, Collins, James J, Feinberg, Andrew P, Daley, George Q

“…Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al . study this question in…”
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RANK + TLR2 + myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis by Zhang, Weixin, Noller, Kathleen, Crane, Janet, Wan, Mei, Wu, Xiaojun, Cahan, Patrick, Cao, Xu

“…Joint destruction is the major clinic burden in patients with rheumatoid arthritis (RA). It is unclear, though, how this autoimmune disease progresses to the…”
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Polycomb Repressive Complex 2 Regulates Normal Development of the Mouse Heart by He, Aibin, Ma, Qing, Cao, Jingjing, von Gise, Alexander, Zhou, Pingzhu, Xie, Huafeng, Zhang, Bing, Hsing, Michael, Christodoulou, Danos C, Cahan, Patrick, Daley, George Q, Kong, Sek Won, Orkin, Stuart H, Seidman, Christine E, Seidman, Jonathan G, Pu, William T

“…RATIONALE:Epigenetic marks are crucial for organogenesis, but their role in heart development is poorly understood. Polycomb repressive complex 2 (PRC2)…”
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Evaluating the transcriptional fidelity of cancer models by Peng, Da, Gleyzer, Rachel, Tai, Wen-Hsin, Kumar, Pavithra, Bian, Qin, Isaacs, Bradley, da Rocha, Edroaldo Lummertz, Cai, Stephanie, DiNapoli, Kathleen, Huang, Franklin W, Cahan, Patrick

“…Cancer researchers use cell lines, patient-derived xenografts, engineered mice, and tumoroids as models to investigate tumor biology and to identify therapies…”
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Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys by Gharaie, Sepideh, Lee, Kyungho, Noller, Kathleen, Lo, Emily K., Miller, Brendan, Jung, Hyun Jun, Newman-Rivera, Andrea M., Kurzhagen, Johanna T., Singla, Nirmish, Welling, Paul A., Fan, Jean, Cahan, Patrick, Noel, Sanjeev, Rabb, Hamid

“…T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR + CD4 - CD8 - (double negative-DN) are T cells that have regulatory properties…”
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The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells by Graubert, Timothy A, Cahan, Patrick, Li, Yedda, Izumi, Masayo

“…Timothy Graubert and colleagues report a high-resolution survey of copy number variation in mouse inbred strains and assess the impact of such variation on…”
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The Transcriptional Landscape of Hematopoietic Stem Cell Ontogeny by McKinney-Freeman, Shannon, Cahan, Patrick, Li, Hu, Lacadie, Scott A., Huang, Hsuan-Ting, Curran, Matthew, Loewer, Sabine, Naveiras, Olaia, Kathrein, Katie L., Konantz, Martina, Langdon, Erin M., Lengerke, Claudia, Zon, Leonard I., Collins, James J., Daley, George Q.

“…Transcriptome analysis of adult hematopoietic stem cells (HSCs) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a…”
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Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids by Velazquez, Jeremy J, LeGraw, Ryan, Moghadam, Farzaneh, Tan, Yuqi, Kilbourne, Jacquelyn, Maggiore, Joseph C, Hislop, Joshua, Liu, Silvia, Cats, Davy, Chuva de Sousa Lopes, Susana M, Plaisier, Christopher, Cahan, Patrick, Kiani, Samira, Ebrahimkhani, Mo R

“…Pluripotent stem cell (PSC)-derived organoids have emerged as novel multicellular models of human tissue development but display immature phenotypes, aberrant…”
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A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development by Cesana, Marcella, Guo, Michael H., Cacchiarelli, Davide, Wahlster, Lara, Barragan, Jessica, Doulatov, Sergei, Vo, Linda T., Salvatori, Beatrice, Trapnell, Cole, Clement, Kendell, Cahan, Patrick, Tsanov, Kaloyan M., Sousa, Patricia M., Tazon-Vega, Barbara, Bolondi, Adriano, Giorgi, Federico M., Califano, Andrea, Rinn, John L., Meissner, Alexander, Hirschhorn, Joel N., Daley, George Q.

“…While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity…”
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Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study by Gao, Xiugong, Li, Rong, Cahan, Patrick, Zhao, Yang, Yourick, Jeffrey J, Sprando, Robert L

“…Abstract Background Hepatocyte-like cells (HLCs) derived from human induced pluripotent stem cells (iPSCs) hold great promise in toxicological applications as…”
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Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells by Su, Emily Y., Fread, Kristen, Goggin, Sarah, Zunder, Eli R., Cahan, Patrick

“…Single-cell methods offer a high-resolution approach for characterizing cell populations. Many studies rely on single-cell transcriptomics to draw conclusions…”
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