Search Results - "Andersen, Stacey"

Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease by Yazar, Seyhan, Alquicira-Hernandez, Jose, Wing, Kristof, Senabouth, Anne, Gordon, M Grace, Andersen, Stacey, Lu, Qinyi, Rowson, Antonia, Taylor, Thomas R P, Clarke, Linda, Maccora, Katia, Chen, Christine, Cook, Anthony L, Ye, Chun Jimmie, Fairfax, Kirsten A, Hewitt, Alex W, Powell, Joseph E

“…The human immune system displays substantial variation between individuals, leading to differences in susceptibility to autoimmune disease. We present…”
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Genome-wide discovery of human splicing branchpoints by Mercer, Tim R, Clark, Michael B, Andersen, Stacey B, Brunck, Marion E, Haerty, Wilfried, Crawford, Joanna, Taft, Ryan J, Nielsen, Lars K, Dinger, Marcel E, Mattick, John S

“…During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming…”
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Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells by Lukowski, Samuel W., Patel, Jatin, Andersen, Stacey B., Sim, Seen-Ling, Wong, Ho Yi, Tay, Joshua, Winkler, Ingrid, Powell, Joseph E., Khosrotehrani, Kiarash

“…The cellular and molecular profiles that govern the endothelial heterogeneity of the circulatory system have yet to be elucidated. Using a data-driven approach…”
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Spliced synthetic genes as internal controls in RNA sequencing experiments by Hardwick, Simon A, Chen, Wendy Y, Wong, Ted, Deveson, Ira W, Blackburn, James, Andersen, Stacey B, Nielsen, Lars K, Mattick, John S, Mercer, Tim R

“…Synthetic spike-in standards (‘sequins’), representing spliced mRNA isoforms, provide internal controls for assessing transcript assembly and quantification…”
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Genotype-free demultiplexing of pooled single-cell RNA-seq by Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D, Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J, Yang, Jian, Mueller, Michael D, Hewitt, Alex W, Pébay, Alice, Montgomery, Grant W, Powell, Joseph E, Coin, Lachlan J M

“…A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag…”
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Spatial Transcriptomics in Kidney Tissue by Raghubar, Arti M, Crawford, Joanna, Jones, Kahli, Lam, Pui Y, Andersen, Stacey B, Matigian, Nicholas A, Ng, Monica S Y, Healy, Helen, Kassianos, Andrew J, Mallett, Andrew J

“…Unlike bulk and single-cell/single-nuclei RNA sequencing methods, spatial transcriptome sequencing (ST-seq) resolves transcriptome expression within the…”
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HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function by Friedman, Clayton E, Cheetham, Seth W, Negi, Sumedha, Mills, Richard J, Ogawa, Masahito, Redd, Meredith A, Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K, Paterson, Scott, De Angelis, Jessica E, Andersen, Stacey B, Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M A, Yoon, Sohye, Faulkner, Geoffrey J, Smith, Kelly A, Porrello, Enzo, Harvey, Richard P, Hogan, Benjamin M, Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E, Palpant, Nathan J

“…Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced…”
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High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection by Nhu, Nguyen Thi Khanh, Phan, Minh-Duy, Hancock, Steven J, Peters, Kate M, Alvarez-Fraga, Laura, Forde, Brian M, Andersen, Stacey B, Miliya, Thyl, Harris, Patrick N A, Beatson, Scott A, Schlebusch, Sanmarie, Bergh, Haakon, Turner, Paul, Brauner, Annelie, Westerlund-Wikström, Benita, Irwin, Adam D, Schembri, Mark A

“…Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. is the second most common cause of neonatal meningitis…”
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ascend: R package for analysis of single-cell RNA-seq data by Senabouth, Anne, Lukowski, Samuel W, Hernandez, Jose Alquicira, Andersen, Stacey B, Mei, Xin, Nguyen, Quan H, Powell, Joseph E

“…Recent developments in single-cell RNA sequencing (scRNA-seq) platforms have vastly increased the number of cells typically assayed in an experiment. Analysis…”
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Representing genetic variation with synthetic DNA standards by Deveson, Ira W, Chen, Wendy Y, Wong, Ted, Hardwick, Simon A, Andersen, Stacey B, Nielsen, Lars K, Mattick, John S, Mercer, Tim R

“…Synthetic DNA spike-ins that recapitulate genetic variation present in human genomes serve as quantitative and qualitative controls for genome sequencing and…”
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Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis by Lukowski, Samuel W., Tuong, Zewen K., Noske, Katharina, Senabouth, Anne, Nguyen, Quan H., Andersen, Stacey B., Soyer, H. Peter, Frazer, Ian H., Powell, Joseph E.

“…Persistent human papillomavirus (HPV) infection is responsible for at least 5% of human malignancies. Most HPV-associated cancers are initiated by the HPV16…”
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Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships by Schwaber, Jessica L, Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K, Trau, Matt, Nielsen, Lars K

“…With the exception of a few master transcription factors, regulators of neutrophil maturation are poorly annotated in the intermediate phenotypes between the…”
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Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cells by Lukowski, Samuel W., Rødahl, Inga, Kelly, Samuel, Yu, Meihua, Gotley, James, Zhou, Chenhao, Millard, Susan, Andersen, Stacey B., Christ, Angelika N., Belz, Gabrielle, Frazer, Ian H., Chandra, Janin

“…Conventional dendritic cells (cDCs) are traditionally subdivided into cDC1 and cDC2 lineages. Batf3 is a cDC1-required transcription factor, and we observed…”
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Development of a novel cell sorting method that samples population diversity in flow cytometry by Osborne, Geoffrey W., Andersen, Stacey B., Battye, Francis L.

“…Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into…”
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Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron Segments by Raghubar, Arti M, Pham, Duy T, Tan, Xiao, Grice, Laura F, Crawford, Joanna, Lam, Pui Yeng, Andersen, Stacey B, Yoon, Sohye, Teoh, Siok Min, Matigian, Nicholas A, Stewart, Anne, Francis, Leo, Ng, Monica S Y, Healy, Helen G, Combes, Alexander N, Kassianos, Andrew J, Nguyen, Quan, Mallett, Andrew J

“…Available transcriptomes of the mammalian kidney provide limited information on the spatial interplay between different functional nephron structures due to…”
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Global Analysis of Transcription Start Sites and Enhancers in Endometrial Stromal Cells and Differences Associated with Endometriosis by Marla, Sushma, Mortlock, Sally, Yoon, Sohye, Crawford, Joanna, Andersen, Stacey, Mueller, Michael D, McKinnon, Brett, Nguyen, Quan, Montgomery, Grant W

“…Identifying tissue-specific molecular signatures of active regulatory elements is critical to understanding gene regulatory mechanisms. In this study,…”
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Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq by Rødahl, Inga, Gotley, James, Andersen, Stacey B., Yu, Meihua, Mehdi, Ahmed M., Christ, Angelika N., Hamilton-Williams, Emma E., Frazer, Ian H., Lukowski, Samuel W., Chandra, Janin

“…Here, we outline detailed protocols to isolate and profile murine splenic dendritic cells (DCs) through advanced flow cytometry of the myeloid compartment and…”
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Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media by Daniszewski, Maciej, Nguyen, Quan, Chy, Hun S, Singh, Vikrant, Crombie, Duncan E, Kulkarni, Tejal, Liang, Helena H, Sivakumaran, Priyadharshini, Lidgerwood, Grace E, Hernández, Damián, Conquest, Alison, Rooney, Louise A, Chevalier, Sophie, Andersen, Stacey B, Senabouth, Anne, Vickers, James C, Mackey, David A, Craig, Jamie E, Laslett, Andrew L, Hewitt, Alex W, Powell, Joseph E, Pébay, Alice

“…We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of…”
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Exceptional memory performance in the Long Life Family Study by Barral, Sandra, Cosentino, Stephanie, Costa, Rosann, Andersen, Stacey L, Christensen, Kaare, Eckfeldt, John H, Newman, Anne B, Perls, Thomas T, Province, Michael A, Hadley, Evan C, Rossi, Winifred K, Mayeux, Richard

“…Abstract Research to understand variability at the highest end of the cognitive performance distribution has been scarce. Our aim was to define a cognitive…”
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Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease by Engel, Jessica A, Lee, Hyun Jae, Williams, Cameron G, Kuns, Rachel, Olver, Stuart, Lansink, Lianne Im, Soon, Megan Sf, Andersen, Stacey B, Powell, Joseph E, Svensson, Valentine, Teichmann, Sarah A, Hill, Geoffrey R, Varelias, Antiopi, Koyama, Motoko, Haque, Ashraful

“…Acute gastrointestinal (GI) graft-versus-host disease (GVHD) is a primary determinant of mortality after allogeneic hematopoietic stem cell transplantation…”
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