Zobrazeno 1 - 10
of 26
pro vyhledávání: '"Emma Dann"'
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-39 (2024)
Abstract Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivi
Externí odkaz:
https://doaj.org/article/3160210e6dc54bf8bf286b1f1b84b2ab
Autor:
Chenqu Suo, Krzysztof Polanski, Emma Dann, Rik G. H. Lindeboom, Roser Vilarrasa-Blasi, Roser Vento-Tormo, Muzlifah Haniffa, Kerstin B. Meyer, Lisa M. Dratva, Zewen Kelvin Tuong, Menna R. Clatworthy, Sarah A. Teichmann
Publikováno v:
Nature Biotechnology.
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::fe6a6f6ace78cdf31eae940f172b0852
https://doi.org/10.1038/s41587-023-01734-7
https://doi.org/10.1038/s41587-023-01734-7
Autor:
Dinithi Sumanaweera, Chenqu Suo, Ana-Maria Cujba, Daniele Muraro, Emma Dann, Krzysztof Polanski, Alexander S. Steemers, Woochan Lee, Amanda J. Oliver, Jong-Eun Park, Kerstin B. Meyer, Bianca Dumitrascu, Sarah A. Teichmann
Single-cell data analysis can infer dynamic changes in cell populations, for example across time, space or in response to perturbation. To compare these dynamics between two conditions, trajectory alignment via dynamic programming (DP) optimization i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::332ab57f231f633a9c123b765a34bbbb
https://doi.org/10.1101/2023.03.08.531713
https://doi.org/10.1101/2023.03.08.531713
Publikováno v:
bioRxiv
Comparing molecular features, including the identification of genes with differential expression (DE) between conditions, is a powerful approach for characterising disease-specific phenotypes. When testing for DE in single-cell RNA sequencing data, c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::93d586e8fa2fa41a0ad90d643dd03e69
https://europepmc.org/articles/PMC10028920/
https://europepmc.org/articles/PMC10028920/
Autor:
Josephine L. Barnes, Peng He, Masahiro Yoshida, Kaylee B. Worlock, Rik G.H. Lindeboom, Chenqu Suo, J. Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Amanda J. Oliver, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T. Herczeg, Robert E. Hynds, Vitor H. Teixeira, Muzlifah Haniffa, Kyungtae Lim, Dawei Sun, Emma L. Rawlins, Krzysztof Polanski, Paul A. Lyons, John C. Marioni, Zewen Kelvin Tuong, Menna R. Clatworthy, James L. Reading, Sam M. Janes, Sarah A. Teichmann, Kerstin B. Meyer, Marko Z. Nikolić
During human development, lungs develop their roles of gas exchange and barrier function. Recent single cell studies have focused on epithelial and mesenchymal cell types, but much less is known about the developing lung immune cells, although the ai
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ba9e470f99f21542bfed3c556bfdae9f
https://doi.org/10.1101/2022.12.13.519713
https://doi.org/10.1101/2022.12.13.519713
Publikováno v:
Nature Biotechnology. 40:245-253
Current computational workflows for comparative analyses of single-cell datasets typically use discrete clusters as input when testing for differential abundance among experimental conditions. However, clusters do not always provide the appropriate r
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c68888ccdb01d112a17da733c83a119b
https://doi.org/10.1038/s41587-021-01033-z
https://doi.org/10.1038/s41587-021-01033-z
Autor:
Chenqu Suo, Krzysztof Polanski, Emma Dann, Rik G.H. Lindeboom, Roser Vilarrasa-Blasi, Roser Vento-Tormo, Muzlifah Haniffa, Kerstin B. Meyer, Lisa M. Dratva, Zewen Kelvin Tuong, Menna R. Clatworthy, Sarah A. Teichmann
Assessment of single-cell gene expression (scRNA-seq) and adaptive immune receptor sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here, we introduceDandelion, a computational pipeline for scVDJ-seq analysis. It enables the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b95ca1a60749960bbce524f1eb989af1
https://doi.org/10.1101/2022.11.18.517068
https://doi.org/10.1101/2022.11.18.517068
Autor:
Alexander Predeus, Anna Arutyunyan, Laura Jardine, Chenqu Suo, Emma Dann, Regina Hoo, Martin Prete, Muzlifah Haniffa, Thomas J. Mitchell, Roser Vento-Tormo, Matthew D. Young
Human females undergo X-inactivation (Xi), whereby one copy of X is randomly inactivated early in development, then propagated through cell division. Because Xi state is inherited, its measurement in populations of cells encodes information about the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2423a988e4866ce369dc8af500382d7f
https://doi.org/10.1101/2022.11.10.515645
https://doi.org/10.1101/2022.11.10.515645
Autor:
Rachel A Botting, Issac Goh, Antony Rose, Simone Webb, Justin Engelbert, Yorick Gitton, Emily Stephenson, Mariana Quiroga Londoño, Michael Mather, Nicole Mende, Ivan Imaz-Rosshandler, Dave Horsfall, Daniela Basurto-Lozada, Nana-Jane Chipampe, Victoria Rook, Pavel Mazin, MS Vijayabaskar, Rebecca Hannah, Laure Gambardella, Kile Green, Stephane Ballereau, Megumi Inoue, Liz Tuck, Valentina Lorenzi, Kwasi Kwakwa, Clara Alsinet, Bayanne Olabi, Mohi Miah, Chloe Admane, Dorin-Mirel Popescu, Meghan Acres, David Dixon, Rowen Coulthard, Steven Lisgo, Deborah J Henderson, Emma Dann, Chenqu Suo, Sarah J Kinston, Jong-eun Park, Krzysztof Polanski, Stijn Van Dongen, Kerstin B Meyer, Marella de Bruijn, James Palis, Sam Behjati, Elisa Laurenti, Nicola K Wilson, Roser Vento-Tormo, Alain Chédotal, Omer Bayraktar, Irene Roberts, Laura Jardine, Berthold Göttgens, Sarah A Teichmann, Muzlifah Haniffa
The yolk sac (YS) represents an evolutionarily-conserved extraembryonic structure that ensures timely delivery of nutritional support and oxygen to the developing embryo. However, the YS remains ill-defined in humans. We therefore assemble a complete
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::40063609b64ec1d12691d74d2fc5041c
https://doi.org/10.1101/2022.08.03.502475
https://doi.org/10.1101/2022.08.03.502475
Autor:
Chenqu Suo, Emma Dann, Issac Goh, Laura Jardine, Vitalii Kleshchevnikov, Jong-Eun Park, Rachel A. Botting, Emily Stephenson, Justin Engelbert, Zewen Kelvin Tuong, Krzysztof Polanski, Nadav Yayon, Chuan Xu, Ondrej Suchanek, Rasa Elmentaite, Cecilia Domínguez Conde, Peng He, Sophie Pritchard, Mohi Miah, Corina Moldovan, Alexander S. Steemers, Martin Prete, John C. Marioni, Menna R. Clatworthy, Muzlifah Haniffa, Sarah A. Teichmann
Recent advances in single cell genomics technologies have facilitated studies on the developing immune system at unprecedented scale and resolution. However, these studies have focused on one or a few organs and were thus limited in understanding the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b5490c12be85c8ef4217f4f5b80e0358
https://doi.org/10.1101/2022.01.17.476665
https://doi.org/10.1101/2022.01.17.476665