Results 11 to 20 of about 1,731,641 (260)

Counterfactual inference for single-cell gene expression analysis [PDF]

, 2021
Abstract Finding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework that prioritizes disease genes by adjusting confounders without prior knowledge of control variables. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of ...
Yongjin Park, Manolis Kellis
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Methods, Challenges and Potentials of Single Cell RNA-seq [PDF]

, 2012
RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several recent studies demonstrate its successful adaption to single cell analysis. This allows new biological insights into cell differentiation, cell-to-cell variation and gene
Daniel Hebenstreit, Hebenstreit, Daniel
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Gene expression atlas of a developing tissue by single cell expression correlation analysis [PDF]

Nature Methods, 2018
ABSTRACT The Drosophila wing disc has been a fundamental model system for the discovery of key signaling pathways and for our understanding of developmental processes. However, a complete map of gene expression in this tissue is lacking. To obtain a complete gene expression atlas in
Josephine Bageritz, Philipp Willnow, Erica Valentini, Svenja Leible, Michael Boutros, Aurelio A. Teleman   +5 more
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Expression quantitative trait loci are highly sensitive to cellular differentiation state [PDF]

, 2009
Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown.
Gerrits, Alice,, Xusheng Wang, Wang, Xusheng,, Breitling, Rainer, Breitling, R., Breitling, Rainer,, Gerald de Haan, Leonid V. Bystrykh, Li, Y., Dontje, B., Dontje, Bert,, Tesson, Bruno M.,, Weersing, Ellen,, Haan, Gerald de,, Bystrykh, L.V., Wang, Xusheng, Ellen Weersing, Ausema, Albertina, De Haan, Gerald, Alice Gerrits, Bert Dontje, de Haan, G., Li, Yang,, Wang, X., Gerrits, A., Bruno M Tesson, Leonid V Bystrykh, Bystrykh, Leonid V.,, Jansen, Ritsert C.,, Gerrits, Alice, Bruno M. Tesson, Jansen, Ritsert C., Rainer Breitling, Dethmers-Ausema, B, Ritsert C Jansen, Ausema, Albertina,, Albertina Ausema, Jansen, R.C., Dontje, Bert, Yang Li, Ritsert C. Jansen, Tesson, B.M., Bystrykh, Leonid V., Weersing, Ellen, de Haan, Gerald; id_orcid, Li, Yang, Tesson, Bruno M.   +46 more
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SCANPY: large-scale single-cell gene expression data analysis [PDF]

Genome Biology, 2018
SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (
F. Alexander Wolf, Philipp Angerer, Fabian J. Theis   +2 more
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Gene expression analysis in microdissected renal tissue - Current challenges and strategies [PDF]

, 2002
The architecture and compartmentalization of the kidney has stimulated the development of an array of microtechniques to study the functional differences between the distinct nephron segments. With the vast amounts of genomic sequence data now available,
Cohen, C. D., Kretzler, M.
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Comparative Analysis of Nuclear Transfer Embryo Derived Mouse Embryonic Stem Cells. Part II: Gene regulation [PDF]

, 2012
In a mouse model nuclear transfer embryo-derived embryonic stem cell lines (ntESCs) of various genetic backgrounds and donor cell types were compared with reference ESCs and analyzed comprehensively at molecular level as a second part of a larger study ...
Julianna Kobolak, Geißler, S., Mamo, S., Horsch, Marion, Horsch, M., Andras Dinnyes, Geissler, Sandra, Mamo, Solomon, Marion Horsch, Kobolak, J., Beckers, Johannes, Solomon Mamo, Kobolak, Julianna, Dinnyes, Andras, Beckers, J., Johannes Beckers, Sandra Geißler, Dinnyes, A.   +17 more
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Gene Expression Analysis by Multiplex Single-Cell RT-PCR [PDF]

, 2019
Brain circuit assemblies comprise different cellular subpopulations that exhibit morphological, electrophysiological, and molecular diversity. Here we describe a protocol which, combined with whole-cell patch-clamp recording and morphological reconstruction, allows the transcriptomic analysis of the recorded cell.
Tricoire, Ludovic, Cauli, Bruno, Lambolez, Bertrand   +2 more
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Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. [PDF]

, 2014
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual
Nusspaumer, G, Holländer, GA, Shikama-Dorn, Noriko, Ponting, Chris P., Nusspaumer, Gretel, Heger, A, Deadman, Mary E., Sansom, SN, Deadman, ME, Shikama-Dorn, N, Holländer, Georg A., Heger, Andreas, Macaulay, IC, Sansom, Stephen N., Zhanybekova, S, Zhanybekova, Saule, Sansom, Stephen, Macaulay, Iain C., Ponting, CP   +18 more
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Single-cell states in the estrogen response of breast cancer cell lines [PDF]

, 2014
Estrogen responsive breast cancer cell lines have been extensively studied to characterize transcriptional patterns in hormone-responsive tumors. Nevertheless, due to current technological limitations, genome-wide studies have typically been limited to ...
Andrea Gamba, Nassa, Giovanni, Roberto Amendola, Mario Nicodemi (81682), Sach Mukherjee (19432), Chris J Oates, Francesco Paolo Casale (526999), Nicodemi, M, Weisz, Alessandro, Gamba, A, Jonathan, W., Alessandro Weisz (90872), Alessandro Weisz, Giorgio Giurato (527000), Giorgio Giurato, Gamba, Andrea, Cora', Davide, Chris J. Oates, Gamba, Andrea Antonio, Armond, Jonathan W., Weisz, A, Amendola, Roberto, Mukherjee, Sach, Casale, Francesco Paolo, Oates, Chris J., Jonathan W. Armond, Mario Nicodemi, Oates, CJ, Giovanni Nassa, Davide Corá, Nassa, G, Corá, Davide, Ro Weisz, Mukherjee, S, Giovanni Nassa (527001), Chris J. Oates (527003), Francesco Paolo Casale, Giurato, Giorgio, Andrea Gamba (181217), Nicodemi, Mario, Sach Mukherjee, Davide Cor?, Giurato, G, Corá, D, Chris, J., Jonathan W Armond, Davide Corá (5649682), Armond, JW, Jonathan W. Armond (527002), Casale, FP   +49 more
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