Results 71 to 80 of about 183,994 (309)

ELLIPSIS: robust quantification of splicing in scRNA-seq

Bioinformatics
Abstract Motivation Alternative splicing is a tightly regulated biological process, that due to its cell type specific behavior, calls for analysis at the single cell level. However, quantifying differential splicing in scRNA-seq is challenging due to low and uneven coverage.
Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal   +5 more
openaire   +4 more sources

Long‐term hippocampal alterations and cognitive impairment in a murine model of surgical sepsis

FEBS Open Bio, EarlyView.
Using a mouse model of surgical sepsis, we tested long‐term memory and analyzed the transcriptome of single cells isolated from the hippocampus. Survivor mice showed worse memory, loss of certain brain cell subpopulations, and abnormal immune cell activity—suggesting that post‐sepsis brain alterations may be linked to cognitive deficits.
Dong Seong Cho, Rebecca Schmitt, Aneesha Dasgupta, Alexandra Ducharme, Jason Doles   +4 more
wiley   +1 more source

Evaluating cell-specific gene expression using single-cell and single-nuclei RNA-sequencing data from human pancreatic islets of the same donors

Scientific Reports
Single-cell and single-nuclei RNA-sequencing (scRNA-seq and snRNA-seq) analyze cell-specific transcriptomes. However, only snRNA-seq applies to frozen biobanked samples.
Karin Engström, Åsa Nilsson, Jones K. Ofori, Nils Wierup, Karl Bacos, Charlotte Ling   +5 more
doaj   +1 more source

GNN-based embedding for clustering scRNA-seq data

Bioinformatics, 2021
Abstract Motivation Single-cell RNA sequencing (scRNA-seq) provides transcriptomic profiling for individual cells, allowing researchers to study the heterogeneity of tissues, recognize rare cell identities and discover new cellular subtypes.
Madalina Ciortan, Matthieu Defrance
openaire   +3 more sources

scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning

, 2023
Annotation of cell-types is a critical step in the analysis of single-cell RNA sequencing (scRNA-seq) data that allows the study of heterogeneity across multiple cell populations.
Lysenko, Artem, Artem Lysenko, Boroevich, Keith A, Sharma, Alok, Tatsuhiko Tsunoda, Jia, Shangru, Tsunoda, Tatsuhiko, Alok Sharma, Keith A Boroevich, Shangru Jia   +9 more
core   +1 more source

The C‐terminal region of KIF26B is indispensable for nephron progenitor condensation and kidney formation in mice

FEBS Open Bio, EarlyView.
KIF26B plays an important role in kidney development. We engineered mice lacking the C‐terminal region of KIF26B and found severe kidney defects, including bilateral renal agenesis, similar to full Kif26b knockout mice. The mutation disrupted nephron progenitor condensation and reduced Gdnf‐Wnt11 signaling, showing that the KIF26B C‐terminal region is ...
Yuta Yamamura, Kengo Furuichi, Hiromitsu Akamatsu, Naoki Yamamoto, Sako Keisuke, Akihiko Koshino, Taichiro Minami, Megumi Oshima, Akinori Hara, Norihiko Sakai, Miho Shimizu, Kenta Takahashi, Minako Yamamura, Shin‐ichi Horike, Takiko Daikoku, Kenichi Harada, Yohei Shinmyo, Hiroshi Kawasaki, Takashi Wada, Yasunori Iwata   +19 more
wiley   +1 more source

ShinyCortex: Exploring Single-Cell Transcriptome Data From the Developing Human Cortex

Frontiers in Neuroscience, 2018
Single-cell mRNA sequencing (scRNA-seq) is a powerful method to identify and classify cell types and reconstruct differentiation trajectories within complex tissues, such as the developing human cortex.
Jorge Kageyama, Damian Wollny, Barbara Treutlein, Barbara Treutlein, Barbara Treutlein, J. Gray Camp   +5 more
doaj   +1 more source

scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing

BMC Genomics, 2023
Abstract Background Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated, the standardization and automation of data analysis are critical to generating hypotheses and discovering biological insights.
Kejie Li, Yu H. Sun, Zhengyu Ouyang, Soumya Negi, Zhen Gao, Jing Zhu, Wanli Wang, Yirui Chen, Sarbottam Piya, Wenxing Hu, Maria I. Zavodszky, Hima Yalamanchili, Shaolong Cao, Andrew Gehrke, Mark Sheehan, Dann Huh, Fergal Casey, Xinmin Zhang, Baohong Zhang   +18 more
openaire   +3 more sources

Merged Adult Human Kidney scRNA-seq dataset

, 2021
A merged human kidney scRNA-seq dataset made from the following scRNA-seq studies: Menon et al. Lake et al. Wu et al. Liao et al.
Fadhl Alakwaa, Adam Tisch, Stephen Blough   +2 more
core   +1 more source

MagmaFlow: A desktop platform for artificial intelligence‐driven expression analysis

FEBS Open Bio, EarlyView.
MagmaFlow is a free, no‐code platform for gene expression analysis. It generates interactive volcano plots, links genes to literature, pathways, and diseases, prioritizes candidates using millions of publications, identifies affected biological processes, builds network diagrams, and exports publication‐ready figures and reports for macOS and Windows ...
Carlos E. Buss, Ao Li, Eduardo H. Gilglioni, Mayank Bansal, Sumeet Pal Singh, Latifa Bakiri, Alessandra K. Cardozo, Esteban N. Gurzov   +7 more
wiley   +1 more source