BrainCellR: A Precise Cell Type Nomenclature R Package for Comparative Analysis Across Brain Single-Cell Datasets

Y Chi, S Marini, GZ Wang - bioRxiv, 2023 - biorxiv.org
cell RNA sequencing (scRNA-seq) has revolutionized the field of neuroscience by enabling
35 comprehensive characterization of cellular … to study individual cells and uncover cell type- …

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

A Kahles, CS Ong, Y Zhong, G Rätsch - Bioinformatics, 2016 - academic.oup.com
RNA-Seq alignments and an annotation file as input to (i) augment the annotation based on
RNA-Seq … (iii) quantify and confirm these events based on the RNA-Seq data and (iv) test for …

CircNet: a database of circular RNAs derived from transcriptome sequencing data

YC Liu, JR Li, CH Sun, E Andrews… - Nucleic acids …, 2016 - academic.oup.com
… -cellular evolution (1) with the phenomenon of the 3′ and 5′ ends covalently joining called
‘exon scramble’ (2) or ‘back-spliced junctions’. In plant cells, … a DNA or RNA sequence to …

[HTML][HTML] Single-cell RNA sequencing of the T helper cell response to house dust mites defines a distinct gene expression signature in airway Th2 cells

CA Tibbitt, JM Stark, L Martens, J Ma, JE Mold… - Immunity, 2019 - cell.com
… Th2 cells play a … -cell RNA sequencing (scRNA-seq) of T helper cells from lymph node,
lung, and airways in the house dust mite (HDM) model of allergic airway disease. scRNA-seq

Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012

L Galluzzi, I Vitale, JM Abrams, ES Alnemri… - Cell Death & …, 2012 - nature.com
… on the use of cell death-related … of cell death are critically evaluated and recommendations
on their definition and use are formulated, hoping that a non-rigid, yet uniform nomenclature

Nomenclature for cellular plasticity: are the terms as plastic as the cells themselves?

JC Mills, BZ Stanger, M Sander - The EMBO Journal, 2019 - embopress.org
… or progenitor cell types). Single‐cell analyses like RNASeq suggest that mature cells
may be relatively fluid even in steady state such that differentiated cells are not as fixed in a …

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

B Tasic, V Menon, TN Nguyen, TK Kim, T Jarsky… - Nature …, 2016 - nature.com
cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis
of single-cell RNA sequencing… Note the change in cell type nomenclature in the paper …

The myeloid cell compartment—cell by cell

K Bassler, J Schulte-Schrepping… - Annual review of …, 2019 - annualreviews.org
… revolution in single-cell genomics, with single-cell RNA sequencing (scRNA-seq) leading the
way, … And lastly, although often considered unimportant, cellular nomenclature will also be …

Long non-coding RNAs: definitions, functions, challenges and recommendations

JS Mattick, PP Amaral, P Carninci… - … reviews Molecular cell …, 2023 - nature.com
… -coding sequences, are cell type specific and regulate many aspects of cell differentiation and
… In this Consensus Statement, we address the definition and nomenclature of lncRNAs and …

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

AF Hill, DM Pegtel, U Lambertz, T Leonardi… - Journal of …, 2013 - Taylor & Francis
… non-coding RNA species have been discovered in cellular … Given the additional complexities
concerning the nomenclature … Although small RNA sequences are thought to have low …