Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Authors
Keywords
-
Journal
PeerJ
Volume 5, Issue -, Pages e2888
Publisher
PeerJ
Online
2017-01-19
DOI
10.7717/peerj.2888
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
- (2016) Jean Fan et al. NATURE METHODS
- Comprehensive analysis of differentially expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma
- (2016) Mengge Huang et al. Oncotarget
- Single-Cell Transcriptomics Bioinformatics and Computational Challenges
- (2016) Olivier B. Poirion et al. Frontiers in Genetics
- Identifications of novel mechanisms in breast cancer cells involving duct-like multicellular spheroid formation after exposure to the Random Positioning Machine
- (2016) Sascha Kopp et al. Scientific Reports
- Normalization and noise reduction for single cell RNA-seq experiments
- (2015) Bo Ding et al. BIOINFORMATICS
- Radioactive 125I seeds inhibit cell growth and epithelial-mesenchymal transition in human glioblastoma multiforme via a ROS-mediated signaling pathway
- (2015) Yunhong Tian et al. BMC CANCER
- Malat1 as an evolutionarily conserved lncRNA, plays a positive role in regulating proliferation and maintaining undifferentiated status of early-stage hematopoietic cells
- (2015) Xian-Yong Ma et al. BMC GENOMICS
- Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
- (2015) Evan Z. Macosko et al. CELL
- Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
- (2015) Florian Buettner et al. NATURE BIOTECHNOLOGY
- Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow
- (2015) Andreas Schlitzer et al. NATURE IMMUNOLOGY
- Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
- (2015) Zhilong Jia et al. PLoS One
- Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
- (2015) A. Zeisel et al. SCIENCE
- Long noncoding RNA MALAT1 associates with the malignant status and poor prognosis in glioma
- (2015) Kang-xiao Ma et al. TUMOR BIOLOGY
- The high expression of TC1 (C8orf4) was correlated with the expression of β-catenin and cyclin D1 and the progression of squamous cell carcinomas of the tongue
- (2015) Peng Zhang et al. TUMOR BIOLOGY
- C8orf4 negatively regulates self-renewal of liver cancer stem cells via suppression of NOTCH2 signalling
- (2015) Pingping Zhu et al. Nature Communications
- A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
- (2014) Yinming Jiao et al. BIOINFORMATICS
- Genome-wide RNA Tomography in the Zebrafish Embryo
- (2014) Jan Philipp Junker et al. CELL
- Single cell dissection of early kidney development: multilineage priming
- (2014) E. W. Brunskill et al. DEVELOPMENT
- Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
- (2014) Fernando H. Biase et al. GENOME RESEARCH
- Deconstructing transcriptional heterogeneity in pluripotent stem cells
- (2014) Roshan M. Kumar et al. NATURE
- Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
- (2014) Barbara Treutlein et al. NATURE
- The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
- (2014) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Normalization of RNA-seq data using factor analysis of control genes or samples
- (2014) Davide Risso et al. NATURE BIOTECHNOLOGY
- Bayesian approach to single-cell differential expression analysis
- (2014) Peter V Kharchenko et al. NATURE METHODS
- Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing
- (2014) Dmitry Usoskin et al. NATURE NEUROSCIENCE
- Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
- (2014) A. P. Patel et al. SCIENCE
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- (2013) Y. Liao et al. BIOINFORMATICS
- HDAC3 is essential for DNA replication in hematopoietic progenitor cells
- (2013) Alyssa R. Summers et al. JOURNAL OF CLINICAL INVESTIGATION
- Accounting for technical noise in single-cell RNA-seq experiments
- (2013) Philip Brennecke et al. NATURE METHODS
- The UCSC Genome Browser database: 2014 update
- (2013) Donna Karolchik et al. NUCLEIC ACIDS RESEARCH
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
- (2012) Andrew McDavid et al. BIOINFORMATICS
- NCBI GEO: archive for functional genomics data sets—update
- (2012) Tanya Barrett et al. NUCLEIC ACIDS RESEARCH
- A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable
- (2011) Hua Tian et al. NATURE
- An intuitive graphical visualization technique for the interrogation of transcriptome data
- (2011) Natascha Bushati et al. NUCLEIC ACIDS RESEARCH
- An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA
- (2011) H. C. Moore et al. RNA
- A flexible R package for nonnegative matrix factorization
- (2010) Renaud Gaujoux et al. BMC BIOINFORMATICS
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools
- (2009) Q. Qi et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
- (2008) Da Wei Huang et al. NUCLEIC ACIDS RESEARCH
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search