SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming
出版年份 2022 全文链接
标题
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming
作者
关键词
-
出版物
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
出版商
Oxford University Press (OUP)
发表日期
2022-03-10
DOI
10.1093/nar/gkac167
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses
- (2021) Songlei Liu et al. NUCLEIC ACIDS RESEARCH
- Integrated analysis of multimodal single-cell data
- (2021) Yuhan Hao et al. CELL
- Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma
- (2020) Aparna Bhaduri et al. Cell Stem Cell
- Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- (2020) Swati Venkat et al. GENOME RESEARCH
- Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism
- (2020) Pia Sommerkamp et al. Cell Stem Cell
- Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
- (2020) Alison D. Tang et al. Nature Communications
- Generalizing RNA velocity to transient cell states through dynamical modeling
- (2020) Volker Bergen et al. NATURE BIOTECHNOLOGY
- Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations
- (2020) Ming-Huei Chen et al. CELL
- The Polygenic and Monogenic Basis of Blood Traits and Diseases
- (2020) Dragana Vuckovic et al. CELL
- Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq
- (2019) Lin Guo et al. MOLECULAR CELL
- Comprehensive Integration of Single-Cell Data
- (2019) Tim Stuart et al. CELL
- A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
- (2019) Charlotte Soneson et al. Nature Communications
- FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control
- (2019) Ivano Legnini et al. NATURE METHODS
- Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data
- (2019) Eldad David Shulman et al. NUCLEIC ACIDS RESEARCH
- Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails
- (2019) Yusheng Liu et al. Nature Communications
- CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones
- (2018) Sören Müller et al. BIOINFORMATICS
- Minimap2: pairwise alignment for nucleotide sequences
- (2018) Heng Li BIOINFORMATICS
- NanoPack: visualizing and processing long-read sequencing data
- (2018) Wouter De Coster et al. BIOINFORMATICS
- Mapping the Mouse Cell Atlas by Microwell-Seq
- (2018) Xiaoping Han et al. CELL
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- Widespread intronic polyadenylation diversifies immune cell transcriptomes
- (2018) Irtisha Singh et al. Nature Communications
- SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants
- (2018) Xiaojun Ren et al. ACS Central Science
- RNA velocity of single cells
- (2018) Gioele La Manno et al. NATURE
- Dimensionality reduction for visualizing single-cell data using UMAP
- (2018) Etienne Becht et al. NATURE BIOTECHNOLOGY
- Spatial organization of the somatosensory cortex revealed by osmFISH
- (2018) Simone Codeluppi et al. NATURE METHODS
- Toward the human cellular microRNAome
- (2017) Matthew N. McCall et al. GENOME RESEARCH
- Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation
- (2017) Yan Song et al. MOLECULAR CELL
- PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes
- (2017) Ruijia Wang et al. NUCLEIC ACIDS RESEARCH
- Alternative polyadenylation of ZEB1 promotes its translation during genotoxic stress in pancreatic cancer cells
- (2017) Ilaria Passacantilli et al. Cell Death & Disease
- Massively parallel digital transcriptional profiling of single cells
- (2017) Grace X. Y. Zheng et al. Nature Communications
- Tissue damage and senescence provide critical signals for cellular reprogramming in vivo
- (2016) Lluc Mosteiro et al. SCIENCE
- Evolution and Biological Roles of Alternative 3′UTRs
- (2016) Christine Mayr TRENDS IN CELL BIOLOGY
- Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
- (2015) Evan Z. Macosko et al. CELL
- The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma
- (2015) Hon-Kit Andus Wong et al. MOLECULAR THERAPY
- Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization
- (2015) Binyamin D. Berkovits et al. NATURE
- TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
- (2015) Antonio Colaprico et al. NUCLEIC ACIDS RESEARCH
- Predicting effective microRNA target sites in mammalian mRNAs
- (2015) Vikram Agarwal et al. eLife
- Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
- (2015) Sean P. Gordon et al. PLoS One
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- PRMT5 enhances generation of induced pluripotent stem cells from dairy goat embryonic fibroblastsviadown-regulation of p53
- (2014) Z. Chu et al. CELL PROLIFERATION
- TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications
- (2014) Hyeshik Chang et al. MOLECULAR CELL
- Genome-wide Functional Analysis Reveals Factors Needed at the Transition Steps of Induced Reprogramming
- (2014) Chao-Shun Yang et al. Cell Reports
- The many faces of calmodulin in cell proliferation, programmed cell death, autophagy, and cancer
- (2013) Martin W. Berchtold et al. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
- In situ sequencing for RNA analysis in preserved tissue and cells
- (2013) Rongqin Ke et al. NATURE METHODS
- Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
- (2013) Magali Soumillon et al. Cell Reports
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Alternative Polyadenylation Mediates MicroRNA Regulation of Muscle Stem Cell Function
- (2012) Stéphane C. Boutet et al. Cell Stem Cell
- Detecting differential usage of exons from RNA-seq data
- (2012) S. Anders et al. GENOME RESEARCH
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
- (2012) Guangchuang Yu et al. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
- CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
- (2012) Tamar Hashimshony et al. Cell Reports
- Origins, evolution, and phenotypic impact of new genes
- (2010) H. Kaessmann GENOME RESEARCH
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
- (2010) Yarden Katz et al. NATURE METHODS
- Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells
- (2009) Christine Mayr et al. CELL
- Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
- (2009) Mo Chen et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types
- (2009) Zhe Ji et al. PLoS One
- Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
- (2009) Z. Ji et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The kinesin KIF1B acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressor
- (2008) S. Schlisio et al. GENES & DEVELOPMENT
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