scSLAM-seq reveals core features of transcription dynamics in single cells
暂无分享,去创建一个
Fabian J Theis | A. Saliba | Marius Lange | Florian Erhard | Marisa A. P. Baptista | T. Hennig | Panagiota Arampatzi | L. Dölken | T. Krammer | Christopher S. Jürges
[1] Jeremy A. Schofield,et al. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. , 2018, Journal of the American Chemical Society.
[2] Yi Zhang,et al. Two-phase differential expression analysis for single cell RNA-seq , 2018, Bioinform..
[3] Erik Sundström,et al. RNA velocity of single cells , 2018, Nature.
[4] Christopher J. Cronin,et al. Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH , 2018, Cell.
[5] Tim De Meyer,et al. Analysis of DNA methylation in cancer: location revisited , 2018, Nature Reviews Clinical Oncology.
[6] Florian Erhard,et al. Dissecting newly transcribed and old RNA using GRAND-SLAM , 2018, Bioinform..
[7] Jesse J. Lipp,et al. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis , 2018, Science.
[8] Paul Hoffman,et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.
[9] Meaghan C. Sullivan,et al. TimeLapse-seq: Adding a temporal dimension to RNA sequencing through nucleoside recoding , 2018, Nature Methods.
[10] Andrew E. Teschendorff,et al. Statistical and integrative system-level analysis of DNA methylation data , 2017, Nature Reviews Genetics.
[11] Johannes Zuber,et al. Thiol-linked alkylation of RNA to assess expression dynamics , 2017, Nature Methods.
[12] R. Satija,et al. Single-cell RNA sequencing to explore immune cell heterogeneity , 2017, Nature Reviews Immunology.
[13] Michael Q. Zhang,et al. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data , 2017, Nature Communications.
[14] Thomas M. Norman,et al. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response , 2016, Cell.
[15] Thomas M. Norman,et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens , 2016, Cell.
[16] A. Regev,et al. Revealing the vectors of cellular identity with single-cell genomics , 2016, Nature Biotechnology.
[17] Aafke A. van den Berg,et al. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes , 2016, bioRxiv.
[18] Christophe Zimmer,et al. A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting , 2016, Nature Communications.
[19] C. Benedict,et al. cGAS-STING Signaling Regulates Initial Innate Control of Cytomegalovirus Infection , 2016, Journal of Virology.
[20] R. Sandberg,et al. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation , 2015, Nature Reviews Genetics.
[21] Joseph L. Herman,et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis , 2015, Nature Methods.
[22] Felix Naef,et al. Structure of silent transcription intervals and noise characteristics of mammalian genes , 2015, Molecular systems biology.
[23] Jason D. Buenrostro,et al. Transient Acquisition of Pluripotency During Somatic Cell Transdifferentiation with iPSC Reprogramming Factors , 2015, Nature Biotechnology.
[24] R. Shamir,et al. ElemeNT: a computational tool for detecting core promoter elements , 2015, Transcription.
[25] Allon M. Klein,et al. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.
[26] Evan Z. Macosko,et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.
[27] L. Dölken,et al. Murine Cytomegalovirus Virion-Associated Protein M45 Mediates Rapid NF-κB Activation after Infection , 2014, Journal of Virology.
[28] P. Kharchenko,et al. Bayesian approach to single-cell differential expression analysis , 2014, Nature Methods.
[29] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[30] Cole Trapnell,et al. Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions , 2014, Nature Biotechnology.
[31] Aleksandra A. Kolodziejczyk,et al. Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.
[32] Åsa K. Björklund,et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.
[33] Rona S. Gertner,et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.
[34] Mikhail Pachkov,et al. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates , 2012, Nucleic Acids Res..
[35] Thomas Bonfert,et al. Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection , 2012, PLoS pathogens.
[36] Peter A. Jones. Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.
[37] Thomas Höfer,et al. Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response , 2012, Molecular systems biology.
[38] S. Kaufmann,et al. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution , 2012, Genome research.
[39] A. van Oudenaarden,et al. Using Gene Expression Noise to Understand Gene Regulation , 2012, Science.
[40] I. Mohr,et al. Transient Reversal of Episome Silencing Precedes VP16-Dependent Transcription during Reactivation of Latent HSV-1 in Neurons , 2012, PLoS pathogens.
[41] B. Roizman,et al. HSV-1 gene expression from reactivated ganglia is disordered and concurrent with suppression of latency-associated transcript and miRNAs , 2011, Proceedings of the National Academy of Sciences.
[42] M. Selbach,et al. Global quantification of mammalian gene expression control , 2011, Nature.
[43] Achim Tresch,et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast , 2011, Molecular systems biology.
[44] Carlos Bustamante,et al. Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II , 2009, Science.
[45] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[46] A. Oudenaarden,et al. Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.
[47] R. Zimmer,et al. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. , 2008, RNA.
[48] D. Brutlag,et al. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[49] T. Shenk,et al. RNAs Are Packaged into Human Cytomegalovirus Virions in Proportion to Their Intracellular Concentration , 2004, Journal of Virology.
[50] Vitaly Epshtein,et al. Cooperation Between RNA Polymerase Molecules in Transcription Elongation , 2003, Science.
[51] P. Khavari,et al. Divergent gene regulation and growth effects by NF-κB in epithelial and mesenchymal cells of human skin , 2003, Oncogene.
[52] T. Shenk,et al. A subset of viral transcripts packaged within human cytomegalovirus particles. , 2000, Science.
[53] Donald Macleod,et al. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA , 1985, Cell.
[54] Extended data : Figures , 2020 .
[55] R. Kalejta. Functions of human cytomegalovirus tegument proteins prior to immediate early gene expression. , 2008, Current topics in microbiology and immunology.