Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

[1]  M. Mello,et al.  Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways , 2021, Scientific reports.

[2]  D. Nam,et al.  Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient , 2020, Genome Medicine.

[3]  A. van Oudenaarden,et al.  Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids , 2020, Nature.

[4]  F. Jamali,et al.  Single dose pharmacokinetics and bioavailability of glucosamine in the rat. , 2002, Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques.

[5]  M. Rattray,et al.  Glucocorticoids rapidly inhibit cell migration through a novel, non-transcriptional HDAC6 pathway. , 2020, Journal of cell science.

[6]  Nikos Koundouros,et al.  Reprogramming of fatty acid metabolism in cancer , 2019, British Journal of Cancer.

[7]  Jonathan S. Packer,et al.  Massively multiplex chemical transcriptomics at single-cell resolution , 2019, Science.

[8]  Jonathan S. Packer,et al.  A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution , 2019, Science.

[9]  L. Lanfumey,et al.  Stress–glucocorticoid–TSC22D3 axis compromises therapy-induced antitumor immunity , 2019, Nature Medicine.

[10]  Cole Trapnell,et al.  A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition , 2019, Nature Genetics.

[11]  Jonathan S. Packer,et al.  A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution , 2019, Science.

[12]  Wei Wang,et al.  A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory , 2019, PLoS Comput. Biol..

[13]  Andrew J. Hill,et al.  The single cell transcriptional landscape of mammalian organogenesis , 2019, Nature.

[14]  Jonathan S. Packer,et al.  Thyroid hormone regulates distinct paths to maturation in pigment cell lineages , 2019, bioRxiv.

[15]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..

[16]  Jie Wu,et al.  The cyclin-dependent kinase inhibitor flavopiridol (alvocidib) inhibits metastasis of human osteosarcoma cells , 2018, Oncotarget.

[17]  Matthew D. Young,et al.  Intra-tumour diversification in colorectal cancer at the single-cell level , 2018, Nature.

[18]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction , 2018, ArXiv.

[19]  L. O’Neill,et al.  A Role for the Krebs Cycle Intermediate Citrate in Metabolic Reprogramming in Innate Immunity and Inflammation , 2018, Front. Immunol..

[20]  Johanna Hardin,et al.  Selecting between‐sample RNA‐Seq normalization methods from the perspective of their assumptions , 2016, Briefings Bioinform..

[21]  Shawn M. Gillespie,et al.  Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer , 2017, Cell.

[22]  Eda Acikgoz,et al.  Ribosome biogenesis mediates antitumor activity of flavopiridol in CD44+/CD24− breast cancer stem cells , 2017, Oncology letters.

[23]  Fan Yang,et al.  Role of histone deacetylase expression levels and activity in the inflammatory responses of patients with chronic hepatitis B. , 2017, Molecular medicine reports.

[24]  Andrew C. Adey,et al.  Single-Cell Transcriptional Profiling of a Multicellular Organism , 2017 .

[25]  K. Yamamoto,et al.  Glucocorticoid receptor control of transcription: precision and plasticity via allostery , 2017, Nature Reviews Molecular Cell Biology.

[26]  Grace X. Y. Zheng,et al.  Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.

[27]  Mariella G. Filbin,et al.  Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma , 2016, Nature.

[28]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[29]  M. Sweet,et al.  Histone Deacetylase Inhibitors Promote Mitochondrial Reactive Oxygen Species Production and Bacterial Clearance by Human Macrophages , 2015, Antimicrobial Agents and Chemotherapy.

[30]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[31]  Aleksandra A. Kolodziejczyk,et al.  Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression , 2015, Nature Communications.

[32]  A. Raj,et al.  Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. , 2015, Molecular cell.

[33]  J. Mariadason,et al.  Mechanisms of Histone Deacetylase Inhibitor-Regulated Gene Expression in Cancer Cells. , 2014, Antioxidants & redox signaling.

[34]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[35]  Y. Tain,et al.  Melatonin prevents neonatal dexamethasone induced programmed hypertension: Histone deacetylase inhibition , 2014, The Journal of Steroid Biochemistry and Molecular Biology.

[36]  S. Kurdistani.  Chromatin: a capacitor of acetate for integrated regulation of gene expression and cell physiology. , 2014, Current opinion in genetics & development.

[37]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[38]  A. Oudenaarden,et al.  Validation of noise models for single-cell transcriptomics , 2014, Nature Methods.

[39]  F. A. Schroeder,et al.  A Selective HDAC 1/2 Inhibitor Modulates Chromatin and Gene Expression in Brain and Alters Mouse Behavior in Two Mood-Related Tests , 2013, PloS one.

[40]  David A. Orlando,et al.  Revisiting Global Gene Expression Analysis , 2012, Cell.

[41]  T. Karagiannis,et al.  Regulation of Immune Responses by Histone Deacetylase Inhibitors , 2012, ISRN hematology.

[42]  M. Salit,et al.  Synthetic Spike-in Standards for Rna-seq Experiments Material Supplemental Open Access License Commons Creative , 2022 .

[43]  M. Sweet,et al.  Histone deacetylases as regulators of inflammation and immunity. , 2011, Trends in immunology.

[44]  W. Miller,et al.  Vorinostat Induces Reactive Oxygen Species and DNA Damage in Acute Myeloid Leukemia Cells , 2011, PloS one.

[45]  S. Zahler,et al.  Flavopiridol Protects Against Inflammation by Attenuating Leukocyte-Endothelial Interaction via Inhibition of Cyclin-Dependent Kinase 9 , 2011, Arteriosclerosis, Thrombosis and Vascular Biology.

[46]  P. François,et al.  Histone deacetylase inhibitors impair innate immune responses to Toll-like receptor agonists and to infection. , 2011, Blood.

[47]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[48]  Justin R. Cross,et al.  ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation , 2009, Science.

[49]  P. Atadja,et al.  Role of histone deacetylase inhibitor-induced reactive oxygen species and DNA damage in LAQ-824/fludarabine antileukemic interactions , 2008, Molecular Cancer Therapeutics.

[50]  Jean-Loup Guillaume,et al.  Fast unfolding of communities in large networks , 2008, 0803.0476.

[51]  W. Plunkett,et al.  Transcription inhibition by flavopiridol: mechanism of chronic lymphocytic leukemia cell death. , 2005, Blood.

[52]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[53]  I. Adcock,et al.  Histone acetylation and deacetylation: importance in inflammatory lung diseases , 2005, European Respiratory Journal.

[54]  Kevin Camphausen,et al.  Transcriptional signature of flavopiridol-induced tumor cell death. , 2004, Molecular cancer therapeutics.

[55]  I. Gojo,et al.  The cyclin-dependent kinase inhibitor flavopiridol induces apoptosis in multiple myeloma cells through transcriptional repression and down-regulation of Mcl-1. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[56]  Andreas Rosenwald,et al.  Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol , 2001, Genome Biology.

[57]  H. Hausen,et al.  Inhibitors of histone deacetylase arrest cell cycle and induce apoptosis in cervical carcinoma cells circumventing human papillomavirus oncogene expression , 2001, Oncogene.

[58]  M. Yoshida,et al.  Mechanism of cell cycle arrest caused by histone deacetylase inhibitors in human carcinoma cells. , 2000, The Journal of antibiotics.

[59]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[60]  Vlad I. Morariu,et al.  Expression , 2015, Principles of Molecular Virology.