Emerging Principles of Gene Expression Programs and Their Regulation.

[1]  E. Fuchs,et al.  Author Correction: Inflammatory memory sensitizes skin epithelial stem cells to tissue damage , 2018, Nature.

[2]  S. Nish,et al.  Lymphocyte Fate and Metabolism: A Clonal Balancing Act. , 2017, Trends in cell biology.

[3]  G. Natoli,et al.  High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins. , 2017, Genes & development.

[4]  G. Wagner,et al.  The origin and evolution of cell types , 2016, Nature Reviews Genetics.

[5]  A. Regev,et al.  Writ large: Genomic dissection of the effect of cellular environment on immune response , 2016, Science.

[6]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[7]  Scott B. Dewell,et al.  Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome. , 2016, Molecular cell.

[8]  R. Xavier,et al.  Trained immunity: A program of innate immune memory in health and disease , 2016, Science.

[9]  Brandon J Thomas,et al.  A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation , 2016, Cell.

[10]  A. Rudensky,et al.  Hallmarks of Tissue-Resident Lymphocytes , 2016, Cell.

[11]  R. Medzhitov,et al.  Tissue biology perspective on macrophages , 2015, Nature Immunology.

[12]  C. Glass,et al.  Molecular control of activation and priming in macrophages , 2015, Nature Immunology.

[13]  Aviv Regev,et al.  Comparative analysis of gene regulatory networks: from network reconstruction to evolution. , 2015, Annual review of cell and developmental biology.

[14]  A. Sandelin,et al.  A Unified Architecture of Transcriptional Regulatory Elements , 2015, bioRxiv.

[15]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[16]  A. Pombo,et al.  Three-dimensional genome architecture: players and mechanisms , 2015, Nature Reviews Molecular Cell Biology.

[17]  C. Glass,et al.  The selection and function of cell type-specific enhancers , 2015, Nature Reviews Molecular Cell Biology.

[18]  G. Natoli,et al.  Transcriptional control of inflammatory responses. , 2014, Cold Spring Harbor perspectives in biology.

[19]  I. Nemenman,et al.  Cellular noise and information transmission. , 2014, Current opinion in biotechnology.

[20]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[21]  R. Medzhitov,et al.  Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages , 2014, Cell.

[22]  G. Natoli,et al.  Chromatin contributions to the regulation of innate immunity. , 2014, Annual review of immunology.

[23]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[24]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[25]  P. Taylor,et al.  Tissue-resident macrophages , 2013, Nature Immunology.

[26]  Thomas A. Wynn,et al.  Macrophage biology in development, homeostasis and disease , 2013, Nature.

[27]  J. Auwerx,et al.  Emerging roles of the corepressors NCoR1 and SMRT in homeostasis. , 2013, Genes & development.

[28]  A. Regev,et al.  Dynamic regulatory network controlling Th17 cell differentiation , 2013, Nature.

[29]  M. Rudnicki,et al.  Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. , 2012, Genes & development.

[30]  Charles Y. Lin,et al.  Transcriptional Amplification in Tumor Cells with Elevated c-Myc , 2012, Cell.

[31]  D. Green,et al.  c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells , 2012, Cell.

[32]  John T. Lis,et al.  Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans , 2012, Nature Reviews Genetics.

[33]  T. Perlmann,et al.  Maintaining differentiated cellular identity , 2012, Nature Reviews Genetics.

[34]  C. Benoist,et al.  PPARγ is a major driver of the accumulation and phenotype of adipose-tissue Treg cells , 2012, Nature.

[35]  Ananda L Roy,et al.  Regulation of primary response genes. , 2011, Molecular cell.

[36]  Aviv Regev,et al.  Strategies to discover regulatory circuits of the mammalian immune system , 2011, Nature Reviews Immunology.

[37]  K. Clément,et al.  Krüppel-like factor 4 regulates macrophage polarization. , 2011, The Journal of clinical investigation.

[38]  A. Bird,et al.  CpG islands and the regulation of transcription. , 2011, Genes & development.

[39]  A. Regev,et al.  Impulse Control: Temporal Dynamics in Gene Transcription , 2011, Cell.

[40]  G. Natoli,et al.  The genomic landscapes of inflammation. , 2011, Genes & development.

[41]  K. Nakai,et al.  The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection , 2010, Nature Immunology.

[42]  Vikki M. Weake,et al.  Inducible gene expression: diverse regulatory mechanisms , 2010, Nature Reviews Genetics.

[43]  J. Ragoussis,et al.  Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.

[44]  T. Enver,et al.  Forcing cells to change lineages , 2009, Nature.

[45]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[46]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[47]  B. Cairns The logic of chromatin architecture and remodelling at promoters , 2009, Nature.

[48]  R. Medzhitov,et al.  Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation , 2009, Cell.

[49]  A. Hoffmann,et al.  A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling , 2009, Cell.

[50]  Aviv Regev,et al.  Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets , 2009, Science.

[51]  Alistair G. Rust,et al.  Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals , 2009, Nature Immunology.

[52]  K. Murphy,et al.  Critical role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis , 2008, Nature.

[53]  Bin Li,et al.  Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics , 2008, PLoS Comput. Biol..

[54]  C. Glass,et al.  Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. , 2006, Genes & development.

[55]  B. Bonavida,et al.  Transcription factor YY1: structure, function, and therapeutic implications in cancer biology , 2006, Oncogene.

[56]  S. Smale,et al.  Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. , 2006, Genes & development.

[57]  J. Raser,et al.  Noise in Gene Expression: Origins, Consequences, and Control , 2005, Science.

[58]  Bruce M. Spiegelman,et al.  Biological Control through Regulated Transcriptional Coactivators , 2004, Cell.

[59]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[60]  J. Nichols,et al.  BMP Induction of Id Proteins Suppresses Differentiation and Sustains Embryonic Stem Cell Self-Renewal in Collaboration with STAT3 , 2003, Cell.

[61]  R. Urrutia,et al.  Sp1- and Krüppel-like transcription factors , 2003, Genome Biology.

[62]  R. Scarpulla Transcriptional activators and coactivators in the nuclear control of mitochondrial function in mammalian cells. , 2002, Gene.

[63]  Christopher K. Glass,et al.  The peroxisome proliferator-activated receptor-γ is a negative regulator of macrophage activation , 1998, Nature.

[64]  T. Braun,et al.  Targeted inactivation of myogenic factor genes reveals their role during mouse myogenesis: a review. , 1996, The International journal of developmental biology.

[65]  E. Wagner,et al.  Complete block of early B cell differentiation and altered patterning of the posterior midbrain in mice lacking Pax5 BSAP , 1994, Cell.

[66]  C. Glass,et al.  Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers. , 2015, Cold Spring Harbor symposia on quantitative biology.

[67]  S. Smale,et al.  Toward an understanding of the gene-specific and global logic of inducible gene transcription. , 2013, Cold Spring Harbor symposia on quantitative biology.

[68]  K. Murphy,et al.  Role for SpiC in the development of red pulp macrophages and splenic iron homeostasis , 2008 .

[69]  Simmie L. Foster,et al.  Gene-specific control of inflammation by TLR-induced chromatin modifications , 2008, Nature.

[70]  Peter Tontonoz,et al.  Reciprocal regulation of inflammation and lipid metabolism by liver X receptors , 2003, Nature Medicine.