Repression of endogenous retroviruses prevents antiviral immune response and is required for mammary gland development.

[1]  Z. Szallasi,et al.  Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers , 2020, Nature Communications.

[2]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[3]  W. Johnson Origins and evolutionary consequences of ancient endogenous retroviruses , 2019, Nature Reviews Microbiology.

[4]  J. Boeke,et al.  LINE-1 derepression in senescent cells triggers interferon and inflammaging , 2018, Nature.

[5]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[6]  F. Supek,et al.  Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours , 2018, Nature Cell Biology.

[7]  Peter A. Jones,et al.  Dual Inhibition of DNA and Histone Methyltransferases Increases Viral Mimicry in Ovarian Cancer Cells. , 2018, Cancer research.

[8]  Param Priya Singh,et al.  Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses , 2018, bioRxiv.

[9]  Melissa J. Davis,et al.  Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling , 2017, Nature Communications.

[10]  Brian Bushnell,et al.  BBMerge – Accurate paired shotgun read merging via overlap , 2017, PloS one.

[11]  E. Fuchs,et al.  Inflammatory Memory Sensitizes Skin Epithelial Stem Cells to Tissue Damage , 2017, Nature.

[12]  S. Ross,et al.  AIM2-Like Receptors Positively and Negatively Regulate the Interferon Response Induced by Cytosolic DNA , 2017, mBio.

[13]  K. Burns Transposable elements in cancer , 2017, Nature Reviews Cancer.

[14]  Wenqing Gao,et al.  Pyroptosis: Gasdermin-Mediated Programmed Necrotic Cell Death. , 2017, Trends in biochemical sciences.

[15]  J. Hiscott,et al.  Crosstalk between Cytoplasmic RIG-I and STING Sensing Pathways. , 2017, Trends in immunology.

[16]  E. Miao,et al.  Programmed cell death as a defence against infection , 2017, Nature Reviews Immunology.

[17]  Peter Bankhead,et al.  QuPath: Open source software for digital pathology image analysis , 2017, Scientific Reports.

[18]  C. Feschotte,et al.  Regulatory activities of transposable elements: from conflicts to benefits , 2016, Nature Reviews Genetics.

[19]  Salvador Aznar Benitah,et al.  Epigenetic control of adult stem cell function , 2016, Nature Reviews Molecular Cell Biology.

[20]  Robin L. Anderson,et al.  OMIP‐032: Two multi‐color immunophenotyping panels for assessing the innate and adaptive immune cells in the mouse mammary gland , 2016, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[21]  G. Vartholomatos,et al.  Genomic analysis of mouse VL30 retrotransposons , 2016, Mobile DNA.

[22]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[23]  L. Que,et al.  A Protocol for the Comprehensive Flow Cytometric Analysis of Immune Cells in Normal and Inflamed Murine Non-Lymphoid Tissues , 2016, PloS one.

[24]  Jason B. Williams,et al.  Antagonism of the STING Pathway via Activation of the AIM2 Inflammasome by Intracellular DNA , 2016, The Journal of Immunology.

[25]  M. Hammell,et al.  TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets , 2015, Bioinform..

[26]  M. Surani,et al.  Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development , 2015, eLife.

[27]  Z. Su,et al.  Identification of cell types from single-cell transcriptomes using a novel clustering method , 2015, Bioinform..

[28]  Rafael A. Irizarry,et al.  Flexible expressed region analysis for RNA-seq with derfinder , 2015, bioRxiv.

[29]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[30]  Mohammad M. Karimi,et al.  Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells , 2014, Genes & development.

[31]  D. O’Carroll,et al.  G9a co-suppresses LINE1 elements in spermatogonia , 2014, Epigenetics & Chromatin.

[32]  C. Tomasetto,et al.  Stromal matrix metalloproteinase-11 is involved in the mammary gland postnatal development , 2014, Oncogene.

[33]  J. Visvader,et al.  Mammary stem cells and the differentiation hierarchy: current status and perspectives , 2014, Genes & development.

[34]  J. Visvader,et al.  Scribble Modulates the MAPK/Fra1 Pathway to Disrupt Luminal and Ductal Integrity and Suppress Tumour Formation in the Mammary Gland , 2014, PLoS genetics.

[35]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[36]  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.

[37]  D. Ingber,et al.  Intraductal Injection for Localized Drug Delivery to the Mouse Mammary Gland , 2013, Journal of visualized experiments : JoVE.

[38]  Ludo Waltman,et al.  A smart local moving algorithm for large-scale modularity-based community detection , 2013, The European Physical Journal B.

[39]  Steven J. M. Jones,et al.  Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells , 2013, Epigenetics & Chromatin.

[40]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[41]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[42]  E. van Nimwegen,et al.  Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8) , 2013, PloS one.

[43]  R. Losson,et al.  Trim24-repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA , 2013, Nature Structural &Molecular Biology.

[44]  Yong Zhang,et al.  Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.

[45]  A. Cardona,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[46]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[47]  Mohammad M. Karimi,et al.  DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. , 2011, Cell stem cell.

[48]  R. Gomis,et al.  Accurate Expression Profiling of Very Small Cell Populations , 2010, PloS one.

[49]  K. Schwertfeger,et al.  Immune Cell Location and Function During Post-Natal Mammary Gland Development , 2010, Journal of Mammary Gland Biology and Neoplasia.

[50]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[51]  G. Fan,et al.  Repression of Retrotransposal Elements in Mouse Embryonic Stem Cells Is Primarily Mediated by a DNA Methylation-independent Mechanism* , 2010, The Journal of Biological Chemistry.

[52]  H. Kimura,et al.  Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET , 2010, Nature.

[53]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[54]  Daniel R. Caffrey,et al.  AIM2 recognizes cytosolic dsDNA and forms a caspase-1 activating inflammasome with ASC , 2009, Nature.

[55]  E. Alnemri,et al.  AIM2 activates the inflammasome and cell death in response to cytoplasmic DNA , 2009, Nature.

[56]  Z. Werb,et al.  Collective epithelial migration and cell rearrangements drive mammary branching morphogenesis. , 2008, Developmental cell.

[57]  Andrew J. Ewald,et al.  Matrix metalloproteinases and the regulation of tissue remodelling , 2007, Nature Reviews Molecular Cell Biology.

[58]  François Vaillant,et al.  Generation of a functional mammary gland from a single stem cell , 2006, Nature.

[59]  Tsutomu Ohta,et al.  Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. , 2005, Genes & development.

[60]  Mina J. Bissell,et al.  Site-specific inductive and inhibitory activities of MMP-2 and MMP-3 orchestrate mammary gland branching morphogenesis , 2003, The Journal of cell biology.

[61]  A. Berns,et al.  Synergistic tumor suppressor activity of BRCA2 and p53 in a conditional mouse model for breast cancer , 2001, Nature Genetics.

[62]  M. Arpin,et al.  The junction-associated protein, zonula occludens-1, localizes to the nucleus before the maturation and during the remodeling of cell-cell contacts. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[64]  J. Léon,et al.  Revised Papers , 2003 .