A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence

Nuclear microRNAs in normal hemopoiesis and cancer

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A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

(2017) Thomas Treiber et al.   MOLECULAR CELL

New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response

(2017) Nelson Rangel et al.   Genes

Robust, universal biomarker assay to detect senescent cells in biological specimens

(2016) Konstantinos Evangelou et al.   AGING CELL

EMT: 2016

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DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation

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Apoptosis or senescence? Which exit route do epithelial cells and fibroblasts preferentially follow?

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Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing

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DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis

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ViableRNaseH1knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function

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SCFCyclin F-dependent degradation of CDC6 suppresses DNA re-replication

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Cellular Reprogramming Using Defined Factors and MicroRNAs

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Specific lipofuscin staining as a novel biomarker to detect replicative and stress-induced senescence. A method applicable in cryo-preserved and archival tissues

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miR-34 miRNAs Regulate Cellular Senescence in Type II Alveolar Epithelial Cells of Patients with Idiopathic Pulmonary Fibrosis

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Mitochondrial miRNA (MitomiR): a new player in cardiovascular health

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A localized nucleolar DNA damage response facilitates recruitment of the homology-directed repair machinery independent of cell cycle stage

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R loops: new modulators of genome dynamics and function

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Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

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Noncoding RNA control of cellular senescence

(2015) Kotb Abdelmohsen et al.   Wiley Interdisciplinary Reviews-RNA

The Regulatory Role of MicroRNAs in EMT and Cancer

(2015) Apostolos Zaravinos   Journal of Oncology

Alternative Lengthening of Telomeres: Recurrent Cytogenetic Aberrations and Chromosome Stability under Extreme Telomere Dysfunction

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HTSeq--a Python framework to work with high-throughput sequencing data

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Guidelines for the use of cell lines in biomedical research

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Are common fragile sites merely structural domains or highly organized “functional” units susceptible to oncogenic stress?

(2014) Alexandros G. Georgakilas et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division

(2014) A. Grob et al.   GENES & DEVELOPMENT

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

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(2014) F. Erhard et al.   GENOME RESEARCH

Intertumor heterogeneity of non-small-cell lung carcinomas revealed by multiplexed mutation profiling and integrative genomics

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Regulation of microRNA biogenesis

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Cellular senescence: from physiology to pathology

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The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

(2014) J. Brosius   Cold Spring Harbor Perspectives in Biology

Genomic alterations on 8p21-p23 are the most frequent genetic events in stage I squamous cell carcinoma of the lung

(2014) JIUN KANG   Experimental and Therapeutic Medicine

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

(2014) Yujia A. Chan et al.   PLoS Genetics

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

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The MicroRNA Biology of the Mammalian Nucleus

(2014) Thomas C Roberts   Molecular Therapy-Nucleic Acids

Stability of miRNA in human urine supports its biomarker potential

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Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

(2013) Sunjong Kwon   BMB Reports

Chromosomal instability (CIN): what it is and why it is crucial to cancer evolution

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Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

The DNA damage checkpoint precedes activation of ARF in response to escalating oncogenic stress during tumorigenesis

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Functional interplay between the DNA-damage-response kinase ATM and ARF tumour suppressor protein in human cancer

(2013) Georgia Velimezi et al.   NATURE CELL BIOLOGY

Adult-specific functions of animal microRNAs

(2013) Kailiang Sun et al.   NATURE REVIEWS GENETICS

Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues

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Modulation of epigenetic regulators and cell fate decisions by miRNAs

(2013) Andreas J Gruber et al.   Epigenomics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

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Is cellular senescence an example of antagonistic pleiotropy?

(2012) Stefano Giaimo et al.   AGING CELL

DNA double-strand break repair within heterochromatic regions: Figure 1

(2012) Johanne M. Murray et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

MicroRNAs in Stress Signaling and Human Disease

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miR-34 and SNAIL form a double-negative feedback loop to regulate epithelial-mesenchymal transitions

(2012) Helge Siemens et al.   CELL CYCLE

Cdc6 Protein Obstructs Apoptosome Assembly and Consequent Cell Death by Forming Stable Complexes with Activated Apaf-1 Molecules

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Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

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Hallmarks of Cancer: The Next Generation

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Cdc6 expression represses E-cadherin transcription and activates adjacent replication origins

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Pre-microRNA and Mature microRNA in Human Mitochondria

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Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments

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Robust MicroRNA Stability in Degraded RNA Preparations from Human Tissue and Cell Samples

(2010) M. Jung et al.   CLINICAL CHEMISTRY

Oncogene-induced senescence: the bright and dark side of the response

(2010) Vassilis G Gorgoulis et al.   CURRENT OPINION IN CELL BIOLOGY

Tumors as Organs: Complex Tissues that Interface with the Entire Organism

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Rapid in situ codetection of noncoding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment

(2010) Mariàngels de Planell-Saguer et al.   Nature Protocols

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Modulation of the E2F1-Driven Cancer Cell Fate by the DNA Damage Response Machinery and Potential Novel E2F1 Targets in Osteosarcomas

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The Sequence Alignment/Map format and SAMtools

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Epithelial-Mesenchymal Transitions in Development and Disease

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G Clustering Is Important for the Initiation of Transcription-Induced R-Loops In Vitro, whereas High G Density without Clustering Is Sufficient Thereafter

(2009) D. Roy et al.   MOLECULAR AND CELLULAR BIOLOGY

Competition between the RNA Transcript and the Nontemplate DNA Strand during R-Loop Formation In Vitro: a Nick Can Serve as a Strong R-Loop Initiation Site

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Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

miRNA in situ hybridization in formaldehyde and EDC–fixed tissues

(2009) John T G Pena et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Protocols to detect senescence-associated beta-galactosidase (SA-βgal) activity, a biomarker of senescent cells in culture and in vivo

(2009) Florence Debacq-Chainiaux et al.   Nature Protocols

Limited Role of Murine ATM in Oncogene-Induced Senescence and p53-Dependent Tumor Suppression

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RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology

(2008) Brian McStay et al.   Annual Review of Cell and Developmental Biology

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

Biological principles of microRNA-mediated regulation: shared themes amid diversity

(2008) Alex S. Flynt et al.   NATURE REVIEWS GENETICS

An Oncogene-Induced DNA Damage Model for Cancer Development

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