Validating transcripts with probes and imaging technology

[1]  Paul J. Choi,et al.  Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells , 2010, Science.

[2]  Ilan Davis,et al.  Making the message clear: visualizing mRNA localization , 2010, Trends in cell biology.

[3]  Alexander van Oudenaarden,et al.  Transcript counting in single cells reveals dynamics of rDNA transcription , 2010, Molecular systems biology.

[4]  Ola Söderberg,et al.  In situ detection and genotyping of individual mRNA molecules , 2010, Nature Methods.

[5]  Keith A. Lidke,et al.  Fast, single-molecule localization that achieves theoretically minimum uncertainty , 2010, Nature Methods.

[6]  C. Zurla,et al.  Single molecule sensitive multivalent polyethylene glycol probes for RNA imaging. , 2010, Bioconjugate chemistry.

[7]  M. Gönen,et al.  Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. , 2010, The Journal of clinical investigation.

[8]  Alexander van Oudenaarden,et al.  Variability in gene expression underlies incomplete penetrance , 2009, Nature.

[9]  Klaus Aktories,et al.  Noise Can Induce Bimodality in Positive Transcriptional Feedback Loops Without Bistability , 2010 .

[10]  H. Clevers,et al.  In situ hybridization to identify gut stem cells. , 2010, Current protocols in stem cell biology.

[11]  J. Troge,et al.  Inferring tumor progression from genomic heterogeneity. , 2010, Genome research.

[12]  Robert H Singer,et al.  Single mRNA tracking in live cells. , 2010, Methods in enzymology.

[13]  Yoav Freund,et al.  Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting , 2009, Current Biology.

[14]  Daniel R. Larson,et al.  A single molecule view of gene expression. , 2009, Trends in cell biology.

[15]  Sung-jun Han,et al.  In situ visualization of gene expression using polymer-coated quantum-dot-DNA conjugates. , 2009, Small.

[16]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[17]  Andrew Tsourkas,et al.  Imaging individual microRNAs in single mammalian cells in situ , 2009, Nucleic acids research.

[18]  James E. Crowe,et al.  Single molecule–sensitive probes for imaging RNA in live cells , 2009, Nature Methods.

[19]  Sanjay Tyagi,et al.  Imaging intracellular RNA distribution and dynamics in living cells , 2009, Nature Methods.

[20]  T. Funatsu,et al.  Single molecule tracking of quantum dot-labeled mRNAs in a cell nucleus. , 2009, Biochemical and biophysical research communications.

[21]  Hans Clevers,et al.  Transcription Factor Achaete Scute-Like 2 Controls Intestinal Stem Cell Fate , 2009, Cell.

[22]  H. Clevers,et al.  Stem cells, self-renewal, and differentiation in the intestinal epithelium. , 2009, Annual review of physiology.

[23]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.

[24]  A. Oudenaarden,et al.  Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.

[25]  Scott A. Rifkin,et al.  Imaging individual mRNA molecules using multiple singly labeled probes , 2008, Nature Methods.

[26]  Shuming Nie,et al.  Bioconjugated quantum dots for in vivo molecular and cellular imaging. , 2008, Advanced drug delivery reviews.

[27]  E. Betzig,et al.  Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics , 2008, Nature Methods.

[28]  Graeme Milligan,et al.  Identification of a serotonin/glutamate receptor complex implicated in psychosis , 2008, Nature.

[29]  R. Singer,et al.  Cell biology of mRNA decay. , 2008, Methods in enzymology.

[30]  D. Dubnau,et al.  Noise in Gene Expression Determines Cell Fate in Bacillus subtilis , 2007, Science.

[31]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[32]  S. Hell.  Far-Field Optical Nanoscopy , 2007, Science.

[33]  Yoshio Umezawa,et al.  Imaging dynamics of endogenous mitochondrial RNA in single living cells , 2007, Nature Methods.

[34]  J. Gerst,et al.  A genomic integration method to visualize localization of endogenous mRNAs in living yeast , 2007, Nature Methods.

[35]  Charles R Cantor,et al.  RNA visualization in live bacterial cells using fluorescent protein complementation , 2007, Nature Methods.

[36]  David Bryder,et al.  Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR , 2006, Proceedings of the National Academy of Sciences.

[37]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.

[38]  David Twomey,et al.  Imaging of multiple mRNA targets using quantum dot based in situ hybridization and spectral deconvolution in clinical biopsies. , 2006, Biochemical and biophysical research communications.

[39]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[40]  D. Tranchina,et al.  Stochastic mRNA Synthesis in Mammalian Cells , 2006, PLoS biology.

[41]  E. Petricoin,et al.  Laser Capture Microdissection , 1996, Science.

[42]  E. Cox,et al.  Real-Time Kinetics of Gene Activity in Individual Bacteria , 2005, Cell.

[43]  Sanjay Tyagi,et al.  Mechanism of mRNA transport in the nucleus. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Tony Yuen,et al.  Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization , 2005, Nucleic acids research.

[45]  W. Gerald,et al.  Gene expression profiling in single cells within tissue , 2005, Nature Methods.

[46]  Wigard P Kloosterman,et al.  In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes , 2005, Nature Methods.

[47]  Chris M. Brown,et al.  Visualization of RNA–protein interactions in living cells: FMRP and IMP1 interact on mRNAs , 2004, The EMBO journal.

[48]  Robert H Singer,et al.  Materials and Methods Som Text Figs. S1 to S8 References and Notes Dynamics of Single Mrnps in Nuclei of Living Cells , 2022 .

[49]  D. Tautz,et al.  A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback , 1989, Chromosoma.

[50]  Diana P Bratu,et al.  Visualizing the distribution and transport of mRNAs in living cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Robert H. Singer,et al.  Fluorescence in situ hybridization: past, present and future , 2003, Journal of Cell Science.

[52]  Robert H. Singer,et al.  Single mRNA Molecules Demonstrate Probabilistic Movement in Living Mammalian Cells , 2003, Current Biology.

[53]  Lawrence M. Lifshitz,et al.  Visualization of single molecules of mRNA in situ. , 2003, Methods in enzymology.

[54]  Robert H Singer,et al.  Gene expression and the myth of the average cell. , 2003, Trends in cell biology.

[55]  Robert H Singer,et al.  Single-Cell Gene Expression Profiling , 2002, Science.

[56]  W. Webb,et al.  Precise nanometer localization analysis for individual fluorescent probes. , 2002, Biophysical journal.

[57]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[58]  I. Weissman,et al.  Stem cells, cancer, and cancer stem cells , 2001, Nature.

[59]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[60]  J. Kolberg,et al.  Single-copy Gene Detection Using Branched DNA (bDNA) In Situ Hybridization , 2001, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[61]  S. Hell,et al.  Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[62]  M vanderPloeg,et al.  Cytochemical nucleic acid research during the twentieth century. , 2000 .

[63]  M. van der Ploeg,et al.  Cytochemical nucleic acid research during the twentieth century. , 2000, European journal of histochemistry : EJH.

[64]  J. Conchello,et al.  Three-dimensional imaging by deconvolution microscopy. , 1999, Methods.

[65]  S. Walker,et al.  Quantitative RT-PCR : Pitfalls and Potential , 1999 .

[66]  S. Shaw,et al.  Using green fluorescent protein fusion proteins to quantitate microtubule and spindle dynamics in budding yeast. , 1999, Methods in cell biology.

[67]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[68]  R. Singer,et al.  Localization of ASH1 mRNA particles in living yeast. , 1998, Molecular cell.

[69]  F S Fay,et al.  Visualization of single RNA transcripts in situ. , 1998, Science.

[70]  K. Kosik,et al.  Sorting of β-Actin mRNA and Protein to Neurites and Growth Cones in Culture , 1998, The Journal of Neuroscience.

[71]  K. Kosik,et al.  Sorting of beta-actin mRNA and protein to neurites and growth cones in culture. , 1998, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[72]  A. Waggoner,et al.  Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes. , 1997, Nucleic acids research.

[73]  K. Kinzler,et al.  Genetic instability in colorectal cancers , 1997, Nature.

[74]  R. W. Davis,et al.  Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[75]  R. Singer,et al.  mRNA and cytoskeletal filaments. , 1997, Current opinion in cell biology.

[76]  H. Tanke,et al.  Heterogeneity in telomere length of human chromosomes. , 1996, Human molecular genetics.

[77]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

[78]  Peter E. Nielsen,et al.  DNA-like double helix formed by peptide nucleic acid , 1994, Nature.

[79]  J Vrolijk,et al.  Fluorescence ratio measurements of double-labeled probes for multiple in situ hybridization by digital imaging microscopy. , 1992, Cytometry.

[80]  J. Ploem,et al.  Multiple fluorescence in situ hybridization. , 1990, Cytometry.