Alexander S Brodsky

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
    Alexander S Brodsky
    Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 6:R64. 2005
  2. ncbi A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry
    Alexander S Brodsky
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 1:922-9. 2002
  3. ncbi Analysis of RNA-protein interactions by flow cytometry
    Alexander S Brodsky
    Dana Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 1 Jimmy Fund Way, SM 922, Boston, MA 02115, USA
    Curr Opin Mol Ther 5:235-40. 2003
  4. ncbi Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
  5. pmc Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription
    Ian A Swinburne
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 16:912-21. 2006
  6. ncbi Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Cell 122:33-43. 2005
  7. pmc Exon expression profiling reveals stimulus-mediated exon use in neural cells
    Adrienne E McKee
    Department of Systems Biology, 200 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Biol 8:R159. 2007
  8. ncbi Identifying proteins that affect mRNA localization in living cells
    Alexander S Brodsky
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, MA 02115, USA
    Methods 26:151-5. 2002
  9. pmc Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors
    Margarida Gama-Carvalho
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av, Prof, Egas Moniz, 1649 028 Lisboa, Portugal
    Genome Biol 7:R113. 2006
  10. ncbi Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation
    Kwaku T Dayie
    Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 317:263-78. 2002

Detail Information

Publications10

  1. pmc Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
    Alexander S Brodsky
    Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 6:R64. 2005
    ..RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows...
  2. ncbi A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry
    Alexander S Brodsky
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 1:922-9. 2002
    ..We propose that this strategy, in combination with emerging coded bead systems, can identify RNAs and RNA sequences important for interacting with RNA-binding proteins on genomic scales...
  3. ncbi Analysis of RNA-protein interactions by flow cytometry
    Alexander S Brodsky
    Dana Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 1 Jimmy Fund Way, SM 922, Boston, MA 02115, USA
    Curr Opin Mol Ther 5:235-40. 2003
    ..The microbead flow cytometric approach is flexible and provides new opportunities for functional genomic studies and small-molecule screening...
  4. ncbi Genome-wide analysis of estrogen receptor binding sites
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 38:1289-97. 2006
    ..Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer...
  5. pmc Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription
    Ian A Swinburne
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 16:912-21. 2006
    ..In sum, we present the mapping in mammalian cells of RNA binding proteins across a portion of the genome that provides insight into the transcriptional assembly of RNA-protein complexes...
  6. ncbi Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Cell 122:33-43. 2005
    ..Furthermore, knockdown of FoxA1 expression blocks the association of ER with chromatin and estrogen-induced gene expression demonstrating the necessity of FoxA1 in mediating an estrogen response in breast cancer cells...
  7. pmc Exon expression profiling reveals stimulus-mediated exon use in neural cells
    Adrienne E McKee
    Department of Systems Biology, 200 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Biol 8:R159. 2007
    ..Although calcium-induced transcription and transcript variation have both been recognized as important sources of gene regulation, the interplay between these two phenomena has not been evaluated on a genome-wide scale...
  8. ncbi Identifying proteins that affect mRNA localization in living cells
    Alexander S Brodsky
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, MA 02115, USA
    Methods 26:151-5. 2002
    ..The technology also allows the swapping of different regions of the RNA to determine the cis requirements for transport. GFP RNA imaging opens many possibilities to examine RNA transport in real time in a variety of different organisms...
  9. pmc Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors
    Margarida Gama-Carvalho
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av, Prof, Egas Moniz, 1649 028 Lisboa, Portugal
    Genome Biol 7:R113. 2006
    ..This observation raises the question of whether U2AF associates with mature mRNA-ribonucleoprotein particles in transit to the cytoplasm, participating in additional cellular functions...
  10. ncbi Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation
    Kwaku T Dayie
    Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 317:263-78. 2002
    ..U23 in the bulge undergoes the largest dynamic change on binding argininamide, while U25 remains flexible, reflecting the large conformational change that is triggered upon ligand binding...