1. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

    Genome Research 25(2):257 (2015) PMID 25378249 PMCID PMC4315299

    We introduce a method for simultaneous prediction of microRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA-targ...
  2. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

    Genome Research 25(2):257 (2015) PMID 25378249 PMCID PMC4315299

    We introduce a method for simultaneous prediction of microRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA-targ...
  3. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.

    Stem Cells 33(2):367 (2015) PMID 25336442 PMCID PMC4305010

    The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs...
  4. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.

    Stem Cells 33(2):367 (2015) PMID 25336442 PMCID PMC4305010

    The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs...
  5. Direct ChIP-Seq significance analysis improves target prediction.

    BMC Genomics 16 Suppl 5:S4 (2015) PMID 26040656 PMCID PMC4460594

    Chromatin immunoprecipitation followed by sequencing of protein-bound DNA fragments (ChIP-Seq) is an effective high-throughput methodology for the identification of context specific DNA fragments that are bound by specific proteins in vivo. Despite significant progress in the bioinformatics anal...
  6. Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme.

    Journal of Neuro-Oncology 119(1):27 (2014) PMID 24792645 PMCID PMC4160150

    Separase, an enzyme that cleaves the chromosomal cohesin during mitosis, is overexpressed in a wide range of human epithelial cancers of breast, bone and prostate (Meyer et al., Clin Cancer Res 15(8):2703-2710, 2009). Overexpression of Separase in animal models results in aneuploidy and tumorige...
  7. Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme.

    Journal of Neuro-Oncology 119(1):27 (2014) PMID 24792645 PMCID PMC4160150

    Separase, an enzyme that cleaves the chromosomal cohesin during mitosis, is overexpressed in a wide range of human epithelial cancers of breast, bone and prostate (Meyer et al., Clin Cancer Res 15(8):2703-2710, 2009). Overexpression of Separase in animal models results in aneuploidy and tumorige...
  8. Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme.

    Journal of Neuro-Oncology 119(1):27 (2014) PMID 24792645 PMCID PMC4160150

    Separase, an enzyme that cleaves the chromosomal cohesin during mitosis, is overexpressed in a wide range of human epithelial cancers of breast, bone and prostate (Meyer et al., Clin Cancer Res 15(8):2703-2710, 2009). Overexpression of Separase in animal models results in aneuploidy and tumorige...
  9. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

    Genes & Development 28(7):765 (2014) PMID 24636986 PMCID PMC4015488

    The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. Here we identify the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a...
  10. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

    Genes & Development 28(7):765 (2014) PMID 24636986 PMCID PMC4015488

    The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. Here we identify the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a...
  11. A molecular signature predictive of indolent prostate cancer.

    Science Translational Medicine 5(202):202ra122 (2013) PMID 24027026 PMCID PMC3943244

    Many newly diagnosed prostate cancers present as low Gleason score tumors that require no treatment intervention. Distinguishing the many indolent tumors from the minority of lethal ones remains a major clinical challenge. We now show that low Gleason score prostate tumors can be distinguished a...
  12. A molecular signature predictive of indolent prostate cancer.

    Science Translational Medicine 5(202):202ra122 (2013) PMID 24027026 PMCID PMC3943244

    Many newly diagnosed prostate cancers present as low Gleason score tumors that require no treatment intervention. Distinguishing the many indolent tumors from the minority of lethal ones remains a major clinical challenge. We now show that low Gleason score prostate tumors can be distinguished a...
  13. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

    PNAS 110(4):1404 (2013) PMID 23297232 PMCID PMC3557069

    Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may be derived from tRNA, but the function of these molecules remains undefined. Here, we demonstrate that one such tRNA-derived fragment, cloned from human mature B cells and designated CU1276, in ...
  14. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

    PNAS 110(4):1404 (2013) PMID 23297232 PMCID PMC3557069

    Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may be derived from tRNA, but the function of these molecules remains undefined. Here, we demonstrate that one such tRNA-derived fragment, cloned from human mature B cells and designated CU1276, in ...
  15. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

    PNAS 110(4):1404 (2013) PMID 23297232 PMCID PMC3557069

    Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may be derived from tRNA, but the function of these molecules remains undefined. Here, we demonstrate that one such tRNA-derived fragment, cloned from human mature B cells and designated CU1276, in ...
  16. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

    PNAS 110(4):1404 (2013) PMID 23297232 PMCID PMC3557069

    Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may be derived from tRNA, but the function of these molecules remains undefined. Here, we demonstrate that one such tRNA-derived fragment, cloned from human mature B cells and designated CU1276, in ...
  17. Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension.

    Circulation: Cardiovascular Genetics 5(3):336 (2012) PMID 22474227 PMCID PMC3380156

    Heritable and idiopathic pulmonary arterial hypertension (PAH) are phenotypically identical and associated with mutations in several genes related to transforming growth factor (TGF) beta signaling, including bone morphogenetic protein receptor type 2, activin receptor-like kinase 1, endoglin, a...
  18. Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension.

    Circulation: Cardiovascular Genetics 5(3):336 (2012) PMID 22474227 PMCID PMC3380156

    Heritable and idiopathic pulmonary arterial hypertension (PAH) are phenotypically identical and associated with mutations in several genes related to transforming growth factor (TGF) beta signaling, including bone morphogenetic protein receptor type 2, activin receptor-like kinase 1, endoglin, a...
  19. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.

    Cell 147(2):370 (2011) PMID 22000015 PMCID PMC3214599

    By analyzing gene expression data in glioblastoma in combination with matched microRNA profiles, we have uncovered a posttranscriptional regulation layer of surprising magnitude, comprising more than 248,000 microRNA (miR)-mediated interactions. These include ∼7,000 genes whose transcripts act a...
  20. An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

    Cell 147(2):370 (2011)

    By analyzing gene expression data in glioblastoma in combination with matched microRNA profiles, we have uncovered a posttranscriptional regulation layer of surprising magnitude, comprising more than 248,000 microRNA (miR)-mediated interactions. These include ∼7,000 genes whose transcripts ...