Preethi H Gunaratne

Summary

Affiliation: University of Houston
Country: USA

Publications

  1. ncbi request reprint Large-scale integration of MicroRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
    Methods Mol Biol 667:297-315. 2010
  2. doi request reprint miRNA data analysis: next-gen sequencing
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
    Methods Mol Biol 822:273-88. 2012
  3. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
  4. pmc Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells
    Peili Gu
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 3:e2548. 2008
  5. pmc Discovery of novel microRNAs in female reproductive tract using next generation sequencing
    Chad J Creighton
    The Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e9637. 2010
  6. ncbi request reprint Embryonic stem cell microRNAs: defining factors in induced pluripotent (iPS) and cancer (CSC) stem cells?
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Curr Stem Cell Res Ther 4:168-77. 2009
  7. pmc A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer
    Ankur K Nagaraja
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Endocrinol 24:447-63. 2010
  8. pmc Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers
    Chad J Creighton
    Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
    Cancer Res 70:1906-15. 2010
  9. pmc Analysis of microRNA expression in the prepubertal testis
    Gregory M Buchold
    Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e15317. 2010
  10. pmc Functional microRNA involved in endometriosis
    Shannon M Hawkins
    Department of Obstetrics and Gynecology, Baylor College of Medicine, 1709 Dryden Drive, Suite 1100, Houston, Texas 77030, USA
    Mol Endocrinol 25:821-32. 2011

Detail Information

Publications32

  1. ncbi request reprint Large-scale integration of MicroRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
    Methods Mol Biol 667:297-315. 2010
    ..These efforts are essential for determining false positive and negative rates of existing algorithms and refining our knowledge on the rules of miRNA-mRNA relationships...
  2. doi request reprint miRNA data analysis: next-gen sequencing
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
    Methods Mol Biol 822:273-88. 2012
    ..We also discuss in greater detail our contributions to this effort...
  3. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
    ..To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence...
  4. pmc Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells
    Peili Gu
    Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 3:e2548. 2008
    ..They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence)...
  5. pmc Discovery of novel microRNAs in female reproductive tract using next generation sequencing
    Chad J Creighton
    The Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e9637. 2010
    ..Our novel miRNAs were detectable in multiple samples, but expressed at low levels and not specific to any one tissue or cell type. To date, this study represents the largest set of samples analyzed together to identify novel miRNAs...
  6. ncbi request reprint Embryonic stem cell microRNAs: defining factors in induced pluripotent (iPS) and cancer (CSC) stem cells?
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Curr Stem Cell Res Ther 4:168-77. 2009
    ..Any perturbation in key ES cell miRNA-mRNA networks during any of the above processes maybe a hallmark of (CSCs)...
  7. pmc A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer
    Ankur K Nagaraja
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Endocrinol 24:447-63. 2010
    ....
  8. pmc Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers
    Chad J Creighton
    Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
    Cancer Res 70:1906-15. 2010
    ....
  9. pmc Analysis of microRNA expression in the prepubertal testis
    Gregory M Buchold
    Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 5:e15317. 2010
    ..These studies provide a foundation for interpretation of miRNA changes associated with testicular pathology and identification of novel components of the miRNA editing machinery in the testis...
  10. pmc Functional microRNA involved in endometriosis
    Shannon M Hawkins
    Department of Obstetrics and Gynecology, Baylor College of Medicine, 1709 Dryden Drive, Suite 1100, Houston, Texas 77030, USA
    Mol Endocrinol 25:821-32. 2011
    ..Thus, miR-29c and other abnormally regulated microRNA appear to play important roles in the pathophysiology of uterine function and dysfunction...
  11. pmc Chromatin changes in dicer-deficient mouse embryonic stem cells in response to retinoic acid induced differentiation
    Jayantha B Tennakoon
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS ONE 8:e74556. 2013
    ....
  12. pmc Dysregulation of uterine signaling pathways in progesterone receptor-Cre knockout of dicer
    Shannon M Hawkins
    Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Endocrinol 26:1552-66. 2012
    ..These data implicate Dicer and appropriate miRNA expression as essential players in the regulation of multiple uterine signaling pathways required for uterine development and appropriate function...
  13. pmc A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions
    Chad J Creighton
    The Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
    RNA 14:2290-6. 2008
    ..The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net...
  14. pmc MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes
    Lawrence A Donehower
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    J Pathol 229:99-110. 2013
    ..Examination of MLH1 expression status and frequencies of APC, KRAS, and BRAF mutation in CRC may provide a useful diagnostic tool that could supplement the standard microsatellite instability assays and influence therapeutic decisions...
  15. pmc Novel MicroRNAs regulating proliferation and apoptosis in uterine papillary serous carcinomas
    Claire M Mach
    Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
    Cancer Lett 335:314-22. 2013
    ..These results expand our insight into the repertoire of human miRNAs and identify novel pathways by which dysregulated miRNA expression promotes uterine cancer growth...
  16. pmc Expression profiling of microRNAs by deep sequencing
    Chad J Creighton
    Dan L Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
    Brief Bioinform 10:490-7. 2009
    ..Here we discuss tools and methodologies for the analysis of microRNA expression data from deep sequencing...
  17. pmc A putative role for microRNA-205 in mammary epithelial cell progenitors
    Stephanie B Greene
    Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Cell Sci 123:606-18. 2010
    ..Additionally, in normal mouse MECs, high expression of miR-205 was observed in stem-cell-enriched cell populations isolated by FACS using established cell-surface markers...
  18. pmc Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
    Jeffrey G Reid
    Department of Chemistry, University of Houston, Houston, Texas 77204, USA
    Genome Res 18:1571-81. 2008
    ....
  19. pmc GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline
    Lang Ma
    Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 5:e1000635. 2009
    ..These studies provide the first evidence for an essential structural role for GASZ in male fertility and epigenetic and post-transcriptional silencing of retrotransposons by stabilizing MILI in nuage...
  20. pmc Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif
    Mark P Hamilton
    Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza Houston M822, Houston, Texas 77030, USA
    Nat Commun 4:2730. 2013
    ..These combined analyses identify pan-cancer oncogenic cotargeting of the phosphoinositide 3-kinase, TGFβ and p53 pathways by the miR-17-19-130 superfamily members. ..
  21. doi request reprint A gold nanoparticle platform for the delivery of functional microRNAs into cancer cells
    Rajib Ghosh
    Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204, USA
    Biomaterials 34:807-16. 2013
    ....
  22. ncbi request reprint A theory for the arrangement of sensory organs in Drosophila
    Huifeng Zhu
    Department of Physics, University of Houston, Houston, Texas 77204, USA
    Chaos 20:013132. 2010
    ..In our theory, miRNA-9a is one of the components of the underlying network and has no special regulatory role. The loss of periodicity in its absence is due to the transfer of the system to a bistable state...
  23. pmc Deletion of Dicer in somatic cells of the female reproductive tract causes sterility
    Ankur K Nagaraja
    Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Mol Endocrinol 22:2336-52. 2008
    ..Thus, our findings reveal diverse and critical roles for Dicer and its miRNA products in the development and function of the female reproductive tract...
  24. pmc miRNA regulatory circuits in ES cells differentiation: a chemical kinetics modeling approach
    Zijun Luo
    Department of Mathematics, University of Houston, Houston, Texas, United States of America
    PLoS ONE 6:e23263. 2011
    ..This approach leads to the computation of a highly selective and drastically reduced list of repressive pairs (M,G) involved in ES cells differentiation...
  25. pmc Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk
    Erika M Munch
    Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 8:e50564. 2013
    ..We further speculate that regulation of these miRNA by a high fat maternal diet enables modulation of fetal metabolism to accommodate significant dietary challenges...
  26. doi request reprint A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma
    Jason M Shohet
    Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas 77204, USA
    Cancer Res 71:3841-51. 2011
    ..Our data reveal host-gene independent functions of MYCN-target microRNAs and demonstrate that MYCN represses both tumor suppressive and proproliferative microRNAs...
  27. pmc Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma
    Chad J Creighton
    Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS ONE 7:e34546. 2012
    ..Here, using TCGA ovarian data, we surveyed the miRNAs, in the context of their predicted gene targets...
  28. pmc Using effective subnetworks to predict selected properties of gene networks
    Gemunu H Gunaratne
    Department of Physics, University of Houston, Houston, Texas, United States of America
    PLoS ONE 5:e13080. 2010
    ..However, since they contain a large number of nodes, the computation of influence networks requires a prohibitively large set of microarray experiments. Furthermore, error estimates of the network make verifiable predictions impossible...
  29. ncbi request reprint Differential mRNA processing in hematopoietic stem cells
    Teresa V Bowman
    Cell and Gene Therapy Center, Baylor College of Medicine, N1030, One Baylor Plaza, Houston, Texas 77030, USA
    Stem Cells 24:662-70. 2006
    ..This change in unspliced transcript level coordinated with increases in gene expression of splicing machinery components. Combined, these results suggest that post-transcriptional regulation is important in HSC activation in vivo...
  30. doi request reprint Histologic subtypes of hepatoblastoma are characterized by differential canonical Wnt and Notch pathway activation in DLK+ precursors
    Dolores Lopez-Terrada
    Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
    Hum Pathol 40:783-94. 2009
    ..The relative Wnt versus Notch activation appears useful in stratifying different subtypes...
  31. pmc Comprehensive molecular characterization of clear cell renal cell carcinoma
    Chad J Creighton
    1 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA 2 Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Nature 499:43-9. 2013
    ..Remodelling cellular metabolism thus constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment. ..
  32. pmc MicroRNA-1258 suppresses breast cancer brain metastasis by targeting heparanase
    Lixin Zhang
    Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
    Cancer Res 71:645-54. 2011
    ....