Genomes and Genes
Melissa J Fazzari
Affiliation: Albert Einstein College of Medicine
- Epigenomics: beyond CpG islandsMelissa J Fazzari
Department of Epidemiology and Social Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Nat Rev Genet 5:446-55. 2004
- Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genomeMasako Suzuki
Department of Genetics Computational Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Genome Res 21:1833-40. 2011....
- CG dinucleotide clustering is a species-specific property of the genomeJacob L Glass
Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA, Division of Hematology Oncology, University of Kentucky, Markey Cancer Center, 800 Rose Street, Lexington KY 40536, USA
Nucleic Acids Res 35:6798-807. 2007..Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters...
- Septin 9 isoform expression, localization and epigenetic changes during human and mouse breast cancer progressionDiana Connolly
Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, 1301 Morris Park Avenue, Bronx, NY 10461, USA
Breast Cancer Res 13:R76. 2011..The mechanisms regulating its expression during tumor initiation and progression in vivo and the oncogenic function of its different isoforms remain elusive...
- DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesisDeanna Acosta
Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
Mamm Genome 22:249-59. 2011..Based on these studies, we present a model in which comparative epigenetic techniques can be used to identify novel candidate genes important for human breast tumorigenesis, in both primary and metastatic tumors...
- Introduction to epigenomics and epigenome-wide analysisMelissa J Fazzari
Division of Biostatistics, Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
Methods Mol Biol 620:243-65. 2010..We will conclude this chapter by identifying issues in building methylation-based models for prediction and potential directions of further statistical research in epigenetics...
- Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of ratsReid F Thompson
Departments of Genetics Computational Genetics, Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA
J Biol Chem 285:15111-8. 2010..These results demonstrate that epigenetic dysregulation is a strong candidate for propagating the cellular memory of intrauterine events, causing changes in expression of nearby genes and long term susceptibility to type 2 diabetes...
- Cytosine methylation dysregulation in neonates following intrauterine growth restrictionFrancine Einstein
Department of Obstetrics, Gynecology and Women s Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS ONE 5:e8887. 2010....
- Experimental approaches to the study of epigenomic dysregulation in ageingReid F Thompson
Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Exp Gerontol 45:255-68. 2010..We describe how such experiments are currently performed, their limitations technically and analytically and their application to ageing research...
- The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human diseaseAndrew S McLellan
Price Center for Genetics and Translational Medicine, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
Epigenomics 1:33-8. 2009..As a result, several avenues of research are now expanding, with cancer epigenomics being complemented by studies of the epigenomics of infectious disease and a neuroepigenomics program...
- CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domainsJacob L Glass
Department of Genetics Computational Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
Mamm Genome 20:633-43. 2009..We conclude that CG dinucleotide periodicity helps to explain some but not all of the relative sequence specificity of mutations of Dnmt3a or Dnmt3L in the establishment of germline cytosine methylation patterns...
- DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancerAmy Sharma
Albert Einstein College of Medicine, Bronx, NY 10461, USA
Wiley Interdiscip Rev Syst Biol Med 2:654-69. 2010..We have thus focused on DNA methylation changes in the pathogenesis of multiple myeloma, which promises to become an excellent model for systems biological studies of epigenomic dysregulation in human disease...
- Akt inhibitors MK-2206 and nelfinavir overcome mTOR inhibitor resistance in diffuse large B-cell lymphomaAdam M Petrich
Montefiore Medical Center, Bronx, New York, USA
Clin Cancer Res 18:2534-44. 2012....
- Comparative isoschizomer profiling of cytosine methylation: the HELP assayBatbayar Khulan
Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Genome Res 16:1046-55. 2006..The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome...
- Prognostic and predictive value of 16p12.1 and 16q22.1 copy number changes in human breast cancerTricia E Downing
Jacobi Medical Center, Department of Internal Medicine, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
Cancer Genet Cytogenet 198:52-61. 2010..0001). The finding that higher q/p ratios occur in younger patients offers a tool to identify high-risk individuals most likely to proceed to high grade...
- Clinical application of molecular profiling in breast cancerJoseph A Sparano
Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Room 47, 1825 Eastchester Road, 2 South, Bronx, NY 10461, USA
Future Oncol 1:485-96. 2005..The completion of these important studies will represent the first step toward integrating molecular profiling into treatment selection for adjuvant therapy in breast cancer...
- Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei S Mikkelsen
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 447:167-77. 2007..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...