Genomes and Genes
Jun S Song
Affiliation: Harvard University
- Model-based analysis of two-color arrays (MA2C)Jun S Song
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
Genome Biol 8:R178. 2007..The tools have been implemented as a stand-alone Java program called MA2C, which can display various plots of statistical analysis for quality control...
- Monte Carlo calculation of rectal dose when using an intrarectal balloon during prostate radiation therapyJun S Song
Department of Radiation Oncology, Brigham and Women s Hospital, Boston, MA, USA
Med Dosim 32:151-6. 2007..Differential dose volume histograms are also computed and compared for individual fields in the anterior expansion of the rectum, and the TPS is again shown to predict higher mean dose in the region by 0.3 approximately 1.0 Gy...
- Defining the rectal dose constraint for permanent radioactive seed implantation of the prostateMichele Albert
Department of Radiation Oncology, Brigham and Women s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
Urol Oncol 26:147-52. 2008..This study was performed to define the rectal dose constraint that would predict late rectal bleeding requiring argon plasma coagulation (APC) following prostate brachy mono-therapy...
- Identifying positioned nucleosomes with epigenetic marks in human from ChIP-SeqYong Zhang
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, 44 Binney St, Boston, MA 02115, USA
BMC Genomics 9:537. 2008..In vivo positioning and covalent modifications of nucleosomes play an important role in epigenetic regulation, but genome-wide studies of positioned nucleosomes and their modifications in human still remain limited...
- Build-up and surface dose measurements on phantoms using micro-MOSFET in 6 and 10 MV x-ray beams and comparisons with Monte Carlo calculationsHong F Xiang
Department of Radiation Oncology, Dana Farber and Brigham Women s Cancer Center, Harvard Medical School, Boston, Massachusetts 02115, USA
Med Phys 34:1266-73. 2007..0%-3.5%, and 1%-2% systematical error due to phantom setup geometry asymmetry. Micro-MOSFET can be used for skin dose measurements in 6 and 10 MV beams with an estimated accuracy of +/- 6%...
- Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITFRizwan Haq
Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
Cancer Cell 23:302-15. 2013..Conversely, treatment of BRAF-mutated melanomas with BRAF inhibitors renders them addicted to oxidative phosphorylation. Our data thus identify an adaptive metabolic program that limits the efficacy of BRAF inhibitors...
- Chromatin structure analyses identify miRNA promotersFatih Ozsolak
Department of Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Genes Dev 22:3172-83. 2008..The high-throughput identification of miRNA promoter and enhancer regulatory elements sheds light on evolution of miRNA transcription and permits rapid identification of transcriptional networks of miRNAs...
- BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibitionRizwan Haq
Division of Medical Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 110:4321-6. 2013..These studies identify MITF-BCL2A1 as a lineage-specific oncogenic pathway in melanoma and underscore its role for improved response to BRAF-directed therapy...
- YY1 regulates melanocyte development and function by cooperating with MITFJuying Li
Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
PLoS Genet 8:e1002688. 2012....
- A comparative study of rectal dose histograms in prostate brachytherapy: some analytic and numerical resultsJun S Song
Department of Radiation Oncology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
Med Phys 32:437-47. 2005..The digitized computation agrees quite well with the pre-digitization numerical integration, within 1% or 0.2 cm3, because of the low dose-gradient effect near the rectum in prostate brachytherapy...
- A high-resolution map of nucleosome positioning on a fission yeast centromereJun S Song
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
Genome Res 18:1064-72. 2008..In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence...
- Microarray blob-defect removal improves array analysisJun S Song
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA
Bioinformatics 23:966-71. 2007....
- High-throughput mapping of the chromatin structure of human promotersFatih Ozsolak
Melanoma Program in Medical Oncology, and Department of Pediatric Oncology, Dana Farber Cancer Institute, Children s Hospital Boston, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
Nat Biotechnol 25:244-8. 2007..This study presents a global view of human nucleosome positioning and provides a high-throughput tool for analyzing chromatin structure in development and disease...
- Lineage-specific transcriptional regulation of DICER by MITF in melanocytesCarmit Levy
Department of Dermatology, Cutaneous Biology Research Center, Mass General Hospital, Harvard Medical School, MA 02115, USA
Cell 141:994-1005. 2010..These observations highlight a central mechanism underlying lineage-specific miRNA regulation which could exist for other cell types during development...
- Quantifying the role of steric constraints in nucleosome positioningH Tomas Rube
Institute for Human Genetics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143 0794, USA, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143 0794, USA, Department of Epidemiology and Biostatistics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143 0794, USA and Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143 0794, USA
Nucleic Acids Res 42:2147-58. 2014..The observed variance gradient suggests an effective nucleosome size of 158 bp, instead of the commonly perceived 147 bp. Our analyses thus clarify the role of statistical positioning in vivo...
- Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targetsDavid S Johnson
Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
Genome Res 18:393-403. 2008..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...