Browsing by Author "Park, Peter"

Now showing items 21-36 of 36

    • Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci 

      Zacharek, Sima J.; Fillmore, Christine M.; Lau, Allison N.; Gludish, David W.; Chou, Alan; Ho, Joshua W.K.; Zamponi, Raffaella; Gazit, Roi; Bock, Christoph; Jäger, Natalie; Smith, Zachary; Kim, Tae-min; Saunders, Arven H.; Wong, Janice; Lee, Joo-Hyeon; Roach, Rebecca R.; Rossi, Derrick; Meissner, Alexander; Gimelbrant, Alexander; Park, Peter; Kim, Carla (Elsevier BV, 2011-09-02)
      Bmi1 is required for the self-renewal of stem cells in many tissues including the lung epithelial stem cells, Bronchioalveolar Stem Cells (BASCs). Imprinted genes, which exhibit expression from only the maternally- or ...

    • Meta-Analysis of Glioblastoma Multiforme versus Anaplastic Astrocytoma Identifies Robust Gene Markers 

      Dreyfuss, Jonathan M; Johnson, Mark Damone; Park, Peter J. (BioMed Central, 2009)
      Background: Anaplastic astrocytoma (AA) and its more aggressive counterpart, glioblastoma multiforme (GBM), are the most common intrinsic brain tumors in adults and are almost universally fatal. A deeper understanding of ...

    • MicroSAGE is Highly Representative and Reproducible but Reveals Major Differences in Gene Expression Among Samples Obtained from Similar Tissues 

      Blackshaw, Seth; Kuo, Winston Patrick; Park, Peter J.; Tsujikawa, Motokazu; Gunnersen, Jenny M; Scott, Hamish S; Boon, Wee-Ming; Tan, Seong-Seng; Cepko, Constance L. (BioMed Central, 2003)
      Background: Serial analysis of gene expression using small amounts of starting material (microSAGE) has not yet been conclusively shown to be representative, reproducible or accurate. Results: We show that microSAGE is ...

    • MNase titration reveals differences between nucleosome occupancy and chromatin accessibility 

      Mieczkowski, Jakub; Cook, April; Bowman, Sarah K.; Mueller, Britta; Alver, Burak H.; Kundu, Sharmistha; Deaton, Aimee M.; Urban, Jennifer A.; Larschan, Erica; Park, Peter J.; Kingston, Robert E.; Tolstorukov, Michael Y. (Nature Publishing Group, 2016)
      Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that ...

    • Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models 

      Liu, Manway; Liberzon, Arthur; Kong, Sek Won Won; Lai, Weil R; Park, Peter J.; Kohane, Isaac Samuel; Kasif, Simon (Public Library of Science, 2007)
      Type 2 diabetes mellitus is a complex disorder associated with multiple genetic, epigenetic, developmental, and environmental factors. Animal models of type 2 diabetes differ based on diet, drug treatment, and gene knockouts, ...

    • Next-generation sequencing-based detection of germline L1-mediated transductions 

      Tica, Jelena; Lee, Eunjung; Untergasser, Andreas; Meiers, Sascha; Garfield, David A.; Gokcumen, Omer; Furlong, Eileen E.M.; Park, Peter J.; Stütz, Adrian M.; Korbel, Jan O. (BioMed Central, 2016)
      Background: While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for ...

    • Normalization and Experimental Design for ChIP-chip Data 

      Peng, Shouyong; Alekseyenko, Artem Anatolievich; Larschan, Erica; Kuroda, Mitzi I.; Park, Peter J. (BioMed Central, 2007)
      Background: Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing ...

    • Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming 

      West, Jason A.; Cook, April; Alver, Burak H.; Stadtfeld, Matthias; Deaton, Aimee; Hochedlinger, Konrad; Park, Peter J.; Tolstorukov, Michael Y.; Kingston, Robert E. (2014)
      Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To ...

    • Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1α 

      Kim, Yeo-Jung; Lee, Hae-June; Kim, Tae-Min; Eisinger-Mathason, TS Karin; Zhang, Alexia Y; Schmidt, Benjamin; Karl, Daniel L; Nakazawa, Michael S; Park, Peter J; Simon, M Celeste; Yoon, Sam S (Wiley Subscription Services, Inc., A Wiley Company, 2012)
      Increased levels of hypoxia and hypoxia-inducible factor 1α (HIF-1α) in human sarcomas correlate with tumor progression and radiation resistance. Prolonged antiangiogenic therapy of tumors not only delays tumor growth but ...

    • Quantized Correlation Coefficient for Measuring Reproducibility of ChIP-chip Data 

      Peng, Shouyong; Kuroda, Mitzi I.; Park, Peter J. (BioMed Central, 2010)
      Background: Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments ...

    • Resolving rates of mutation in the brain using single-neuron genomics 

      Evrony, Gilad D; Lee, Eunjung; Park, Peter J; Walsh, Christopher A (eLife Sciences Publications, Ltd, 2016)
      Whether somatic mutations contribute functional diversity to brain cells is a long-standing question. Single-neuron genomics enables direct measurement of somatic mutation rates in human brain and promises to answer this ...

    • rSW-seq: Algorithm for Detection of Copy Number Alterations in Deep Sequencing Data 

      Kim, Tae-Min; Luquette, Lovelace J.; Xi, Ruibin; Park, Peter J. (BioMed Central, 2010)
      Background: Recent advances in sequencing technologies have enabled generation of large-scale genome sequencing data. These data can be used to characterize a variety of genomic features, including the DNA copy number ...

    • Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context 

      Alekseyenko, Artyom A.; Gelbart, Marnie; Tolstorukov, Michael Y.; Gorchakov, Andrey A.; Larschan, Erica; Gu, Tingting; Minoda, Aki; Riddle, Nicole C.; Schwartz, Yuri B.; Elgin, Sarah C. R.; Karpen, Gary H.; Pirrotta, Vincenzo; Ho, Joshua Wing Kei; Peng, Shouyong; Plachetka, Annette; Kharchenko, Peter Vasili; Jung, Youngsook; Kuroda, Mitzi I.; Park, Peter J. (Public Library of Science, 2012)
      The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent ...

    • The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework 

      Sui, Shannan Ho; Merrill, Emily; Gehlenborg, Nils; Haseley, Psalm; Sytchev, Ilya; Park, Richard; Rocca-Serra, Philippe; Corlosquet, Stephane; Gonzalez-Beltran, Alejandra; Maguire, Eamonn; Hofmann, Oliver; Park, Peter; Das, Sudeshna; Sansone, Susanna-Assunta; Hide, Winston (American Medical Informatics Association, 2013)
      Comparisons of stem cell experiments at both molecular and semantic levels remain challenging due to inconsistencies in results, data formats, and descriptions among biomedical research discoveries. The Harvard Stem Cell ...

    • Systematic Identification of Synergistic Drug Pairs Targeting HIV 

      Tan, Xu; Hu, Long; Luquette, Lovelace J.; Gao, Geng; Liu, Yifang; Qu, Hongjing; Xi, Ruibin; Lu, Zhi John; Park, Peter J.; Elledge, Stephen J. (2012)
      The systematic identification of effective drug combinations has been hindered by the unavailability of methods that can explore the large combinatorial search space of drug interactions. Here we present a multiplex screening ...

    • Vector Algebra in the Analysis of Genome-Wide Expression Data 

      Kuruvilla, Finny G; Park, Peter J.; Schreiber, Stuart L. (BioMed Central, 2002)
      Background: Data from thousands of transcription-profiling experiments in organisms ranging from yeast to humans are now publicly available. How best to analyze these data remains an important challenge. A variety of tools ...