Now showing items 1-11 of 11

    • Analysis of somatic retrotransposition in human cancers 

      Lee, Eunjung; Iskow, Rebecca; Yang, Lixing; Gokcumen, Omer; Haseley, Psalm; Luquette, Lovelace J.; Lohr, Jens Guenter; Harris, Christopher C; Ding, Li; Wilson, Richard K.; Wheeler, David A.; Gibbs, Richard A; Kucherlapati, Raju; Lee, Charles; Kharchenko, Peter Vasili; Park, Peter J. (BioMed Central, 2012)
    • Bayesian approach to single-cell differential expression analysis 

      Kharchenko, Peter Vasili; Silberstein, Lev; Scadden, David Thomas (Springer Nature, 2014)
      Single-cell data provide a means to dissect the composition of complex tissues and specialized cellular environments. However, the analysis of such measurements is complicated by high levels of technical noise and intrinsic ...
    • Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis 

      Fan, Jean; Salathia, Neeraj; Liu, Rui; Kaeser, Gwendolyn E.; Yung, Yun C.; Herman, Joseph L.; Kaper, Fiona; Fan, Jian-Bing; Zhang, Kun; Chun, Jerold; Kharchenko, Peter V. (2016)
      The transcriptional state of a cell reflects a variety of biological factors, from persistent cell-type specific features to transient processes such as cell cycle. Depending on biological context, all such aspects of ...
    • Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain 

      Riddle, Nicole C.; Jung, Youngsook; Gu, Tingting; Alekseyenko, Artyom A.; Asker, Dalal; Gui, Hongxing; Kharchenko, Peter Vasili; Minoda, Aki; Plachetka, Annette; Schwartz, Yuri B.; Tolstorukov, Michael Y.; Kuroda, Mitzi I.; Pirrotta, Vincenzo; Karpen, Gary H.; Park, Peter J.; Elgin, Sarah C. R. (Public Library of Science, 2012)
      Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, ...
    • Estimating Enrichment of Repetitive Elements from High-throughput Sequence Data 

      Day, Daniel Sindt; Luquette, Lovelace j; Park, Peter J.; Kharchenko, Peter Vasili (BioMed Central, 2010)
      We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our ...
    • Expression Dynamics of a Cellular Metabolic Network 

      Kharchenko, Peter Vasili; Church, George McDonald; Vitkup, Dennis (Nature Publishing Group, 2005)
      Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our results demonstrate ...
    • Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner 

      Woo, Caroline J; Kharchenko, Peter Vasili; Daheron, Laurence Marie; Park, Peter J.; Kingston, Robert Edward (BioMed Central, 2013)
    • Identifying Metabolic Enzymes with Multiple Types of Association Evidence 

      Kharchenko, Peter Vasili; Chen, Lifeng; Freund, Yoav; Vitkup, Dennis; Church, George McDonald (BioMed Central, 2006)
      Background: Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such ...
    • Influence of Metabolic Network Structure and Function on Enzyme Evolution 

      Vitkup, Dennis; Kharchenko, Peter Vasili; Wagner, Andreas (BioMed Central, 2006)
      Background: Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. ...
    • Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia 

      Landau, Dan Avi; Clement, Kendell; Ziller, Michael Johannes; Boyle, Patrick; Fan, Jean; Gu, Hongcang; Stevenson, Kristen; Sougnez, Carrie; Wang, Lili; Li, Shuqiang; Kotliar, Dylan; Zhang, Wandi; Ghandi, Mahmoud; Garraway, Levi Alexander; Fernandes, Stacey M.; Livak, Kenneth J.; Gabriel, Stacey; Gnirke, Andreas; Lander, Eric Steven; Brown, Jennifer Ruth; Neuberg, Donna S.; Kharchenko, Peter Vasili; Hacohen, Nir; Getz, Gad A; Meissner, Alexander; Wu, Catherine J. (Elsevier BV, 2014)
      Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic ...
    • 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 ...