Now showing items 1-20 of 34

    • 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)
    • Ascorbic Acid Prevents Loss of Dlk1-Dio3 Imprinting and Facilitates Generation of All-iPS Cell Mice from Terminally Differentiated B Cells 

      Stadtfeld, Matthias; Apostolou, Effie; Chen, Taiping; Oi, Steen; Bestor, Tim; Ferrari, Francesco; Choi, Jiho; Walsh, Ryan Michael; Kim, Sang Yong; Shioda, Toshi; Park, Peter J.; Hochedlinger, Konrad (Nature Publishing Group, 2012)
      The generation of induced pluripotent stem cells (iPSCs) often results in aberrant epigenetic silencing of the imprinted Dlk1-Dio3 gene cluster, compromising the ability to generate entirely iPSC-derived adult mice ('all-iPSC ...
    • ChIP-chip versus ChIP-seq: Lessons for Experimental Design and Data Analysis 

      Ho, Joshua Wing Kei; Bishop, Eric; Karchenko, Peter V; Nègre, Nicolas; White, Kevin P; Park, Peter J. (BioMed Central, 2011)
      Background: Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription ...
    • Combining Gene Expression Data from Different Generations of Oligonucleotide Arrays 

      Hwang, Kyu-Baek; Kong, Sek Won; Greenberg, Steven A.; Park, Peter J. (BioMed Central, 2004)
      Background: One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a ...
    • Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types 

      Day, Daniel S.; Zhang, Bing; Stevens, Sean M.; Ferrari, Francesco; Larschan, Erica N.; Park, Peter J.; Pu, William T. (BioMed Central, 2016)
      Background: For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the ...
    • Comprehensive molecular characterization of gastric adenocarcinoma 

      Bass, Adam J.; Thorsson, Vesteinn; Shmulevich, Ilya; Reynolds, Sheila M.; Miller, Michael; Bernard, Brady; Hinoue, Toshinori; Laird, Peter W.; Curtis, Christina; Shen, Hui; Weisenberger, Daniel J.; Schultz, Nikolaus; Shen, Ronglai; Weinhold, Nils; Kelsen, David P.; Bowlby, Reanne; Chu, Andy; Kasaian, Katayoon; Mungall, Andrew J.; Robertson, A. Gordon; Sipahimalani, Payal; Cherniack, Andrew; Getz, Gad; Liu, Yingchun; Noble, Michael S.; Pedamallu, Chandra; Sougnez, Carrie; Taylor-Weiner, Amaro; Akbani, Rehan; Lee, Ju-Seog; Liu, Wenbin; Mills, Gordon B.; Yang, Da; Zhang, Wei; Pantazi, Angeliki; Parfenov, Michael; Gulley, Margaret; Piazuelo, M. Blanca; Schneider, Barbara G.; Kim, Jihun; Boussioutas, Alex; Sheth, Margi; Demchok, John A.; Rabkin, Charles S.; Willis, Joseph E.; Ng, Sam; Garman, Katherine; Beer, David G.; Pennathur, Arjun; Raphael, Benjamin J.; Wu, Hsin-Ta; Odze, Robert; Kim, Hark K.; Bowen, Jay; Leraas, Kristen M.; Lichtenberg, Tara M.; Weaver, Stephanie; McLellan, Michael; Wiznerowicz, Maciej; Sakai, Ryo; Lawrence, Michael S.; Cibulskis, Kristian; Lichtenstein, Lee; Fisher, Sheila; Gabriel, Stacey B.; Lander, Eric S.; Ding, Li; Niu, Beifang; Ally, Adrian; Balasundaram, Miruna; Birol, Inanc; Brooks, Denise; Butterfield, Yaron S. N.; Carlsen, Rebecca; Chu, Justin; Chuah, Eric; Chun, Hye-Jung E.; Clarke, Amanda; Dhalla, Noreen; Guin, Ranabir; Holt, Robert A.; Jones, Steven J.M.; Lee, Darlene; Li, Haiyan A.; Lim, Emilia; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Karen L.; Nip, Ka Ming; Schein, Jacqueline E.; Tam, Angela; Thiessen, Nina; Beroukhim, Rameen; Carter, Scott L.; Cherniack, Andrew D.; Cho, Juok; DiCara, Daniel; Frazer, Scott; Gehlenborg, Nils; Heiman, David I.; Jung, Joonil; Kim, Jaegil; Lin, Pei; Meyerson, Matthew; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Saksena, Gordon; Schumacher, Steven E.; Stojanov, Petar; Tabak, Barbara; Voet, Doug; Rosenberg, Mara; Zack, Travis I.; Zhang, Hailei; Zou, Lihua; Protopopov, Alexei; Santoso, Netty; Lee, Semin; Zhang, Jianhua; Mahadeshwar, Harshad S.; Tang, Jiabin; Ren, Xiaojia; Seth, Sahil; Yang, Lixing; Xu, Andrew W.; Song, Xingzhi; Xi, Ruibin; Bristow, Christopher A.; Hadjipanayis, Angela; Seidman, Jonathan; Chin, Lynda; Park, Peter J.; Kucherlapati, Raju; Ling, Shiyun; Rao, Arvind; Weinstein, John N.; Kim, Sang-Bae; Lu, Yiling; Mills, Gordon; Bootwalla, Moiz S.; Lai, Phillip H.; Triche, Timothy; Van Den Berg, David J.; Baylin, Stephen B.; Herman, James G.; Murray, Bradley A.; Askoy, B. Arman; Ciriello, Giovanni; Dresdner, Gideon; Gao, Jianjiong; Gross, Benjamin; Jacobsen, Anders; Lee, William; Ramirez, Ricardo; Sander, Chris; Senbabaoglu, Yasin; Sinha, Rileen; Sumer, S. Onur; Sun, Yichao; Thorsson, Vésteinn; Iype, Lisa; Kramer, Roger W.; Kreisberg, Richard; Rovira, Hector; Tasman, Natalie; Ng, Santa Cruz Sam; Haussler, David; Stuart, Josh M.; Verhaak, Roeland G.W.; Leiserson, Mark D. M.; Taylor, Barry S.; Black, Aaron D.; Carney, Julie Ann; Gastier-Foster, Julie M.; Helsel, Carmen; McAllister, Cynthia; Ramirez, Nilsa C.; Tabler, Teresa R.; Wise, Lisa; Zmuda, Erik; Penny, Robert; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Curely, Erin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Shelton, Troy; Shelton, Candace; Sherman, Mark; Benz, Christopher; Lee, Jae-Hyuk; Fedosenko, Konstantin; Manikhas, Georgy; Potapova, Olga; Voronina, Olga; Belyaev, Smitry; Dolzhansky, Oleg; Rathmell, W. Kimryn; Brzezinski, Jakub; Ibbs, Matthew; Korski, Konstanty; Kycler, Witold; ŁaŸniak, Radoslaw; Leporowska, Ewa; Mackiewicz, Andrzej; Murawa, Dawid; Murawa, Pawel; Spychała, Arkadiusz; Suchorska, Wiktoria M.; Tatka, Honorata; Teresiak, Marek; Abdel-Misih, Raafat; Bennett, Joseph; Brown, Jennifer; Iacocca, Mary; Rabeno, Brenda; Kwon, Sun-Young; Kemkes, Ariane; Curley, Erin; Alexopoulou, Iakovina; Engel, Jay; Bartlett, John; Albert, Monique; Park, Do-Youn; Dhir, Rajiv; Luketich, James; Landreneau, Rodney; Janjigian, Yelena Y.; Cho, Eunjung; Ladanyi, Marc; Tang, Laura; McCall, Shannon J.; Park, Young S.; Cheong, Jae-Ho; Ajani, Jaffer; Camargo, M. Constanza; Alonso, Shelley; Ayala, Brenda; Jensen, Mark A.; Pihl, Todd; Raman, Rohini; Walton, Jessica; Wan, Yunhu; Eley, Greg; Mills Shaw, Kenna R.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean Claude; Davidsen, Tanja; Hutter, Carolyn M.; Sofia, Heidi J.; Burton, Robert; Chudamani, Sudha; Liu, Jia (2014)
      Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular ...
    • EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering 

      Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J. (BioMed Central, 2015)
      Background: RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity ...
    • 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 ...
    • hiHMM: Bayesian non-parametric joint inference of chromatin state maps 

      Sohn, Kyung-Ah; Ho, Joshua W. K.; Djordjevic, Djordje; Jeong, Hyun-hwan; Park, Peter J.; Kim, Ju Han (Oxford University Press, 2015)
      Motivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed ...
    • The histone chaperone CAF-1 safeguards somatic cell identity 

      Cheloufi, Sihem; Elling, Ulrich; Hopfgartner, Barbara; Jung, Youngsook L; Murn, Jernej; Ninova, Maria; Hubmann, Maria; Badeaux, Aimee I; Ang, Cheen Euong; Tenen, Danielle; Wesche, Daniel J; Abazova, Nadezhda; Hogue, Max; Tasdemir, Nilgun; Brumbaugh, Justin; Rathert, Philipp; Jude, Julian; Ferrari, Francesco; Blanco, Andres; Fellner, Michaela; Wenzel, Daniel; Zinner, Marietta; Vidal, Simon E; Bell, Oliver; Stadtfeld, Matthias; Chang, Howard Y.; Almouzni, Genevieve; Lowe, Scott W; Rinn, John; Wernig, Marius; Aravin, Alexei; Shi, Yang; Park, Peter; Penninger, Josef M; Zuber, Johannes; Hochedlinger, Konrad (2016)
      Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory ...
    • Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Drosophila Dosage Compensation 

      Larschan, Erica; Soruco, Marcela M. L.; Lee, Ok-Kyung; Peng, Shouyong; Bishop, Eric; Chery, Jessica; Goebel, Karen; Feng, Jessica; Park, Peter J.; Kuroda, Mitzi I. (Public Library of Science, 2012)
      Sex chromosome dosage compensation in Drosophila provides a model for understanding how chromatin organization can modulate coordinate gene regulation. Male Drosophila increase the transcript levels of genes on the single ...
    • Identification of rare germline copy number variations over-represented in five human cancer types 

      Park, Richard W; Kim, Tae-Min; Kasif, Simon; Park, Peter J (BioMed Central, 2015)
      Background: Copy number variations (CNVs) are increasingly recognized as significant disease susceptibility markers in many complex disorders including cancer. The availability of a large number of chromosomal copy number ...
    • 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)
    • The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts 

      Saini, Natalie; Roberts, Steven A.; Klimczak, Leszek J.; Chan, Kin; Grimm, Sara A.; Dai, Shuangshuang; Fargo, David C.; Boyer, Jayne C.; Kaufmann, William K.; Taylor, Jack A.; Lee, Eunjung; Cortes-Ciriano, Isidro; Park, Peter J.; Schurman, Shepherd H.; Malc, Ewa P.; Mieczkowski, Piotr A.; Gordenin, Dmitry A. (Public Library of Science, 2016)
      Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding ...
    • Impact of sequencing depth in ChIP-seq experiments 

      Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W.K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (Oxford University Press, 2014)
      In a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiment, an important consideration in experimental design is the minimum number of sequenced reads required to obtain statistically ...
    • Improving Identification of Differentially Expressed Genes in Microarray Studies Using Information From Public Databases 

      Kim, Richard D; Park, Peter J. (BioMed Central, 2004)
      Summary: The process of identifying differentially expressed genes in miroarray studies with small sample sizes can be improved substantially by extracting information from a large number of datasets accumulated in public ...
    • Integration of Heterogeneous Expression Data Sets Extends the Role of the Retinol Pathway in Diabetes and Insulin Resistance 

      Park, Peter J.; Kong, Sek Won Won; Tebaldi, Toma; Lai, Weil R.; Kasif, Simon; Kohane, Isaac Samuel (Oxford University Press, 2009)
      Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project ...
    • Large-Scale Quality Analysis of Published ChIP-seq Data 

      Marinov, Georgi K.; Kundaje, Anshul; Park, Peter J.; Wold, Barbara J. (Genetics Society of America, 2014)
      ChIP-seq has become the primary method for identifying in vivo protein–DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and ...
    • 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 ...