Browsing by Author "Yuan, Guo-Cheng"

Now showing items 1-20 of 21

    • BCL11A Enhancer Dissection by Cas9-Mediated in Situ Saturating Mutagenesis 

      Canver, Matthew Charles; Smith, Elenoe; Pinello, Luca; Sanjana, Neville E.; Shalem, Ophir; Chen, Diane; Schupp, Patrick G.; Vinjamur, Divya S.; Garcia, Sara P.; Luc, Sidinh; Kurita, Ryo; Fujiwara, Yuko; Maeda, Takahiro; Yuan, Guo-Cheng; Zhang, Feng; Orkin, Stuart Holland; Bauer, Daniel Evan; Nakamura, Yukio (Nature, 2015-09-16)

    • Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis 

      Saadatpour, Assieh; Guo, Guoji; Orkin, Stuart H; Yuan, Guo-Cheng (BioMed Central, 2014)
      Background: A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. Recent advances in ...

    • Chromatin signature of widespread monoallelic expression 

      Nag, Anwesha; Savova, Virginia; Fung, Ho-Lim; Miron, Alexander; Yuan, Guo-Cheng; Zhang, Kun; Gimelbrant, Alexander A (eLife Sciences Publications, Ltd, 2013)
      In mammals, numerous autosomal genes are subject to mitotically stable monoallelic expression (MAE), including genes that play critical roles in a variety of human diseases. Due to challenges posed by the clonal nature of ...

    • The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing 

      Stelloh, Cary; Reimer, Michael H.; Pulakanti, Kirthi; Blinka, Steven; Peterson, Jonathan; Pinello, Luca; Jia, Shuang; Roumiantsev, Sergei; Hessner, Martin J.; Milanovich, Samuel; Yuan, Guo-Cheng; Rao, Sridhar (BioMed Central, 2016)
      Background: The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in off-loading cohesin to ...

    • Combination inhibition of PI3K and mTORC1 yields durable remissions in orthotopic patient-derived xenografts of HER2-positive breast cancer brain metastases 

      Ni, Jing; Ramkissoon, Shakti H.; Xie, Shaozhen; Goel, Shom; Stover, Daniel G.; Guo, Hanbing; Luu, Victor; Marco, Eugenio; Ramkissoon, Lori A.; Kang, Yun Jee; Hayashi, Marika; Nguyen, Quang-De; Ligon, Azra H.; Du, Rose; Claus, Elizabeth B.; Alexander, Brian M.; Yuan, Guo-Cheng; Wang, Zhigang C.; Iglehart, J. Dirk; Krop, Ian E.; Roberts, Thomas M.; Winer, Eric P.; Lin, Nancy U.; Ligon, Keith L.; Zhao, Jean J. (2016)
      Brain metastases represent the greatest clinical challenge in treating HER2-positive breast cancer. We report the development of orthotopic patient-derived xenografts (PDXs) of HER2-expressing breast cancer brain metastases ...

    • Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia 

      Wu, Jennifer N.; Pinello, Luca; Yissachar, Elinor; Wischhusen, Jonathan W.; Yuan, Guo-Cheng; Roberts, Charles W. M. (BioMed Central, 2015)
      Background: Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription ...

    • Genomic Sequence is Highly Predictive of Local Nucleosome Depletion 

      Yuan, Guo-Cheng; Liu, Jun (Public Library of Science, 2008)
      The regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these ...

    • GiniClust: detecting rare cell types from single-cell gene expression data with Gini index 

      Jiang, Lan; Chen, Huidong; Pinello, Luca; Yuan, Guo-Cheng (BioMed Central, 2016)
      High-throughput single-cell technologies have great potential to discover new cell types; however, it remains challenging to detect rare cell types that are distinct from a large population. We present a novel computational ...

    • Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring 

      Lao, Taotao; Glass, Kimberly; Qiu, Weiliang; Polverino, Francesca; Gupta, Kushagra; Morrow, Jarrett; Mancini, John Dominic; Vuong, Linh; Perrella, Mark A; Hersh, Craig P; Owen, Caroline A; Quackenbush, John; Yuan, Guo-Cheng; Silverman, Edwin K; Zhou, Xiaobo (BioMed Central, 2015)
      Background: The HHIP gene, encoding Hedgehog interacting protein, has been implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS), and our subsequent studies identified a ...

    • High fat diet enhances stemness and tumorigenicity of intestinal progenitors 

      Beyaz, Semir; Mana, Miyeko D.; Roper, Jatin; Kedrin, Dmitriy; Saadatpour, Assieh; Hong, Sue-Jean; Bauer-Rowe, Khristian E.; Xifaras, Michael E.; Akkad, Adam; Arias, Erika; Pinello, Luca; Katz, Yarden; Shinagare, Shweta; Abu-Remaileh, Monther; Mihaylova, Maria M.; Lamming, Dudley W.; Dogum, Rizkullah; Guo, Guoji; Bell, George W.; Selig, Martin; Nielsen, G. Petur; Gupta, Nitin; Ferrone, Cristina R.; Deshpande, Vikram; Yuan, Guo-Cheng; Orkin, Stuart H.; Sabatini, David M.; Yilmaz, Ömer H. (2016)
      Little is known about how pro-obesity diets regulate tissue stem and progenitor cell function. Here we find that high fat diet (HFD)-induced obesity augments the numbers and function of Lgr5+ intestinal stem-cells (ISCs) ...

    • The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells 

      Beyaz, Semir; Kim, Ji Hyung; Pinello, Luca; Xifaras, Michael E; Hu, Yu; Huang, Jialiang; Kerenyi, Marc A; Das, Partha Pratim; Barnitz, R Anthony; Herault, Aurelie; Dogum, Rizkullah; Haining, William Nicholas; Yilmaz, Omer Hidir; Passegue, Emmanuelle; Yuan, Guo-Cheng; Orkin, Stuart Holland; Winau, Florian (Springer Nature, 2016)

    • Integrated Spatial Genomics Reveals Global Architecture of Single Nuclei 

      Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, ShengBao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long (Springer Science and Business Media LLC, 2021-01-27)
      Identifying the relationships between chromosome structures, nuclear bodies, chromatin states, and gene expression is an overarching goal of nuclear organization studies1–4. Because individual cells appear to be highly ...

    • Mitochondrial iron chelation ameliorates cigarette-smoke induced bronchitis and emphysema in mice 

      Cloonan, Suzanne M.; Glass, Kimberly; Laucho-Contreras, Maria E.; Bhashyam, Abhiram R.; Cervo, Morgan; Pabón, Maria A.; Konrad, Csaba; Polverino, Francesca; Siempos, Ilias I.; Perez, Elizabeth; Mizumura, Kenji; Ghosh, Manik C.; Parameswaran, Harikrishnan; Williams, Niamh C.; Rooney, Kristen T.; Chen, Zhi-Hua; Goldklang, Monica P.; Yuan, Guo-Cheng; Moore, Stephen C.; Demeo, Dawn L.; Rouault, Tracey A.; D’Armiento, Jeanine M.; Schon, Eric A.; Manfredi, Giovanni; Quackenbush, John; Mahmood, Ashfaq; Silverman, Edwin K.; Owen, Caroline A.; Choi, Augustine M.K. (2015)
      Chronic obstructive pulmonary disease (COPD) is linked to both cigarette smoking and genetic determinants. We have previously identified iron-responsive element binding protein 2 (IRP2) as an important COPD susceptibility ...

    • A Motif-Independent Metric for DNA Sequence Specificity 

      Pinello, Luca; Lo Bosco, Giosuè; Hanlon, Bret; Yuan, Guo-Cheng (BioMed Central, 2011)
      Background: Genome-wide mapping of protein-DNA interactions has been widely used to investigate biological functions of the genome. An important question is to what extent such interactions are regulated at the DNA sequence ...

    • A network model for angiogenesis in ovarian cancer 

      Glass, Kimberly; Quackenbush, John; Spentzos, Dimitrios; Haibe-Kains, Benjamin; Yuan, Guo-Cheng (BioMed Central, 2015)
      Background: We recently identified two robust ovarian cancer subtypes, defined by the expression of genes involved in angiogenesis, with significant differences in clinical outcome. To identify potential regulatory mechanisms ...

    • Passing Messages between Biological Networks to Refine Predicted Interactions 

      Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng (Public Library of Science, 2013)
      Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks ...

    • Predicting chromatin organization using histone marks 

      Huang, Jialiang; Marco, Eugenio; Pinello, Luca; Yuan, Guo-Cheng (BioMed Central, 2015)
      Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have ...

    • Robust lineage reconstruction from high-dimensional single-cell data 

      Giecold, Gregory; Marco, Eugenio; Garcia, Sara P.; Trippa, Lorenzo; Yuan, Guo-Cheng (Oxford University Press, 2016)
      Single-cell gene expression data provide invaluable resources for systematic characterization of cellular hierarchy in multi-cellular organisms. However, cell lineage reconstruction is still often associated with significant ...

    • Sexually-dimorphic targeting of functionally-related genes in COPD 

      Glass, Kimberly; Quackenbush, John; Silverman, Edwin K; Celli, Bartolome; Rennard, Stephen I; Yuan, Guo-Cheng; DeMeo, Dawn L (BioMed Central, 2014)
      Background: There is growing evidence that many diseases develop, progress, and respond to therapy differently in men and women. This variability may manifest as a result of sex-specific structures in gene regulatory ...

    • Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5 + Intestinal Stem Cells 

      Kim, Tae-Hee; Saadatpour, Assieh; Guo, Guoji; Saxena, Madhurima; Cavazza, Alessia; Desai, Niyati; Jadhav, Unmesh Jaysing; Jiang, Lan; Rivera, Miguel Nicolas; Orkin, Stuart Holland; Yuan, Guo-Cheng; Shivdasani, Ramesh Arjun (Elsevier BV, 2016-08)
      Lgr5+ intestinal stem cells (ISC) drive epithelial self-renewal, and their immediate progeny – intestinal bipotential progenitors – produce absorptive and secretory lineages via lateral inhibition. To define features of ...