Now showing items 1-13 of 13

    • Augmenting and Directing Robust, Long-Range CRISPR-Mediated Activation in Human Cells 

      Tak, Y. Esther; Horng, Joy E.; Perry, Nicholas T.; Schultz, Hayley; Iyer, Sowmya; Yao, Qiuming; Zou, Luli S.; Aryee, Martin; Pinello, Luca; Joung, Keith (Springer Science and Business Media LLC, 2021-08-05)
      Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the ...
    • 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)
    • BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair 

      Hatchi, Elodie; Skourti-Stathaki, Konstantina; Ventz, Steffen; Pinello, Luca; Yen, Angela; Kamieniarz-Gdula, Kinga; Dimitrov, Stoil; Pathania, Shailja; McKinney, Kristine M.; Eaton, Matthew L.; Kellis, Manolis; Hill, Sarah J.; Parmigiani, Giovanni; Proudfoot, Nicholas J.; Livingston, David M. (Cell Press, 2015)
      Summary The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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)
    • A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis 

      Giancarlo, Raffaele; Lo Bosco, Giosué; Pinello, Luca; Utro, Filippo (BioMed Central, 2013)
      Background: Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from statistics to computer science. Following Handl et al., it can be ...
    • 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 ...
    • 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 ...
    • STAT5 Outcompetes STAT3 To Regulate the Expression of the Oncogenic Transcriptional Modulator BCL6 

      Walker, Sarah Rebecca; Nelson, E; Yeh, Jennifer E; Pinello, Luca; Yuan, Guocheng; Frank, David Alan (American Society for Microbiology, 2013)
      Inappropriate activation of the transcription factors STAT3 and STAT5 has been shown to drive cancer pathogenesis through dysregulation of genes involved in cell survival, growth, and differentiation. Although STAT3 and ...
    • Therapeutic Base Editing of Human Hematopoietic Stem Cells 

      Zeng, Jing; Wu, Yuxuan; Ren, Chunyan; Bonanno, Jasmine; Shen, Anne H.; Shea, Devlin; Gehrke, Jason M.; Clement, Kendell; Luk, Kevin; Yao, Qiuming; Kim, Rachel; Wolfe, Scot A.; Manis, John; Pinello, Luca; Joung, Keith; Bauer, Daniel (Springer Science and Business Media LLC, 2020-03-16)
      Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to permanently remedy blood disorders, although its application in engrafting hematopoietic stem cells (HSCs) ...