Now showing items 1-12 of 12

    • Bringing LTL Model Checking to Biologists 

      Ahmed, Z; Benque, D; Berezin, S; Dahl, ACE; Fisher, Jasmin; Hall, Benjamin Andrew; Ishtiaq, S et al.
      The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphical user interface, it allows rapid development of complex models of gene and protein interaction ...
    • BTR: training asynchronous Boolean models using single-cell expression data 

      Lim, Chee Yee; Wang, Huange; Woodhouse, Steven; Piterman, Nir; Wernisch, Lorenz; Fisher, Jasmin; Göttgens, Berthold (BioMed Central, 2016-09-06)
      Background Rapid technological innovation for the generation of single-cell genomics data presents new challenges and opportunities for bioinformatics analysis. One such area lies in the development of new ways to train ...
    • BTR: training asynchronous Boolean models using single-cell expression data 

      Lim, Chee; Wang, Huange; Woodhouse, Steven; Piterman, Nir; Wernisch, Lorenz; Fisher, Jasmin; Göttgens, Berthold (2016-09-06)
      Abstract Background Rapid technological innovation for the generation of single-cell genomics data presents new challenges and opportunities for bioinformatics analysis. One ...
    • Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia. 

      Silverbush, Dana; Grosskurth, Shaun; Wang, Dennis; Powell, Francoise; Gottgens, Berthold; Dry, Jonathan; Fisher, Jasmin (American Association for Cancer Research, 2017-02)
      Personalized therapy is a major goal of modern oncology, as patient responses vary greatly even within a histologically defined cancer subtype. This is especially true in acute myeloid leukemia (AML), which exhibits striking ...
    • Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics 

      Wang, Dennis YQ; Cardelli, Luca; Phillips, Andrew; Piterman, Nir; Fisher, Jasmin (2009-12-22)
      Abstract Background The epidermal growth factor receptor (EGFR) signaling pathway plays a key role in regulation of cellular growth and development. While highly studied, it is still not fully understood how the signal is ...
    • Decoding the Regulatory Network for Blood Development from Single-Cell Gene Expression Measurements 

      Moignard, Victoria Rachel; Woodhouse, Steven; Haghverdi, Laleh; Lilly, Andrew J; Tanaka, Yosuke; Wilkinson, Adam; Buettner, Florian et al. (Nature Publishing Group, 2015-02-09)
      Reconstruction of the molecular pathways controlling organ development has been hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a strategy to address this problem that combines gene ...
    • Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform 

      Chuang, Ryan; Hall, Benjamin Andrew; Benque, David; Cook, Byron; Ishtiaq, Samin; Piterman, Nir; Taylor, Alex et al. (NPG, 2015-02-03)
      Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing ...
    • Linear Temporal Logic for Biologists in BMA 

      Hall, Benjamin Andrew; Piterman, Nir; Fisher, Jasmin (Springer, 2016-09)
    • Processing, visualising and reconstructing network models from single cell data 

      Woodhouse, Steven; Moignard, Victoria Rachel; Göttgens, Berthold; Fisher, Jasmin (Nature Publishing Group, 2015-11-18)
      New single-cell technologies readily permit gene expression profiling of thousands of cells at single-cell resolution. In this review we will discuss methods for visualisation and interpretation of single-cell gene expression ...
    • Program Synthesis Meets Deep Learning for Decoding Regulatory Networks 

      Fisher, Jasmin; Woodhouse, S
      With ever growing data sets spanning DNA sequencing all the way to single-cell transcriptomics, we are now facing the question of how can we turn this vast amount of information into knowledge. How do we integrate these ...
    • SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data 

      Woodhouse, Steven; Piterman, Nir; Wintersteiger, Christoph M; Göttgens, Berthold; Fisher, Jasmin (2018-05-25)
      Abstract Background Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and ...
    • Single cell analyses of regulatory network perturbations using enhancer targeting TAL Effectors suggest novel roles for PU.1 during haematopoietic specification 

      Wilkinson, Adam; Kawata, Viviane KS; Schütte, Judith; Gao, Xuefei; Antoniou, Stella; Baumann, Claudia; Woodhouse, Steven et al. (The Company of Biologists, 2014-09-24)
      Transcription factors (TFs) act within wider regulatory networks to control cell identity and fate. Numerous TFs including Scl/Tal1 and PU.1 are known regulators of developmental and adult haematopoiesis, but how they act ...