Journal Articles

    MONET: a toolbox integrating top-performing methods for network modularisation
    M. Tomasoni, S. Gomez, J. Crawford, W. Zhang, S. Choobdar, D. Marbach, S. Bergmann.
    Bioinformatics, April 2020.
    (Paper) (Source code)
    Incorporating biological structure into machine learning models in biomedicine
    J. Crawford, C. S. Greene.
    Current Opinion in Biotechnology, Jan 2020.
    (Paper) (Manuscript repo)
    Assessment of network module identification across complex diseases
    S. Choobdar, M. E. Ahsen, J. Crawford, M. Tomasoni, D. Lamparter, J. Lin, B. Hescott, X. Hu, J. Mercer, T. Natoli, R. Narayan, The DREAM Module Identification Challenge Consortium, A. Subramanian, J.D. Zhang, G. Stolovitzky, Z. Kutalik, K. Lage, D. Slonim, J. Saez-Rodriguez, L. J. Cowen, S. Bergmann, D. Marbach.
    Nature Methods, Sep 2019.
    (Paper) (Data and code)
    Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs
    J. Listgarten, M. Weinstein, B. Kleinstiver, A.A. Sousa, J.K. Joung, J. Crawford, K. Gao, M. Elibol, L. Hoang, J. Doench, N. Fusi.
    Nature Biomedical Engineering, Jan 2018.
    (Paper) (Source code)

Preprints

    Gene expression and DNA methylation consistently predict cancer mutation states
    J. Crawford, B. C. Christensen, M. Chikina, C. S. Greene.
    (bioRxiv preprint) (Source code)
    Generative neural networks separate common and specific transcriptional responses
    A. J. Lee, D. L. Mould, J. Crawford, D. Hu, R. K. Powers, G. Doing, J. C. Costello, D. A. Hogan, C. S. Greene.
    (bioRxiv preprint) (Source code)
    Graph biased feature selection of genes is better than random for many genes
    J. Crawford, C. S. Greene.
    (bioRxiv preprint) (Source code)
    NOTE: no peer-reviewed submission currently planned for this work.

Presentations

    "Prediction of cancer mutation states using multiple data modalities reveals the utility and consistency of gene expression and DNA methylation."
    Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB), 2021. (Poster)
    "Open Community Challenge Reveals Molecular Network Modules With Key Roles in Diseases."
    Intelligent Systems for Molecular Biology (ISMB), 2018. (Slides) (Poster)
    "Detangling PPI Networks to Uncover Functionally Meaningful Clusters."
    Workshop on Computational Network Biology: Modeling, Analysis and Control (CNB-MAC), 2017. (Slides)
    "A Double Spectral Approach to Disease Module Identification."
    RECOMB/ISCB Conference on Regulatory and Systems Genomics (RSG), 2016. (Slides)