Journal Articles

    Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction
    J. Crawford, M. Chikina, C. S. Greene.
    Bioinformatics Advances, January 2024.
    (Paper) (Source code)
    CAJAL enables analysis and integration of single-cell morphological data using metric geometry
    K. W. Govek, P. Nicodemus, Y. Lin, J. Crawford, A. B. Saturnino, H. Cui, K. Zoga, M. P. Hart, P. G. Camara.
    Nature Communications, March 2023.
    (Paper) (Source code)
    The effect of nonlinear signal in classification problems using gene expression
    B. J. Heil, J. Crawford, C. S. Greene.
    PLoS Computational Biology, March 2023.
    (Paper) (Source code)
    SOPHIE: 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.
    Genomics, Proteomics & Bioinformatics, October 2022.
    (Paper) (Source code)
    wenda_gpu: fast domain adaptation for genomic data
    A. A. Hippen, J. Crawford, J. R. Gardner, C. S. Greene.
    Bioinformatics, October 2022.
    (Paper) (Source code)
    Widespread redundancy in -omics profiles of cancer mutation states
    J. Crawford, B. C. Christensen, M. Chikina, C. S. Greene.
    Genome Biology, June 2022.
    (Paper) (Source code)
    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, January 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, September 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, January 2018.
    (Paper) (Source code)

Preprints

    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

    "Widespread redundancy in -omics profiles of cancer mutation states." Intelligent Systems for Molecular Biology (ISMB), 2022. (Slides)(Poster)
    "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)