2,486 research outputs found

    AAS227 - Synthesizing Understanding from Data with yt

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    This is a talk I gave at the AAS227 about yt.  yt is available at yt-project.org.<div><br></div><div>While I am listed as the author of this talk, the yt community is composed of more than a hundred code contributors and mailing list participants, and we are grateful to their involvement and support.</div><div><br></div><div>Additionally, the yt project is built on other members of the scientific software ecosystem such as Jupyter, NumPy, Cython, h5py and hdf5, Matplotlib, and Sympy.</div

    Network-based classification of breast cancer metastasis

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    Mapping the pathways that give rise to metastasis is one of the key challenges of breast cancer research. Recently, several large-scale studies have shed light on this problem through analysis of gene expression profiles to identify markers correlated with metastasis. Here, we apply a protein-network-based approach that identifies markers not as individual genes but as subnetworks extracted from protein interaction databases. The resulting subnetworks provide novel hypotheses for pathways involved in tumor progression. Although genes with known breast cancer mutations are typically not detected through analysis of differential expression, they play a central role in the protein network by interconnecting many differentially expressed genes. We find that the subnetwork markers are more reproducible than individual marker genes selected without network information, and that they achieve higher accuracy in the classification of metastatic versus non-metastatic tumors
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