• Music Cognition, Perception, and Pattern Recognition

    Efforts to have computers mimic human behavior can only succeed if the computer is using the same types of criteria as a human. We have explored the ability of a computer to recognize patterns in music in a similar way to a human being. The result of this work is a system for the machine recognition of musical patterns [1-7]. We frame the problem of recognition of musical patterns as…

  • The study of microRNAs in cancer

    MicroRNAs (miRNAs) are small non-coding RNAs that can regulate gene expression and that are frequently altered in human cancers. Computational approaches can help us understand how miRNAs are dysregulated and potentially offer new therapies.

  • Cultivated Meat Modeling Consortium (CMMC)

    The mission of the Cultivated Meat Modeling Consortium (CMMC) is to accelerate the delivery of affordable high-quality cultivated meat products through the use of computer modeling.

  • Cancer Target Discovery and Development

    The goal of the CTD2 Network is to understand how tumor heterogeneity leads to drug resistance in order to develop optimal combinations of chemotherapy or small molecules in combination with immunotherapy.

  • Probabilistic Boolean Networks

    Probabilistic Boolean Networks are a class of models of genetic regulatory networks.

  • Pan-Cancer Atlas

    From the analysis of over 11,000 tumors from 33 of the most prevalent forms of cancer, the Pan-Cancer Atlas provides a uniquely comprehensive, in-depth, and interconnected understanding of how, where, and why tumors arise in humans.

  • Genomic and molecular characterization of preterm birth

    A family-based study of preterm birth with whole-genome sequencing, RNA sequencing, DNA methylation, and clinical data.

  • Stack Filters

    Stack filters are a class of nonlinear digital filters used in many signal and image processing applications.

  • Multiscale Methods

    Many phenomena and signals have structure on multiple scales. We have developed methods to analyze such multiscale structures.

  • Monotone Boolean Functions

    Our mathematical work on monotone Boolean functions, which is one of the most widely studied classes of Boolean functions.

  • CRI iAtlas

    The Cancer Research Institute (CRI) iAtlas is an interactive web-based platform and set of analytic tools for studying interactions between tumors and the immune microenvironment.

  • Biocellion

    A high-performance computing framework for simulation of agent-based multicellular models

  • Human Tumor Atlas Network

    Data Coordinating Center for the Human Tumor Atlas Network

  • Network Visualization

    Both of the network visualization tools below have been developed by our lab member Bill Longabaugh. Publications: Longabaugh, W.J.R. Combing the hairball with BioFabric: a new approach for visualization of large networks. BMC Bioinformatics, 13:275, 2012. Publications: Paquette, S.M., Leinonen, K., Longabaugh, W.J.R. BioTapestry now provides a web application and improved drawing and layout tools  F1000Research 5:39, 2016. Longabaugh, W.J.R. BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory…

  • The ISB Cancer Genomics Cloud

    The ISB Cancer Genomics Cloud (ISB-CGC) is democratizing access to NCI Cancer Data and coupling it with unprecedented computational power to allow researchers to explore and analyze this vast data-space.