Regulatory Networks

Application of the Dynamic Regulatory Events Miner (DREM) to study amino acid starvation response in yeast.


Our group develops computational methods for understanding the dynamics, interactions and conservation of complex biological systems. As new high-throughput biological data sources become available, they hold the promise of revolutionizing molecular biology by providing a large-scale view of cellular activity. However, each type of data is noisy, contains many missing values and only measures a single aspect of cellular activity. Our computational focus is on methods for large scale data integration. We primarily rely on machine learning and statistical methods. Most of our work is carried out in close collaboration with experimentalists. Many of the computational tools we develop are available and widely used.

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Latest Publications

Full list of publications


  • 09/2018

    We are leading the HuBMAP Computational Tools Center The Human BioMolecular Atlas Program (HuBMAP) is a large, national effort to develop a 3D map of the human body. As part of this program the NIH has funded 15 centers to collected new data, develop new technologies and develop computational methods for the analysis of the data. We are heading one of these centers, which is a part of the HuBMAP Integration, Visualization & Engagement (HIVE) effort. Our center will focus on the development of computational methods for the processing, analysis, modeling and retrieval of the HuBMAP data and on the interactions between users and the MAP. In addition to 4 investigators from CMU our center also includes co-PIs for UCSC and the UK and investigators from Google Brain. See CMU Press Release , Post-Gazette story , and KDKA radio story

  • 02/2018

    Matt awarded NIH Postdoctoral Fellowship Matt Ruffalo received a NIH postdoctoral fellowship grant from the NCI. Matt has been a postdoc in our group since 2016. Matt works on the analysis of cancer genomics data and his proposal focused on methods for integrating genomics data from several different sources to predict survival and drug response. Congratulations Matt!

  • 12/2017

    Bar-Joseph receives FORE Systems Professorship. In a ceremony attended by some of the FORE Systems founders, Ziv Bar-Joseph has been awarded the FORE Systems chair in computational biology and machine learning. While the chair is a great personal honor, it is in large part due to the amazing work over the years by all the students and postdocs in our group!

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