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


  • 07/2015

    Neuroscience-based algorithms make for better networks. A new paper we published in PLoS Computational Biology shows that the methods used by the brain to optimize the topology of neural networks (termed pruning) lead to effective and robust computational networks as well. As part of this work, we have experimentally characterized the pruning rates in developing mice and showed that using similar rates to construct computer communication networks improves their ability to efficiently route messages. This paper further expands the set of Algorithms in Nature we have been working on for the last 5 years. The work has been highlighted by a CMU press release , a press release from the Salk Institute, and a few other venues (for example, Tech Times )

  • 07/2015

    Ercument Cicek accepts new faculty position. Ercument, who is a postdoc in our group since 2013 (also a Lane fellow co-advised by Kathryn Roeder) has accepted a faculty position in the Computer Science department at Bilkent University, one of the leading research universities in Turkey. We wish him good luck on this exciting new appointment!

  • 01/2015

    CACM publishes a new paper from our group. Communication of the ACM (CACM), the top and most widely read computer science journal publishes a paper we wrote on biological distributed computing as the cover story for their first issue of 2015. The paper summarizes several recent studies by us and others in this area. With the success of the BDA workshop we recently organized it seems that this idea is catching up and more and more people are looking into biological systems to gain insights into the design of complex distributed networks and systems. See also an interview CACM recorded with co-author Saket Navlakha discussing the area and the paper.

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