Jason Ernst
PhD Student
Machine Learning Department
School of Computer Science
Carnegie Mellon University

Advisor: Ziv Bar-Joseph
Research Group: Systems Biology Group

Email: jernst@cs.cmu.edu
Office: Wean Hall 3721
Office Phone: 412-268-1549

Publications

  • J. Ernst, Q.K. Beg, K.A. Kay, G. Balazsi, Z.N. Oltvai, Z. Bar-Joseph.
    A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli.
    PLoS Computational Biology 4(3): e1000044, 2008.
    Supporting Website

  • A. Vazquez, Q.K. Beg, M.A. de Menezes, J. Ernst, Z. Bar-Joseph, A.-L. Barabási, L.G. Boros, Z.N. Oltvai.
    Impact of the solvent capacity constraint on E. coli metabolism.
    BMC Systems Biology, 2:7, 2008.

  • J. Ernst, O. Vainas, C.T. Harbison, I. Simon, and Z. Bar-Joseph.
    Reconstructing dynamic regulatory maps.
    Nature-EMBO Molecular Systems Biology, 3:74, 2007.
    Supporting website

  • Q.K. Beg, A. Vazquez, J. Ernst, M.A. de Menezes, Z. Bar-Joseph, A.-L. Barabási, and Z.N. Oltvai.
    Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
    Proceedings of the National Academy of Sciences, 104: pp.12663-12668, 2007.

  • J. Ernst and Z. Bar-Joseph.
    STEM: a tool for the analysis of short time series gene expression data    .
    BMC Bioinformatics, 7:191, 2006.
    Supporting website

  • I. Simon, Z. Siegfried, J. Ernst, and Z. Bar-Joseph.
    Combined static and dynamic analysis for determining the quality of time-series expression profiles.
    Nature Biotechnology, 23(12) pp. 1503-1508, 2005.
    Supporting website

  • J. Ernst, G.J. Nau, and Z. Bar-Joseph.
    Clustering Short Time Series Gene Expression Data.
    Bioinformatics (Proceedings of ISMB 2005), 21 Suppl. 1, pp. i159-i168, 2005.
    Supporting website

    Software
  • Dynamic Regulatory Events Miner (DREM)

  • Short Time-series Expression Miner (STEM)

    Press
  • STEM and DREM: The Link (page 17)
  • STEM: BioInform 7/18/2005 (subscription required), CMU Tech Transfer Annual Report 2005 (page 14)
  • Nature Biotechnology Paper: Pittsburgh Post-Gazette, Red Herring, BioITWorld, Drug Discovery & Development, CMU Press Release