Over 150 publications can be found on Google Scholar, or on this local archive.

Pre-prints

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Books and Book-Length Articles

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Selected Refereed Publications

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Other Scholarly Works

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Patents

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Open-Source Software

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Other Scholarly Writings

  1. T Hashimoto✝, DJ Gresham, D Botstein, EM Airoldi. A linear model framework for genome-scale functional analysis based on the gene ontology. Princeton University, 2009.

  2. EM Airoldi. Weak convergence of probability measures, with an application to Girone-Cifarelli (in Italian). Institute for Quantitative Methods, Bocconi University, 1998.


Open-source Software     (Google Scholar archive)

  1. SGD, an R package. Implements stochastic approximation methods for parameter estimation.

  2. iGraph 1.0.0, an R package, and Python and C libraries. Implements methods to analyze graphs.

  3. ABQuant, R functions, and Python and C libraries. Implements methods for estimating absolute protein concentrations from Mass Spectrometry data. (Single processor and MPI.)

  4. CPlate, R functions, and Python and C libraries. Implements methods for estimating nucleosomes insertions, deletions, and their primary and alternative positions within a population of cells from paired-end mRNA-sequencing data. (Single processor and MPI.)

  5. MISO, Python and C libraries. Implements methods for estimating expression of alternatively spliced isoforms from paired-end mRNA-sequencing data. (Single processor and MPI.)

  6. TPE, an R package. Implements tree preserving embedding.

  7. networkTomography, an R package. Implements methods for estimating latent time series on a graph, including those published in JASA. Includes 3 data sets of point-to-point time series.

  8. Tetrahedron 3D, a JAVA applet to explore the geometry of 2x2 contingency tables.