There are three data sets provided here in Matlab format (*.mat).
Please cite the relevant paper (listed in full below) if using this
data.

1) eColi_singleClass_11perClass.mat*
   -this is the pre-processed data set from Chapter 4 of my thesis, and
    also a subset of the pre-processed data in our paper 
    "Multiple Alignment of Continuous Time Series".
   -it is a single class, LC-MS data set, with 2400 features (m/z bins)
    and 400 time points per time series, with 11 experimental replicates
   [data generated by the laboratory of Andrew Emili]

2) uvDiode_3Class_7perClass.mat
   -this is the data (which has been sub-sampled and log transformed 
    from the original)
    appearing in our paper "Bayesian Detection of Infrequent 
    Differences in Sets of Time Series with Shared Structure"
   -it is a 3 class, LC-UV data set of the plant Arabidopsis thaliana,
    where the first class is the 'no treatment'
    (indexes 1:7), and the 2nd and 3rd class are treatments (indexes
    8:14, 15:21)
   -each time series is 134 time points long, with 1 feature (280nm 
    wavelength) [data generated by the laboratory of Sean Cutler]

3) spikeInSerum_2Class_7perClass.mat
   -this is the pre-processed data set from Chapter 6 of my thesis, and
    also the data used in our paper "Difference detection in 
    LC-MS data for protein biomarker discovery".
   -it is a two class, LC-MS data set, with 2400 features (m/z bins)
    and 501 time points.
   -there are 7 replicates in each class, where the first class
    is the base mixture (indexes 1:7), and the second class
    is the base+spike-in (indexes(8:14)
   -NOTE: to obtain the ground truth LC-MS, please refer to
    http://www.cs.toronto.edu/~jenn/LCMS/index.html#data
   [data generated by the laboratory of Andrew Emili]
   

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References
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1. Jennifer Listgarten (2006) Analysis of Sibling Time Series Data: Alignment and
Difference Detection, Ph.D. Thesis, Department of Computer Science, University of
Toronto

2. Bayesian Detection of Infrequent Differences in Sets of Time Series with
Shared Structure.  Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Rachel
Puckrin and Sean Cutler, To appear in Advances in Neural Information Processing
Systems 19, MIT Press, Cambridge, MA, 2007 (NIPS 2006).

3. Difference detection in LC-MS data for protein biomarker discovery.  
Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong and Andrew
Emili, To appear in Bioinformatics, by way of ECCB 2006 (European Conference on
Computational Biology)

4. Multiple alignment of continuous time series.  Jennifer Listgarten, Radford
M. Neal, Sam T. Roweis and Andrew Emili, in Advances in Neural Information
Processing Systems 17, MIT Press, Cambridge, MA, 2005 (NIPS 2004).