Medical, Biological, and Chemical Applications

In addition to work in medical informatics, I have worked on medical image processing. Numerical methods for classifying cytology specimens (e.g., pap smears) were compared in [J09]. In collaboration with medical researchers, methods for identifying chromosomes were developed in [J53] and [C23].

The structure of a protein provides critical information in determining its function. A new algorithm for determining the 3-dimensional configuration of proteins was described in [J73], and its use was demonstrated on a backbone model of proteins. In [J76] and [J84] we proposed two fast screening algorithms for finding proteins whose structure is expected to be similar to one presented for classification. The relation between the structure of the connectivity graph and the essentiality of a protein in its interaction network was investigated in [J88].

Konstantin Berlin, David Fushman, and I studied the use of nuclear magnetic resonance (NMR) measurements in determining protein shape. First we developed a fast algorithm for predicting residual dipolar couplings [J94], and then we used it to determine structure of docked complexes [J95]. Similar work with the rotational diffusion tensor [J00] also yielded accurate docking structures.

[C23]

John M. Conroy, Robert L. Becker Jr., William Lefkowitz, Kewi L. Christopher, Rawatmal B. Surana, Timothy J. O'Leary, Dianne P. O'Leary, and Tamara G. Kolda, ``Hidden Markov Models for Chromosome Identification," Proceedings of the 14th IEEE Symposium on Computer-Based Medical Systems (CBMS'01), 2001.

[J09]

Timothy J. O'Leary, Dianne P. O'Leary, Mary C. Habbersett, and Chester J. Herman, ``Classification of gynecologic flow cytometry data: a comparison of methods,'' J. of Analytical and Quantitative Cytology 3 (1981) 135-142.

[J53]

John M. Conroy, Tamara G. Kolda, Dianne P. O'Leary, and Timothy J. O'Leary, ``Chromosome Identification Using Hidden Markov Models: Comparison with Neural Network, Singular Value Decomposition, Principal Components Analysis, and Fisher Discriminant Analysis," Laboratory Investigation, 80 (2000) 1629-1641.

[J73]

Daniel M. Dunlavy, Dianne P. O'Leary, Dmitri Klimov, and D. Thirumalai, ``HOPE: A Homotopy Optimization Method for Protein Structure Prediction," Journal of Computational Biology, 12, No. 10 (2005), pp. 1275-1288.

[J76]

Elena Zotenko, Dianne P. O'Leary, and Teresa M. Przytycka, ``Secondary Structure Spatial Conformation Footprint: A Novel Method for Fast Protein Structure Comparison," BMC Structural Biology, (2006), 6:12, doi:10.1186/1472-6807-6-12

[J84]

Elena Zotenko, Rezarta Islamaj Dogan, W. John Wilbur, Dianne P. O'Leary, and Teresa M. Przytycka, ``Structural Footprinting in Protein Structure Comparison: The Impact of Structural Fragments," BMC Structural Biology, (2007) 7:53 DOI:10.1186/1472-6807-7-53.

[J88]

Elena Zotenko, Julian Mestre, Dianne P. O'Leary, and Teresa M. Przytycka, ``Why Do Hubs in the Yeast Protein Interaction Network Tend to be Essential: Re-examining the Connection between the Network Topology and Essentiality," PLoS Computational Biology, 4(8):e1000140 (2008) (16 pages) doi:10.1371/journal.pcbi.1000140

[J94]

Konstantin Berlin, Dianne P. O'Leary, and David Fushman, ``Improvement and Analysis of Computational Methods for Prediction of Residual Dipolar Couplings," Journal of Magnetic Resonance 201 (2009) 25-33. http://dx.doi.org/10.1016/j.jmr.2009.07.028

[J95]

Konstantin Berlin, Dianne P. O'Leary, and David Fushman, ``Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings," Journal of the American Chemical Society, 132(26) (2010) 8961-–8972. DOI: 10.1021/ja100447p

[J100]

Konstantin Berlin, Dianne P. O'Leary, and David Fushman, ``Fast Approximations of the Rotational Diffusion Tensor and Their Application to Structural Assembly of Molecular Complexes," Proteins: Structure, Function, and Bioinformatics, 79(7) (2011) 2268-–2281. DOI: 10.1002/prot.23053 http://onlinelibrary.wiley.com/doi/10.1002/prot.23053/abstract