• Monte Carlo simulation & Markov chain convergence
  • Ji C, Schmidler SC. Adaptive MCMC for Bayesian Variable Selection Problems. In preparation for Statistics and Computing special issue on Adaptive MC.
  • Woodard DB, Schmidler SC, Huber M. Conditions for Torpid Mixing of Parallel and Simulated Tempering on Multimodal Distributions. Submitted to Stochastic Processes and their Applications.
  • Woodard DB, Schmidler SC, Huber M (2008). Conditions for Rapid Mixing of Parallel and Simulated Tempering on Multimodal Distributions. Annals of Applied Probability, (to appear).
  • Cooke B, Schmidler SC. Preserving the Boltzmann Ensemble in Replica-Exchange Molecular Dynamics Simulations. Submitted to Journal of Chemical Physics.
  • Woodard D, Schmidler SC. Torpid Mixing of the Equi-Energy Sampler on the Mean-Field Potts Model. In preparation for Annals of Statistics.
• Statistical shape analysis
  • Schmidler SC. Bayesian Flexible Shape Matching With Applications to Structural Bioinformatics. Submitted to Journal of the American Statistical Association.
  • Schmidler SC (2006). Fast Bayesian Shape Matching Using Geometric Algorithms (with discussion). Bayesian Statistics 8, Eds. J.M. Bernardo, S. Bayarri, J.O. Berger, A.P. Dawid, D. Heckerman, A.F.M. Smith and M. West, Oxford University Press, pp 471-490.
  • Rodriguez A, Schmidler SC. Bayesian Protein Structure Alignment. In preparation for Journal of Computational Biology.
  • Wang R, Schmidler SC. Bayesian Multiple and Flexible Protein Structure Alignment. In preparation for Journal of Computational Biology.
  • Rodriguez A, Schmidler SC. Combining Sequence and Structure Information in Protein Alignments. Under revision for resubmission.
• Bayesian sequence segmentation
  • Schmidler SC, Liu JL, Brutlag DB. Bayesian Modeling of Non-local Interactions in Protein Sequences: Prediction of &Beta-Sheets. Submitted to Journal of Computational Biology.
  • Schmidler SC, Liu JL, Brutlag DB. Stochastic Segment Interaction Models for Biological Sequence Analysis. Under revision for Journal of the American Statistical Association.
  • Schmidler, SC, Liu, JS, Brutlag, DL (2000). Bayesian segmentation of protein secondary structure. Journal of Computational Biology, Vol 7, No 1/2, pp 233-248
  • Schmidler SC, Liu JS, Brutlag DL (1999). Bayesian protein structure prediction. Case Studies in Bayesian Statistics, Vol 5, 363-378.
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• Parameter estimation in Gibbs random fields
  • Schmidler SC, Lucas J, Oas TG (2007). Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction. Journal of Computational Biology, Vol 14, No 10, pp 1287-1310. (Dataset reference list)
  • Cooke B, Schmidler SC (2008). Statistical Prediction and Molecular Dynamics Simulation. Biophysical Journal, Vol 95, No 9 (to appear).
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• Parameter estimation in dynamical systems
  • Cooke B, Schmidler SC (2008). Statistical Prediction and Molecular Dynamics Simulation. Biophysical Journal, Vol 95, No 9 (to appear).
  • Sanders GD, Schmidler SC (2007). Effect of HPV Vaccine Characteristics and Implementation Strategies on Incidence of Disease. Medical Decision Making, 28(1): E14. (refereed abstract).
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• Bayesian experimental design
  • Lucas JE, Oas TG, Schmidler SC. Bayesian Experimental Design in Bioinformatics: Application to Helical Peptide Studies. Submitted to Journal of Computational Biology.
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• Protein Structure Alignment
  • Schmidler SC. Bayesian Flexible Shape Matching With Applications to Structural Bioinformatics. Submitted to Journal of the American Statistical Association.
  • Schmidler SC (2006). Fast Bayesian Shape Matching Using Geometric Algorithms (with discussion). Bayesian Statistics 8, Eds. J.M. Bernardo, S. Bayarri, J.O. Berger, A.P. Dawid, D. Heckerman, A.F.M. Smith and M. West, Oxford University Press, pp 471-490.
  • Wu, TD, Schmidler, SC, Hastie, T, Brutlag, DL (1998). Regression analysis of multiple protein structures. Journal of Computational Biology, Vol 5, No 3, pp 585-595. (preprint version with color figures)
  • Wu TD, Hastie T, Schmidler SC, Brutlag DL (1998). Regression analysis of multiple protein structures. Proceedings Second Annual Conference on Computational Molecular Biology (RECOMB '98), ACM press, 1998, 276-284.
  • Wu TD, Schmidler SC, Hastie T, Brutlag DL (1998). Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins. In Pacific Symposium on Biocomputing '98, World Scientific Publishing, Singapore, 507-518.
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• Protein Structure Prediction
  • Schmidler SC, Liu JL, Brutlag DB. Bayesian Modeling of Non-local Interactions in Protein Sequences: Prediction of β-Sheets. Submitted to Journal of Computational Biology.
  • Schmidler SC, Liu JL, Brutlag DB. Stochastic Segment Interaction Models for Biological Sequence Analysis. Under revision for Journal of the American Statistical Association.
  • Schmidler, SC, Liu, JS, Brutlag, DL (2000). Bayesian segmentation of protein secondary structure. Journal of Computational Biology, Vol 7, No 1/2, pp 233-248
  • Schmidler SC, Liu JS, Brutlag DL (1999). Bayesian protein structure prediction. Case Studies in Bayesian Statistics, Vol 5, 363-378.
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• Helix-coil theory
  • Lucas JE, Oas TG, Schmidler SC. Statistical Model Selection and Synthesis of Multiple Data Sources for the Statistical Thermodynamics of Helix-Coil Transitions. In preparation for Journal of Molecular Biology
  • Lucas JE, Oas TG, Schmidler SC. Bayesian Experimental Design in Bioinformatics: Application to Helical Peptide Studies. Submitted to Journal of Computational Biology.
  • Ji C, Schmidler SC. Adaptive MCMC for Bayesian Variable Selection Problems. In preparation for Statistics and Computing special issue on Adaptive MC.
  • Schmidler SC, Lucas J, Oas TG (2007). Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction. Journal of Computational Biology, Vol 14, No 10, pp 1287-1310. (Dataset reference list)
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• Molecular simulation and protein folding
  • Cooke B, Schmidler SC. Preserving the Boltzmann Ensemble in Replica-Exchange Molecular Dynamics Simulations. Submitted to Journal of Chemical Physics.
  • Cooke B, Schmidler SC (2008). Statistical Prediction and Molecular Dynamics Simulation. Biophysical Journal, Vol 95, No 9 (to appear).
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• Single-molecule force spectroscopy
  • Guo S, Ray C, Lad N, Kirkpatrick A, Schmidler SC, Akhremitchev BB. Accounting for the Linkers and Multiple Ruptures in Dynamic Force Spectroscopy Experiments.
  • Valiaev A, Zauscher S, Schmidler SC. Statistical Analysis of AFM Force Spectroscopy Curves. Submitted to Biophysical Journal.
  • Valiaev A, Lim DW, Schmidler SC, Clark RL, Chilkoti, A, Zauscher, S (2008). Hydration and Conformational Mechanics of Single End-Tethered Elastin-Like Polypeptides. Journal of the American Chemical Society, Vol 130, No 33, pp 10939-10946. (Suppl. material)
  • Valiaev A, Lim DW, Chilkoti A, Schmidler SC, Zauscher S (2006). Polypeptide-Solvent Interactions Measured by Single Molecule Force Spectroscopy. In Mechanical Behavior of Biological and Biomimetic Materials, Bushby A.J, Ferguson V.L., Ko C.-C., Oyen, M.-L., Eds., Materials Research Society Symposium Proceedings, Vol. 898E, MRS, Warrendale, PA.
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• Other computational biology
  • Colinas J, Bohrer G, Iordanov B, Schmidler SC, Benfey PN. Relationships Between Sequence Length and Gene Expression and the Epigenetic Regulation of Gene Expression by Non-Coding Sequences. Submitted to PLoS ONE.
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Other:

• Jiang T, Tomasi C, Schmidler SC. (2007) How to Dispatch Observers to Track an Evolving Boundary. ACM/IEEE International Conference on Distributed Smart Cameras (ICDSC '07), pp 305-312.
• Schmidler SC (2003). Discussion of "A Statistical Approach to Modeling Genomic Aberrations in Cancer Cells" by Newton et al. Bayesian Statistics 7, Oxford University Press.
• Lansky, A, Friedman M, Getoor L, Schmidler S, Short, N. (1995). The COLLAGE/Khoros Link: Planning for Image Processing Tasks. Proceedings of the 1995 AAAI Spring Symposium on Integrated Planning Architectures.
• Jiang T, Tomasi C, Schmidler SC. Decision-theoretic Observer Dispatch for Tracking an Evolving Boundary. Submitted to IEEE Transactions on Signal Processing.