• Monte Carlo simulation & Markov chain convergence
  • Wolpert RL, Schmidler SC (2012). α-Stable Limit Laws for Harmonic Mean Estimators of Marginal Likelihoods. Statistica Sinica, Vol 22, No 3, pp 1233-51.
  • Woodard DB, Schmidler SC, Huber M (2009). Sufficient Conditions for Torpid Mixing of Parallel and Simulated Tempering. Electronic Journal of Probability, Vol 14, pp 780-804.
  • Ji C, Schmidler SC (2013). Adaptive Markov Chain Monte Carlo for Bayesian Variable Selection. Journal of Computational and Graphical Statistics, Vol 22, No 3, pp 708-728.
  • Woodard DB, Schmidler SC, Huber M (2009). Conditions for Rapid Mixing of Parallel and Simulated Tempering on Multimodal Distributions. Annals of Applied Probability, Vol 19, No 2, pp 617-640.
  • Cooke B, Schmidler SC (2008). Preserving the Boltzmann Ensemble in Replica-Exchange Molecular Dynamics Simulations. Journal of Chemical Physics, Vol 129, No 16, 164112. (copyright notice, abstract)
  (Also selected to appear in Virtual Journal of Biological Physics Research, Vol 16, No 9.)
   

• Statistical shape analysis
  • Herman JL, Challis CJ, Novak A, Hein J, Schmidler SC (2014). Simultaneous Bayesian Estimation of Alignment and Phylogeny Under a Joint Sequence-Structure Model. Molecular Biology and Evolution, Vol 31, No 9, pp 2251-66.
  • Wang R, Schmidler SC (2014). Bayesian Multiple Protein Structure Alignment. Proceedings 18th Annual Conference on Computational Molecular Biology (RECOMB 2014), Lecture Notes in Computer Science, Volume 8394, pp 326-339.
  • Challis CJ, Schmidler SC (2012). A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny. Molecular Biology and Evolution, Vol 29, No 11, pp 3575-87.
  • Rodriguez A, Schmidler SC (2014). Bayesian Protein Structure Alignment. Annals of Applied Statistics, Vol 8, No 4, pp 2068-95.
  • 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.
   

• Bayesian sequence segmentation
  • 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.
   

• 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 10, 4497-4511. abstract
   

• Parameter estimation in dynamical systems
  • Daniels KG, Tonthat NK, McClure DR, Chang Y, Liu X, Schumacher MA, Fierke CA, Schmidler SC, Oas TG (2014). Ligand Concentration Regulates the Pathways of Coupled Protein Folding and Binding. Journal of the American Chemical Society, (to appear)
  • Cooke B, Schmidler SC (2008). Statistical Prediction and Molecular Dynamics Simulation. Biophysical Journal, Vol 95, No 10, 4497-4511. abstract
  • 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).
   

• Bayesian experimental design
  • Zheng N, Schmidler SC, Marks D, Brady D (2011). Computer experiment and global optimization of layered monocentric lens systems. Optik - International Journal for Light and Electron Optics, Vol 123, No 14, pp 1249-59.
  • Lucas JE, Oas TG, Schmidler SC. Bayesian Experimental Design in Bioinformatics: Application to Helical Peptide Studies. Submitted to Journal of Computational Biology.
  • 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.
   

• Protein Structure Alignment
  • Herman JL, Challis CJ, Novak A, Hein J, Schmidler SC (2014). Simultaneous Bayesian Estimation of Alignment and Phylogeny Under a Joint Sequence-Structure Model. Molecular Biology and Evolution, Vol 31, No 9, pp 2251-66.
  • Wang R, Schmidler SC (2014). Bayesian Multiple Protein Structure Alignment. Proceedings 18th Annual Conference on Computational Molecular Biology (RECOMB 2014), Lecture Notes in Computer Science, Volume 8394, pp 326-339.
  • Challis CJ, Schmidler SC (2012). A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny. Molecular Biology and Evolution, Vol 29, No 11, pp 3575-87.
  • Rodriguez A, Schmidler SC (2014). Bayesian Protein Structure Alignment. Annals of Applied Statistics, Vol 8, No 4, pp 2068-95.
  • 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.
   

• 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.
   

• Helix-coil theory
  • 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 (2013). Adaptive Markov Chain Monte Carlo for Bayesian Variable Selection. Journal of Computational and Graphical Statistics, Vol 22, No 3, pp 708-728.
  • 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)
   

• Molecular simulation and protein folding
  • Daniels KG, Tonthat NK, McClure DR, Chang Y, Liu X, Schumacher MA, Fierke CA, Schmidler SC, Oas TG (2014). Ligand Concentration Regulates the Pathways of Coupled Protein Folding and Binding. Journal of the American Chemical Society, (to appear)
  • Cooke B, Schmidler SC (2008). Preserving the Boltzmann Ensemble in Replica-Exchange Molecular Dynamics Simulations. Journal of Chemical Physics, Vol 129, No 16, 164112. (copyright notice, abstract)
  (Also selected to appear in Virtual Journal of Biological Physics Research, Vol 16, No 9.)
  • Cooke B, Schmidler SC (2008). Statistical Prediction and Molecular Dynamics Simulation. Biophysical Journal, Vol 95, No 10, 4497-4511. abstract
   

• Single-molecule force spectroscopy
  • Valiaev A, Zauscher S, Schmidler SC. Statistical Analysis of AFM Force Spectroscopy Curves. Submitted to Biophysical Journal. Software (matlab)
  • 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.
   

• Other computational biology
  • Wilson MA, Iversen ES, Clyde MA, Schmidler SC, Schildkraut JM (2010). Bayesian Model Search and Multilevel Inference for SNP Association Studies. Annals of Applied Statistics, Vol 4, No 3, pp 1342-64.
  • Colinas J, Bohrer G, Iordanov B, Schmidler SC, Benfey PN (2008). Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression. PLoS ONE, Vol 3, No 11, pp e3670.
   

Other:

• Estrada R, Tomasi C, Schmidler SC, Farsiu, S (2014). Tree Topology Estimation. IEEE Transactions on Pattern Analysis and Machine Intelligence, (to appear).
• Zheng N, Schmidler SC, Marks D, Brady D (2011). Computer experiment and global optimization of layered monocentric lens systems. Optik - International Journal for Light and Electron Optics, Vol 123, No 14, pp 1249-59.
• Jia B, Li J, Huang S, Schmidler SC, Wu YK (2010). Electron Beam Energy Spread Measurements Using Optical Klystron Radiation. Physical Review Special Topics - Accelerators and Beams, Vol 13, No 8, 080702 pp 1-14.
• 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.