Duke Probability Theory and Applications
   Search Help Login Join pdf version printable version

Publications of Scott C. Schmidler    :chronological  alphabetical  combined  bibtex listing:

Papers Published

  1. Hughes, RG; Zhao, S; Oas, TG; Schmidler, SC, Efficient enumeration and visualization of helix-coil ensembles., Biophys J, vol. 123 no. 3 (February, 2024), pp. 317-333 [doi]  [abs]
  2. Mathews, J; Schmidler, SC, Finite sample complexity of sequential Monte Carlo estimators on multimodal target distributions, Annals of Applied Probability, vol. 34 no. 1 (February, 2024), pp. 1199-1223, Institute of Mathematical Statistics [doi]  [abs]
  3. Mathews, J; Van Itallie, E; Wiehe, K; Schmidler, SC, Computing the inducibility of B cell lineages under a context-dependent model of affinity maturation: Applications to sequential vaccine design., bioRxiv (October, 2023) [doi]  [abs]
  4. Schmidler, SC; Hughes, RG; Oas, TG; Zhao, S, Efficient Enumeration and Visualization of Helix-coil Ensembles., bioRxiv (September, 2023) [doi]  [abs]
  5. Marion, J; Mathews, J; Schmidler, SC, Finite-sample complexity of sequential Monte Carlo estimators, Annals of Statistics, vol. 51 no. 3 (June, 2023), pp. 1357-1375, Institute of Mathematical Statistics [doi]  [abs]
  6. Wu, K; Schmidler, S; Chen, Y, Minimax mixing time of the Metropolis-adjusted Langevin algorithm for log-concave sampling, Journal of Machine Learning Research, vol. 23 (July, 2022)  [abs]
  7. Tonner, PD; Darnell, CL; Bushell, FML; Lund, PA; Schmid, AK; Schmidler, SC, A Bayesian non-parametric mixed-effects model of microbial growth curves, edited by Papin, JA, PLOS Computational Biology, vol. 16 no. 10 (October, 2020), pp. e1008366-e1008366, Public Library of Science (PLoS) [doi]  [abs]
  8. Larson, G; Thorne, JL; Schmidler, S, Incorporating nearest-neighbor site dependence into protein evolution models, Journal of Computational Biology, vol. 27 no. 3 (March, 2020), pp. 361-375, Mary Ann Liebert Inc [doi]  [abs]
  9. Larson, G; Thorne, JL; Schmidler, S, Modeling dependence in evolutionary inference for proteins, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10812 LNBI (January, 2018), pp. 122-137, Springer International Publishing, ISBN 9783319899282 [doi]  [abs]
  10. Darnell, CL; Tonner, PD; Gulli, JG; Schmidler, SC; Schmid, AK, Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis, edited by Shank, EA, mSystems, vol. 2 no. 5 (October, 2017), pp. e00032-e00017, American Society for Microbiology [doi]  [abs]
  11. VanDerwerken, D; Schmidler, SC, Monitoring joint convergence of MCMC samplers, Journal of Computational and Graphical Statistics, vol. 26 no. 3 (July, 2017), pp. 558-568, Informa UK Limited [doi]  [abs]
  12. Cooke, B; Herzog, DP; Mattingly, JC; Mckinle, SA; Schmidler, SC, Geometric ergodicity of two-dimensional hamiltonian systems with a Lennard-Jones-like repulsive potential, Communications in Mathematical Sciences, vol. 15 no. 7 (January, 2017), pp. 1987-2025, International Press of Boston [doi]  [abs]
  13. Ben-Shachar, R; Schmidler, S; Koelle, K, Drivers of inter-individual variation in Dengue viral load dynamics, edited by Ferguson, NM, PLoS Computational Biology, vol. 12 no. 11 (November, 2016), pp. e1005194-e1005194, Public Library of Science (PLoS) [doi]  [abs]
  14. Estrada, R; Tomasi, C; Schmidler, SC; Farsiu, S, Tree topology estimation, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37 no. 8 (August, 2015), pp. 1688-1701, Institute of Electrical and Electronics Engineers (IEEE) [doi]  [abs]
  15. Rodriguez, A; Schmidler, SC, Bayesian protein structure alignment, Annals of Applied Statistics, vol. 8 no. 4 (December, 2014), pp. 2068-2095, Institute of Mathematical Statistics, ISSN 1932-6157 [doi]  [abs]
  16. Daniels, KG; Tonthat, NK; McClure, DR; Chang, Y-C; Liu, X; Schumacher, MA; Fierke, CA; Schmidler, SC; Oas, TG, Ligand concentration regulates the pathways of coupled protein folding and binding., J Am Chem Soc, vol. 136 no. 3 (January, 2014), pp. 822-825 [24364358], [doi]  [abs]
  17. Herman, JL; Challis, CJ; Novák, A; Hein, J; Schmidler, SC, Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure, Molecular Biology and Evolution, vol. 31 no. 9 (January, 2014), pp. 2251-2266, Oxford University Press (OUP), ISSN 0737-4038 [doi]  [abs]
  18. Wang, R; Schmidler, SC, Bayesian multiple protein structure alignment, edited by Sharan, R, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8394 LNBI (January, 2014), pp. 326-339, SPRINGER INT PUBLISHING AG, ISSN 0302-9743, ISBN 9783319052687 [doi]  [abs]
  19. Wang, R; Schmidler, SC, Bayesian multiple protein structure alignment, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8394 LNBI (January, 2014), pp. 326-339, Springer International Publishing, ISBN 9783319052687 [doi]  [abs]
  20. Ji, C; Schmidler, SC, Adaptive Markov chain Monte Carlo for Bayesian variable selection, Journal of Computational and Graphical Statistics, vol. 22 no. 3 (December, 2013), pp. 708-728, Informa UK Limited, ISSN 1061-8600 [Gateway.cgi], [doi]  [abs]
  21. Challis, CJ; Schmidler, SC, A stochastic evolutionary model for protein structure alignment and phylogeny, Molecular Biology and Evolution, vol. 29 no. 11 (November, 2012), pp. 3575-3587, Oxford University Press (OUP) [22723302], [doi]  [abs]
  22. Wolpert, RL; Schmidler, SC, α-Stable limit laws for harmonic mean estimators of marginal likelihoods, Statistica Sinica, vol. 22 no. 3 (July, 2012), pp. 1233-1251, Statistica Sinica (Institute of Statistical Science), ISSN 1017-0405 [Gateway.cgi], [doi]  [abs]
  23. Zheng, N; Schmidler, SC; Marks, D; Brady, D, Computer experiment and global optimization of layered monocentric lens systems, Optik, vol. 123 no. 14 (July, 2012), pp. 1249-1259, Elsevier BV, ISSN 0030-4026 [doi]  [abs]
  24. Wilson, MA; Iversen, ES; Clyde, MA; Schmidler, SC; Schildkraut, JM, BAYESIAN MODEL SEARCH AND MULTILEVEL INFERENCE FOR SNP ASSOCIATION STUDIES., Ann Appl Stat, vol. 4 no. 3 (September, 2010), pp. 1342-1364, Institute of Mathematical Statistics, ISSN 1932-6157 [21179394], [doi]  [abs]
  25. Jia, B; Li, J; Huang, S; Schmidler, SC; Wu, YK, Electron beam energy spread measurements using optical klystron radiation, Physical Review Special Topics - Accelerators and Beams, vol. 13 no. 8 (August, 2010), pp. 080702, American Physical Society (APS), ISSN 1098-4402 [repository], [doi]  [abs]
  26. Wiehe, K; Kepler, TB; Schmidler, SC, P19-50. Simulation of an MPER peptide samples epitope conformations of two broadly neutralizing antibodies, Retrovirology, vol. 6 no. S3 (October, 2009), pp. P370-P370, Springer Science and Business Media LLC, ISSN 1742-4690 [doi]
  27. Woodard, DB; Schmidler, SC; Huber, M, Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions, Annals of Applied Probability, vol. 19 no. 2 (April, 2009), pp. 617-640, Institute of Mathematical Statistics, ISSN 1050-5164 [doi]  [abs]
  28. Woodard, DB; Schmidler, SC; Huber, M, Sufficient conditions for torpid mixing of parallel and simulated tempering, Electronic Journal of Probability, vol. 14 (January, 2009), pp. 780-804, Institute of Mathematical Statistics, ISSN 1083-6489 [doi]  [abs]
  29. Cooke, B; Schmidler, SC, Statistical Prediction and Molecular Dynamics Simulation, Biophysical Journal, vol. 95 no. 10 (November, 2008), pp. 4497-4511, Elsevier BV [18676654], [doi]  [abs]
  30. Cooke, B; Schmidler, SC, Preserving the Boltzmann ensemble in replica-exchange molecular dynamics, The Journal of Chemical Physics, vol. 129 no. 16 (October, 2008), pp. 164112, AIP Publishing [19045252], [doi]  [abs]
  31. Valiaev, A; Dong, WL; Schmidler, S; Clark, RL; Chilkoti, A; Zauscher, S, Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides, Journal of the American Chemical Society, vol. 130 no. 33 (August, 2008), pp. 10939-10946, American Chemical Society (ACS) [18646848], [doi]  [abs]
  32. Colinas, J; Schmidler, SC; Bohrer, G; Iordanov, B; Benfey, PN, Intergenic and genic sequence lengths have opposite relationships with respect to gene expression., PloS one, vol. 3 no. 11 (January, 2008), pp. e3670 [18989364], [doi]  [abs]
  33. Schmidler, SC; Lucas, JE; Oas, TG, Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction., J Comput Biol, vol. 14 no. 10 (December, 2007), pp. 1287-1310, ISSN 1066-5277 [18047425], [doi]  [abs]
  34. Schmidler, SC, Fast Bayesian Shape Matching Using Geometric Algorithms, in Bayesian Statistics 8, edited by J.M. Bernardo, S. Bayarri, J.O. Berger, A.P. Dawid, D. Heckerman, A.F.M. Smith and M. West (July, 2007), pp. 481-500, Oxford University PressOxford, ISBN 9780199214655 [doi]  [abs]
  35. Jiang, T; Tomasi, C; Schmidler, SC, How to dispatch observers to track an evolving boundary, in ACM/IEEE International Conference on Distributed Smart Cameras (ICDSC '07),, 2007 1st ACM/IEEE International Conference on Distributed Smart Cameras, ICDSC (2007), pp. 305-312, IEEE [doi]  [abs]
  36. Jiang, T; Tomasi, C; Schmidler, SC, How to dispatch observers to track an evolving boundary, 2007 First ACM/IEEE International Conference on Distributed Smart Cameras (2007), pp. 295-+, IEEE, ISBN 978-1-4244-1353-9
  37. Valiaev, A; Dong, WL; Chilkoti, A; Schmidler, S; Zauscher, S, Polypeptide-solvent interactions measured by single molecule force spectroscopy, Materials Research Society Symposium Proceedings, vol. 898 (2005), pp. 92-97, ISSN 0272-9172 [doi]  [abs]
  38. Schmidler, SC, Discussion of "A Statistical Approach to Modeling Genomic Aberrations in Cancer Cells" by Newton et. al, Bayesian Statistics7 (2003), Oxford University Press
  39. Schmidler, SC; Liu, JS; Brutlag, DL, Bayesian segmentation of protein secondary structure, Journal of Computational Biology, vol. 7 no. 1-2 (July, 2000), pp. 233-248, Mary Ann Liebert Inc, ISSN 1066-5277 [10890399], [doi]  [abs]
  40. Schmidler, SC; Liu, JS; Brutlag, DL, Probabilistic modeling for protein structure prediction, FASEB JOURNAL, vol. 13 no. 7 (April, 1999), pp. A1542-A1542, FEDERATION AMER SOC EXP BIOL, ISSN 0892-6638 [Gateway.cgi]
  41. Schmidler, SC; Liu, JS; Brutlag, DL, Bayesian protein structure prediction, Case Studies in Bayesian Statistics, vol. 5 (1999), pp. 363-378
  42. Wu, TD; Hastie, T; Schmidler, SC; Brutlag, DL, Regression analysis of multiple protein structures, Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB, vol. 5 no. 3 (January, 1998), pp. 276-284, ACM oress, ISSN 1066-5277 [9773352], [doi]  [abs]
  43. Wu, TD; Schmidler, SC; Hastie, T; Brutlag, DL, Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins., Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1998), pp. 509-520, World Scientific Publishing, Singapore, ISSN 2335-6936 [9697208]  [abs]
  44. Wu, TD; Schmidler, SC; Hastie, T; Brutlag, DL, Regression analysis of multiple protein structures, Journal of Computational Biology, vol. 5 no. 3 (1998), pp. 597-607, ISSN 1066-5277 [9773352], [doi]  [abs]
  45. Lansky, AL; Friedman, M; Getoor, L; Schmidler, S; Short, N, The COLLAGE/KHOROS Link: Planning for Image Processing Tasks, AAAI Spring Symposium - Technical Report, vol. SS-95-04 (January, 1995), pp. 67-76  [abs]