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

Papers Published

1. Mathews, J; Van Itallie, E; Li, Y; Wiehe, K; Schmidler, SC. "Computing the inducibility of broadly neutralizing antibodies under a context-dependent model of affinity maturation: applications to sequential vaccine design.." Journal of immunology (Baltimore, Md. : 1950) (September, 2025): vkaf234. [doi]  [abs]
2. Li, Y; Mathews, J; Schmidler, SC. "On Gibbs Sampling for Endpoint-Conditioned Neighbor-Dependent Sequence Evolution Models." Journal of Computational and Graphical Statistics (January, 2025): 1-6. [doi]  [abs]
3. Hughes, RG; Zhao, S; Oas, TG; Schmidler, SC. "Efficient enumeration and visualization of helix-coil ensembles.." Biophys J 123.3 (February, 2024): 317-333. [doi]  [abs]
4. Mathews, J; Schmidler, SC. "Finite sample complexity of sequential Monte Carlo estimators on multimodal target distributions." Annals of Applied Probability 34.1 (February, 2024): 1199-1223. [doi]  [abs]
5. 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]
6. Schmidler, SC; Hughes, RG; Oas, TG; Zhao, S. "Efficient Enumeration and Visualization of Helix-coil Ensembles.." bioRxiv (September, 2023). [doi]  [abs]
7. Marion, J; Mathews, J; Schmidler, SC. "Finite-sample complexity of sequential Monte Carlo estimators." Annals of Statistics 51.3 (June, 2023): 1357-1375. [doi]  [abs]
8. Wu, K; Schmidler, S; Chen, Y. "Minimax mixing time of the Metropolis-adjusted Langevin algorithm for log-concave sampling." Journal of Machine Learning Research 23 (July, 2022).  [abs]
9. Tonner, PD; Darnell, CL; Bushell, FML; Lund, PA; Schmid, AK; Schmidler, SC. "A Bayesian non-parametric mixed-effects model of microbial growth curves." PLOS Computational Biology 16.10 (October, 2020): e1008366-e1008366. [doi]  [abs]
10. Larson, G; Thorne, JL; Schmidler, S. "Incorporating nearest-neighbor site dependence into protein evolution models." Journal of Computational Biology 27.3 (March, 2020): 361-375. [doi]  [abs]
11. Tonner, PD; Darnell, CL; Bushell, FML; Lund, PA; Schmid, AK; Schmidler, SC. "A Bayesian Non-parametric Mixed-Effects Model of Microbial Phenotypes." Cold Spring Harbor Laboratory (October, 2019). [doi]
12. 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) 10812 LNBI (January, 2018): 122-137. [doi]  [abs]
13. Darnell, CL; Tonner, PD; Gulli, JG; Schmidler, SC; Schmid, AK. "Systematic discovery of Archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis." mSystems 2.5 (October, 2017): e00032-e00017. [doi]  [abs]
14. VanDerwerken, D; Schmidler, SC. "Monitoring joint convergence of MCMC samplers." Journal of Computational and Graphical Statistics 26.3 (July, 2017): 558-568. [doi]  [abs]
15. 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 15.7 (January, 2017): 1987-2025. [doi]  [abs]
16. Ben-Shachar, R; Schmidler, S; Koelle, K. "Drivers of inter-individual variation in Dengue viral load dynamics." PLoS Computational Biology 12.11 (November, 2016): e1005194-e1005194. [doi]  [abs]
17. Estrada, R; Tomasi, C; Schmidler, SC; Farsiu, S. "Tree topology estimation." IEEE Transactions on Pattern Analysis and Machine Intelligence 37.8 (August, 2015): 1688-1701. [doi]  [abs]
18. Rodriguez, A; Schmidler, SC. "Bayesian protein structure alignment." Annals of Applied Statistics 8.4 (December, 2014): 2068-2095. [doi]  [abs]
19. 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 136.3 (January, 2014): 822-825. [24364358], [doi]  [abs]
20. 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 31.9 (January, 2014): 2251-2266. [doi]  [abs]
21. 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) 8394 LNBI (January, 2014): 326-339. [doi]  [abs]
22. 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 8394 LNBI (January, 2014): 326-339. [doi]  [abs]
23. VanDerwerken, DN; Schmidler, SC. "Parallel Markov Chain Monte Carlo." (December, 2013).
24. Ji, C; Schmidler, SC. "Adaptive Markov chain Monte Carlo for Bayesian variable selection." Journal of Computational and Graphical Statistics 22.3 (December, 2013): 708-728. [Gateway.cgi], [doi]  [abs]
25. Challis, CJ; Schmidler, SC. "A stochastic evolutionary model for protein structure alignment and phylogeny." Molecular Biology and Evolution 29.11 (November, 2012): 3575-3587. [22723302], [doi]  [abs]
26. Wolpert, RL; Schmidler, SC. "α-Stable limit laws for harmonic mean estimators of marginal likelihoods." Statistica Sinica 22.3 (July, 2012): 1233-1251. [Gateway.cgi], [doi]  [abs]
27. Zheng, N; Schmidler, SC; Marks, D; Brady, D. "Computer experiment and global optimization of layered monocentric lens systems." Optik 123.14 (July, 2012): 1249-1259. [doi]  [abs]
28. Wilson, MA; Iversen, ES; Clyde, MA; Schmidler, SC; Schildkraut, JM. "BAYESIAN MODEL SEARCH AND MULTILEVEL INFERENCE FOR SNP ASSOCIATION STUDIES.." Ann Appl Stat 4.3 (September, 2010): 1342-1364. [21179394], [doi]  [abs]
29. 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 13.8 (August, 2010): 080702. [repository], [doi]  [abs]
30. Wiehe, K; Kepler, TB; Schmidler, SC. "P19-50. Simulation of an MPER peptide samples epitope conformations of two broadly neutralizing antibodies." Retrovirology 6.S3 (October, 2009): P370-P370. [doi]
31. Woodard, DB; Schmidler, SC; Huber, M. "Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions." Annals of Applied Probability 19.2 (April, 2009): 617-640. [doi]  [abs]
32. Woodard, DB; Schmidler, SC; Huber, M. "Sufficient conditions for torpid mixing of parallel and simulated tempering." Electronic Journal of Probability 14 (January, 2009): 780-804. [doi]  [abs]
33. Cooke, B; Schmidler, SC. "Statistical prediction and molecular dynamics simulation." Biophysical Journal 95.10 (November, 2008): 4497-4511. [18676654], [doi]  [abs]
34. Cooke, B; Schmidler, SC. "Preserving the Boltzmann ensemble in replica-exchange molecular dynamics." The Journal of Chemical Physics 129.16 (October, 2008): 164112. [19045252], [doi]  [abs]
35. 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 130.33 (August, 2008): 10939-10946. [18646848], [doi]  [abs]
36. 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 3.11 (January, 2008): e3670. [18989364], [doi]  [abs]
37. Schmidler, SC; Lucas, JE; Oas, TG. "Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction.." J Comput Biol 14.10 (December, 2007): 1287-1310. [18047425], [doi]  [abs]
38. Schmidler, SC. "Fast Bayesian Shape Matching Using Geometric Algorithms." Bayesian Statistics 8 (July, 2007): 471-490. [doi]  [abs]
39. Jiang, T; Tomasi, C; Schmidler, SC. "How to dispatch observers to track an evolving boundary." 2007 1st ACM/IEEE International Conference on Distributed Smart Cameras, ICDSCACM/IEEE International Conference on Distributed Smart Cameras (ICDSC '07), (2007): 305-312. [doi]  [abs]
40. 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): 295-+.
41. Valiaev, A; Dong, WL; Chilkoti, A; Schmidler, S; Zauscher, S. "Polypeptide-solvent interactions measured by single molecule force spectroscopy." Materials Research Society Symposium Proceedings 898 (2005): 92-97. [doi]  [abs]
42. Schmidler, SC. "Discussion of "A Statistical Approach to Modeling Genomic Aberrations in Cancer Cells" by Newton et. al." Bayesian Statistics7 (2003).
43. Schmidler, SC; Liu, JS; Brutlag, DL. "Bayesian segmentation of protein secondary structure." Journal of Computational Biology 7.1-2 (July, 2000): 233-248. [10890399], [doi]  [abs]
44. Schmidler, SC; Liu, JS; Brutlag, DL. "Probabilistic modeling for protein structure prediction." FASEB JOURNAL 13.7 (April, 1999): A1542-A1542. [Gateway.cgi]
45. Schmidler, SC; Liu, JS; Brutlag, DL. "Bayesian protein structure prediction." Case Studies in Bayesian Statistics 5 (1999): 363-378.
46. 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 5.3 (January, 1998): 276-284. [9773352], [doi]  [abs]
47. 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): 509-520. [9697208]  [abs]
48. Wu, TD; Schmidler, SC; Hastie, T; Brutlag, DL. "Regression analysis of multiple protein structures." Journal of Computational Biology 5.3 (1998): 597-607. [9773352], [doi]  [abs]
49. Lansky, AL; Friedman, M; Getoor, L; Schmidler, S; Short, N. "The COLLAGE/KHOROS Link: Planning for Image Processing Tasks." Aaai Spring Symposium Technical Report SS-95-04 (January, 1995): 67-76.  [abs]