Scott C. Schmidler | Scholars@Duke

Scott C. Schmidler
Associate Professor of Statistical Science

Current Appointments & Affiliations

Associate Professor of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2010
Associate Professor in the Department of Computer Science, Computer Science, Trinity College of Arts & Sciences 2011

Contact Information

223D Old Chem, Durham, NC 27708-0251
Box 90251, Isds, Durham, NC 27708-0251
scott.schmidler@duke.edu (919) 684-8064
http://www.stat.duke.edu/~scs/

Background
Education, Training, & Certifications
- Ph.D., Stanford University 2002
- B.A., University of California at Berkeley 1995
Duke Appointment History
- Assistant Professor in the Institute of Statistics and Decision Sciences, Statistical Science, Trinity College of Arts & Sciences 2006 - 2010
- Assistant Professor in the Institute of Statistics and Decision Sciences, Statistical Science, Trinity College of Arts & Sciences 2002 - 2006
- Lecturer, University, Statistical Science, Trinity College of Arts & Sciences 2000 - 2002
Research
Selected Grants
- Deep Topological Sampling of Protein Structures - non-competing renewal for Year 2 awarded by National Institutes of Health 2017 - 2021
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- EMSW21-RTG: Geometric, Topological awarded by National Science Foundation 2011 - 2018
- Advances in Scalable Monte Carlo Algorithms for Bayesian Statistics awarded by National Science Foundation 2014 - 2017
- Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
- Mechanistic Studies of Complex Protein Folding Reactions awarded by National Institutes of Health 2008 - 2013
- Bayesian Analysis of Shapes and Curves with Applications in Bioinformatics awarded by National Science Foundation 2006 - 2007
- Statistical Models of Biopolymer Sequence and Folding awarded by National Science Foundation 2002 - 2005
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Darnell, CL, Tonner, PD, Gulli, JG, Schmidler, SC, and Schmid, AK. "Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis." Msystems 2, no. 5 (September 19, 2017). Full Text
  - VanDerwerken, D, and Schmidler, SC. "Monitoring Joint Convergence of MCMC Samplers." Journal of Computational and Graphical Statistics 26, no. 3 (July 3, 2017): 558-568. Full Text
  - Cooke, B, Herzog, DP, Mattingly, JC, Mckinle, SA, and Schmidler, SC. "Geometric ergodicity of two-dimensional hamiltonian systems with a Lennard-Jones-like repulsive potential." Communications in Mathematical Sciences 15, no. 7 (January 1, 2017): 1987-2025. Full Text Open Access Copy
  - Ben-Shachar, R, Schmidler, S, and Koelle, K. "Drivers of Inter-individual Variation in Dengue Viral Load Dynamics." Plos Computational Biology 12, no. 11 (November 17, 2016): e1005194-null. Full Text
  - Estrada, R, Tomasi, C, Schmidler, SC, and Farsiu, S. "Tree Topology Estimation." Ieee Transactions on Pattern Analysis and Machine Intelligence 37, no. 8 (August 2015): 1688-1701. Full Text
  - Herman, JL, Challis, CJ, Novák, Á, Hein, J, and Schmidler, SC. "Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure." Molecular Biology and Evolution 31, no. 9 (September 2014): 2251-2266. Full Text
  - Daniels, KG, Tonthat, NK, McClure, DR, Chang, Y-C, Liu, X, Schumacher, MA, Fierke, CA, Schmidler, SC, and Oas, TG. "Ligand concentration regulates the pathways of coupled protein folding and binding." J Am Chem Soc 136, no. 3 (January 22, 2014): 822-825. Full Text Link to Item
  - Rodriguez, A, and Schmidler, SC. "BAYESIAN PROTEIN STRUCTURE ALIGNMENT." The Annals of Applied Statistics 8, no. 4 (January 2014): 2068-2095. Full Text
  - Wang, R, and 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 1, 2014): 326-339. Full Text
  - Ji, C, and Schmidler, SC. "Adaptive Markov Chain Monte Carlo for Bayesian Variable Selection." Journal of Computational and Graphical Statistics 22, no. 3 (July 2013): 708-728. Full Text
  - Challis, CJ, and Schmidler, SC. "A stochastic evolutionary model for protein structure alignment and phylogeny." Mol Biol Evol 29, no. 11 (November 2012): 3575-3587. Full Text Link to Item
  - Wolpert, RL, and Schmidler, SC. "α-Stable limit laws for harmonic mean estimators of marginal likelihoods." Statistica Sinica 22, no. 3 (July 1, 2012): 1233-1251. Full Text
  - Zheng, N, Schmidler, SC, Marks, D, and Brady, D. "Computer experiment and global optimization of layered monocentric lens systems." Optik 123, no. 14 (July 2012): 1249-1259. Full Text
  - Wilson, MA, Iversen, ES, Clyde, MA, Schmidler, SC, and Schildkraut, JM. "Bayesian model search and multilevel inference for SNP association studies." The Annals of Applied Statistics 4, no. 3 (September 2010): 1342-1364. Full Text Open Access Copy
  - Jia, B, Li, J, Huang, S, Schmidler, SC, and Wu, YK. "Electron beam energy spread measurements using optical klystron radiation." Physical Review Special Topics Accelerators and Beams 13, no. 8 (August 4, 2010). Full Text Open Access Copy
  - Wiehe, K, Kepler, TB, and Schmidler, SC. "P19-50. Simulation of an MPER peptide samples epitope conformations of two broadly neutralizing antibodies." Retrovirology 6, no. SUPPL. 3 (October 22, 2009). Full Text
  - Woodard, DB, Schmidler, SC, and Huber, M. "Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions." Annals of Applied Probability 19, no. 2 (April 1, 2009): 617-640. Full Text Open Access Copy
  - Woodard, DB, Schmidler, SC, and Huber, M. "Sufficient conditions for torpid mixing of parallel and simulated tempering." Electronic Journal of Probability 14 (January 1, 2009): 780-804. Full Text
  - Cooke, B, and Schmidler, SC. "Statistical prediction and molecular dynamics simulation." Biophys J 95, no. 10 (November 15, 2008): 4497-4511. Full Text Link to Item
  - Cooke, B, and Schmidler, SC. "Preserving the Boltzmann ensemble in replica-exchange molecular dynamics." J Chem Phys 129, no. 16 (October 28, 2008): 164112-. Full Text Link to Item
  - Valiaev, A, Lim, DW, Schmidler, S, Clark, RL, Chilkoti, A, and Zauscher, S. "Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides." Journal of the American Chemical Society 130, no. 33 (August 2008): 10939-10946. Full Text
  - Colinas, J, Schmidler, SC, Bohrer, G, Iordanov, B, and Benfey, PN. "Intergenic and genic sequence lengths have opposite relationships with respect to gene expression." Plos One 3, no. 11 (January 2008): e3670-null. Full Text Open Access Copy
  - Schmidler, SC, Lucas, JE, and Oas, TG. "Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction." Journal of Computational Biology : a Journal of Computational Molecular Cell Biology 14, no. 10 (December 2007): 1287-1310. Full Text
  - Jiang, T, Tomasi, C, and Schmidler, SC. "How to Dispatch Observers to Track an Evolving Boundary." 2007 First Acm/Ieee International Conference on Distributed Smart Cameras (September 2007). Full Text
  - Valiaev, A, Dong, WL, Chilkoti, A, Schmidler, S, and Zauscher, S. "Polypeptide-solvent interactions measured by single molecule force spectroscopy." Materials Research Society Symposium Proceedings 898 (2005): 92-97.
  - Schmidler, SC. "Discussion of "A Statistical Approach to Modeling Genomic Aberrations in Cancer Cells" by Newton et. al." Bayesian Statistics7 (2003). (Academic Article)
  - Schmidler, SC, Liu, JS, and Brutlag, DL. "Bayesian segmentation of protein secondary structure." Journal of Computational Biology : a Journal of Computational Molecular Cell Biology 7, no. 1-2 (February 2000): 233-248. Full Text
  - Schmidler, SC, Liu, JS, and Brutlag, DL. "Bayesian segmentation of protein secondary structure." J Comput Biol 7, no. 1-2 (February 2000): 233-248. Full Text Link to Item
  - Schmidler, SC, Liu, JS, and Brutlag, DL. "Probabilistic modeling for protein structure prediction." FASEB JOURNAL 13, no. 7 (April 23, 1999): A1542-A1542. Link to Item
  - Schmidler, SC, Liu, JS, and Brutlag, DL. "Bayesian protein structure prediction." Case Studies in Bayesian Statistics 5 (1999): 363-378. (Academic Article)
  - "Regression analysis of multiple protein structures." Proceedings of the Annual International Conference on Computational Molecular Biology, Recomb (January 1, 1998): 276-284.
  - Wu, TD, Schmidler, SC, Hastie, T, and Brutlag, DL. "Regression analysis of multiple protein structures." Journal of Computational Biology 5, no. 3 (1998): 597-607. (Academic Article)
  - Wu, TD, Schmidler, SC, Hastie, T, and Brutlag, DL. "Regression analysis of multiple protein structures." Journal of Computational Biology : a Journal of Computational Molecular Cell Biology 5, no. 3 (January 1998): 585-595. Full Text
  - Wu, TD, Schmidler, SC, Hastie, T, and Brutlag, DL. "Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins." Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (January 1998): 509-520.
- Conference Papers
  - Larson, G, Thorne, JL, and Schmidler, S. "Modeling Dependence in Evolutionary Inference for Proteins." January 1, 2018. Full Text
  - Wang, R, and Schmidler, SC. "Bayesian Multiple Protein Structure Alignment." : Springer International Publishing, 2014. Full Text
Teaching & Mentoring
Recent Courses

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Conference Papers

Recent Courses