Scholars@Duke
Scott C. Schmidler

Scott C. Schmidler

Associate Professor of Statistical Science
Statistical Science
Box 90251, Department of Statistical Science, Durham, NC 27708-0251
212 Old Chem, Durham, NC 27708-0251

Scholarly Works - Journal articles

ABSEIL: A polypeptide helicity and ensemble prediction tool.

Journal article J Mol Biol · September 15, 2026 Nascent helicity in polypeptides and unfolded proteins arises from local structure formation and represents one of the earliest events in a protein folding reaction. Nascent helicity may also influence the physical properties of intrinsically disordered re ... Full text Link to item Cite

The effect of osmolytes on peptide helicity: Experiments and predictions.

Journal article Protein Sci · February 2026 Nascent helicity in polypeptides and unfolded proteins is a type of rapid local structure formation that could represent the earliest events in a protein folding reaction. Nascent helicity may also influence the physical properties of intrinsically disorde ... Full text Link to item Cite

Computing the inducibility of broadly neutralizing antibodies under a context-dependent model of affinity maturation: applications to sequential vaccine design.

Journal article J Immunol · January 21, 2026 A key challenge in B-cell lineage-based vaccine design is understanding the "inducibility" of target neutralizing antibodies-the ability of these antibodies to be elicited by presentation of an immunogen. Induction relies on a combination of stochastic div ... Full text Link to item Cite

On Gibbs Sampling for Endpoint-Conditioned Neighbor-Dependent Sequence Evolution Models

Journal article Journal of Computational and Graphical Statistics · January 1, 2026 In 2008, Hobolth described an algorithm for sampling paths in models of DNA sequence evolution with neighbor dependence. We show that this algorithm fails to sample the desired target distribution, and provide a simple Metropolis acceptance step correction ... Full text Cite

Efficient enumeration and visualization of helix-coil ensembles.

Journal article Biophys J · February 6, 2024 Helix-coil models are routinely used to interpret circular dichroism data of helical peptides or predict the helicity of naturally-occurring and designed polypeptides. However, a helix-coil model contains significantly more information than mean helicity a ... Full text Link to item Cite

Finite sample complexity of sequential Monte Carlo estimators on multimodal target distributions

Journal article Annals of Applied Probability · February 1, 2024 We prove finite sample complexities for sequential Monte Carlo (SMC) algorithms which require only local mixing times of the associated Markov kernels. Our bounds are particularly useful when the target distribution is multimodal and global mixing of the M ... Full text Cite

Computing the inducibility of B cell lineages under a context-dependent model of affinity maturation: Applications to sequential vaccine design.

Journal article bioRxiv · October 17, 2023 A key challenge in B cell lineage-based vaccine design is understanding the inducibility of target neutralizing antibodies. We approach this problem through the use of detailed stochastic modeling of the somatic hypermutation process that occurs during aff ... Full text Link to item Cite

Efficient Enumeration and Visualization of Helix-coil Ensembles.

Journal article bioRxiv · September 17, 2023 Helix-coil models are routinely used to interpret CD data of helical peptides or predict the helicity of naturally-occurring and designed polypeptides. However, a helix-coil model contains significantly more information than mean helicity alone, as it defi ... Full text Open Access Link to item Cite

Finite-sample complexity of sequential Monte Carlo estimators

Journal article Annals of Statistics · June 1, 2023 We present bounds for the finite-sample error of sequential Monte Carlo samplers on static spaces. Our approach explicitly relates the performance of the algorithm to properties of the chosen sequence of distributions and mixing properties of the associate ... Full text Cite

Minimax mixing time of the Metropolis-adjusted Langevin algorithm for log-concave sampling

Journal article Journal of Machine Learning Research · July 1, 2022 We study the mixing time of the Metropolis-adjusted Langevin algorithm (MALA) for sampling from a log-smooth and strongly log-concave distribution. We establish its optimal minimax mixing time under a warm start. Our main contribution is two-fold. First, f ... Cite

A Bayesian non-parametric mixed-effects model of microbial growth curves

Journal article PLOS Computational Biology · October 26, 2020 Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety ... Full text Cite

Incorporating nearest-neighbor site dependence into protein evolution models

Journal article Journal of Computational Biology · March 1, 2020 Evolutionary models of proteins are widely used for statistical sequence alignment and inference of homology and phylogeny. However, the vast majority of these models rely on an unrealistic assumption of independent evolution between sites. Here we focus o ... Full text Cite

Systematic discovery of Archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis

Journal article mSystems · October 31, 2017 To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, sali ... Full text Cite

Monitoring joint convergence of MCMC samplers

Journal article Journal of Computational and Graphical Statistics · July 3, 2017 We present a diagnostic for monitoring convergence of a Markov chain Monte Carlo (MCMC) sampler to its target distribution. In contrast to popular existing methods, we monitor convergence to the joint target distribution directly rather than a select scala ... Full text Cite

Geometric ergodicity of two-dimensional hamiltonian systems with a Lennard-Jones-like repulsive potential

Journal article Communications in Mathematical Sciences · January 1, 2017 We establish ergodicity of the Langevin dynamics for a simple two-particle system involving a Lennard-Jones type potential. Moreover, we show that the dynamics is geometrically ergodic; that is, the system converges to stationarity exponentially fast. Meth ... Full text Open Access Cite

Drivers of inter-individual variation in Dengue viral load dynamics

Journal article PLoS Computational Biology · November 1, 2016 Dengue is a vector-borne viral disease of humans that endemically circulates in many tropical and subtropical regions worldwide. Infection with dengue can result in a range of disease outcomes. A considerable amount of research has sought to improve our un ... Full text Cite

Tree topology estimation

Journal article IEEE Transactions on Pattern Analysis and Machine Intelligence · August 1, 2015 Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree-what connects to what-from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar g ... Full text Cite

Bayesian protein structure alignment

Journal article Annals of Applied Statistics · December 1, 2014 The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary time ... Full text Cite

Ligand concentration regulates the pathways of coupled protein folding and binding.

Journal article J Am Chem Soc · January 22, 2014 Coupled ligand binding and conformational change plays a central role in biological regulation. Ligands often regulate protein function by modulating conformational dynamics, yet the order in which binding and conformational change occurs are often hotly d ... Full text Link to item Cite

Bayesian multiple protein structure alignment

Journal article Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2014 Multiple protein structure alignment is an important tool in computational biology, with numerous algorithms published in the past two decades. However, recently literature highlights a growing recognition of the inconsistencies among alignments from diffe ... Full text Cite

Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure

Journal article Molecular Biology and Evolution · January 1, 2014 For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures genera ... Full text Cite

Adaptive Markov chain Monte Carlo for Bayesian variable selection

Journal article Journal of Computational and Graphical Statistics · December 17, 2013 We describe adaptive Markov chain Monte Carlo (MCMC) methods for sampling posterior distributions arising from Bayesian variable selection problems. Point-mass mixture priors are commonly used in Bayesian variable selection problems in regression. However, ... Full text Cite

A stochastic evolutionary model for protein structure alignment and phylogeny

Journal article Molecular Biology and Evolution · November 1, 2012 We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix ... Full text Cite

Computer experiment and global optimization of layered monocentric lens systems

Journal article Optik · July 1, 2012 In this paper we derive a general analytical solution for a monocentric lens system and present a global optimization method combining sequential design for global optimization and an expected improvement algorithm for global optimization for the design an ... Full text Cite

α-Stable limit laws for harmonic mean estimators of marginal likelihoods

Journal article Statistica Sinica · July 1, 2012 The task of calculating marginal likelihoods arises in a wide array of statistical inference problems, including the evaluation of Bayes factors for model selection and hypothesis testing. Although Markov chain Monte Carlo methods have simplified many post ... Full text Cite

BAYESIAN MODEL SEARCH AND MULTILEVEL INFERENCE FOR SNP ASSOCIATION STUDIES.

Journal article Ann Appl Stat · September 1, 2010 Technological advances in genotyping have given rise to hypothesis-based association studies of increasing scope. As a result, the scientific hypotheses addressed by these studies have become more complex and more difficult to address using existing analyt ... Full text Open Access Link to item Cite

Electron beam energy spread measurements using optical klystron radiation

Journal article Physical Review Special Topics - Accelerators and Beams · August 4, 2010 Full text Open Access Cite

Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions

Journal article Annals of Applied Probability · April 1, 2009 We give conditions under which a Markov chain constructed via parallel or simulated tempering is guaranteed to be rapidly mixing, which are applicable to a wide range of multimodal distributions arising in Bayesian statistical inference and statistical mec ... Full text Open Access Cite

Sufficient conditions for torpid mixing of parallel and simulated tempering

Journal article Electronic Journal of Probability · January 1, 2009 We obtain upper bounds on the spectral gap of Markov chains constructed by parallel and simulated tempering, and provide a set of sufficient conditions for torpid mixing of both techniques. Combined with the results of [22], these results yield a two-sided ... Full text Cite

Statistical prediction and molecular dynamics simulation

Journal article Biophysical Journal · November 15, 2008 We describe a statistical approach to the validation and improvement of molecular dynamics simulations of macromolecules. We emphasize the use of molecular dynamics simulations to calculate thermodynamic quantities that may be compared to experimental meas ... Full text Cite

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics

Journal article The Journal of Chemical Physics · October 28, 2008 We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulat ... Full text Cite

Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides

Journal article Journal of the American Chemical Society · August 20, 2008 We investigated the effect of temperature, ionic strength, solvent polarity, and type of guest residue on the force-extension behavior of single, end-tethered elastin-like polypeptides (ELPs), using single molecule force spectroscopy (SMFS). ELPs are stimu ... Full text Cite

Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.

Journal article PloS one · January 2008 Eukaryotic genomes are mostly composed of noncoding DNA whose role is still poorly understood. Studies in several organisms have shown correlations between the length of the intergenic and genic sequences of a gene and the expression of its corresponding m ... Full text Open Access Cite

Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction.

Journal article J Comput Biol · December 2007 Analysis of biopolymer sequences and structures generally adopts one of two approaches: use of detailed biophysical theoretical models of the system with experimentally-determined parameters, or largely empirical statistical models obtained by extracting p ... Full text Link to item Cite

How to dispatch observers to track an evolving boundary

Journal article 2007 1st ACM/IEEE International Conference on Distributed Smart Cameras, ICDSC · 2007 Some distributed-sensing applications make it necessary to dispatch a limited number of observers (ships, vehicles, or airplanes with cameras; field workers with chemical kits; high-flying balloons with atmospheric sensors) to track the evolving boundary o ... Full text Cite

Polypeptide-solvent interactions measured by single molecule force spectroscopy

Journal article Materials Research Society Symposium Proceedings · 2005 Stimulus-responsive biomolecules have attracted a large research interest because of their potential application in various areas such as drug delivery, actuators and sensing devices at the nanoscale. Using single-molecule force spectroscopy (SMFS) we stud ... Cite

Bayesian segmentation of protein secondary structure

Journal article Journal of Computational Biology · July 10, 2000 We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local window of residues, sliding this window along the length of the sequence. In Co ... Full text Cite

Probabilistic modeling for protein structure prediction

Journal article FASEB JOURNAL · April 23, 1999 Link to item Cite

Bayesian protein structure prediction

Journal article Case Studies in Bayesian Statistics · 1999 Cite

Regression analysis of multiple protein structures

Journal article Journal of Computational Biology · 1998 Cite

Regression analysis of multiple protein structures

Journal article Proceedings of the Annual International Conference on Computational Molecular Biology RECOMB · January 1, 1998 A general framework is presented for analyzing multiple protein structures. A family of related protein structures may be analyzed using statistical regression methods. The analysis requires alternating steps of finding correspondences among the protein st ... Full text Cite

Regression analysis of multiple protein structures

Journal article Journal of Computational Biology · 1998 A general framework is presented for analyzing multiple protein structures using statistical regression methods. The regression approach can superimpose protein structures rigidly or with shear. Also, this approach can superimpose multiple structures expli ... Cite

Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins.

Journal article Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 1998 A novel approach for analyzing multiple protein structures is presented. A family of related protein structures may be characterized by an affine model, obtained by applying transformation matrices that permit both rotation and shear. The affine model and ... Cite