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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

Selected Publications


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

Conference 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

Modeling dependence in evolutionary inference for proteins

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2018 Protein structure alignment is a classic problem of computational biology, and is widely used to identify structural and functional similarity and to infer homology among proteins. Previously a statistical model for protein structural evolution has been in ... 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

Bayesian multiple protein structure alignment

Conference 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