Forecasting Competitions with Correlated Events

with Rafael Frongillo, Anish Thilagar & Bo Waggoner (accepted)

Interpretable Metric Learning in Comparative Metagenomics: The Adaptive Haar-like Distance

PLOS Computational Biology (2024)
with E.D. Gorman

Sparsification of Covariance Matrices of K-regular Trees

Proceedings of the 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (2024)

with S. Svihla

Sparsification of large ultrametric matrices: insights into the microbial Tree of Life

Proceedings of the Royal Society A: Mathematical, Physical, and Engineering Sciences (2023)

with E.D. Gorman

Getting the lay of the land in discrete space: A survey of metric dimension and its applications

SIAM Review (2023)

with R.C. Tillquist & R.M. Frongillo

On latent idealized models in symbolic datasets: unveiling signals in noisy sequencing data

Journal of Mathematical Biology (2023)

with A. Pearson

Levenshtein graphs: Resolvability, automorphisms & determining sets

Journal of Discrete Mathematics (2023)

with P. Ruth

Truncated metric dimension for finite graphs

Discrete Applied Mathematics (2022)

with R.M. Frongillo, J. Geneson, R.C. Tillquist & E. Ji

Resolvability of Hamming Graphs

SIAM Journal on Discrete Mathematics (2020)

with L. Laird, R.C. Tillquist & S. Becker

Stochastic Analysis of Minimal Automata Growth for Generalized Strings

Methodology and Computing in Applied Probability (2020)

with I. Char

Hidden independence in unstructured probabilistic models

Proceedings of the 31st International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (2020)

with A. Pearson

Low-dimensional representation of genomic sequences

Journal of Mathematical Biology (2019)

with R.C. Tillquist

Metric Dimension

Scholarpedia (2019)

with R.C. Tillquist & R.M. Frongillo

Quantum Computation

Scholarpedia (2018)

with J. Pieper

Balance Trees Reveal Microbial Niche Differentiation

mSystems (2017)

with J.T. Morton, J. Sanders, R.A. Quinn, D. McDonald, A. Gonzalez, Y. Vazquez-Baeza, J.A. Navas-Molina, S.J. Song, J.L. Metcalf, E.E. Hyde, P.C. Dorrestein & R. Knight

RNA Pol II transcription model and interpre- tation of GRO-seq data

Journal of Mathematical Biology (2017)

with J.G. Azofeifa, M.A. Allen & R.D. Dowell

An annotation agnostic algorithm for detecting nascent RNA transcripts in GRO-seq

IEEE/ACM Transactions on Computational Biology and Bioinformatics (2017)

with J.G. Azofeifa, M.A. Allen & R.D. Dowell

Approximation of sojourn-times via maximal couplings: Motif frequency distributions

Journal of Mathematical Biology (2014)

with S. Chestnut 

FStitch: A fast and simple algorithm for detecting nascent RNA transcripts

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (2014)

with J. Azofeifa, M. A. Allen & R. D. Dowell 

Mathematical approaches for describing microbial populations: practice and theory for extrapolation of rich environments

In “The Human Microbiota”, ISBN: 978-0-470-47989-6 (2013)

with R. Knight

Random Cayley digraphs of diameter 2 and given degree

Discrete Mathematics and Theoretical Computer Science (2012)

with P. Potocnik, J. Siran & M. C. Wilson

Estimation of Distribution Overlap of Urn Models

PLOS ONE (2012)

with J. Hampton

Toward the asymptotic count of bi-modular hidden patterns under proba- bilistic dynamical sources: a case study

Proceedings of the 23rd International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (2012)

with L. Lhothe 

Extrapolation of urn models via Poissonization: accurate mea- surements of the microbial unknown

PLOS ONE (2011)

with R. Gouet & J. Reeder

UniFrac: an effective distance metric for microbial community comparison

Multidisciplinary Journal of Microbial Ecology (2011)

with C. Lozupone,  D. Knights, J. Stombaugh & R. Knight 

Variables Aleatorias y Simulación Estocástica

Editorial JC Sáez, SBN: 978-956-306-068-3 (2011)

Chiral histidine selection by D-ribose RNA

RNA Journal (2010)

with M. Illangasekare, R. Turk, G. C. Peterson & M. Yarus

Natural and artificial RNAs occupy the same restricted region of sequence space

RNA Journal (2010)

with R. Kennedy,  Z. Wu, C. Zhang, M. Yarus, H. De Sterck & R. Knight

Occupancy distributions in Markov chains via Doeblin’s ergodicity coefficient

Proceedings of he 21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms (2010)

with S. Chestnut 

Prediction of unseen proportions in urn models with restricted sampling

Proceedings of the Sixth Workshop on Analytic Algorithmics and Combinatorics (2009)

Comparison of methods for estimating the nucleotide substitution matrix

BMC Bioinformatics (2008)

with M. Oscamou, D. McDonald, V.-B. Yap, G. A. Huttley & R. Knight

Information, probability, and the abundance of the simplest RNA active sites

Frontiers in Bioscience (2008)

with R. Kennedy, M. Yarus & R. Knight

Multiple pattern matching: A Markov chain approach

Journal of Mathematical Biology (2008)

with M.D. Betterton & R. Knight

Semi-supervised learning of a Markovian metric

Proceedings of the 2008 SIAM International Conference on Data Mining (2008)

with A.S. Bijral & G. Grudic

Markovian embeddings of general random strings

Proceedings of the Fifth Workshop on Analytic Algorithmics and Combinatorics (2008)

Minimal Markov chain embeddings of pattern problems

Proceedings of the 2007 Information Theory and Applications Workshop (2007)

Uniqueness of polynomial canonical representations

Proceedings of the 2007 Conference on Analysis of Algorithms (2007)

Uniform formulae for coefficients of meromorphic functions in two variables. Part I.

SIAM Journal of Discrete Mathematics (2006)

Mixed powers of generating functions

Proceedings of the Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities (2006)