Topological entropy of DNA sequences. - David Koslicki (Bioinform., 2011)

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. - David Koslicki; Simon Foucart; Gail Rosen (Bioinform., 2013)

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition. - Saikat Chatterjee; David Koslicki; Siyuan Dong; Nicolas Innocenti; Lu Cheng 004; Yueheng Lan; Mikko Vehkaperä; Mikael Skoglund; Lars K. Rasmussen; Erik Aurell; Jukka Corander (Bioinform., 2014)

Sparse Recovery by Means of Nonnegative Least Squares. - Simon Foucart; David Koslicki (IEEE Signal Process. Lett., 2014)

On Entropy-Based Data Mining. - Andreas Holzinger; Matthias Hörtenhuber; Christopher C. Mayer; Martin Bachler; Siegfried Wassertheurer; Armando J. Pinho; David Koslicki (Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014)

Reference-free comparison of microbial communities via de Bruijn graphs. - Serghei Mangul; David Koslicki (BCB, 2016)

IndeCut evaluates performance of network motif discovery algorithms. - Mitra Ansariola; Molly Megraw; David Koslicki (Bioinform., 2018)

Workshop on Microbiomics, Metagenomics, and Metabolomics. - Soha Hassoun; Yasser El-Manzalawy; Georg Gerber; David Koslicki; Gail Rosen (BCB, 2019)

Improving MinHash via the containment index with applications to metagenomic analysis. - David Koslicki; Hooman Zabeti (Appl. Math. Comput., 2019)

Finer Metagenomic Reconstruction via Biodiversity Optimization. - Simon Foucart; David Koslicki (NeurIPS, 2020)

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. - Varuni Sarwal; Serghei Mangul; David Koslicki (IPDPS Workshops, 2022)

WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data. - Wei Wei; David Koslicki (WABI, 2022)

The minimizer Jaccard estimator is biased and inconsistent. - Mahdi Belbasi; Antonio Blanca; Robert S. Harris; David Koslicki; Paul Medvedev (Bioinform., 2022)

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices. - Shaopeng Liu; David Koslicki (Bioinform., 2022)

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. - E. C. Wood; Amy Glen; Lindsey G. Kvarfordt; Finn Womack; Liliana Acevedo; Timothy S. Yoon; Chunyu Ma; Veronica Flores; Meghamala Sinha; Yodsawalai Chodpathumwan; Arash Termehchy; Jared C. Roach; et al. (BMC Bioinform., 2022)

Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph. - Chunyu Ma; Zhihan Zhou 001; Han Liu 001; David Koslicki (CoRR, 2022)

PressPurt: network sensitivity to press perturbations under interaction uncertainty. - David Koslicki; Dana Gibbon; Mark Novak (F1000Research, 2022)

The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. - Antonio Blanca; Robert S. Harris; David Koslicki; Paul Medvedev (J. Comput. Biol., 2022)

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac. - Wei Wei; Andrew Millward; David Koslicki (Bioinform., 2023)

ARAX: a graph-based modular reasoning tool for translational biomedicine. - Amy Glen; Chunyu Ma; Luis Mendoza; Finn Womack; E. C. Wood; Meghamala Sinha; Liliana Acevedo; Lindsey G. Kvarfordt; Ross C. Peene; Shaopeng Liu; Andrew S. Hoffman; Jared C. Roach; et al. (Bioinform., 2023)

Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. - Mahmudur Rahman Hera; David Koslicki (WABI, 2024)

Metagenomic functional profiling: to sketch or not to sketch? - Mahmudur Rahman Hera; Shaopeng Liu; Wei Wei; Judith S. Rodríguez; Chunyu Ma; David Koslicki (Bioinform., 2024)

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. - Luiz Irber; N. Tessa Pierce-Ward; Mohamed Abuelanin; Harriet Alexander; Abhishek Anant; Keya Barve; Colton Baumler; Olga B. Botvinnik; Phillip Brooks; Daniel Dsouza; Gautier Laurent; Mahmudur Rahman Hera; et al. (J. Open Source Softw., 2024)

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. - David Koslicki; Stephen White; Chunyu Ma; Alexei Novikov (Bioinform., 2024)

ANI distance matrix of 25412 KOs generated using sourmash. - Shaopeng Liu; Wei Wei; David Koslicki (Zenodo, 2024)

Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis. - Adam Park; David Koslicki (RECOMB, 2025)

Estimation of Substitution and Indel Rates via k-mer Statistics. - Mahmudur Rahman Hera; Paul Medvedev; David Koslicki; Antonio Blanca (WABI, 2025)

Estimating similarity and distance using FracMinHash. - Mahmudur Rahman Hera; David Koslicki (Algorithms Mol. Biol., 2025)