David Koslicki

27 papers A* 1B 1C 3Journal 18Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
Elucidating Transitions of
J. Comput. Biol.
Adam Park, David Koslicki
2025 J jnl
Estimating similarity and distance using FracMinHash.
Algorithms Mol. Biol.
Mahmudur Rahman Hera, David Koslicki
2025 C conf
Estimation of Substitution and Indel Rates via k-mer Statistics.
WABI
Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, Antonio Blanca
2025 B conf
Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis.
RECOMB
Adam Park, David Koslicki
2024 C conf
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation.
WABI
Mahmudur Rahman Hera, David Koslicki
2024 J jnl
Metagenomic functional profiling: to sketch or not to sketch?
Bioinform.
Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S. Rodríguez, Chunyu Ma, David Koslicki
2024 J jnl
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets.
J. Open Source Softw.
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, Hannah Eve Houts, Lisa K. Johnson, Fabian Klötzl, David Koslicki, Marisa Lim, Ricky Lim, Bradley Nelson, Ivan Ogasawara, Taylor Reiter, Camille Scott, Andreas Sjödin, Daniel S. Standage, S. Joshua Swamidass, Connor Tiffany, Pranathi Vemuri, Erik Young, C. Titus Brown
2023 J jnl
ARAX: a graph-based modular reasoning tool for translational biomedicine.
Bioinform.
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, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki
2023 J jnl
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples:
Bioinform.
Wei Wei, Andrew Millward, David Koslicki
2022 J jnl
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.
Bioinform.
Shaopeng Liu, David Koslicki
2022 J jnl
Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph.
CoRR
Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki
2022 J jnl
PressPurt: network sensitivity to press perturbations under interaction uncertainty.
F1000Research
David Koslicki, Dana Gibbon, Mark Novak
2022 J jnl
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.
BMC Bioinform.
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, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey
2022 — conf
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.
IPDPS Workshops
Varuni Sarwal, Serghei Mangul, David Koslicki
2022 J jnl
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches.
J. Comput. Biol.
Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
2022 J jnl
The minimizer Jaccard estimator is biased and inconsistent.
Bioinform.
Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
2022 C conf
WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data.
WABI
Wei Wei, David Koslicki
2020 A* conf
Finer Metagenomic Reconstruction via Biodiversity Optimization.
NeurIPS
Simon Foucart, David Koslicki
2019 J jnl
Improving MinHash via the containment index with applications to metagenomic analysis.
Appl. Math. Comput.
David Koslicki, Hooman Zabeti
2019 — conf
Workshop on Microbiomics, Metagenomics, and Metabolomics.
BCB
Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen
2018 J jnl
IndeCut evaluates performance of network motif discovery algorithms.
Bioinform.
Mitra Ansariola, Molly Megraw, David Koslicki
2016 — conf
Reference-free comparison of microbial communities via de Bruijn graphs.
BCB
Serghei Mangul, David Koslicki
2014 — ch.
On Entropy-Based Data Mining.
Interactive Knowledge Discovery and Data Mining in Biomedical Informatics
Andreas Holzinger, Matthias Hörtenhuber, Christopher C. Mayer, Martin Bachler, Siegfried Wassertheurer, Armando J. Pinho, David Koslicki
2014 J jnl
SEK: sparsity exploiting
Bioinform.
Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander
2014 J jnl
Sparse Recovery by Means of Nonnegative Least Squares.
IEEE Signal Process. Lett.
Simon Foucart, David Koslicki
2013 J jnl
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.
Bioinform.
David Koslicki, Simon Foucart, Gail Rosen
2011 J jnl
Topological entropy of DNA sequences.
Bioinform.
David Koslicki