David Koslicki

According to our database, David Koslicki authored at least 21 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2024

<tt>YACHT</tt>: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.

David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov

Bioinform., February, 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, 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

J. Open Source Softw., 2024

Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation.

Mahmudur Rahman Hera, David Koslicki

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

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, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki

Bioinform., March, 2023

Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: <i>L</i>2UniFrac.

Wei Wei, Andrew Millward, David Koslicki

Bioinform., 2023

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

PressPurt: network sensitivity to press perturbations under interaction uncertainty.

David Koslicki, Dana Gibbon, Mark Novak

F1000Research, 2022

Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph.

Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki

CoRR, 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, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey

BMC Bioinform., 2022

WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data.

Wei Wei, David Koslicki

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.

Varuni Sarwal, Serghei Mangul, David Koslicki

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

2020

Finer Metagenomic Reconstruction via Biodiversity Optimization.

Simon Foucart, David Koslicki

Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

2019

Improving MinHash via the containment index with applications to metagenomic analysis.

David Koslicki, Hooman Zabeti

Appl. Math. Comput., 2019

Workshop on Microbiomics, Metagenomics, and Metabolomics.

Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

IndeCut evaluates performance of network motif discovery algorithms.

Mitra Ansariola, Molly Megraw, David Koslicki

Bioinform., 2018

2016

Reference-free comparison of microbial communities via de Bruijn graphs.

Serghei Mangul, David Koslicki

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2014

On Entropy-Based Data Mining.

Andreas Holzinger, Matthias Hörtenhuber, Christopher C. Mayer, Martin Bachler, Siegfried Wassertheurer, Armando J. Pinho, David Koslicki

Proceedings of the Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014

Sparse Recovery by Means of Nonnegative Least Squares.

Simon Foucart, David Koslicki

IEEE Signal Process. Lett., 2014

SEK: sparsity exploiting <i>k</i>-mer-based estimation of bacterial community composition.

Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander

Bioinform., 2014

2013

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.

David Koslicki, Simon Foucart, Gail Rosen

Bioinform., 2013

2011

Topological entropy of DNA sequences.

David Koslicki

Bioinform., 2011