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2020 – today
- 2024
[j11]David Koslicki
, Stephen White, Chunyu Ma, Alexei Novikov:
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinform. 40(2) (2024)- [c6]Mahmudur Rahman Hera, David Koslicki:
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. WABI 2024: 6:1-6:16 - 2023
- [j10]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:
ARAX: a graph-based modular reasoning tool for translational biomedicine. Bioinform. 39(3) (2023) - [j9]Wei Wei, Andrew Millward, David Koslicki:
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac. Bioinform. 39(Supplement-1): 57-65 (2023) - 2022
- [j8]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:
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. BMC Bioinform. 23(1): 400 (2022) - [j7]Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev:
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. J. Comput. Biol. 29(2): 155-168 (2022) - [c5]Varuni Sarwal, Serghei Mangul, David Koslicki:
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. IPDPS Workshops 2022: 217 - [c4]Wei Wei, David Koslicki:
WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data. WABI 2022: 15:1-15:22 - [i2]Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki:
Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph. CoRR abs/2212.01384 (2022) - [i1]David Koslicki, Dana Gibbon, Mark Novak:
PressPurt: network sensitivity to press perturbations under interaction uncertainty. F1000Research 11: 173 (2022) - 2020
- [c3]Simon Foucart, David Koslicki:
Finer Metagenomic Reconstruction via Biodiversity Optimization. NeurIPS 2020
2010 – 2019
- 2019
- [j6]David Koslicki, Hooman Zabeti:
Improving MinHash via the containment index with applications to metagenomic analysis. Appl. Math. Comput. 354: 206-215 (2019) - [c2]Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen:
Workshop on Microbiomics, Metagenomics, and Metabolomics. BCB 2019: 618 - 2018
- [j5]Mitra Ansariola, Molly Megraw, David Koslicki:
IndeCut evaluates performance of network motif discovery algorithms. Bioinform. 34(9): 1514-1521 (2018) - 2016
- [c1]Serghei Mangul, David Koslicki:
Reference-free comparison of microbial communities via de Bruijn graphs. BCB 2016: 68-77 - 2014
- [j4]Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander:
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition. Bioinform. 30(17): 2423-2431 (2014) - [j3]Simon Foucart, David Koslicki:
Sparse Recovery by Means of Nonnegative Least Squares. IEEE Signal Process. Lett. 21(4): 498-502 (2014) - [p1]Andreas Holzinger, Matthias Hörtenhuber, Christopher C. Mayer, Martin Bachler, Siegfried Wassertheurer, Armando J. Pinho, David Koslicki:
On Entropy-Based Data Mining. Interactive Knowledge Discovery and Data Mining in Biomedical Informatics 2014: 209-226 - 2013
- [j2]David Koslicki, Simon Foucart, Gail Rosen:
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinform. 29(17): 2096-2102 (2013) - 2011
- [j1]David Koslicki:
Topological entropy of DNA sequences. Bioinform. 27(8): 1061-1067 (2011)
Coauthor Index
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