David Koslicki

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 27

Top Venues

bioRxiv : the preprint server for biology

Bioinformatics (Oxford, England)

GigaScience

Journal of mathematical biology

Pennsylvania State University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Pennsylvania State University Aug 20 2019

United States

Associate Professor :: Computer Science and Engineering

Oregon State University Sep 01 2013 - Aug 20 2019

United States

Assistant professor :: Mathematics

Publications

David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics (Oxford, England) 40 (2) (2024)
Adam Park, David Koslicki
Prokrustean Graph: A substring index supporting rapid enumeration across a range of k-mer sizes. bioRxiv : the preprint server for biology (2024)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics (Oxford, England) 40 (2) (2024)
Adam Park, David Koslicki
Prokrustean Graph: A substring index supporting rapid enumeration across a range of k-mer sizes. bioRxiv : the preprint server for biology (2024)
Adam Park, David Koslicki
Prokrustean Graph: A substring index supporting rapid enumeration across a range of k-mer sizes. bioRxiv : the preprint server for biology (2024)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics (Oxford, England) 40 (2) (2024)
Chunyu Ma, Shaopeng Liu, David Koslicki
MetagenomicKG: a knowledge graph for metagenomic applications. bioRxiv : the preprint server for biology (2024)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics (Oxford, England) 40 (2) (2024)
Chunyu Ma, Shaopeng Liu, David Koslicki
MetagenomicKG: a knowledge graph for metagenomic applications. bioRxiv : the preprint server for biology (2024)
Mahmudur Rahman Hera, David Koslicki
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. bioRxiv : the preprint server for biology (2024)
Mahmudur Rahman Hera, David Koslicki
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. bioRxiv : the preprint server for biology (2024)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Wei Wei, Andrew Millward, David Koslicki
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L 2 UniFrac. bioRxiv : the preprint server for biology (2023)
Amy K 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. Bioinformatics (Oxford, England) 39 (3) (2023)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. bioRxiv : the preprint server for biology (2023)
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra A T Moxon, Anne E Thessen, Shervin Abdollahi, Sergio E Baranzini, Basazin Belhu, William E Byrd, Lawrence Chung, Andrew B Crouse, Marc P Duby, Stephen S Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer J Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte A Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Phillip J Mease, Sandrine Muller, Christopher John Mungall, Stephen A Ramsey, Jared C Roach, Irit R Rubin, Shepherd H Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I Su, Casey Ta, Paul B Watkins, Mark D Williams, Chunlei Wu, Colleen H Xu, null null
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges. Journal of clinical and translational science 7 (1) (2023)
Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki
KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description. GigaScience 12 (2023)
Wei Wei, Andrew Millward, David Koslicki
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L 2 UniFrac. bioRxiv : the preprint server for biology (2023)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. bioRxiv : the preprint server for biology (2023)
Mahmudur Rahman Hera, N Tessa Pierce, David Koslicki
Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash. Genome research (2023)
Wei Wei, Andrew Millward, David Koslicki
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac. Bioinformatics (Oxford, England) 39 (39 Suppl 1) (2023)
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. bioRxiv : the preprint server for biology (2023)
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J Brito, C Titus Brown, Jan P Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip Thomas Lanken Conradsen Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fábio Malcher Miranda, Serghei Mangul, Vanessa R Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C Piro, Jacob S Porter, Simon Rasmussen, Evan R Rees, Knut Reinert, Bernhard Y Renard, Espen Mikal Robertsen, Gail L Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stéphane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature methods 19 (4) (2022)
Fernando Meyer, Till-Robin Lesker, David Koslicki, Adrian Fritz, Alexey Gurevich, Aaron E Darling, Alexander Sczyrba, Andreas Bremges, Alice C McHardy
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. Nature protocols 16 (4) (2021)
David Koslicki, Mark Novak
Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations. Journal of mathematical biology 76 (4) (2017)

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Publication Activity (10 Years)

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David Koslicki