David Koslicki

Associate Professor of Computer Science and Engineering and Biology

David Koslicki

Research Summary

Developing efficient algorithms to extract insight from high-throughput sequencing data.

Huck Graduate Students

Huck Affiliations

Links

Publication Tags

Genome Genes Metagenomics Methodology Metagenome Bioinformatics Software Sampling Statistics Painting Strain Viruses Matlab Datasets Alignment Health Benchmarking Databases Nucleotides Method Availability Linux Classifiers Biological Property Mutation

Most Recent Papers

The minimizer Jaccard estimator is biased and inconsistent

Mahdi Belbasi, A Blanca Pimentel, R Harris, David Koslicki, P Medvedev, ISMB 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, 2022, Journal of Computational Biology on p. 155-168

PressPurt: network sensitivity to press perturbations under interaction uncertainty

David Koslicki, Dana Gibbon, Mark Novak, 2022, F1000Research

Critical Assessment of Metagenome Interpretation

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 Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T.L.C. 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, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, 2022, Nature Methods

Technology dictates algorithms: recent developments in read alignment

Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul, 2021, Genome Biology

Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit

Fernando Meyer, Till Robin Lesker, David Koslicki, Adrian Fritz, Alexey Gurevich, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges, Alice C. McHardy, 2021, Nature Protocols

Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems

Karamarie Fecho, James Balhoff, Chris Bizon, William E. Byrd, Sui Hang, David Koslicki, Stefano E. Rensi, Patrick L. Schmitt, Mathias J. Wawer, Mark Williams, Stanley C. Ahalt, 2021, Clinical and Translational Science

Finer Metagenomic Reconstruction via Biodiversity Optimization

Simon Foucart, David Koslicki, 2020, Advances in Neural Information Processing Systems on p. 14

Metalign

Nathan Lapierre, Mohammed Alser, Eleazar Eskin, David Koslicki, Serghei Mangul, 2020, Genome Biology

Erratum

Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki, Serghei Mangul, 2020, BMC Biology

Most-Cited Papers

Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. Demaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvočiutė, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K.H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael D. Barton, Thomas Lingner, Hsin Hung Lin, Yu Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy, 2017, Nature Methods on p. 1063-1071

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

Loes M. Olde Loohuis, Serghei Mangul, Anil P.S. Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P. Boks, Catherine Lomen-Hoerth, Martina Wiedau-Pazos, Rita M. Cantor, Willem M. De Vos, René S. Kahn, Eleazar Eskin, Roel A. Ophoff, 2018, Translational Psychiatry

Sparse recovery by means of nonnegative least squares

Simon Foucart, David Koslicki, 2014, IEEE Signal Processing Letters on p. 498-502

On entropy-based data mining

Andreas Holzinger, Matthias Hörtenhuber, Christopher Mayer, Martin Bachler, Siegfried Wassertheurer, Armando J. Pinho, David Koslicki, 2014, Lecture Notes in Computer Science on p. 209-226

Striped UniFrac

Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez, Rob Knight, 2018, Nature Methods on p. 847-848

Quikr

David Koslicki, Simon Foucart, Gail Rosen, 2013, Bioinformatics on p. 2096-2102

MetaPalette

David Koslicki, Daniel Falush, 2016, mSystems on p. e00020--16

WGSQuikr

David Koslicki, Simon Foucart, Gail Rosen, 2014, PLoS One on p. e91784

Assessing taxonomic metagenome profilers with OPAL

Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy, David Koslicki, 2019, Genome Biology on p. 51

Coding sequence density estimation via topological pressure

David Koslicki, Daniel J. Thompson, 2015, Journal of Mathematical Biology on p. 45-69