David Koslicki
Associate Professor of Computer Science and Engineering and Biology
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W354 Westgate
University Park, PA - dmk333@psu.edu
- 814-865-1611
Research Summary
Developing efficient algorithms to extract insight from high-throughput sequencing data.
Huck Graduate Students
Huck Affiliations
Links
Publication Tags
Metagenomics Entropy Genes Genome Metagenome Databases Software Sampling Methodology Painting Viruses Datasets Microbiota Matlab Health Benchmarking Method Bioinformatics Linux Availability Classifiers Microorganisms Need Classifier Data MiningMost Recent Papers
The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches
A Blanca Pimentel, R Harris, David Koslicki, P Medvedev, 2021, RECOMB
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
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
Improving the usability and comprehensiveness of microbial databases
Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki, Serghei Mangul, 2020, BMC Biology
Improving MinHash via the containment index with applications to metagenomic analysis
David Koslicki, Hooman Zabeti, 2019, Applied Mathematics and Computation on p. 206-215
MiCoP
Nathan Lapierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin, 2019, BMC Genomics
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
Workshop on Microbiomics, Metagenomics, and Metabolomics
Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen, 2019, on p. 618--618
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
Sparse recovery by means of nonnegative least squares
Simon Foucart, David Koslicki, 2014, IEEE Signal Processing Letters on p. 498-502
Topological entropy of DNA sequences
David Koslicki, 2011, Bioinformatics on p. 1061-1067
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
Quikr
David Koslicki, Simon Foucart, Gail Rosen, 2013, Bioinformatics on p. 2096-2102
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
WGSQuikr
David Koslicki, Simon Foucart, Gail Rosen, 2014, PLoS One on p. e91784
MetaPalette
David Koslicki, Daniel Falush, 2016, mSystems on p. e00020--16
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
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
News Articles Featuring David Koslicki
Sep 24, 2020
Penn State Microbiome Center elects new executive committee
The Penn State Microbiome Center in the Huck Institutes of the Life Sciences recently elected six new members to join its executive committee. The new members, along with 11 others who remained on the committee, started their two-year term in July.
Full Article