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
Genome Genes Sampling Entropy Metagenomics Uncertainty Metagenome Methodology Bioinformatics Availability Painting Matlab Databases Viruses Health Microbiota Method Datasets Prediction Linux Classifiers Microorganisms Community Complex Networks Data MiningMost Recent Papers
Metalign
Nathan Lapierre, Mohammed Alser, Eleazar Eskin, David Koslicki, Serghei Mangul, 2020, Genome 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
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
EMDUniFrac
Jason McClelland, David Koslicki, 2018, Journal of Mathematical Biology on p. 935-949
IndeCut evaluates performance of network motif discovery algorithms
Mitra Ansariola, Molly Megraw, David Koslicki, 2018, Bioinformatics on p. 1514-1521
Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations
David Koslicki, Mark Novak, 2018, Journal of Mathematical Biology on p. 877-909
The Biomedical Data Translator Program: Conception, Culture, and Community
David Koslicki, 2018, Clinical and Translational Science on p. 1--4
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
Topological entropy of DNA sequences
David Koslicki, 2011, Bioinformatics on p. 1061-1067
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
Quikr
David Koslicki, Simon Foucart, Gail Rosen, 2013, Bioinformatics on p. 2096-2102
WGSQuikr
David Koslicki, Simon Foucart, Gail Rosen, 2014, PLoS One on p. e91784
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
MetaPalette
David Koslicki, Daniel Falush, 2016, mSystems on p. e00020--16
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
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