David Koslicki

Associate Professor of Computer Science and Engineering

David Koslicki

Research Summary

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

Graduate Students

Huck Affiliations

Links

Publication Tags

Genes Genome Sampling Metagenomics Chemical Analysis Entropy Painting Viruses Uncertainty Software Metagenome Bacteria Availability Bioinformatics Community Methodology Benchmarking Organisms Matlab Health Prediction Metric Linux Classifiers Microorganisms

Most Recent Papers

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

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

MetaPalette

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

Substitution Markov chains and Martin boundaries

David Koslicki, Manfred Denker, 2016, Rocky Mountain Journal of Mathematics on p. 1963-1985

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

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 (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) on p. 209-226

Topological entropy of DNA sequences

David Koslicki, 2011, Bioinformatics on p. 1061-1067

Quikr

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

WGSQuikr

David Koslicki, Simon Foucart, Gail Rosen, 2014, PloS one

MetaPalette

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

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

SEK

Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander, 2014, Bioinformatics on p. 2423-2431

Coding sequence density estimation via topological pressure

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