David Koslicki

Associate Professor of Computer Science and Engineering and Biology

W205C 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

Bioinformatics and Genomics

Microbiome Center

Publication Tags

Genome Genes Metagenomics Bioinformatics Metagenome Strain Viruses Health Painting Statistics Sampling Datasets Computational Biology Matlab Software Availability Linux Classifiers Time Recovery Chemical Analysis Data Mining Biological Property Genomics Mutation

Most Recent Publications

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

Shaopeng Liu, David Koslicki, ISMB

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey, 2022, BMC Bioinformatics

WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data

Wei Wei, David Koslicki, 2022,

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Deepak R. Unni, Sierra A.T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J. Harry Caufield, Paul A. Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall, Liliana Acevedo, Stanley C. Ahalt, John Alden, Ahmed Alkanaq, Nada Amin, Ricardo Avila, Jim Balhoff, Sergio E. Baranzini, Andrew Baumgartner, William Baumgartner, Basazin Belhu, MacKenzie Brandes, Namdi Brandon, Noel Burtt, William Byrd, Jackson Callaghan, Marco Alvarado Cano, Steven Carrell, Remzi Celebi, James Champion, Zhehuan Chen, Mei Jan Chen, Lawrence Chung, Kevin Cohen, Tom Conlin, David Koslicki, 2022, Clinical and Translational Science on p. 1848-1855

Progress toward a universal biomedical data translator

Karamarie Fecho, Anne E. Thessen, Sergio E. Baranzini, Chris Bizon, Jennifer J. Hadlock, Sui Huang, Ryan T. Roper, Noel Southall, Casey Ta, Paul B. Watkins, Mark D. Williams, Hao Xu, William Byrd, Vlado Dančík, Marc P. Duby, Michel Dumontier, Gustavo Glusman, Nomi L. Harris, Eugene W. Hinderer, Greg Hyde, Adam Johs, Andrew I. Su, Guangrong Qin, Qian Zhu, Jennifer Dougherty, Conrad Huang, Andrew Magis, Brett Smith, Remzi Celebi, Zhehuan Chen, Ricardo De Miranda Azevedo, Vincent Emonet, Jay Lee, Chunhua Weng, Arif Yilmaz, Keum Joo Kim, Eugene Santos, Lucas Tonstad, Luke Veenhuis, Chase Yakaboski, Liliana Acevedo, Steven Carrell, Eric Deutsch, Amy Glen, Andrew Hoffman, David Koslicki, Lindsey Kvarfordt, Zheng Liu, Shaopeng Liu, Chunyu Ma, 2022, Clinical and Translational Science on p. 1838-1847

CMash: Fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

Shaopeng Liu, David Koslicki, 2022, Bioinformatics on p. I28-I35

The minimizer Jaccard estimator is biased and inconsistent

Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev, 2022, Bioinformatics on p. I169-I176

PressPurt: network sensitivity to press perturbations under interaction uncertainty

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

Critical Assessment of Metagenome Interpretation: the second round of challenges

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

The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches

Antonio Blanca, A Blanca Pimentel, Robert S. Harris, David Koslicki, Paul Medvedev, 2022, Journal of Computational Biology on p. 155-168

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

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

Sparse recovery by means of nonnegative least squares

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

Striped UniFrac: enabling microbiome analysis at unprecedented scale

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: A method for rapid reconstruction of bacterial communities via compressive sensing

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

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

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

WGSQuikr: Fast whole-genome shotgun metagenomic classification

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