David Koslicki
Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Computer Science and Engineering and Biology
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W205C Westgate
University Park, PA - dmk333@psu.edu
- 814-865-1611
Research Summary
Developing efficient algorithms to extract insight from high-throughput sequencing data.
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Metagenomics Genes Genome Metagenome Benchmarking Health Painting Strain Viruses Sampling Matlab Datasets Linux Availability Bioinformatics Classifiers Software Entropy Chemical Analysis Recovery Classifier Data Mining Biological Property Methodology GenomicsMost Recent Publications
The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches
A Blanca, R Harris, D Koslicki, Paul Medvedev, Proceedings of the 25th Annual Conference on Research in Computational Molecular Biology, RECOMB 2021
L2-UniFrac: taking averages with respect to a phylogenetically informed metric
Wei Wei, Andrew , David Koslicki, ISMB 2023
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L<sub>2</sub>UniFrac
Wei Wei, Andrew Millward, David Koslicki, 2023, Bioinformatics on p. I57-I65
Deriving Confidence Intervals for Mutation Rates Across a Wide Range of Evolutionary Distances Using FracMinHash
Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki, 2023, Genome Research
ARAX: a graph-based modular reasoning tool for translational biomedicine
Amy K. Glen, Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G. Kvarfordt, Ross C. Peene, Shaopeng Liu, Andrew S. Hoffman, Jared C. Roach, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki, 2023, Bioinformatics
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki, 2023, GigaScience
KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description
Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki, 2022, GigaScience
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,
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
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
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
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
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
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
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
Quikr: A method for rapid reconstruction of bacterial communities via compressive sensing
David Koslicki, Simon Foucart, Gail Rosen, 2013, Bioinformatics on p. 2096-2102
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
WGSQuikr: Fast whole-genome shotgun metagenomic classification
David Koslicki, Simon Foucart, Gail Rosen, 2014, PLoS One on p. e91784
News Articles Featuring David Koslicki
Sep 21, 2023
Huck-supported graduate degree programs transition to new leadership
David Koslicki and Greg Shearer have stepped into the leadership roles for the Huck's Bioinformatics and Genomics (BG) and Physiology graduate programs.
Full Article
Mar 29, 2023
The Microbiome Center announces a free bioinformatics resource for Penn State
The Penn State Microbiome Center, in coordination with the lab of Associate Professor David Koslicki, is offering access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) to all Penn State faculty, staff and students for free.
Full Article
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