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.
Huck Graduate Students
Huck Affiliations
Links
Most Recent Publications
A synthetic microbiota designed through meta-analysis provides insight to community function in Clostridioides difficile resistance.
Susan Tian, Min Soo Kim, Jingcheng Zhao, Kerim Heber, Fuhua Hao, D Koslicki, A Patterson, Jordan Bisanz, Cell Host & Microbe
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
Identifying and Targeting TNF Signaling in Idiopathic Multicentric Castleman's Disease
Melanie D. Mumau, Michael V. Gonzalez, Chunyu Ma, Abiola H. Irvine, Mateo Sarmiento Bustamante, Saishravan Shyamsundar, Luke Y.C. Chen, David Koslicki, David C. Fajgenbaum, 2025, New England Journal of Medicine on p. 616-618
Pioneering a new field of computational pharmacophenomics to unlock the life-saving potential of existing medicines
David C. Fajgenbaum, Sally Nijim, Grant Mitchell, Matej Macak, Chris Bizon, Alexander Tropsha, David Koslicki, 2025, The Lancet Haematology on p. e94-e96
Metagenomic functional profiling: to sketch or not to sketch?
Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S. Rodriguez, Chunyu Ma, David Koslicki, 2024, Bioinformatics on p. ii165-ii173
Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation
Mahmudur Rahman Hera, David Koslicki, 2024,
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets
Luiz Irber, David Koslicki, 2024, Journal of Open Source Science
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov, 2024, Bioinformatics
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, Basazin Belhu, William E. Byrd, Lawrence Chung, Andrew Crouse, Marc P. Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J. Mungall, Stephen A. Ramsey, Jared Roach, Irit Rubin, Shepherd H. Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I. Su, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu, 2023, Journal of Clinical and Translational Science
L2-UniFrac: taking averages with respect to a phylogenetically informed metric
Wei Wei, Andrew , David Koslicki, 2023, ISMB 2023
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
Technology dictates algorithms: recent developments in read alignment
Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul, 2021, Genome Biology
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
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
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
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
Metalign: Efficient alignment-based metagenomic profiling via containment min hash
Nathan Lapierre, Mohammed Alser, Eleazar Eskin, David Koslicki, Serghei Mangul, 2020, Genome Biology
MiCoP: Microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
Nathan Lapierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin, 2019, BMC Genomics
News Articles Featuring David Koslicki
Mar 25, 2025
Translator for biomedical research aims to speed up patient care
$12.8M, five-year project brings together multiple institutions to improve and expand NIH Biomedical Data Translator
Full Article
Mar 03, 2025
Synthetic microbiome therapy suppresses bacterial infection without antibiotics
Precise, targeted treatment using limited strains of gut bacteria effectively protected against C. difficile infection, severe symptoms and recurrent infections in mice.
Full Article
Sep 30, 2024
One Health Microbiome Center launches new video series
The Penn State One Health Microbiome Center (OHMC) announced the launch of a new video series highlighting the center's state-of-the-art resources, research capabilities and collaborative efforts in microbiome sciences.
Full Article
Jan 05, 2024
The stories that defined 2023 for the One Health Microbiome Center
A list of the top 10 most popular Penn State News articles about the One Health Microbiome Center
Full Article
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