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
Shuchang Tian, Min Kim, Jingcheng Zhao, Kerim Heber, Fuhua Hao, David Koslicki, A Patterson, J Bisanz, Cell Press
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
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
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, Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki, 2023, Genome Research on p. 1061-1068
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
A translational approach to identifying and targeting TNF signaling in idiopathic multicentric Castleman disease
Melanie Mumau, Abiola Irvine, Chunyu Ma, Sheila Pierson, Brent Shaw, Michael Gonzalez, Daniel Korn, Tracey Sikora, Grant Mitchell, David Koslicki, others, 2023, Blood on p. 3921
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki, 2023, GigaScience
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
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
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
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
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
News Articles Featuring David Koslicki
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