David Koslicki

Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Computer Science and Engineering and Biology

David Koslicki

Research Summary

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

Huck Graduate Students

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Genes Metagenomics Genome Metagenome Benchmarking Methodology Strain Painting Viruses Sampling Entropy Recovery Data Mining Chemical Analysis Software Datasets Method Bacteria Technology Visualization Genomics Plasmids Organisms Time Schizophrenia

Most 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

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

David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov, 2024, Oxford Journal of Bioinformatics

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

Wei Wei, Andrew Millward, David Koslicki, 2023, Bioinformatics on p. I57-I65

Mahmudur Rahman Hera, Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki, 2023, Genome Research on p. 1061-1068

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

Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki, 2023, GigaScience

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

Most-Cited Papers

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

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

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

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

Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy, David Koslicki, 2019, Genome Biology on p. 51

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

David Koslicki, Simon Foucart, Gail Rosen, 2014, PLoS One on p. e91784