• BS, Mathematics, Washington State University, 2006
• Ph D, Mathematics, Pennsylvania State University, 2012

Journal Articles

Fernando Meyer, Till Robin Lesker, David Koslicki, Adrian Fritz, Alexey Gurevich, Aaron E Darling, Alexander Sczyrba, Andreas Bremges and Alice C McHardy, 2021, "Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit", Nature Protocols

Nathan LaPierre, Mahammed Alser, Eleazar Eskin, David Koslicki and Serghei Mangul, 2020, "Metalign: efficient alignment-based metagenomic profiling via containment min hash", Genome Biology, 21, (242), pp. 15

Caitlin Loeffler, Aaron Karlsberg, Lana S Martin, Eleazar Eskin, David Koslicki and Serghei Mangul, 2020, "Improving the usability and comprehensiveness of microbial databases", BMC Biology, 18, (37)

Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C McHardy and David Koslicki, 2019, "Assessing taxonomic metagenome profilers with OPAL", Genome biology, 20, (1), pp. 51

David Koslicki and Hooman Zabeti, 2019, "Improving MinHash via the containment index with applications to metagenomic analysis", Applied Mathematics and Computation, 354, pp. 206--215

Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C Wu, David Koslicki and Eleazar Eskin, 2019, "MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples", BMC genomics, 20, (5), pp. 423

Jason McClelland and David Koslicki, 2018, "EMDUniFrac: exact linear time computation of the unifrac metric and identification of differentially abundant organisms", Journal of mathematical biology, 77, (4), pp. 935--949

David Koslicki and Mark Novak, 2018, "Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations", Journal of mathematical biology, 76, (4), pp. 877--909

Daniel McDonald, V\'azquez-Baeza, Yoshiki, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez and Rob Knight, 2018, "Striped UniFrac: enabling microbiome analysis at unprecedented scale", Nature methods, 15, (11), pp. 847

David Koslicki, 2018, "The Biomedical Data Translator Program: Conception, Culture, and Community", Clinical and Translational Science, (https://doi.org/10.1111/cts.12592), pp. 1--4

David Koslicki, 2018, "Toward a universal biomedical data translator", Clinical and Translational Science, (doi.org/10.1111/cts.12591), pp. 1--5

Loes M Olde Loohuis, Serghei Mangul, Anil Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P Boks, Catherine Lomen-Hoerth, Martina Wiedau-Pazos and others, 2018, "Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia", Nature Translational Psychiatry, 8, (96), pp. 9

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Dr\"oge, Johannes, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms and others, 2017, "Critical assessment of metagenome interpretation—a benchmark of metagenomics software", Nature methods, 14, (11), pp. 1063

Mitra Ansariola, Molly Megraw and David Koslicki, 2017, "IndeCut evaluates performance of network motif discovery algorithms", Bioinformatics, 34, (9), pp. 1514--1521

David Koslicki and Daniel Falush, 2016, "MetaPalette: A K-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation", MSystems, 1, (3), pp. e00020--16

David Koslicki, Manfred H Denker and others, 2016, "Substitution Markov chains and Martin boundaries", Rocky Mountain Journal of Mathematics, 46, (6), pp. 1963--1985

David Koslicki, Saikat Chatterjee, Damon Shahrivar, Alan Walker, Suzanna C Francis, Louise J Fraser, Vehkaper\"a, Mikko, Yueheng Lan and Jukka Corander, 2015, "ARK: Aggregation of Reads by k-Means for estimation of bacterial community composition", PloS one, 10, (10), pp. e0140644

David Koslicki and Daniel James Thompson, 2015, "Coding sequence density estimation via topological pressure", Journal of mathematical biology, 70, (1-2), pp. 45--69

Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Vehkaper\"a, M, Mikael Skoglund, Lars K Rasmussen, Erik Aurell and others, 2014, "SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition", Bioinformatics; accepted with Minor Revision on 18-03-2014

Simon Foucart and David Koslicki, 2014, "Sparse recovery by means of nonnegative least squares", IEEE Signal Processing Letters, 21, (4), pp. 498--502

David Koslicki, Simon Foucart and Gail Rosen, 2014, "WGSQuikr: fast whole-genome shotgun metagenomic classification", PloS one, 9, (3), pp. e91784

David Koslicki, Simon Foucart and Gail Rosen, 2013, "Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing", Bioinformatics, 29, (17), pp. 2096--2102

David Koslicki, 2011, "Topological entropy of DNA sequences", Bioinformatics, 27, (8), pp. 1061--1067

Karamarie Fecho, James Balhoff, Chris Bizon, William Byrd, Sui Hang, David Koslicki, Stefano Rensi, Patrick Schmitt, Mathias Wawer, Mark Williams and Stanley Ahalt, , "Application of MCAT Questions as a Testing Tool and Evaluation Metric for Knowledge Graph-based Reasoning Systems", Clinical and Translational Science

Conference Proceedings

Antonio Blanca Pimentel, Robert Scott Harris, David Koslicki and Paul Medvedev, 2021, "The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches", RECOMB, 2021

Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki and Gail Rosen, 2019, "Workshop on Microbiomics, Metagenomics, and Metabolomics", pp. 618--618

Serghei Mangul and David Koslicki, 2016, "Reference-free comparison of microbial communities via de Bruijn graphs", (http://doi.acm.org/10.1145/2975167.29751), pp. 68--77

Simon Foucart and David Koslicki, , "Finer Metagenomic Reconstruction via Biodiversity Optimization", Advances in Neural Information Processing Systems 33 (NeurIPS 2020), 33, pp. 14

Other

David Koslicki, 2012, "SUBSTITUTION MARKOV CHAINS WITH APPLICATIONS TO MOLECULAR EVOLUTION"

• June 2020 - May 2022, "QuBBD: Fast, Efficient Mathematical Approach to the Analysis of the Human Microbiome through Biodiversity Optimization," (Sponsor: National Science Foundation).

• January 2020 - May 2020, "Biomedical Data Translator Development of Autonomous Relay Agent: RTX," (Sponsor: Oregon State University).

• College of Science Impact Award, Oregon State University, October 2018

Service to Penn State:

• Committee Work, Committee Member, Bioinformatics and Genomics qualification exam committee, The Huck Institutes of the Life Sciences, Qualification exam committee, April 2020

• Committee Work, Committee Member, Executive Committee Member, The Huck Institutes of the Life Sciences Microbiome center, Executive Committee of the Penn State Microbiome Center, July 2020

• Committee Work, Committee Member, Safety Committee, May 2020

• Committee Work, Member, Committee Member, Graduate Committee, August 2019

Service to External Organizations:

• Organizing Conferences and Service on Conference Committees, Committee Member, Program committee member for the ACM conference on bioinformatics, computational biology, and health informatics (BCB), ACM BCB, February 2019 - February 2019

• Organizing Conferences and Service on Conference Committees, Co-Organizer, Computational Genomics Summer Institute (CGSI) Co-organizer, Computational Genomics Summer Institute (CGSI), December 2018 - August 2019

• Organizing Conferences and Service on Conference Committees, Co-Organizer, Computational Genomics Summer Institute (CGSI) Co-organizer, Computational Genomics Summer Institute (CGSI), December 2017 - August 2018

• Organizing Conferences and Service on Conference Committees, Co-Organizer, Computational Genomics Summer Institute (CGSI) Co-organizer, December 2016 - July 2017

• Service to Public and Private Organizations, Board Member, Critical Assessment of Metagenomic Interpretation (CAMI) advisory board member, CAMI, January 2015