David Koslicki
David Koslicki
Department of Mathematics, Oregon State University
Verified email at math.oregonstate.edu - Homepage
TitleCited byYear
Critical assessment of metagenome interpretation—a benchmark of metagenomics software
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ...
Nature methods 14 (11), 1063, 2017
1842017
Sparse recovery by means of nonnegative least squares
S Foucart, D Koslicki
IEEE Signal Processing Letters 21 (4), 498-502, 2014
422014
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
D Koslicki, S Foucart, G Rosen
Bioinformatics 29 (17), 2096-2102, 2013
422013
Topological entropy of DNA sequences
D Koslicki
Bioinformatics 27 (8), 1061-1067, 2011
392011
On entropy-based data mining
A Holzinger, M Hörtenhuber, C Mayer, M Bachler, S Wassertheurer, ...
Interactive Knowledge Discovery and Data Mining in Biomedical Informatics …, 2014
382014
WGSQuikr: fast whole-genome shotgun metagenomic classification
D Koslicki, S Foucart, G Rosen
PloS one 9 (3), e91784, 2014
322014
Transcriptome analysis in whole blood reveals increased microbial 1 diversity in schizophrenia
LMO Loohuis, S Mangul, A Ori, G Jospin, D Koslicki, HT Yang, T Wu, ...
Nature Translational Psychiatry 8 (96), 9, 2018
22*2018
SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition
S Chatterjee, D Koslicki, S Dong, N Innocenti, L Cheng, Y Lan, ...
Bioinformatics; accepted with Minor Revision on 18-03-2014, 2014
162014
MetaPalette: A K-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation
D Koslicki, D Falush
MSystems 1 (3), e00020-16, 2016
132016
Coding sequence density estimation via topological pressure
D Koslicki, DJ Thompson
Journal of mathematical biology 70 (1-2), 45-69, 2015
10*2015
Improving MinHash via the containment index with applications to metagenomic analysis
D Koslicki, H Zabeti
Applied Mathematics and Computation 354, 206-215, 2019
82019
Toward a universal biomedical data translator
TBDT Consortium
Clinical and Translational Science, 1--5, 2018
7*2018
ARK: Aggregation of Reads by k-Means for estimation of bacterial community composition
D Koslicki, S Chatterjee, D Shahrivar, AW Walker, SC Francis, LJ Fraser, ...
PloS one 10 (10), e0140644, 2015
7*2015
SUBSTITUTION MARKOV CHAINS WITH APPLICATIONS TO MOLECULAR EVOLUTION
D Koslicki
The Pennsylvania State University, 2012
72012
Assessing taxonomic metagenome profilers with OPAL
F Meyer, A Bremges, P Belmann, S Janssen, AC McHardy, D Koslicki
Genome biology 20 (1), 51, 2019
52019
Critical Assessment of Metagenome Interpretation–a benchmark of computational metagenomics software. bioRxiv, 99127
A Sczyrba, P Belmann, D Koslicki, S Janssen, J Droege, I Gregor
Google Scholar, 2017
52017
Striped UniFrac: enabling microbiome analysis at unprecedented scale
D McDonald, Y Vázquez-Baeza, D Koslicki, J McClelland, N Reeve, Z Xu, ...
Nature methods 15 (11), 847, 2018
42018
EMDUniFrac: exact linear time computation of the unifrac metric and identification of differentially abundant organisms
J McClelland, D Koslicki
Journal of mathematical biology 77 (4), 935-949, 2018
42018
Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations
D Koslicki, M Novak
Journal of mathematical biology 76 (4), 877-909, 2018
42018
IndeCut evaluates performance of network motif discovery algorithms
M Ansariola, M Megraw, D Koslicki
Bioinformatics 34 (9), 1514-1521, 2017
32017
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