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David Koslicki
David Koslicki
Computer Science and Engineering, Biology, Huck Institutes of the Life Sciences, Penn State
Verified email at psu.edu - Homepage
Title
Cited by
Cited by
Year
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), 1063-1071, 2017
5532017
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia
LMO Loohuis, S Mangul, A Ori, G Jospin, D Koslicki, HT Yang, T Wu, ...
Nature Translational Psychiatry 8 (96), 9, 2018
80*2018
Sparse recovery by means of nonnegative least squares
S Foucart, D Koslicki
IEEE Signal Processing Letters 21 (4), 498-502, 2014
662014
Topological entropy of DNA sequences
D Koslicki
Bioinformatics 27 (8), 1061-1067, 2011
632011
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
D Koslicki, S Foucart, G Rosen
Bioinformatics 29 (17), 2096-2102, 2013
602013
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), 847-848, 2018
582018
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
552014
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
522016
Assessing taxonomic metagenome profilers with OPAL
F Meyer, A Bremges, P Belmann, S Janssen, AC McHardy, D Koslicki
Genome biology 20 (1), 1-10, 2019
492019
Toward a universal biomedical data translator
TBDT Consortium
Clinical and Translational Science, 1--5, 2018
46*2018
WGSQuikr: fast whole-genome shotgun metagenomic classification
D Koslicki, S Foucart, G Rosen
PloS one 9 (3), e91784, 2014
462014
Critical Assessment of Metagenome Interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
322022
Improving minhash via the containment index with applications to metagenomic analysis
D Koslicki, H Zabeti
Applied Mathematics and Computation 354, 206-215, 2019
292019
Technology dictates algorithms: recent developments in read alignment
M Alser, J Rotman, D Deshpande, K Taraszka, H Shi, PI Baykal, HT Yang, ...
Genome biology 22 (1), 1-34, 2021
282021
Metalign: efficient alignment-based metagenomic profiling via containment min hash
N LaPierre, M Alser, E Eskin, D Koslicki, S Mangul
Genome biology 21 (1), 1-15, 2020
252020
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
F Meyer, TR Lesker, D Koslicki, A Fritz, A Gurevich, AE Darling, A Sczyrba, ...
Nature protocols 16 (4), 1785-1801, 2021
202021
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
192018
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
192014
Clinical data: sources and types, regulatory constraints, applications
SC Ahalt, CG Chute, K Fecho, G Glusman, J Hadlock, CO Taylor, ER Pfaff, ...
Clinical and translational science 12 (4), 329, 2019
172019
Improving the usability and comprehensiveness of microbial databases
C Loeffler, A Karlsberg, LS Martin, E Eskin, D Koslicki, S Mangul
BMC biology 18 (1), 1-6, 2020
16*2020
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Articles 1–20