David Koslicki
David Koslicki
Computer Science and Engineering, Biology, Huck Institutes of the Life Sciences, Penn State
Verified email at - Homepage
Cited by
Cited by
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
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
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), 249, 2021
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
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
Assessing taxonomic metagenome profilers with OPAL
F Meyer, A Bremges, P Belmann, S Janssen, AC McHardy, D Koslicki
Genome biology 20, 1-10, 2019
Sparse recovery by means of nonnegative least squares
S Foucart, D Koslicki
IEEE Signal Processing Letters 21 (4), 498-502, 2014
Topological entropy of DNA sequences
D Koslicki
Bioinformatics 27 (8), 1061-1067, 2011
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
Toward a universal biomedical data translator
TBDT Consortium
Clinical and Translational Science, 1--5, 2018
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
D Koslicki, D Falush
MSystems 1 (3), 10.1128/msystems. 00020-16, 2016
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
D Koslicki, S Foucart, G Rosen
Bioinformatics 29 (17), 2096-2102, 2013
Metalign: efficient alignment-based metagenomic profiling via containment min hash
N LaPierre, M Alser, E Eskin, D Koslicki, S Mangul
Genome biology 21, 1-15, 2020
WGSQuikr: fast whole-genome shotgun metagenomic classification
D Koslicki, S Foucart, G Rosen
PloS one 9 (3), e91784, 2014
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
DR Unni, SAT Moxon, M Bada, M Brush, R Bruskiewich, JH Caufield, ...
Clinical and translational science 15 (8), 1848-1855, 2022
Improving minhash via the containment index with applications to metagenomic analysis
D Koslicki, H Zabeti
Applied Mathematics and Computation 354, 206-215, 2019
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
Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers
L Irber, PT Brooks, T Reiter, NT Pierce-Ward, MR Hera, D Koslicki, ...
BioRxiv, 2022.01. 11.475838, 2022
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
N LaPierre, S Mangul, M Alser, I Mandric, NC Wu, D Koslicki, E Eskin
BMC genomics 20, 1-10, 2019
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine
EC Wood, AK Glen, LG Kvarfordt, F Womack, L Acevedo, TS Yoon, C Ma, ...
BMC bioinformatics 23 (1), 400, 2022
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