David Koslicki

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Serghei MangulAssistant Professor at USCVerified email at usc.edu
Eleazar EskinUniversity of California, Los AngelesVerified email at cs.ucla.edu
Simon FoucartProfessor of Mathematics, Texas A&M UniversityVerified email at tamu.edu
Gail RosenProfessor of ECE, Drexel UniversityVerified email at ece.drexel.edu
Roel A. OphoffProfessor of Psychiatry and Human Genetics, University of California Los AngelesVerified email at ucla.edu
Anil Ori, PhDDepartment of Psychiatry, Amsterdam UMC, the NetherlandsVerified email at amsterdamumc.nl
Willem M de VosProfessor @ Microbiology Wageningen Netherlands @Helsinki FinlandVerified email at wur.nl
Loes Olde LoohuisAssistant professor at UCLAVerified email at mednet.ucla.edu
Alice Carolyn McHardyHelmholtz Centre for Infection Research, GermanyVerified email at helmholtz-hzi.de
Saikat ChatterjeeKTH - Royal Institute of TechnologyVerified email at kth.se
Mikko VehkaperäNokia Mobile NetworksVerified email at nokia.com
Christopher Clemens MayerAIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Medical Signal AnalysisVerified email at ait.ac.at
Martin BachlerResearch Engineer, AIT Austrian Institute of Technology GmbH, Center for Health & BioresourcesVerified email at ait.ac.at
Daniel FalushShanghai Institute of Immunity and InfectionVerified email at ips.ac.cn
Alexander SczyrbaForschungszentrum Jülich (IBG-5), Bielefeld University, Centrum for Biotechnology (CeBiTec)Verified email at fz-juelich.de
Aaron DarlingIllumina Australia; Professor @ University of Technology SydneyVerified email at illumina.com
Alan WalkerProfessor, Rowett Institute, University of AberdeenVerified email at abdn.ac.uk
Nicolas InnocentiSvipe ABVerified email at innocenti.se
Mikael SkoglundKTH Royal Institute of TechnologyVerified email at kth.se
Erik AurellProfessor of Biological Physics, KTH-Royal Institute of TechnologyVerified email at kth.se

David Koslicki

Computer Science and Engineering, Biology, Huck Institutes of the Life Sciences, Penn State

Verified email at psu.edu - Homepage

Computational genomics Metagenomics Probability Knowledge Graphs


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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	805	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	253	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	126	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	113*	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	103	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	92	2019
Sparse recovery by means of nonnegative least squares S Foucart, D Koslicki IEEE Signal Processing Letters 21 (4), 498-502, 2014	80	2014
Topological entropy of DNA sequences D Koslicki Bioinformatics 27 (8), 1061-1067, 2011	77	2011
Toward a universal biomedical data translator TBDT Consortium Clinical and Translational Science, 1--5, 2018	70*	2018
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	68	2014
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	65	2016
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	64	2022
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	64	2020
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing D Koslicki, S Foucart, G Rosen Bioinformatics 29 (17), 2096-2102, 2013	61	2013
Improving minhash via the containment index with applications to metagenomic analysis D Koslicki, H Zabeti Applied Mathematics and Computation 354, 206-215, 2019	58	2019
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	55	2022
WGSQuikr: fast whole-genome shotgun metagenomic classification D Koslicki, S Foucart, G Rosen PloS one 9 (3), e91784, 2014	54	2014
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	50	2021
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	40	2019
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches A Blanca, RS Harris, D Koslicki, P Medvedev Journal of Computational Biology 29 (2), 155-168, 2022	36	2022

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