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Items: 14

1.

Assessing taxonomic metagenome profilers with OPAL.

Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D.

Genome Biol. 2019 Mar 4;20(1):51. doi: 10.1186/s13059-019-1646-y.

2.

Striped UniFrac: enabling microbiome analysis at unprecedented scale.

McDonald D, Vázquez-Baeza Y, Koslicki D, McClelland J, Reeve N, Xu Z, Gonzalez A, Knight R.

Nat Methods. 2018 Nov;15(11):847-848. doi: 10.1038/s41592-018-0187-8. No abstract available.

PMID:
30377368
3.

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.

Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA.

Transl Psychiatry. 2018 May 10;8(1):96. doi: 10.1038/s41398-018-0107-9.

4.

EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms.

McClelland J, Koslicki D.

J Math Biol. 2018 Oct;77(4):935-949. doi: 10.1007/s00285-018-1235-9. Epub 2018 Apr 25.

PMID:
29691633
5.

IndeCut evaluates performance of network motif discovery algorithms.

Ansariola M, Megraw M, Koslicki D.

Bioinformatics. 2018 May 1;34(9):1514-1521. doi: 10.1093/bioinformatics/btx798.

PMID:
29236975
6.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

7.

Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations.

Koslicki D, Novak M.

J Math Biol. 2018 Mar;76(4):877-909. doi: 10.1007/s00285-017-1163-0. Epub 2017 Jul 22.

PMID:
28735343
8.

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.

Koslicki D, Falush D.

mSystems. 2016 Jun 7;1(3). pii: e00020-16. eCollection 2016 May-Jun.

9.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Koslicki D, Chatterjee S, Shahrivar D, Walker AW, Francis SC, Fraser LJ, Vehkaperä M, Lan Y, Corander J.

PLoS One. 2015 Oct 23;10(10):e0140644. doi: 10.1371/journal.pone.0140644. eCollection 2015.

10.

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition.

Chatterjee S, Koslicki D, Dong S, Innocenti N, Cheng L, Lan Y, Vehkaperä M, Skoglund M, Rasmussen LK, Aurell E, Corander J.

Bioinformatics. 2014 Sep 1;30(17):2423-31. doi: 10.1093/bioinformatics/btu320. Epub 2014 May 7.

11.

WGSQuikr: fast whole-genome shotgun metagenomic classification.

Koslicki D, Foucart S, Rosen G.

PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.

12.

Coding sequence density estimation via topological pressure.

Koslicki D, Thompson DJ.

J Math Biol. 2015 Jan;70(1-2):45-69. doi: 10.1007/s00285-014-0754-2. Epub 2014 Jan 22.

PMID:
24448658
13.

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.

Koslicki D, Foucart S, Rosen G.

Bioinformatics. 2013 Sep 1;29(17):2096-102. doi: 10.1093/bioinformatics/btt336. Epub 2013 Jun 20.

PMID:
23786768
14.

Topological entropy of DNA sequences.

Koslicki D.

Bioinformatics. 2011 Apr 15;27(8):1061-7. doi: 10.1093/bioinformatics/btr077. Epub 2011 Feb 10.

PMID:
21317142

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