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Items: 39

1.

How to normalize metatranscriptomic count data for differential expression analysis.

Klingenberg H, Meinicke P.

PeerJ. 2017 Oct 17;5:e3859. doi: 10.7717/peerj.3859. eCollection 2017.

2.

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.

3.

MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data.

Kaever A, Landesfeind M, Feussner K, Mosblech A, Heilmann I, Morgenstern B, Feussner I, Meinicke P.

Metabolomics. 2015;11(3):764-777. Epub 2014 Oct 10.

4.

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.

Aßhauer KP, Wemheuer B, Daniel R, Meinicke P.

Bioinformatics. 2015 Sep 1;31(17):2882-4. doi: 10.1093/bioinformatics/btv287. Epub 2015 May 7.

5.

UProC: tools for ultra-fast protein domain classification.

Meinicke P.

Bioinformatics. 2015 May 1;31(9):1382-8. doi: 10.1093/bioinformatics/btu843. Epub 2014 Dec 23.

6.

Predicting the functional repertoire of an organism from unassembled RNA-seq data.

Landesfeind M, Meinicke P.

BMC Genomics. 2014 Nov 20;15:1003. doi: 10.1186/1471-2164-15-1003.

7.

Exploring neighborhoods in the metagenome universe.

Aßhauer KP, Klingenberg H, Lingner T, Meinicke P.

Int J Mol Sci. 2014 Jul 14;15(7):12364-78. doi: 10.3390/ijms150712364.

8.

Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software.

Landesfeind M, Kaever A, Feussner K, Thurow C, Gatz C, Feussner I, Meinicke P.

PeerJ. 2014 Mar 13;2:e239. doi: 10.7717/peerj.239. eCollection 2014.

9.

Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

Kaever A, Landesfeind M, Feussner K, Morgenstern B, Feussner I, Meinicke P.

PLoS One. 2014 Feb 28;9(2):e89297. doi: 10.1371/journal.pone.0089297. eCollection 2014.

10.

Land use type significantly affects microbial gene transcription in soil.

Nacke H, Fischer C, Thürmer A, Meinicke P, Daniel R.

Microb Ecol. 2014 May;67(4):919-30. doi: 10.1007/s00248-014-0377-6. Epub 2014 Feb 20.

PMID:
24553913
11.

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.

Klingenberg H, Aßhauer KP, Lingner T, Meinicke P.

Bioinformatics. 2013 Apr 15;29(8):973-80. doi: 10.1093/bioinformatics/btt077. Epub 2013 Feb 15.

12.

Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities.

Danielsen L, Thürmer A, Meinicke P, Buée M, Morin E, Martin F, Pilate G, Daniel R, Polle A, Reich M.

Ecol Evol. 2012 Aug;2(8):1935-48. doi: 10.1002/ece3.305. Epub 2012 Jul 12.

13.

MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data.

Kaever A, Landesfeind M, Possienke M, Feussner K, Feussner I, Meinicke P.

J Biomed Biotechnol. 2012;2012:263910. doi: 10.1155/2012/263910. Epub 2012 Apr 5.

14.

Improving Hidden Markov Models for classification of human immunodeficiency virus-1 subtypes through linear classifier learning.

Bulla I, Schultz AK, Meinicke P.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(1):Article 1. doi: 10.2202/1544-6115.1680.

PMID:
22499688
15.

Metabolic priming by a secreted fungal effector.

Djamei A, Schipper K, Rabe F, Ghosh A, Vincon V, Kahnt J, Osorio S, Tohge T, Fernie AR, Feussner I, Feussner K, Meinicke P, Stierhof YD, Schwarz H, Macek B, Mann M, Kahmann R.

Nature. 2011 Oct 5;478(7369):395-8. doi: 10.1038/nature10454.

PMID:
21976020
16.

CoMet--a web server for comparative functional profiling of metagenomes.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W518-23. doi: 10.1093/nar/gkr388. Epub 2011 May 26.

17.

Mixture models for analysis of the taxonomic composition of metagenomes.

Meinicke P, Asshauer KP, Lingner T.

Bioinformatics. 2011 Jun 15;27(12):1618-24. doi: 10.1093/bioinformatics/btr266. Epub 2011 May 5.

18.

Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses.

Lingner T, Kataya AR, Antonicelli GE, Benichou A, Nilssen K, Chen XY, Siemsen T, Morgenstern B, Meinicke P, Reumann S.

Plant Cell. 2011 Apr;23(4):1556-72. doi: 10.1105/tpc.111.084095. Epub 2011 Apr 12.

19.

The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development.

Nahlik K, Dumkow M, Bayram O, Helmstaedt K, Busch S, Valerius O, Gerke J, Hoppert M, Schwier E, Opitz L, Westermann M, Grond S, Feussner K, Goebel C, Kaever A, Meinicke P, Feussner I, Braus GH.

Mol Microbiol. 2010 Nov;78(4):964-79. doi: 10.1111/j.1365-2958.2010.07384.x. Epub 2010 Sep 27.

20.

Predicting phenotypic traits of prokaryotes from protein domain frequencies.

Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P.

BMC Bioinformatics. 2010 Sep 24;11:481. doi: 10.1186/1471-2105-11-481.

21.

DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS.

Subramanian AR, Hiran S, Steinkamp R, Meinicke P, Corel E, Morgenstern B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W19-22. doi: 10.1093/nar/gkq442. Epub 2010 May 23.

22.

Treephyler: fast taxonomic profiling of metagenomes.

Schreiber F, Gumrich P, Daniel R, Meinicke P.

Bioinformatics. 2010 Apr 1;26(7):960-1. doi: 10.1093/bioinformatics/btq070. Epub 2010 Feb 19.

PMID:
20172941
23.

UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.

Meinicke P.

BMC Genomics. 2009 Sep 2;10:409. doi: 10.1186/1471-2164-10-409.

24.

Orphelia: predicting genes in metagenomic sequencing reads.

Hoff KJ, Lingner T, Meinicke P, Tech M.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W101-5. doi: 10.1093/nar/gkp327. Epub 2009 May 8.

25.

MarVis: a tool for clustering and visualization of metabolic biomarkers.

Kaever A, Lingner T, Feussner K, Göbel C, Feussner I, Meinicke P.

BMC Bioinformatics. 2009 Mar 20;10:92. doi: 10.1186/1471-2105-10-92.

26.

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.

Meinicke P, Lingner T, Kaever A, Feussner K, Göbel C, Feussner I, Karlovsky P, Morgenstern B.

Algorithms Mol Biol. 2008 Jun 26;3:9. doi: 10.1186/1748-7188-3-9.

27.

Word correlation matrices for protein sequence analysis and remote homology detection.

Lingner T, Meinicke P.

BMC Bioinformatics. 2008 Jun 3;9:259. doi: 10.1186/1471-2105-9-259.

28.

Gene prediction in metagenomic fragments: a large scale machine learning approach.

Hoff KJ, Tech M, Lingner T, Daniel R, Morgenstern B, Meinicke P.

BMC Bioinformatics. 2008 Apr 28;9:217. doi: 10.1186/1471-2105-9-217.

29.

Evolutionary optimization of sequence kernels for detection of bacterial gene starts.

Mersch B, Glasmachers T, Meinicke P, Igel C.

Int J Neural Syst. 2007 Oct;17(5):369-81.

PMID:
18098369
30.

Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection.

Igel C, Glasmachers T, Mersch B, Pfeifer N, Meinicke P.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Apr-Jun;4(2):216-26.

PMID:
17473315
31.

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites.

Tech M, Morgenstern B, Meinicke P.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W588-90.

32.

Remote homology detection based on oligomer distances.

Lingner T, Meinicke P.

Bioinformatics. 2006 Sep 15;22(18):2224-31. Epub 2006 Jul 12.

PMID:
16837522
33.

P-value based visualization of codon usage data.

Meinicke P, Brodag T, Fricke WF, Waack S.

Algorithms Mol Biol. 2006 Jun 29;1(1):10.

34.

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R.

BMC Bioinformatics. 2006 Mar 16;7:142.

35.
36.

Principal surfaces from unsupervised kernel regression.

Meinicke P, Klanke S, Memisevic R, Ritter H.

IEEE Trans Pattern Anal Mach Intell. 2005 Sep;27(9):1379-91.

PMID:
16173183
37.

TICO: a tool for improving predictions of prokaryotic translation initiation sites.

Tech M, Pfeifer N, Morgenstern B, Meinicke P.

Bioinformatics. 2005 Sep 1;21(17):3568-9. Epub 2005 Jun 30.

PMID:
15994191
38.

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites.

Meinicke P, Tech M, Morgenstern B, Merkl R.

BMC Bioinformatics. 2004 Oct 28;5:169.

39.

BCI Competition 2003--Data set IIb: support vector machines for the P300 speller paradigm.

Kaper M, Meinicke P, Grossekathoefer U, Lingner T, Ritter H.

IEEE Trans Biomed Eng. 2004 Jun;51(6):1073-6.

PMID:
15188881

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