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Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B. Bolger AM, et al. Among authors: lohse m. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1. Bioinformatics. 2014. PMID: 24695404 Free PMC article.
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.
Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B. Lohse M, et al. Plant Cell Environ. 2014 May;37(5):1250-8. doi: 10.1111/pce.12231. Epub 2013 Dec 17. Plant Cell Environ. 2014. PMID: 24237261
OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets.
Lohse M, Drechsel O, Kahlau S, Bock R. Lohse M, et al. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W575-81. doi: 10.1093/nar/gkt289. Epub 2013 Apr 22. Nucleic Acids Res. 2013. PMID: 23609545 Free PMC article.
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis.
Lohse M, Nunes-Nesi A, Kr├╝ger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B. Lohse M, et al. Plant Physiol. 2010 Jun;153(2):642-51. doi: 10.1104/pp.109.152553. Epub 2010 Apr 13. Plant Physiol. 2010. PMID: 20388663 Free PMC article.
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. Lohse M, et al. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7. doi: 10.1093/nar/gks540. Epub 2012 Jun 8. Nucleic Acids Res. 2012. PMID: 22684630 Free PMC article.
Algorithm-driven artifacts in median polish summarization of microarray data.
Giorgi FM, Bolger AM, Lohse M, Usadel B. Giorgi FM, et al. Among authors: lohse m. BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553. BMC Bioinformatics. 2010. PMID: 21070630 Free PMC article.
A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize.
Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M. Usadel B, et al. Among authors: lohse m. Plant Cell Environ. 2009 Sep;32(9):1211-29. doi: 10.1111/j.1365-3040.2009.01978.x. Epub 2009 Mar 24. Plant Cell Environ. 2009. PMID: 19389052
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data.
Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B. Ryngajllo M, et al. Among authors: lohse m. Front Plant Sci. 2011 Sep 12;2:43. doi: 10.3389/fpls.2011.00043. eCollection 2011. Front Plant Sci. 2011. PMID: 22639594 Free PMC article.
The Interplay between Carbon Availability and Growth in Different Zones of the Growing Maize Leaf.
Czedik-Eysenberg A, Arrivault S, Lohse MA, Feil R, Krohn N, Encke B, Nunes-Nesi A, Fernie AR, Lunn JE, Sulpice R, Stitt M. Czedik-Eysenberg A, et al. Among authors: lohse ma. Plant Physiol. 2016 Oct;172(2):943-967. doi: 10.1104/pp.16.00994. Epub 2016 Aug 31. Plant Physiol. 2016. PMID: 27582314 Free PMC article.
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