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Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B. Bolger AM, et al. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1. Bioinformatics. 2014. PMID: 24695404 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: bolger am. BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553. BMC Bioinformatics. 2010. PMID: 21070630 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. Among authors: bolger am. 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.
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.
Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. Schmidt MH, et al. Among authors: bolger am. Plant Cell. 2017 Oct;29(10):2336-2348. doi: 10.1105/tpc.17.00521. Epub 2017 Oct 12. Plant Cell. 2017. PMID: 29025960 Free PMC article.
Evolution of a complex locus for terpene biosynthesis in solanum.
Matsuba Y, Nguyen TT, Wiegert K, Falara V, Gonzales-Vigil E, Leong B, Schäfer P, Kudrna D, Wing RA, Bolger AM, Usadel B, Tissier A, Fernie AR, Barry CS, Pichersky E. Matsuba Y, et al. Among authors: bolger am. Plant Cell. 2013 Jun;25(6):2022-36. doi: 10.1105/tpc.113.111013. Epub 2013 Jun 11. Plant Cell. 2013. PMID: 23757397 Free PMC article.
The genome of the stress-tolerant wild tomato species Solanum pennellii.
Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. Bolger A, et al. Among authors: bolger me. Nat Genet. 2014 Sep;46(9):1034-8. doi: 10.1038/ng.3046. Epub 2014 Jul 27. Nat Genet. 2014. PMID: 25064008 Free PMC article.
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.
Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B. Schwacke R, et al. Among authors: bolger am. Mol Plant. 2019 Jun 3;12(6):879-892. doi: 10.1016/j.molp.2019.01.003. Epub 2019 Jan 9. Mol Plant. 2019. PMID: 30639314 Free article.
Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function.
Klap C, Yeshayahou E, Bolger AM, Arazi T, Gupta SK, Shabtai S, Usadel B, Salts Y, Barg R. Klap C, et al. Among authors: bolger am. Plant Biotechnol J. 2017 May;15(5):634-647. doi: 10.1111/pbi.12662. Epub 2016 Dec 27. Plant Biotechnol J. 2017. PMID: 27862876 Free PMC article.
Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer.
Brouwer P, Bräutigam A, Buijs VA, Tazelaar AO, van der Werf A, Schlüter U, Reichart GJ, Bolger A, Usadel B, Weber AP, Schluepmann H. Brouwer P, et al. Among authors: bolger a. Front Plant Sci. 2017 Mar 31;8:442. doi: 10.3389/fpls.2017.00442. eCollection 2017. Front Plant Sci. 2017. PMID: 28408911 Free PMC article.
Computational aspects underlying genome to phenome analysis in plants.
Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Bolger AM, et al. Plant J. 2019 Jan;97(1):182-198. doi: 10.1111/tpj.14179. Plant J. 2019. PMID: 30500991 Free PMC article. Review.
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