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Integrating genome assemblies with MAIA.
Nijkamp J, Winterbach W, van den Broek M, Daran JM, Reinders M, de Ridder D. Nijkamp J, et al. Bioinformatics. 2010 Sep 15;26(18):i433-9. doi: 10.1093/bioinformatics/btq366. Bioinformatics. 2010. PMID: 20823304 Free PMC article.
De novo detection of copy number variation by co-assembly.
Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D. Nijkamp JF, et al. Bioinformatics. 2012 Dec 15;28(24):3195-202. doi: 10.1093/bioinformatics/bts601. Epub 2012 Oct 9. Bioinformatics. 2012. PMID: 23047563
Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.
van den Broek M, Bolat I, Nijkamp JF, Ramos E, Luttik MA, Koopman F, Geertman JM, de Ridder D, Pronk JT, Daran JM. van den Broek M, et al. Among authors: nijkamp jf. Appl Environ Microbiol. 2015 Sep;81(18):6253-67. doi: 10.1128/AEM.01263-15. Epub 2015 Jul 6. Appl Environ Microbiol. 2015. PMID: 26150454 Free PMC article.
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.
Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM. Nijkamp JF, et al. Microb Cell Fact. 2012 Mar 26;11:36. doi: 10.1186/1475-2859-11-36. Microb Cell Fact. 2012. PMID: 22448915 Free PMC article.
Laboratory evolution of new lactate transporter genes in a jen1Δ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis.
de Kok S, Nijkamp JF, Oud B, Roque FC, de Ridder D, Daran JM, Pronk JT, van Maris AJ. de Kok S, et al. Among authors: nijkamp jf. FEMS Yeast Res. 2012 May;12(3):359-374. doi: 10.1111/j.1567-1364.2012.00787.x. Epub 2012 Jan 18. FEMS Yeast Res. 2012. PMID: 22257278 Free article.