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Full Text	Issue Date	Title	Author(s)
	2011	The human gut microbiome: are we our enterotypes?	Siezen, R.J.; Kleerebezem, M.
	2011	Microbial sunscreens.	Siezen, R.J.
	2011	Searching in microbial genomes for encoded small proteins.	Boekhorst, J.; Wilson, G.; Siezen, R.J.
	2011	Single-cell genomics: unravelling the genomes of unculturable microorganisms.	Jager, V.C.L. de; Siezen, R.J.
	2011	Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis	Machielsen, R.; Siezen, R.J.; Hijum, S.A.F.T. van; Hylckama Vlieg, J.E. van
	2011	SNP/RD Typing of Mycobacterium tuberculosis Beijing Strains Reveals Local and Worldwide Disseminated Clonal Complexes.	Schurch, A.C.; Kremer, K.; Hendriks, A.C.; Freyee, B.; McEvoy, C.R.; Crevel, R. van; Boeree, M.J.; Helden, P. van; Warren, R.M.; Siezen, R.J.; Soolingen, D. van
	2011	Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases.	Been, M.W.H.J. de; Francke, C.; Siezen, R.J.; Abee, T.
	2011	Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis.	Schurch, A.C.; Kremer, K.; Kiers, A.; Boeree, M.J.; Siezen, R.J.; Soolingen, D. van
	2011	Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior.	Francke, C.; Groot Kormelink, T.; Hagemeijer, Y.; Overmars, L.; Sluijter, V.; Moezelaar, R.; Siezen, R.J.
	2011	Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays	Siezen, R.J.; Bayjanov, J.; Felis, G.E.; Sijde, M.R. van der; Starrenburg, M.; Molenaar, D.; Sanders, M.W.W.; Hijum, S.A. van; Hylckama Vlieg, J.E. van
	2011	Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.	Schurch, A.C.; Kremer, K.; Warren, R.M.; Hung, N.V.; Zhao, Y.; Wan, K.; Boeree, M.J.; Siezen, R.J.; Smith, N.H.; Soolingen, D. van
	2010	Genomic tracing of epidemics and disease outbreaks.	Schurch, A.C.; Siezen, R.J.
	2010	A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus.	Been, M.W.H.J. de; Tempelaars, M.H.; Schaik, Wvan; Moezelaar, R.; Siezen, R.J.; Abee, T.
	2010	Probiotics genomics	Siezen, R.J.; Wilson, G.
	2010	Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays	Siezen, R.J.; Wilson, G.; Todt, T.
	2010	Genomics of microalgae, fuel for the future?	Brooijmans, R.J.W.; Siezen, R.J.
	2010	Genome (re-)annotation and open-source annotation pipelines	Siezen, R.J.; Hijum, S.A.F.T. van
	2010	LAB-Secretome : a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria	Zhou, M.; Theunissen, D.H.J.; Wels, M.W.W.; Siezen, R.J.
	2010	PanCGHweb: a web tool for genotype calling in pangenome CGH data.	Bayjanov, J.; Siezen, R.J.; Hijum, S.A.F.T. van
	2010	High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.	Schurch, A.C.; Kremer, K.; Daviena, O.; Kiers, A.; Boeree, M.J.; Siezen, R.J.; Soolingen, D. van
	2010	Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.	Siezen, R.J.; Bayjanov, J.; Renckens, B.A.M.; Wels, M.W.W.; Hijum, S.A.F.T. van; Molenaar, D.; Hylckama Vlieg, J.E. van
	2010	Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches.	Siezen, R.J.; Tzeneva, V.A.; Castioni, A.; Wels, M.W.W.; Phan, H.T.; Rademaker, J.L.; Starrenburg, M.J.; Kleerebezem, M; Molenaar, D.; Hylckama Vlieg, J.E. van
	2010	The extracellular biology of the lactobacilli.	Kleerebezem, M; Hols, P.; Bernard, E.; Rolain, T.; Zhou, M.; Siezen, R.J.; Bron, P.A.
	2010	The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale.	Schurch, A.C.; Kremer, K.; Kiers, A.; Daviena, O.; Boeree, M.J.; Siezen, R.J.; Smith, N.H.; Soolingen, D. van
	2010	The proteolytic system of lactic acid bacteria revisited : a genomic comparison	Liu, M.; Bayjanov, J.; Renckens, B.A.M.; Nauta, A.; Siezen, R.J.
	2010	A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.	Medema, M.H.; Zhou, M.; Hijum, S.A.F.T. van; Gloerich, J.; Wessels, H.J.; Siezen, R.J.; Strous, M.
	2010	A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.	Medema, M.H.; Zhou, M.; Hijum, S.A.F.T. van; Gloerich, J.; Wessels, H.J.; Siezen, R.J.; Strous, M.
	2009	Genomis of a deep-sea and sub-seafloor microbes	Siezen, R.J.; Wilson, G.
	2009	Genomics of plant-associated microbes	Baarlen, P. van; Siezen, R.J.
	2009	Bioleaching genomics	Siezen, R.J.; Wilson, G.
	2009	Hydrocarbon-degrading bacteria: the oil-spill clean-up crew	Brooijmans, R.J.W.; Pastink, M.I.; Siezen, R.J.
	2009	Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome.	Wels, M.W.W.; Bongers, R.S.; Boekhorst, J.; Molenaar, D.; Sturme, M.; Vos, W.M. de; Siezen, R.J.; Kleerebezem, M
	2009	In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.	Liu, M.; Siezen, R.J.; Nauta, A.
	2009	Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carnea.	Patel, A.K.; Oosterwijk, N. van; Singh, V.K.; Rozeboom, H.J.; Kalk, K.H.; Siezen, R.J.; Jagannadham, M.V.; Dijkstra, B.W.
	2009	PanCGH: a genotype-calling algorithm for pangenome CGH data.	Bayjanov, J.; Wels, M.W.W.; Starrenburg, M.; Hylckama Vlieg, J.E. van; Siezen, R.J.; Molenaar, D.
	2008	Natural products genomics.	Siezen, R.J.; Khayatt, B.
	2008	Genomics of biological wastewater treatment	Siezen, R.J.; Galardini, M.
	2008	Genomics of dairy fermentations.	Siezen, R.J.; Bachmann, H.
	2008	Wine Genomics	Siezen, R.J.
	2008	Unpublished but public microbial genomes with biotechnological relevance.	Siezen, R.J.; Wilson, G.
	2008	Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria.	Liu, M.; Nauta, A.; Francke, C.; Siezen, R.J.
	2008	Challenges in plant cellular pathway reconstruction based on gene expression profiling.	Baarlen, P.; Esse, HP van; Siezen, R.J.; Thomma, B.P.
	2008	The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.	Been, M. de; Bart, M.J.; Abee, T.; Siezen, R.J.; Francke, C.
	2008	Genetic analysis of the capsid gene of genotype GII.2 noroviruses.	Iritani, N.; Vennema, H.; Siebenga, J.J.; Siezen, R.J.; Renckens, B.; Seto, Y.; Kaida, A.; Koopmans, M.
	2008	Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.	Siezen, R.J.; Starrenburg, M.J.; Boekhorst, J.; Renckens, B.; Molenaar, D.; Vlieg, J.E. van Hylckama
	2008	Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria.	Lambert, J.M.; Siezen, R.J.; Vos, W.M. de; Kleerebezem, M
	2008	Co-regulation of metabolic genes is better explained by flux coupling than by network distance.	Notebaart, R.A.; Teusink, B.; Siezen, R.J.; Papp, B.
	2008	LocateP : genome-scale subcellular-location predictor for bacterial proteins	Zhou, M.; Boekhorst, J.; Francke, C.; Siezen, R.J.
	2008	An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters	Wels, M.; Groot Kormelink, T.; Kleerebezem, M.; Siezen, R.J.; Francke, C.
	2008	A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.	Francke, C.; Kerkhoven, R.; Wels, M.; Siezen, R.J.

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