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Sacha van Hijum

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Oligonucleotide Array Sequence Analysis

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Gene Expression Regulation, Bacterial

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Prokaryotic Cells

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Publications

TOP 3
Sacha A F T van Hijum; Elaine E Vaughan; Rudi F Vogel
Application of state-of-art sequencing technologies to indigenous food fermentations.
Thomas H A Ederveen; Lex Overmars; Sacha A F T van Hijum
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.
Jumamurat R Bayjanov; Roland J Siezen; Marjo Jc Starrenburg; Marijke R van der Sijde; Sacha A F T van Hijum
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.

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All Publications

2013: Sacha A F T van Hijum; Elaine E Vaughan; Rudi F Vogel
Application of state-of-art sequencing technologies to indigenous food fermentations.
Current opinion in biotechnology 2013;24(2):178-86.
2013: Thomas H A Ederveen; Lex Overmars; Sacha A F T van Hijum
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.
PloS one 2013;8(5):e63523.
2013: Jumamurat R Bayjanov; Roland J Siezen; Marjo Jc Starrenburg; Marijke R van der Sijde; Sacha A F T van Hijum
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.
BMC microbiology 2013;13():68.
2013: Kingsley C Anukam; Jos Boekhorst; Gregory B Gloor; Jean M Macklaim; Gregor Reid; Bernadet Renckens; Sacha A F T van Hijum; Roland J Siezen
Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.
PloS one 2013;8(3):e59239.
2013: Stuart Ainsworth; Francesca Bottacini; Victor de Jager; Jennifer Mahony; Sacha A F T van Hijum; Aldert L Zomer; Douwe van Sinderen
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.
Genome announcements 2013;1(1):.
2013: Lilly M Verhagen; Julian A Villalba; Aldert Zomer; Mailis Maes; Sacha A F T van Hijum; Jacobus H de Waard; Berenice Del Nogal; Marc Eleveld; Peter Wm Hermans
A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children.
BMC genomics 2013;14():74.
2013: Fabio Gori; Mike S M Jetten; Huub J M Op den Camp; Susannah Green Tringe; Sacha A F T van Hijum; Gianluigi Folino; Elena Marchiori
Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.
BMC genomics 2013;14():7.
2012: Lars Axelsson; Hans Blom; Jos Boekhorst; Michiel Kleerebezem; Kristine Naterstad; Bernadet Renckens; Ida Rud; Sacha A F T van Hijum; Roland Siezen
Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730).
Journal of bacteriology 2012;194(9):2391-2.
2012: Priyanka Nannapaneni; Leif Steil; Uwe Völker; Maren Depke; Michael Hecker; Falk Hertwig; Ulrike Mäder; Sacha A F T van Hijum
Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification.
Microbiology (Reading, England) 2012;158(Pt 3):696-707.
2012: Tilman J Todt; Sacha A F T van Hijum; Michiel Wels; Roger S Bongers; Roland S Siezen; Michiel Kleerebezem
Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.
PloS one 2012;7(9):e45097.
2012: Aldert Zomer; Hester J Bootsma; Peter Burghout; Peter W M Hermans; Sacha A F T van Hijum
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
PloS one 2012;7(8):e43012.
2012: Jumamurat R Bayjanov; Douwe Molenaar; Roland Siezen; Vesela A Tzeneva; Sacha A F T van Hijum
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
BMC genomics 2012;13():170.
2011: Bas E Dutilh; Kees-Jan Françoijs; Harry R Harhangi; Bart de Wild; Mike S.M. Jetten; Rasa Jurgelenaite; Huub J M Op den Camp; Markus Schmid; Marc Strous; Hendrik G Stunnenberg; Radek Szklarczyk; Sacha A F T van Hijum; Martijn A Huynen
FACIL: Fast and Accurate Genetic Code Inference and Logo.
Bioinformatics (Oxford, England) 2011;27(14):1929-33.
2011: Ronnie Machielsen; Roland Siezen; Sacha A F T van Hijum; Johan E T van Hylckama Vlieg
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.
Applied and environmental microbiology 2011;77(2):555-63.
2010: Sander Sieuwerts; Douwe Molenaar; Sacha A F T van Hijum; Marke Beerthuyzen; Marc J A Stevens; Patrick W M Janssen; Colin J Ingham; Frank A M de Bok; Willem M de Vos; Johan E T van Hylckama Vlieg
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus.
Applied and environmental microbiology 2010;76(23):7775-84.
2010: Michel A Westenberg; Jos B T M Roerdink; Oscar P Kuipers; Sacha A F T van Hijum
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
Bioinformatics (Oxford, England) 2010;26(22):2922-3.
2010: Roland J Siezen; Sacha A F T van Hijum
Genome (re-)annotation and open-source annotation pipelines.
Microbial biotechnology 2010;3(4):362-9.
2010: Stefan P W de Vries; Sacha A F T van Hijum; Wolfgang Schueler; Kristian Riesbeck; John P Hays; Peter W M Hermans; Hester J Bootsma
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen.
Journal of bacteriology 2010;192(14):3574-83.
2010: Roland Siezen; Jumamurat Bayjanov; Bernadet Renckens; Michiel Wels; Sacha A F T van Hijum; Douwe Molenaar; Johan E T van Hylckama Vlieg
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.
Journal of bacteriology 2010;192(10):2649-50.
2010: Jumamurat R Bayjanov; Roland Siezen; Sacha A F T van Hijum
PanCGHweb: a web tool for genotype calling in pangenome CGH data.
Bioinformatics (Oxford, England) 2010;26(9):1256-7.
2010: Marnix H Medema; Miaomiao Zhou; Sacha A F T van Hijum; Jolein Gloerich; Hans J C T Wessels; Roland Siezen; Marc Strous
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
BMC genomics 2010;11():299.
2009: Sacha A F T van Hijum; Marnix H Medema; Oscar P Kuipers
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.
Microbiology and molecular biology reviews : MMBR 2009;73(3):481-509, Table of Contents.
2009: Evert-Jan Blom; Jos B T M Roerdink; Oscar P Kuipers; Sacha A F T van Hijum
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.
Bioinformatics (Oxford, England) 2009;25(4):550-1.
2009: Rutger W W Brouwer; Sacha A F T van Hijum; Oscar P Kuipers
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.
Bioinformatics (Oxford, England) 2009;25(1):139-40.
2008: Rasmus Larsen; Sacha A F T van Hijum; Jan Martinussen; Oscar P Kuipers; Jan Kok
Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons.
Applied and environmental microbiology 2008;74(15):4768-71.
2008: Evert-Jan Blom; Sacha A F T van Hijum; Klaas J Hofstede; Remko Silvis; Jos B T M Roerdink; Oscar P Kuipers
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites.
BMC bioinformatics 2008;9():535.
2008: Evert Jan Blom; Rainer Breitling; Klaas Jan Hofstede; Jos B T M Roerdink; Sacha A F T van Hijum; Oscar P Kuipers
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.
BMC genomics 2008;9():495.
2008: Sacha A F T van Hijum; Richard J S Baerends; Aldert L Zomer; Harma A Karsens; Victoria Martin-Requena; Oswaldo Trelles; Jan Kok; Oscar P Kuipers
Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons.
BMC bioinformatics 2008;9():93.
2007: Evert-Jan Blom; Dinne W J Bosman; Sacha A F T van Hijum; Rainer Breitling; Lars Tijsma; Remko Silvis; Jos B T M Roerdink; Oscar P Kuipers
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.
Bioinformatics (Oxford, England) 2007;23(9):1161-3.
2007: Ewa Szalowska; Sacha A F T van Hijum; Han Roelofsen; Annemiek Hoek; roel vonk; Gerard te Meerman
Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.
Biotechnology progress 2007;23(1):217-24.
2006: Tomas G Kloosterman; Wouter T Hendriksen; Jetta J E Bijlsma; Hester J Bootsma; Sacha A F T van Hijum; Jan Kok; Peter W M Hermans; Oscar P Kuipers
Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae.
The Journal of biological chemistry 2006;281(35):25097-109.
2006: Anne de Jong; Sacha A F T van Hijum; Jetta J E Bijlsma; Jan Kok; Oscar P Kuipers
BAGEL: a web-based bacteriocin genome mining tool.
Nucleic acids research 2006;34(Web Server issue):W273-9.
2006: Naomi E Kramer; Sacha A F T van Hijum; Jan Knol; Jan Kok; Oscar P Kuipers
Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance.
Antimicrobial agents and chemotherapy 2006;50(5):1753-61.
2006: Sacha A F T van Hijum; Slavko Kralj; Lukasz K Ozimek; Lubbert Dijkhuizen; Ineke G H van Geel-Schutten
Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria.
Microbiology and molecular biology reviews : MMBR 2006;70(1):157-76.
2006: Casper J Albers; Ritsert C Jansen; Jan Kok; Oscar P Kuipers; Sacha A F T van Hijum
SIMAGE: simulation of DNA-microarray gene expression data.
BMC bioinformatics 2006;7():205.
2005: Chris D den Hengst; Sacha A F T van Hijum; Jan Geurts; Arjen Nauta; Jan Kok; Oscar P Kuipers
The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.
The Journal of biological chemistry 2005;280(40):34332-42.
2005: Jan Kok; Girbe Buist; Aldert L Zomer; Sacha A F T van Hijum; Oscar P Kuipers
Comparative and functional genomics of lactococci.
FEMS microbiology reviews 2005;29(3):411-33.
2005: Sacha A F T van Hijum; Aldert L Zomer; Oscar P Kuipers; Jan Kok
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
Nucleic acids research 2005;33(Web Server issue):W560-6.
2005: Charlotte Barrière; Maria Veiga-da-Cunha; Nicolas Pons; Eric Guédon; Sacha A F T van Hijum; Jan Kok; Oscar P Kuipers; Dusko S Ehrlich; Pierre Renault
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site.
Journal of bacteriology 2005;187(11):3752-61.
2005: Sacha A F T van Hijum; Anne de Jong; Richard J S Baerends; Harma A Karsens; Naomi E Kramer; Rasmus Larsen; Chris D den Hengst; Casper J Albers; Jan Kok; Oscar P Kuipers
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
BMC genomics 2005;6():77.
2004: Morris A Swertz; E O De Brock; Sacha A F T van Hijum; Anne de Jong; Girbe Buist; Richard J S Baerends; Jan Kok; Oscar P Kuipers; Ritsert C Jansen
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
Bioinformatics (Oxford, England) 2004;20(13):2075-83.
2004: Sacha A F T van Hijum; E Szalowska; M J E C van der Maarel; Lubbert Dijkhuizen
Biochemical and molecular characterization of a levansucrase from Lactobacillus reuteri.
Microbiology (Reading, England) 2004;150(Pt 3):621-30.
2004: Lukasz K Ozimek; Sacha A F T van Hijum; Gerrit A van Koningsveld; M J E C van der Maarel; GH van Geel-Schutten; Lubbert Dijkhuizen
Site-directed mutagenesis study of the three catalytic residues of the fructosyltransferases of Lactobacillus reuteri 121.
FEBS letters 2004;560(1-3):131-3.
2004: Jorge García de la Nava; Sacha A F T van Hijum; Oswaldo Trelles
Saturation and quantization reduction in microarray experiments using two scans at different sensitivities.
Statistical applications in genetics and molecular biology 2004;3():Article11.
2003: Jorge García de la Nava; Sacha A F T van Hijum; Oswaldo Trelles
PreP: gene expression data pre-processing.
Bioinformatics (Oxford, England) 2003;19(17):2328-9.
2003: Sacha A F T van Hijum; Aldert L Zomer; Oscar P Kuipers; Jan Kok
Projector: automatic contig mapping for gap closure purposes.
Nucleic acids research 2003;31(22):e144.
2003: Sacha A F T van Hijum; Anne de Jong; Girbe Buist; Jan Kok; Oscar P Kuipers
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.
Bioinformatics (Oxford, England) 2003;19(12):1580-2.
2003: Sacha A F T van Hijum; M J E C van der Maarel; Lubbert Dijkhuizen
Kinetic properties of an inulosucrase from Lactobacillus reuteri 121.
FEBS letters 2003;534(1-3):207-10.
2003: Sacha A F T van Hijum; Jorge García de la Nava; Oswaldo Trelles; Jan Kok; Oscar P Kuipers
MicroPreP: a cDNA microarray data pre-processing framework.
Applied bioinformatics 2003;2(4):241-4.
2002: Sacha A F T van Hijum; GH van Geel-Schutten; H Rahaoui; M J E C van der Maarel; Lubbert Dijkhuizen
Characterization of a novel fructosyltransferase from Lactobacillus reuteri that synthesizes high-molecular-weight inulin and inulin oligosaccharides.
Applied and environmental microbiology 2002;68(9):4390-8.
2002: Oscar P Kuipers; Anne de Jong; Richard J S Baerends; Sacha A F T van Hijum; Aldert L Zomer; Harma A Karsens; Chris D den Hengst; Naomi E Kramer; Girbe Buist; Jan Kok
Transcriptome analysis and related databases of Lactococcus lactis.
Antonie van Leeuwenhoek 2002;82(1-4):113-22.
2001: Sacha A F T van Hijum; K Bonting; M J E C van der Maarel; Lubbert Dijkhuizen
Purification of a novel fructosyltransferase from Lactobacillus reuteri strain 121 and characterization of the levan produced.
FEMS microbiology letters 2001;205(2):323-8.