Epernicus: Sacha AFT van Hijum, Dr.P.H.

Sacha AFT van Hijum, Dr.P.H.

Positions:
Senior Scientist

NIZO Food Research (Food Valley, Netherlands)

Group Leader

Bacterial Genomics

Radboud University Nijmegen Medical Center (Nijmegen, Netherlands)
Advisor:
Roland Siezen
Degrees:

Dr.P.H., Biology, University of Groningen (Groningen, Netherlands)
Past Advisors:

Uwe Völker (as Senior Scientist)

Oscar P. Kuipers (as Senior Scientist)

Jan Kok (as Senior Scientist)

Lubbert Dijkhuizen (as Graduate Student - Ph.D.)
Research:
Bioinformatics of prokaryotes, transcriptomics, proteomics, gene regulatory networks

Communities:

Sacha van Hijum's Genealogy

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Sacha van Hijum's Publications (28)

The relative value of operon predictions.
Brouwer RW, Kuipers OP, van Hijum SA

Briefings in bioinformatics. 2008 Sep;9(5):367-75
Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons.
Larsen R, van Hijum SA, Martinussen J, Kuipers OP, Kok J

Applied and environmental microbiology. 2008 Aug;74(15):4768-71
Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons.
van Hijum SA, Baerends RJ, Zomer AL, Karsens HA, Martin-Requena V, Trelles O, Kok J, Kuipers OP

BMC bioinformatics. 2008;9:93
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.
Blom EJ, Bosman DW, van Hijum SA, Breitling R, Tijsma L, Silvis R, Roerdink JB, Kuipers OP

Bioinformatics (Oxford, England). 2007 May 1;23(9):1161-3
Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.
Szalowska E, van Hijum SA, Roelofsen H, Hoek A, Vonk RJ, te Meerman GJ

Biotechnology progress. 2007 Jan-Feb;23(1):217-24
Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae.
Kloosterman TG, Hendriksen WT, Bijlsma JJ, Bootsma HJ, van Hijum SA, Kok J, Hermans PW, Kuipers OP

The Journal of biological chemistry. 2006 Sep 1;281(35):25097-109
BAGEL: a web-based bacteriocin genome mining tool.
de Jong A, van Hijum SA, Bijlsma JJ, Kok J, Kuipers OP

Nucleic acids research. 2006 Jul 1;34(Web Server issue):W273-9
Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance.
Kramer NE, van Hijum SA, Knol J, Kok J, Kuipers OP

Antimicrobial agents and chemotherapy. 2006 May;50(5):1753-61
Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria.
van Hijum SA, Kralj S, Ozimek LK, Dijkhuizen L, van Geel-Schutten IG

Microbiology and molecular biology reviews : MMBR. 2006 Mar;70(1):157-76
SIMAGE: simulation of DNA-microarray gene expression data.
Albers CJ, Jansen RC, Kok J, Kuipers OP, van Hijum SA

BMC bioinformatics. 2006;7:205
The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.
den Hengst CD, van Hijum SA, Geurts JM, Nauta A, Kok J, Kuipers OP

The Journal of biological chemistry. 2005 Oct 7;280(40):34332-42
Comparative and functional genomics of lactococci.
Kok J, Buist G, Zomer AL, van Hijum SA, Kuipers OP

FEMS microbiology reviews. 2005 Aug;29(3):411-33
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
van Hijum SA, Zomer AL, Kuipers OP, Kok J

Nucleic acids research. 2005 Jul 1;33(Web Server issue):W560-6
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site.
Barrière C, Veiga-da-Cunha M, Pons N, Guédon E, van Hijum SA, Kok J, Kuipers OP, Ehrlich DS, Renault P

Journal of bacteriology. 2005 Jun;187(11):3752-61
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
van Hijum SA, de Jong A, Baerends RJ, Karsens HA, Kramer NE, Larsen R, den Hengst CD, Albers CJ, Kok J, Kuipers OP

BMC genomics. 2005;6(1):77
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
Swertz MA, De Brock EO, Van Hijum SA, De Jong A, Buist G, Baerends RJ, Kok J, Kuipers OP, Jansen RC

Bioinformatics (Oxford, England). 2004 Sep 1;20(13):2075-83
Biochemical and molecular characterization of a levansucrase from Lactobacillus reuteri.
van Hijum SA, Szalowska E, van der Maarel MJ, Dijkhuizen L

Microbiology (Reading, England). 2004 Mar;150(Pt 3):621-30
Site-directed mutagenesis study of the three catalytic residues of the fructosyltransferases of Lactobacillus reuteri 121.
Ozimek LK, van Hijum SA, van Koningsveld GA, van Der Maarel MJ, van Geel-Schutten GH, Dijkhuizen L

FEBS letters. 2004 Feb 27;560(1-3):131-3
Saturation and quantization reduction in microarray experiments using two scans at different sensitivities.
García de la Nava J, van Hijum S, Trelles O

Statistical applications in genetics and molecular biology. 2004;3:Article11
PreP: gene expression data pre-processing.
García de la Nava J, van Hijum S, Trelles O

Bioinformatics (Oxford, England). 2003 Nov 22;19(17):2328-9
Projector: automatic contig mapping for gap closure purposes.
van Hijum SA, Zomer AL, Kuipers OP, Kok J

Nucleic acids research. 2003 Nov 15;31(22):e144
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.
van Hijum SA, de Jong A, Buist G, Kok J, Kuipers OP

Bioinformatics (Oxford, England). 2003 Aug 12;19(12):1580-2
Kinetic properties of an inulosucrase from Lactobacillus reuteri 121.
van Hijum SA, van der Maarel MJ, Dijkhuizen L

FEBS letters. 2003 Jan 16;534(1-3):207-10
MicroPreP: a cDNA microarray data pre-processing framework.
van Hijum SA, García de la Nava J, Trelles O, Kok J, Kuipers OP

Applied bioinformatics. 2003;2(4):241-4
Characterization of a novel fructosyltransferase from Lactobacillus reuteri that synthesizes high-molecular-weight inulin and inulin oligosaccharides.
van Hijum SA, van Geel-Schutten GH, Rahaoui H, van der Maarel MJ, Dijkhuizen L

Applied and environmental microbiology. 2002 Sep;68(9):4390-8

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Sacha AFT van Hijum, Dr.P.H.

Senior Scientist

Group Leader

Bioinformatics of prokaryotes, transcriptomics, proteomics, gene regulatory networks

Sacha van Hijum's Genealogy

Sacha van Hijum's Publications (28)