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2009 (1) 2006 (2) 2005 (3) 2004 (4) 2003 (3) 2002 (6) 2001 and before (11) Books (2)

2009

    Genome-wide gene expression profiling of SCID mice with T-cell-mediated Colitis
    Brudzewsky D, Pedersen AE, Claesson MH, Gad M, Kristensen NN, Lage K, Jensen T, Tommerup N, Larsen LA, Knudsen S, Tümer Z
    Scand J Immunol;69(5):437-46, 2009
    PubMed

2006

    Transcriptome analysis of FSH and FSH variant stimulation in granulosa cells from IVM patients reveals novel regulated genes
    Perlman S, Bouquin T, van den Hazel B, Jensen TH, Schambye HT, Knudsen S, Okkels JS
    Mol Hum Reprod, 12, 135-44, 2006
    PubMed
    Identification of novel genes regulated in the developing human ventral mesencephalon
    Jorgensen JR, Juliusson B, Henriksen KF, Hansen C, Knudsen S, Petersen TN, Blom N, Seiger A, Wahlberg LU
    Experimental neurology, 198(2):427-37, 2006
    PubMed

2005

    Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering
    Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J
    Applied and environmental microbiology, 71, 6465-6472, 2005
    PubMed
    New weakly expressed cell cycle-regulated genes in yeast
    Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S
    Yeast, 22, 1191-201, 2005
    PubMed
    Implementation of a gene expression index cal-culation method based on the PDNN model
    Nielsen HB, Gautier L, Knudsen S
    Bioinformatics, 1;21, 687-8, 2005
    PubMed

2004

    Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy
    Strøm CC, Kruhøffer M, Knudsen S, Stensgaard-Hansen F, Jonassen TE, Ørntoft TF, Haunsø S, Sheikh SP
    Comparative and Functional Genomics 5, 459-470, 2004
    PubMed
    Implementation of a gene expression index calculatation method based on the PDNN model
    Bjørn Nielsen H, Gautier L, Knudsen S
    Bioinformatics, 1;21, 687-8, 2004
    PubMed
    Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
    Willenbrock H, Juncker AS, Schmiegelow K, Knudsen S, Ryder LP
    Leukemia, 18, 1270-7, 2004
    PubMed
    The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing
    Theilgaard-Monch K, Knudsen S, Follin P, Borregaard N
    Journal of Immunology, 172, 7684-93, 2004
    PubMed

2003

    GenePublisher: Automated analysis of DNA microarray data
    Knudsen S, Workman C, Sicheritz-Ponten T, Friis C
    Nucleic Acids Res, 31, 3471-76, 2003
    PubMed
    Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Nielsen HB, Wernersson R, Knudsen S
    Nucleic Acids Res.,31, 3491-6, 2003
    PubMed
    Classification of Dukes´ B and C colorectal cancers using expression arrays
    Frederiksen CM, Knudsen S, Laurberg S, Ørntoft TF
    Journal of Cancer Research and Clinical Oncology, 129,263-271, 2003
    PubMed

2002

    A new non-linear normalization method for reducing variability in DNA microarray experiments
    Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielsen HB, Saxild HH, Nielsen C, Brunak S, Knudsen S
    Genome Biol., 3, research0048.1-0048.16, 2002
    PubMed
    Neural network predicts sequence of TP53 gene based on DNA chip
    Spicker S, Wikman F, Lu ML, Cordon-Cardo C, Workman C, Orntoft TF, Brunak S, Knudsen S
    Bioinformatics, 18, 1133-1134, 2002
    PubMed
    Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
    Nielsen HB, Knudsen S
    Bioinformatics, 18, 321-322, 2002
    PubMed
    Prediction of human protein function from post-translational modifications and localization features
    Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Stærfeldt HH, Rapacki K, Workman C, Andersen CAF, Knudsen S, Krogh A, Valencia A, Brunak S
    J. Mol. Biol., 319, 1257-1265, 2002
    PubMed
    Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions
    Jarmer H, Berka R, Knudsen S, Saxild HH
    FEMS Microbiology letters, 206, 197-200, 2002
    PubMed
    Reproducibility of transcriptome analyses using oligonucleotide microarrays: an interlaboratory comparison of chemostat cultures of Saccharomyces cerevisiae
    Piper M, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk J
    Journal of Biological Chemistry, 277, 37001-37008, 2002
    PubMed

2001

    Sigma A recognition sites in the Bacillus subtilis genome
    Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S
    Microbiology, 147, 2417-24, 2001
    PubMed
    Identification of gene expression patterns in superficial and invasive human bladder cancer
    Thykjaer T, Workman C, Kruhoffer M, Demtroder K, Wolf H, Andersen LD, Frederiksen CM, Knudsen S, Ørntoft TF
    Cancer Res., 61,2492-2499, 2001
    PubMed

2000

    Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
    Jensen LJ, Knudsen S
    Bioinformatics 16, 326-333, 2000
    PubMed
    The frequency of mutators in populations of Escherichia coli
    Boe L, Danielsen M, Knudsen S, Petersen JB, Maymann J, Jensen PR
    Mutat. Res., 448, 47-55, 2000
    PubMed

1999

    Promoter 2.0: for the Recognition of PolII Promoter Sequences and
    Knudsen S
    Bioinformatics, 15, 356-361, 1999
    PubMed

1998

    The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Eschericia coli and Pseudomonas fluorescens
    Hansen LH, Knudsen S, Sorensen SJ
    Curr. Microbiol., 36, 341-347, 1998
    PubMed

1997

    Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts
    Knudsen S, Brunak S
    RNA, 3, 697-701, 1997
    PubMed

1992

    G/C rich tract in 5' end of human introns
    Engelbrecht J, Knudsen S, Brunak S
    J. Mol. Biol., 227, 108-113, 1992

1991

    Prediction of human mRNA donor and acceptor sites from the DNA sequence
    Brunak S, Engelbrecht J, Knudsen S
    J. Mol. Biol., 220, 49-65, 1991

1990

    Neural Network Detects Errors in the assignment of pre-mRNA splice sites
    Brunak S, Engelbrecht J, Knudsen S
    Nucleic Acids Res., 18, 4797-4801, 1990
    Cleaning up gene databases
    Brunak S, Engelbrecht J, Knudsen S
    Nature, 343, 123, 1990


Books

    A Biologist's Guide to Analysis of DNA Microarray Data, 2nd edition
    Knudsen S
    John Wiley & Sons, New York, 2004
    Details
    A Biologist's Guide to Analysis of DNA Microarray Data, 1st edition
    Knudsen S
    John Wiley & Sons, New York, 2002
    Details

2009 (1) 2006 (2) 2005 (3) 2004 (4) 2003 (3) 2002 (6) 2001 and before (11) Books (2)