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2014 (6) 2013 (4) 2012 (3) 2011 (4) 2010 (6) 2009 (3) 2008 and before (19)

2014

    Oxidative stress response pathways: Fission yeast as archetype.
    Papadakis MA, Workman CT
    Critical Reviews in Microbiology. 2014 Feb 27, 2014
    PubMed
    RNA-protein interactions: an overview
    Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT
    Methods in Molecular Biology 2014;1097:491-521., 2014
    PubMed
    Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials.
    Gulez G, Altintas A, Fazli M, Dechesne A, Workman CT, Tolker-Nielsen T, Smets BF
    Microbiologyopen. 2014 Jun 10., 2014
    PubMed
    Synthetic promoter library for modulation of actinorhodin production in Streptomyces coelicolor A3(2).
    Sohoni SV, Fazio A, Workman CT, Mijakovic I, Lantz AE
    PLoS One. 2014 Jun 25;9(6):e99701, 2014
    PubMed
    Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and β-cell protection.
    Christensen DP, Gysemans C, Lundh M, Dahllöf MS, Noesgaard D, Schmidt SF, Mandrup S, Birkbak N, Workman CT, Piemonti L, Blaabjerg L, Monzani V, Fossati G, Mascagni P, Paraskevas S, Aikin RA, Billestrup N, Grunnet LG, Dinarello CA, Mathieu C, Mandrup-Poulsen T
    PNAS, Proceedings of the National Academy of Sciences 2014 Jan 21;111(3):1055-9., 2014
    PubMed
    A DNA binding-site landscape and regulatory network analysis for the family of NAC stress response transcription factors in Arabidopsis thaliana.
    Lindemose S, Jensen KM, Van de Velde Jan, O’Shea C, Heyndrickx KS, Workman CT, Vandepoele Klaas, Skriver K, De Masi F
    Nucleic Acids Research. 2014 Aug 1;42(12):7681-93., 2014
    PubMed

2013

    The SH2 domain interaction landscape.
    Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, Mann M, Mayer BJ, Castagnoli L, Cesareni G
    Cell Reports. 2013 Apr 25;3(4):1293-305., 2013
    PubMed
    Mapping Condition Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae.
    Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J
    G3 (Bethesda) 3(11):1979-95 doi:10.1534/g3.113.006601, 2013
    PubMed
    ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.
    Jensen MK, Lindemose S, Masi Fd, Reimer JJ, Nielsen M, Perera V, Workman CT, Turck F, Grant MR, Mundy J, Petersen M, Skriver K
    FEBS Open Bio 3:321-7 doi:10.1016/j.fob.2013.07.006, 2013
    PubMed
    MicroRNA profiling in ocular adnexal lymphoma: A role for MYC and NFKB1 mediated dysregulation of microRNA expression in aggressive disease.
    Hother C, Rasmussen P, Joshi T, Reker D, Ralfkiaer U, Workman C, Heegaard S, Ralfkiaer E, Grønbæk K
    Investigative Ophthalmology & Visual Science. 54(8):5169-75 doi:10.1167/iovs.13-12272, 2013
    PubMed

2012

    Differential protein pathways in 1,25-dihydroxyvitamin d(3) and dexamethasone modulated tolerogenic human dendritic cells.
    Ferreira GB, Kleijwegt FS, Waelkens E, Lage K, Nikolic T, Hansen DA, Workman CT, Roep BO, Overbergh L, Mathieu C
    Journal of Proteome Research. 2012 Feb 3;11(2):941-71, 2012
    PubMed
    Transcriptome dynamics of Pseudomonas putida KT2440 under water stress.
    Gülez G, Dechesne A, Workman CT, Smets BF
    Applied and Environmental Microbiology. 2012 Feb;78(3):676-83, 2012
    PubMed
    Gene prioritization for livestock diseases by data integration.
    Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT
    Physiological Genomics. 2012 Mar 1;44(5):305-17, 2012
    PubMed

2011

    Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using \"-omics\" techniques
    Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, Nielsen J, Olsson L
    Microb. Cell Fact. 10:27 doi:10.1186/1475-2859-10-27, 2011
    PubMed
    Evolutionary dynamics of bacteria in a human host environment
    Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MO, Molin S
    Proceedings of the National Academy of Sciences U.S.A. 108(18):7481-6 doi:10.1073/pnas.1018249108, 2011
    PubMed
    Relevant URL
    Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
    Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S
    Genet. Epidemiol. 35(5):318-32 doi:10.1002/gepi.20580, 2011
    PubMed
    Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine
    Polur H, Joshi T, Workman CT, Lavekar G, Kouskoumvekaki I
    Molecular Informatics, February 10, 2011

2010

    Early adaptive developments of Pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts.
    Rau MH, Hansen SK, Johansen HK, Thomsen LE, Workman CT, Nielsen KF, Jelsbak L, Høiby N, Yang L, Molin S
    Environmental Microbiology . 2010 Jun;12(6):1643-58., 2010
    PubMed
    Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains
    Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J
    Nature Communication 1:145 doi:10.1038/ncomms1150, 2010
    PubMed
    Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status
    Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C
    PLoS ONE 5(12):e15031 doi:10.1371/journal.pone.0015031, 2010
    PubMed
    Novel insights into the global proteome responses of insulin-producing INS-1E cells to different degrees of endoplasmic reticulum stress
    D\\\'Hertog W, Maris M, Ferreira GB, Verdrengh E, Lage K, Hansen DA, Cardozo AK, Workman CT, Moreau Y, Eizirik DL, Waelkens E, Overbergh L, Mathieu C
    Journal of Proteome Research. 9(10):5142-52 doi:10.1021/pr1004086, 2010
    PubMed
    Equitoxic Doses of 5-Azacytidine and 5-Aza-2ŒDeoxycytidine Induce Diverse Immediate and Overlapping Heritable Changes in the Transcriptome
    Qiu X, Hother C, Ralfkiær UM, Søgaard A, Lu Q, Workman CT, Liang G, Jones PA, Grønbæk K
    PLoS ONE 5(9) doi:10.1371/journal.pone.0012994, 2010
    PubMed
    Dissecting spatio-temporal protein networks driving human heart development and related disorders
    Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA
    Mol. Syst. Biol. 6:381 doi:10.1038/msb.2010.36, 2010
    PubMed

2009

    Predicting functionality of protein-DNA interactions by integrating diverse evidence.
    Ucar D, Beyer A, Parthasarathy S, Workman CT
    Bioinformatics. 2009 Jun 15;25(12):i137-44., 2009
    PubMed
    IL-1 receptor antagonism and muscle gene expression in patients with type 2 diabetes.
    Berchtold LA, Larsen CM, Vaag A, Faulenbach M, Workman CT, Kruhøffer M, Donath M, Mandrup-Poulsen T
    European Cytokine Network . 2009 Jun;20(2):81-7., 2009
    PubMed
    Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D
    Ferreira GB, van Etten E, Lage K, Hansen DA, Moreau Y, Workman CT, Waer M, Verstuyf A, Waelkens E, Overbergh L, Mathieu C
    Proteomics 9(14):3752-64 doi:10.1002/pmic.200800848, 2009
    PubMed

2008

    Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach
    Ferreira GB, Overbergh L, Etten EV, Lage K, D’Hertog W, Hansen DA, Maris M, Moreau Y, Workman CT, Waelkens E, Mathieu C
    Proteomics Clinical Applications, Volume 2 Issue 9, Pages 1349 - 1360, 2008
    Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design
    Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J
    BMC Genomics 2008, 9:341, 2008

2007

    DASS: efficient discovery and p-value calculation of substructures in unordered data.
    Hollunder J, Friedel M, Beyer A, Workman CT, Wilhelm T
    Bioinformatics. 2007 Jan 1;23(1):77-83., 2007
    PubMed
    Integration of biological networks and gene expression data using Cytoscape.
    Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
    Nature Protocols. 2007;2(10):2366-82., 2007
    PubMed
    Integrative analysis for finding genes and networks involved in diabetes and other complex diseases
    Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F
    Genome Biol. 8(11):R253, 2007
    PubMed

2006

    A systems approach to mapping DNA damage response pathways.
    Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T
    Science. 2006 May 19;312(5776):1054-9., 2006
    PubMed
    Integrated assessment and prediction of transcription factor binding.
    Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T
    PLoS Computational Biology. 2006 Jun 16;2(6):e70., 2006
    PubMed

2005

    enoLOGOS: a versatile web tool for energy normalized sequence logos.
    Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV
    Nucleic Acids Research. 2005 Jul 1;33(Web Server issue):W389-92., 2005
    PubMed

2004

    Blood cell gene expression profiling in rheumatoid arthritis; Discriminative genes and effect of rheumatoid factor
    Bovin LF, Rieneck K, Workman C, Nielsen H, Sorensen SF, Skjodt H, Florescu A, Brunak S, Bendtzen K
    Immunol. Lett. 93:217-26, 2004
    PubMed

2003

    GenePublisher: Automated analysis of DNA microarray data
    Knudsen S, Workman C, Sicheritz-Ponten T, Friis C
    Nucleic Acids Res. 31(13):3471-6, 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(9):research0048, 2002
    PubMed
    DNA Microarray analysis of fim mutations in Escherichia coli
    Schembri MA, Ussery D, Workman C, Hasman H, Klemm P
    Mol. Genet. Genomics 267(6):721-9, 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(8):1133-4, 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(5):1257-65, 2002
    PubMed
    Gene expression analysis and gene regulation: from DNA microarrays to comparative genomics
    Workman C
    Ph.D. thesis, 2002

2001

    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(6):2492-9, 2001
    PubMed
    Enrichment of regulatory signals in conserved non-coding genomic sequence
    Levy S, Hannenhalli S, Workman C
    Bioinformatics 17(10):871-7, 2001
    PubMed

1999

    No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    Workman C, Krogh A
    Nucleic Acids Res. 27(24):4816-22, 1999
    PubMed
    Modeling regulatory networks with weight matrices
    Weaver D, Workman C, Stormo GD
    Pac Symp Biocomput:112-23, 1999
    PubMed

2014 (6) 2013 (4) 2012 (3) 2011 (4) 2010 (6) 2009 (3) 2008 and before (19)