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Items: 1 to 50 of 58

1.

Protease Activity Profiling of Snake Venoms Using High-Throughput Peptide Screening.

Kalogeropoulos K, Treschow AF, Auf dem Keller U, Escalante T, Rucavado A, Gutiérrez JM, Laustsen AH, Workman CT.

Toxins (Basel). 2019 Mar 19;11(3). pii: E170. doi: 10.3390/toxins11030170.

2.

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans.

La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MØ, Pope PB, Martens EC, Hachem MA, Westereng B.

Nat Commun. 2019 Feb 22;10(1):905. doi: 10.1038/s41467-019-08812-y.

3.

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

Thodberg M, Thieffry A, Bornholdt J, Boyd M, Holmberg C, Azad A, Workman CT, Chen Y, Ekwall K, Nielsen O, Sandelin A.

Nucleic Acids Res. 2019 Feb 28;47(4):1671-1691. doi: 10.1093/nar/gky1227.

4.

Glucose-Dependent Promoters for Dynamic Regulation of Metabolic Pathways.

Maury J, Kannan S, Jensen NB, Öberg FK, Kildegaard KR, Forster J, Nielsen J, Workman CT, Borodina I.

Front Bioeng Biotechnol. 2018 May 22;6:63. doi: 10.3389/fbioe.2018.00063. eCollection 2018.

5.

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data.

Kannan S, Sams T, Maury J, Workman CT.

ACS Synth Biol. 2018 Mar 16;7(3):832-841. doi: 10.1021/acssynbio.7b00223. Epub 2018 Feb 19.

6.

Correction to: Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells.

Nielsen JC, Lino FSO, Rasmussen TG, Thykær J, Workman CT, Basso TO.

Appl Microbiol Biotechnol. 2018 Jan;102(1):513. doi: 10.1007/s00253-017-8643-4.

7.

Familial co-occurrence of congenital heart defects follows distinct patterns.

Ellesøe SG, Workman CT, Bouvagnet P, Loffredo CA, McBride KL, Hinton RB, van Engelen K, Gertsen EC, Mulder BJM, Postma AV, Anderson RH, Hjortdal VE, Brunak S, Larsen LA.

Eur Heart J. 2018 Mar 21;39(12):1015-1022. doi: 10.1093/eurheartj/ehx314.

8.

Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells.

Nielsen JC, Senne de Oliveira Lino F, Rasmussen TG, Thykær J, Workman CT, Basso TO.

Appl Microbiol Biotechnol. 2017 Nov;101(22):8237-8248. doi: 10.1007/s00253-017-8548-2. Epub 2017 Oct 10. Erratum in: Appl Microbiol Biotechnol. 2017 Nov 25;:.

9.

Modifiable risk factors promoting neurodegeneration is associated with two novel brain degradation markers measured in serum.

Neergaard JS, Dragsbæk K, Christiansen C, Nielsen HB, Workman CT, Brix S, Henriksen K, Karsdal MA.

Neurochem Int. 2017 Sep;108:303-308. doi: 10.1016/j.neuint.2017.05.002. Epub 2017 May 10.

PMID:
28499950
10.

The identification and functional annotation of RNA structures conserved in vertebrates.

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9.

11.

RAIN: RNA-protein Association and Interaction Networks.

Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J.

Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw167. Print 2017. Erratum in: Database (Oxford). 2017 Jan 1;2017(1):.

12.

A scored human protein-protein interaction network to catalyze genomic interpretation.

Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K.

Nat Methods. 2017 Jan;14(1):61-64. doi: 10.1038/nmeth.4083. Epub 2016 Nov 28.

13.

High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells.

Altıntaş A, Davidsen K, Garde C, Mortensen UH, Brasen JC, Sams T, Workman CT.

Free Radic Biol Med. 2016 Dec;101:143-153. doi: 10.1016/j.freeradbiomed.2016.10.006. Epub 2016 Oct 11.

PMID:
27742413
14.

15-year follow-up of the Second Nordic Mantle Cell Lymphoma trial (MCL2): prolonged remissions without survival plateau.

Eskelund CW, Kolstad A, Jerkeman M, Räty R, Laurell A, Eloranta S, Smedby KE, Husby S, Pedersen LB, Andersen NS, Eriksson M, Kimby E, Bentzen H, Kuittinen O, Lauritzsen GF, Nilsson-Ehle H, Ralfkiaer E, Ehinger M, Sundström C, Delabie J, Karjalainen-Lindsberg ML, Workman CT, Garde C, Elonen E, Brown P, Grønbaek K, Geisler CH.

Br J Haematol. 2016 Nov;175(3):410-418. doi: 10.1111/bjh.14241. Epub 2016 Jul 5.

PMID:
27378674
15.

Major differences between human atopic dermatitis and murine models, as determined by using global transcriptomic profiling.

Ewald DA, Noda S, Oliva M, Litman T, Nakajima S, Li X, Xu H, Workman CT, Scheipers P, Svitacheva N, Labuda T, Krueger JG, Suárez-Fariñas M, Kabashima K, Guttman-Yassky E.

J Allergy Clin Immunol. 2017 Feb;139(2):562-571. doi: 10.1016/j.jaci.2016.08.029. Epub 2016 Oct 1.

PMID:
27702671
16.

Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer.

Joshi T, Elias D, Stenvang J, Alves CL, Teng F, Lyng MB, Lykkesfeldt AE, Brünner N, Wang J, Gupta R, Workman CT, Ditzel HJ.

Oncotarget. 2016 Aug 30;7(35):57239-57253. doi: 10.18632/oncotarget.11136.

17.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S.

NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016.

18.

Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans.

Donkin I, Versteyhe S, Ingerslev LR, Qian K, Mechta M, Nordkap L, Mortensen B, Appel EV, Jørgensen N, Kristiansen VB, Hansen T, Workman CT, Zierath JR, Barrès R.

Cell Metab. 2016 Feb 9;23(2):369-78. doi: 10.1016/j.cmet.2015.11.004. Epub 2015 Dec 6.

19.

Quantification of oxidative stress phenotypes based on high-throughput growth profiling of protein kinase and phosphatase knockouts.

Altıntaş A, Martini J, Mortensen UH, Workman CT.

FEMS Yeast Res. 2016 Feb;16(1):fov101. doi: 10.1093/femsyr/fov101. Epub 2015 Nov 11.

PMID:
26564984
20.

Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways.

Ewald DA, Malajian D, Krueger JG, Workman CT, Wang T, Tian S, Litman T, Guttman-Yassky E, Suárez-Fariñas M.

BMC Med Genomics. 2015 Oct 12;8:60. doi: 10.1186/s12920-015-0133-x.

21.

miR-18b overexpression identifies mantle cell lymphoma patients with poor outcome and improves the MIPI-B prognosticator.

Husby S, Ralfkiaer U, Garde C, Zandi R, Ek S, Kolstad A, Jerkeman M, Laurell A, Räty R, Pedersen LB, Pedersen A, Ehinger M, Sundström C, Karjalainen-Lindsberg ML, Delabie J, Clasen-Linde E, Brown P, Cowland JB, Workman CT, Geisler CH, Grønbæk K.

Blood. 2015 Apr 23;125(17):2669-77. doi: 10.1182/blood-2014-06-584193. Epub 2015 Mar 3.

22.

Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast.

Clément-Ziza M, Marsellach FX, Codlin S, Papadakis MA, Reinhardt S, Rodríguez-López M, Martin S, Marguerat S, Schmidt A, Lee E, Workman CT, Bähler J, Beyer A.

Mol Syst Biol. 2014 Nov 28;10:764. doi: 10.15252/msb.20145123.

23.

A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.

Jiang L, Edwards SM, Thomsen B, Workman CT, Guldbrandtsen B, Sørensen P.

BMC Bioinformatics. 2014 Sep 24;15:315. doi: 10.1186/1471-2105-15-315.

24.

Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells.

Re A, Workman CT, Waldron L, Quattrone A, Brunak S.

Stem Cell Res. 2014 Sep;13(2):316-28. doi: 10.1016/j.scr.2014.07.008. Epub 2014 Aug 4.

25.

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. doi: 10.1371/journal.pone.0099701. eCollection 2014.

26.

A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.

Lindemose S, Jensen MK, Van de Velde J, O'Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, De Masi F.

Nucleic Acids Res. 2014 Jul;42(12):7681-93. doi: 10.1093/nar/gku502. Epub 2014 Jun 9.

27.

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, Altıntaş A, Fazli M, Dechesne A, Workman CT, Tolker-Nielsen T, Smets BF.

Microbiologyopen. 2014 Aug;3(4):457-69. doi: 10.1002/mbo3.180. Epub 2014 Jun 10.

28.

RNA-protein interactions: an overview.

Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT.

Methods Mol Biol. 2014;1097:491-521. doi: 10.1007/978-1-62703-709-9_23. Review.

PMID:
24639174
29.

Oxidative stress response pathways: Fission yeast as archetype.

Papadakis MA, Workman CT.

Crit Rev Microbiol. 2015;41(4):520-35. doi: 10.3109/1040841X.2013.870968. Review.

PMID:
24576188
30.

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.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):1055-9. doi: 10.1073/pnas.1320850111. Epub 2014 Jan 6.

31.

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). 2013 Nov 6;3(11):1979-95. doi: 10.1534/g3.113.006601.

32.

ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.

Jensen MK, Lindemose S, de Masi F, Reimer JJ, Nielsen M, Perera V, Workman CT, Turck F, Grant MR, Mundy J, Petersen M, Skriver K.

FEBS Open Bio. 2013 Jul 29;3:321-7. doi: 10.1016/j.fob.2013.07.006. eCollection 2013.

33.

MicroRNA profiling in ocular adnexal lymphoma: a role for MYC and NFKB1 mediated dysregulation of microRNA expression in aggressive disease.

Hother C, Rasmussen PK, Joshi T, Reker D, Ralfkiær U, Workman CT, Heegaard S, Ralfkiær E, Grønbæk K.

Invest Ophthalmol Vis Sci. 2013 Aug 5;54(8):5169-75. doi: 10.1167/iovs.13-12272.

PMID:
23821202
34.

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 Rep. 2013 Apr 25;3(4):1293-305. doi: 10.1016/j.celrep.2013.03.001. Epub 2013 Mar 28.

35.

Gene prioritization for livestock diseases by data integration.

Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT.

Physiol Genomics. 2012 Mar 1;44(5):305-17. doi: 10.1152/physiolgenomics.00047.2011. Epub 2012 Jan 10.

PMID:
22234994
36.

Transcriptome dynamics of Pseudomonas putida KT2440 under water stress.

Gülez G, Dechesne A, Workman CT, Smets BF.

Appl Environ Microbiol. 2012 Feb;78(3):676-83. doi: 10.1128/AEM.06150-11. Epub 2011 Dec 2.

37.

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.

J Proteome Res. 2012 Feb 3;11(2):941-71. doi: 10.1021/pr200724e. Epub 2011 Dec 15.

PMID:
22103328
38.

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.

Proc Natl Acad Sci U S A. 2011 May 3;108(18):7481-6. doi: 10.1073/pnas.1018249108. Epub 2011 Apr 25.

39.

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. 2011 Jul;35(5):318-32. doi: 10.1002/gepi.20580. Epub 2011 Apr 11.

PMID:
21484861
40.

Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine.

Polur H, Joshi T, Workman CT, Lavekar G, Kouskoumvekaki I.

Mol Inform. 2011 Mar 14;30(2-3):181-7. doi: 10.1002/minf.201000163. Epub 2011 Feb 10.

PMID:
27466772
41.

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.

Nat Commun. 2010;1:145. doi: 10.1038/ncomms1150.

PMID:
21266995
42.

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. 2010 Dec 1;5(12):e15031. doi: 10.1371/journal.pone.0015031.

43.

Equitoxic doses of 5-azacytidine and 5-aza-2'deoxycytidine 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. 2010 Sep 29;5(9). pii: e12994. doi: 10.1371/journal.pone.0012994.

44.

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.

J Proteome Res. 2010 Oct 1;9(10):5142-52. doi: 10.1021/pr1004086.

PMID:
20839851
45.

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. 2010 Jun 22;6:381. doi: 10.1038/msb.2010.36.

46.

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.

Environ Microbiol. 2010 Jun;12(6):1643-58. doi: 10.1111/j.1462-2920.2010.02211.x. Epub 2010 Apr 7.

PMID:
20406284
47.

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. 2009 Jul;9(14):3752-64. doi: 10.1002/pmic.200800848.

PMID:
19639594
48.

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.

Eur Cytokine Netw. 2009 Jun;20(2):81-7. doi: 10.1684/ecn.2009.0152.

49.

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. doi: 10.1093/bioinformatics/btp213.

50.

Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach.

Ferreira GB, Overbergh L, van Etten E, Lage K, D'Hertog W, Hansen DA, Maris M, Moreau Y, Workman CT, Waelkens E, Mathieu C.

Proteomics Clin Appl. 2008 Sep;2(9):1349-60. doi: 10.1002/prca.200800110. Epub 2008 Jul 21.

PMID:
21136928

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