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Items: 1 to 50 of 67

1.

Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal.

Wu P, Heins ZJ, Muller J, Katsnelson L, de Bruijn I, Abeshouse AA, Schultz N, Fenyö D, Gao J.

Mol Cell Proteomics. 2019 Jul 15. pii: mcp.TIR119.001673. doi: 10.1074/mcp.TIR119.001673. [Epub ahead of print]

2.

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.

Herlemann DPR, Markert S, Meeske C, Andersson AF, de Bruijn I, Hentschker C, Unfried F, Becher D, Jürgens K, Schweder T.

Appl Environ Microbiol. 2019 Jul 18;85(15). pii: e00825-19. doi: 10.1128/AEM.00825-19. Print 2019 Aug 1.

PMID:
31152013
3.

Impact of a quadrivalent inactivated influenza vaccine on influenza-associated complications and health care use in children aged 6 to 35 months: Analysis of data from a phase III trial in the Northern and Southern Hemispheres.

Pepin S, Samson SI, Alvarez FP, Dupuy M, Gresset-Bourgeois V, De Bruijn I.

Vaccine. 2019 Mar 22;37(13):1885-1888. doi: 10.1016/j.vaccine.2019.01.059. Epub 2019 Feb 8.

4.

Efficacy, immunogenicity, and safety of a quadrivalent inactivated influenza vaccine in children aged 6-35 months: A multi-season randomised placebo-controlled trial in the Northern and Southern Hemispheres.

Pepin S, Dupuy M, Borja-Tabora CFC, Montellano M, Bravo L, Santos J, de Castro JA, Rivera-Medina DM, Cutland C, Ariza M, Diez-Domingo J, Gonzalez CD, Martinón-Torres F, Papadopoulou-Alataki E, Theodoriadou M, Kazek-Duret MP, Gurunathan S, De Bruijn I; GQM05 Study Group.

Vaccine. 2019 Mar 22;37(13):1876-1884. doi: 10.1016/j.vaccine.2018.11.074. Epub 2018 Dec 14.

5.

Cross-species interference of gene expression.

de Bruijn I, Verhoeven KJF.

Nat Commun. 2018 Nov 27;9(1):5019. doi: 10.1038/s41467-018-07353-0.

6.

Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors.

Pareja F, Brandes AH, Basili T, Selenica P, Geyer FC, Fan D, Da Cruz Paula A, Kumar R, Brown DN, Gularte-Mérida R, Alemar B, Bi R, Lim RS, de Bruijn I, Fujisawa S, Gardner R, Feng E, Li A, da Silva EM, Lozada JR, Blecua P, Cohen-Gould L, Jungbluth AA, Rakha EA, Ellis IO, Edelweiss MIA, Palazzo J, Norton L, Hollmann T, Edelweiss M, Rubin BP, Weigelt B, Reis-Filho JS.

Nat Commun. 2018 Aug 30;9(1):3533. doi: 10.1038/s41467-018-05886-y.

7.

Cell entry of a host-targeting protein of oomycetes requires gp96.

Trusch F, Loebach L, Wawra S, Durward E, Wuensch A, Iberahim NA, de Bruijn I, MacKenzie K, Willems A, Toloczko A, Diéguez-Uribeondo J, Rasmussen T, Schrader T, Bayer P, Secombes CJ, van West P.

Nat Commun. 2018 Jun 14;9(1):2347. doi: 10.1038/s41467-018-04796-3.

8.

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.

Carrión VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, Medema MH, Eberl L, Raaijmakers JM.

ISME J. 2018 Sep;12(9):2307-2321. doi: 10.1038/s41396-018-0186-x. Epub 2018 Jun 13.

PMID:
29899517
9.

Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis.

Al-Jubury A, Lu C, Kania PW, von Gersdorff Jørgensen L, Liu Y, de Bruijn I, Raaijmakers J, Buchmann K.

J Fish Dis. 2018 Jul;41(7):1147-1152. doi: 10.1111/jfd.12810. Epub 2018 Apr 19.

PMID:
29671884
10.

Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.

Gómez Expósito R, de Bruijn I, Postma J, Raaijmakers JM.

Front Microbiol. 2017 Dec 18;8:2529. doi: 10.3389/fmicb.2017.02529. eCollection 2017. Review.

11.

Exploring fish microbial communities to mitigate emerging diseases in aquaculture.

de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM.

FEMS Microbiol Ecol. 2018 Jan 1;94(1). doi: 10.1093/femsec/fix161. Review.

PMID:
29206925
12.

Quadrivalent inactivated influenza vaccine (VaxigripTetra™).

Gresset-Bourgeois V, Leventhal PS, Pepin S, Hollingsworth R, Kazek-Duret MP, De Bruijn I, Samson SI.

Expert Rev Vaccines. 2018 Jan;17(1):1-11. doi: 10.1080/14760584.2018.1407650. Epub 2017 Nov 27. Review.

PMID:
29157068
13.

Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer.

Weigelt B, Comino-Méndez I, de Bruijn I, Tian L, Meisel JL, García-Murillas I, Fribbens C, Cutts R, Martelotto LG, Ng CKY, Lim RS, Selenica P, Piscuoglio S, Aghajanian C, Norton L, Murali R, Hyman DM, Borsu L, Arcila ME, Konner J, Reis-Filho JS, Greenberg RA, Robson ME, Turner NC.

Clin Cancer Res. 2017 Nov 1;23(21):6708-6720. doi: 10.1158/1078-0432.CCR-17-0544. Epub 2017 Aug 1.

14.

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF.

ISME J. 2017 Nov;11(11):2538-2551. doi: 10.1038/ismej.2017.108. Epub 2017 Jul 21.

15.

Potential for Biocontrol of Hairy Root Disease by a Paenibacillus Clade.

Bosmans L, De Bruijn I, Gerards S, Moerkens R, Van Looveren L, Wittemans L, Van Calenberge B, Paeleman A, Van Kerckhove S, De Mot R, Rozenski J, Rediers H, Raaijmakers JM, Lievens B.

Front Microbiol. 2017 Mar 22;8:447. doi: 10.3389/fmicb.2017.00447. eCollection 2017.

16.

Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases.

Ng CKY, Bidard FC, Piscuoglio S, Geyer FC, Lim RS, de Bruijn I, Shen R, Pareja F, Berman SH, Wang L, Pierga JY, Vincent-Salomon A, Viale A, Norton L, Sigal B, Weigelt B, Cottu P, Reis-Filho JS.

Clin Cancer Res. 2017 Aug 1;23(15):4402-4415. doi: 10.1158/1078-0432.CCR-16-3115. Epub 2017 Mar 28.

17.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

Bagnoud A, Chourey K, Hettich RL, de Bruijn I, Andersson AF, Leupin OX, Schwyn B, Bernier-Latmani R.

Nat Commun. 2016 Oct 14;7:12770. doi: 10.1038/ncomms12770.

18.

Agar composition affects in vitro screening of biocontrol activity of antagonistic microorganisms.

Bosmans L, De Bruijn I, De Mot R, Rediers H, Lievens B.

J Microbiol Methods. 2016 Aug;127:7-9. doi: 10.1016/j.mimet.2016.05.004. Epub 2016 May 7.

PMID:
27166668
19.

Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina.

Liu Y, Zachow C, Raaijmakers JM, de Bruijn I.

Int J Mol Sci. 2016 Jan 21;17(1). pii: E140. doi: 10.3390/ijms17010140.

20.

Diversity and Activity of Lysobacter Species from Disease Suppressive Soils.

Gómez Expósito R, Postma J, Raaijmakers JM, De Bruijn I.

Front Microbiol. 2015 Nov 16;6:1243. doi: 10.3389/fmicb.2015.01243. eCollection 2015.

21.

Comparative genomics and metabolic profiling of the genus Lysobacter.

de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J, Patel N, Postma J, Dorrestein PC, Kobayashi D, Raaijmakers JM.

BMC Genomics. 2015 Nov 23;16:991. doi: 10.1186/s12864-015-2191-z.

22.

Uterine adenosarcomas are mesenchymal neoplasms.

Piscuoglio S, Burke KA, Ng CK, Papanastasiou AD, Geyer FC, Macedo GS, Martelotto LG, de Bruijn I, De Filippo MR, Schultheis AM, Ioris RA, Levine DA, Soslow RA, Rubin BP, Reis-Filho JS, Weigelt B.

J Pathol. 2016 Feb;238(3):381-8. doi: 10.1002/path.4675. Epub 2015 Dec 28.

23.

A minimalistic microbial food web in an excavated deep subsurface clay rock.

Bagnoud A, de Bruijn I, Andersson AF, Diomidis N, Leupin OX, Schwyn B, Bernier-Latmani R.

FEMS Microbiol Ecol. 2016 Jan;92(1). pii: fiv138. doi: 10.1093/femsec/fiv138. Epub 2015 Nov 4.

PMID:
26542073
24.

Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms.

Bonnichsen L, Bygvraa Svenningsen N, Rybtke M, de Bruijn I, Raaijmakers JM, Tolker-Nielsen T, Nybroe O.

Microbiology. 2015 Dec;161(12):2289-97. doi: 10.1099/mic.0.000191. Epub 2015 Sep 28.

25.

Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia.

Liu Y, Rzeszutek E, van der Voort M, Wu CH, Thoen E, Skaar I, Bulone V, Dorrestein PC, Raaijmakers JM, de Bruijn I.

PLoS One. 2015 Aug 28;10(8):e0136241. doi: 10.1371/journal.pone.0136241. eCollection 2015.

26.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

27.

Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP.

Song C, Sundqvist G, Malm E, de Bruijn I, Kumar A, van de Mortel J, Bulone V, Raaijmakers JM.

BMC Microbiol. 2015 Feb 14;15:29. doi: 10.1186/s12866-015-0367-y.

28.

The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization.

Zachow C, Jahanshah G, de Bruijn I, Song C, Ianni F, Pataj Z, Gerhardt H, Pianet I, Lämmerhofer M, Berg G, Gross H, Raaijmakers JM.

Mol Plant Microbe Interact. 2015 Jul;28(7):800-10. doi: 10.1094/MPMI-12-14-0406-R. Epub 2015 Jul 9.

29.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
30.

Functional characterization of a tyrosinase gene from the oomycete Saprolegnia parasitica by RNAi silencing.

Saraiva M, de Bruijn I, Grenville-Briggs L, McLaggan D, Willems A, Bulone V, van West P.

Fungal Biol. 2014 Jul;118(7):621-9. doi: 10.1016/j.funbio.2014.01.011. Epub 2014 Feb 22.

31.

Deciphering microbial landscapes of fish eggs to mitigate emerging diseases.

Liu Y, de Bruijn I, Jack AL, Drynan K, van den Berg AH, Thoen E, Sandoval-Sierra V, Skaar I, van West P, Diéguez-Uribeondo J, van der Voort M, Mendes R, Mazzola M, Raaijmakers JM.

ISME J. 2014 Oct;8(10):2002-14. doi: 10.1038/ismej.2014.44. Epub 2014 Mar 27.

32.

The Gac regulon of Pseudomonas fluorescens SBW25.

Cheng X, de Bruijn I, van der Voort M, Loper JE, Raaijmakers JM.

Environ Microbiol Rep. 2013 Aug;5(4):608-19. doi: 10.1111/1758-2229.12061. Epub 2013 Apr 30.

PMID:
23864577
33.

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P.

PLoS Genet. 2013 Jun;9(6):e1003272. doi: 10.1371/journal.pgen.1003272. Epub 2013 Jun 13.

34.

Immune gene expression in trout cell lines infected with the fish pathogenic oomycete Saprolegnia parasitica.

de Bruijn I, Belmonte R, Anderson VL, Saraiva M, Wang T, van West P, Secombes CJ.

Dev Comp Immunol. 2012 Sep;38(1):44-54. doi: 10.1016/j.dci.2012.03.018. Epub 2012 Apr 19.

PMID:
22522286
35.

Host-targeting protein 1 (SpHtp1) from the oomycete Saprolegnia parasitica translocates specifically into fish cells in a tyrosine-O-sulphate-dependent manner.

Wawra S, Bain J, Durward E, de Bruijn I, Minor KL, Matena A, Löbach L, Whisson SC, Bayer P, Porter AJ, Birch PR, Secombes CJ, van West P.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2096-101. doi: 10.1073/pnas.1113775109. Epub 2012 Jan 20.

36.

Deciphering the rhizosphere microbiome for disease-suppressive bacteria.

Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM.

Science. 2011 May 27;332(6033):1097-100. doi: 10.1126/science.1203980. Epub 2011 May 5.

37.

The putative RxLR effector protein SpHtp1 from the fish pathogenic oomycete Saprolegnia parasitica is translocated into fish cells.

van West P, de Bruijn I, Minor KL, Phillips AJ, Robertson EJ, Wawra S, Bain J, Anderson VL, Secombes CJ.

FEMS Microbiol Lett. 2010 Sep 1;310(2):127-37. doi: 10.1111/j.1574-6968.2010.02055.x. Epub 2010 Jul 9.

38.

Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics.

Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M.

FEMS Microbiol Rev. 2010 Nov;34(6):1037-62. doi: 10.1111/j.1574-6976.2010.00221.x. Review.

39.

Dedifferentiated peripheral chondrosarcomas: regulation of EXT-downstream molecules and differentiation-related genes.

Rozeman LB, de Bruijn IH, Bacchini P, Staals EL, Bertoni F, Bovée JV, Hogendoorn PC.

Mod Pathol. 2009 Nov;22(11):1489-98. doi: 10.1038/modpathol.2009.120. Epub 2009 Sep 4.

40.

Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens.

Mazzola M, de Bruijn I, Cohen MF, Raaijmakers JM.

Appl Environ Microbiol. 2009 Nov;75(21):6804-11. doi: 10.1128/AEM.01272-09. Epub 2009 Aug 28.

41.

Diversity and functional analysis of LuxR-type transcriptional regulators of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens.

de Bruijn I, Raaijmakers JM.

Appl Environ Microbiol. 2009 Jul;75(14):4753-61. doi: 10.1128/AEM.00575-09. Epub 2009 May 15.

42.

Trivalent inactivated subunit influenza vaccine Influvac: 25-Year experience of safety and immunogenicity.

Giezeman KM, Nauta J, de Bruijn IA, Palache AM.

Vaccine. 2009 Apr 21;27(18):2414-7. doi: 10.1016/j.vaccine.2009.02.008. Epub 2009 Feb 12.

PMID:
19368782
43.

Regulation of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens by the ClpP protease.

de Bruijn I, Raaijmakers JM.

J Bacteriol. 2009 Mar;191(6):1910-23. doi: 10.1128/JB.01558-08. Epub 2008 Dec 29.

44.

Safety and immunogenicity of two subunit influenza vaccines in healthy children, adults and the elderly: a randomized controlled trial in China.

Zhu FC, Zhou W, Pan H, Lu L, Gerez L, Nauta J, Giezeman K, de Bruijn I.

Vaccine. 2008 Aug 18;26(35):4579-84. doi: 10.1016/j.vaccine.2008.05.082. Epub 2008 Jun 17.

PMID:
18602729
45.

Stimulation of chitin synthesis rescues Candida albicans from echinocandins.

Walker LA, Munro CA, de Bruijn I, Lenardon MD, McKinnon A, Gow NA.

PLoS Pathog. 2008 Apr 4;4(4):e1000040. doi: 10.1371/journal.ppat.1000040.

46.

Antibody induction by virosomal, MF59-adjuvanted, or conventional influenza vaccines in the elderly.

de Bruijn I, Meyer I, Gerez L, Nauta J, Giezeman K, Palache B.

Vaccine. 2007 Dec 21;26(1):119-27. Epub 2007 Nov 12.

PMID:
18063446
47.

Massetolide A biosynthesis in Pseudomonas fluorescens.

de Bruijn I, de Kock MJ, de Waard P, van Beek TA, Raaijmakers JM.

J Bacteriol. 2008 Apr;190(8):2777-89. Epub 2007 Nov 9.

48.

Functional outcome after peroneal nerve injury.

de Bruijn IL, Geertzen JH, Dijkstra PU.

Int J Rehabil Res. 2007 Dec;30(4):333-7.

PMID:
17975454
49.

The PKC, HOG and Ca2+ signalling pathways co-ordinately regulate chitin synthesis in Candida albicans.

Munro CA, Selvaggini S, de Bruijn I, Walker L, Lenardon MD, Gerssen B, Milne S, Brown AJ, Gow NA.

Mol Microbiol. 2007 Mar;63(5):1399-413.

50.

Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species.

de Bruijn I, de Kock MJ, Yang M, de Waard P, van Beek TA, Raaijmakers JM.

Mol Microbiol. 2007 Jan;63(2):417-28.

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