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Items: 1 to 50 of 57

1.

An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens.

Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S.

Front Microbiol. 2019 May 7;10:924. doi: 10.3389/fmicb.2019.00924. eCollection 2019.

2.

Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima.

Gore-Lloyd D, Sumann I, Brachmann AO, Schneeberger K, Ortiz-Merino RA, Moreno-Beltrán M, Schläfli M, Kirner P, Santos Kron A, Rueda-Mejia MP, Somerville V, Wolfe KH, Piel J, Ahrens CH, Henk D, Freimoser FM.

Mol Microbiol. 2019 May 12. doi: 10.1111/mmi.14272. [Epub ahead of print]

PMID:
31081214
3.

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.

Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH.

Nucleic Acids Res. 2018 Sep 28;46(17):8953-8965. doi: 10.1093/nar/gky726.

4.

Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris.

Lardi M, Liu Y, Giudice G, Ahrens CH, Zamboni N, Pessi G.

Int J Mol Sci. 2018 Apr 1;19(4). pii: E1049. doi: 10.3390/ijms19041049.

5.

Seasonal Dynamics of Glyphosate and AMPA in Lake Greifensee: Rapid Microbial Degradation in the Epilimnion During Summer.

Huntscha S, Stravs MA, Bühlmann A, Ahrens CH, Frey JE, Pomati F, Hollender J, Buerge IJ, Balmer ME, Poiger T.

Environ Sci Technol. 2018 Apr 17;52(8):4641-4649. doi: 10.1021/acs.est.8b00314. Epub 2018 Mar 27.

PMID:
29584408
6.

Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower.

Zengerer V, Schmid M, Bieri M, Müller DC, Remus-Emsermann MNP, Ahrens CH, Pelludat C.

Front Microbiol. 2018 Feb 9;9:145. doi: 10.3389/fmicb.2018.00145. eCollection 2018.

7.

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level.

Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH.

Front Microbiol. 2018 Jan 30;9:63. doi: 10.3389/fmicb.2018.00063. eCollection 2018.

8.

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH.

Genome Res. 2017 Dec;27(12):2083-2095. doi: 10.1101/gr.218255.116. Epub 2017 Nov 15.

9.

Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.

Marti R, Schmid M, Kulli S, Schneeberger K, Naskova J, Knøchel S, Ahrens CH, Hummerjohann J.

Appl Environ Microbiol. 2017 Jul 17;83(15). pii: e00628-17. doi: 10.1128/AEM.00628-17. Print 2017 Aug 1.

10.

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.

Remus-Emsermann MNP, Schmid M, Gekenidis MT, Pelludat C, Frey JE, Ahrens CH, Drissner D.

Stand Genomic Sci. 2016 Sep 26;11:75. doi: 10.1186/s40793-016-0190-6. eCollection 2016.

11.

Long-Chain Alkyl Cyanides: Unprecedented Volatile Compounds Released by Pseudomonas and Micromonospora Bacteria.

Montes Vidal D, von Rymon-Lipinski AL, Ravella S, Groenhagen U, Herrmann J, Zaburannyi N, Zarbin PH, Varadarajan AR, Ahrens CH, Weisskopf L, Müller R, Schulz S.

Angew Chem Int Ed Engl. 2017 Apr 3;56(15):4342-4346. doi: 10.1002/anie.201611940. Epub 2017 Mar 9.

PMID:
28276609
12.

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi.

Hilber-Bodmer M, Schmid M, Ahrens CH, Freimoser FM.

BMC Microbiol. 2017 Jan 5;17(1):4. doi: 10.1186/s12866-016-0908-z.

13.

Short communication: Heat-resistant Escherichia coli as potential persistent reservoir of extended-spectrum β-lactamases and Shiga toxin-encoding phages in dairy.

Marti R, Muniesa M, Schmid M, Ahrens CH, Naskova J, Hummerjohann J.

J Dairy Sci. 2016 Nov;99(11):8622-8632. doi: 10.3168/jds.2016-11076. Epub 2016 Aug 24.

14.

Isotropic thin PTCDA films on GaN(0 0 0 1).

Ahrens C, Flege JI, Jaye C, Fischer DA, Schmidt T, Falta J.

J Phys Condens Matter. 2016 Nov 30;28(47):475003. Epub 2016 Sep 26.

PMID:
27667820
15.

Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures.

Lardi M, Murset V, Fischer HM, Mesa S, Ahrens CH, Zamboni N, Pessi G.

Int J Mol Sci. 2016 May 27;17(6). pii: E815. doi: 10.3390/ijms17060815.

16.

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.

Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E.

BMC Genomics. 2016 Apr 23;17:302. doi: 10.1186/s12864-016-2602-9.

17.

Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms.

Turnbull L, Toyofuku M, Hynen AL, Kurosawa M, Pessi G, Petty NK, Osvath SR, Cárcamo-Oyarce G, Gloag ES, Shimoni R, Omasits U, Ito S, Yap X, Monahan LG, Cavaliere R, Ahrens CH, Charles IG, Nomura N, Eberl L, Whitchurch CB.

Nat Commun. 2016 Apr 14;7:11220. doi: 10.1038/ncomms11220.

18.

Volatile Organic Compounds from Native Potato-associated Pseudomonas as Potential Anti-oomycete Agents.

De Vrieze M, Pandey P, Bucheli TD, Varadarajan AR, Ahrens CH, Weisskopf L, Bailly A.

Front Microbiol. 2015 Nov 23;6:1295. doi: 10.3389/fmicb.2015.01295. eCollection 2015.

19.

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli.

Urfer M, Bogdanovic J, Lo Monte F, Moehle K, Zerbe K, Omasits U, Ahrens CH, Pessi G, Eberl L, Robinson JA.

J Biol Chem. 2016 Jan 22;291(4):1921-32. doi: 10.1074/jbc.M115.691725. Epub 2015 Dec 1.

20.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members.

Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.

21.

σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111.

Lardi M, Aguilar C, Pedrioli A, Omasits U, Suppiger A, Cárcamo-Oyarce G, Schmid N, Ahrens CH, Eberl L, Pessi G.

Appl Environ Microbiol. 2015 Jun 15;81(12):4077-89. doi: 10.1128/AEM.00694-15. Epub 2015 Apr 3.

22.

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH.

J Proteomics. 2014 Aug 28;108:269-83. doi: 10.1016/j.jprot.2014.05.011. Epub 2014 May 27.

PMID:
24878426
23.

Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism.

Stekhoven DJ, Omasits U, Quebatte M, Dehio C, Ahrens CH.

J Proteomics. 2014 Mar 17;99:123-37. doi: 10.1016/j.jprot.2014.01.015. Epub 2014 Jan 28.

PMID:
24486812
24.

A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum.

Koch M, Delmotte N, Ahrens CH, Omasits U, Schneider K, Danza F, Padhi B, Murset V, Braissant O, Vorholt JA, Hennecke H, Pessi G.

Appl Environ Microbiol. 2014 Apr;80(7):2094-101. doi: 10.1128/AEM.03314-13. Epub 2014 Jan 24.

25.

Protter: interactive protein feature visualization and integration with experimental proteomic data.

Omasits U, Ahrens CH, Müller S, Wollscheid B.

Bioinformatics. 2014 Mar 15;30(6):884-6. doi: 10.1093/bioinformatics/btt607. Epub 2013 Oct 24.

26.

Response of Burkholderia cenocepacia H111 to micro-oxia.

Pessi G, Braunwalder R, Grunau A, Omasits U, Ahrens CH, Eberl L.

PLoS One. 2013 Sep 2;8(9):e72939. doi: 10.1371/journal.pone.0072939. eCollection 2013.

27.

Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions.

Carlier AL, Omasits U, Ahrens CH, Eberl L.

Mol Plant Microbe Interact. 2013 Nov;26(11):1325-33. doi: 10.1094/MPMI-05-13-0152-R.

28.

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.

Omasits U, Quebatte M, Stekhoven DJ, Fortes C, Roschitzki B, Robinson MD, Dehio C, Ahrens CH.

Genome Res. 2013 Nov;23(11):1916-27. doi: 10.1101/gr.151035.112. Epub 2013 Jul 22.

29.

The hemolymph proteome of fed and starved Drosophila larvae.

Handke B, Poernbacher I, Goetze S, Ahrens CH, Omasits U, Marty F, Simigdala N, Meyer I, Wollscheid B, Brunner E, Hafen E, Lehner CF.

PLoS One. 2013 Jun 20;8(6):e67208. doi: 10.1371/journal.pone.0067208. Print 2013.

30.

The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.

Schmid N, Pessi G, Deng Y, Aguilar C, Carlier AL, Grunau A, Omasits U, Zhang LH, Ahrens CH, Eberl L.

PLoS One. 2012;7(11):e49966. doi: 10.1371/journal.pone.0049966. Epub 2012 Nov 20.

31.

Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover.

Deng Y, Schmid N, Wang C, Wang J, Pessi G, Wu D, Lee J, Aguilar C, Ahrens CH, Chang C, Song H, Eberl L, Zhang LH.

Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15479-84. Epub 2012 Sep 4.

32.

The HUPO initiative on Model Organism Proteomes, iMOP.

Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.

Proteomics. 2012 Feb;12(3):340-5. doi: 10.1002/pmic.201290014.

PMID:
22290800
33.

A mighty small heart: the cardiac proteome of adult Drosophila melanogaster.

Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, Reedy MC, Zmasek CM, Gucek M, Cole RN, Van Eyk JE, Bodmer R, O'Rourke B, Bernstein SI, Foster DB.

PLoS One. 2011 Apr 25;6(4):e18497. doi: 10.1371/journal.pone.0018497.

34.

Generating and navigating proteome maps using mass spectrometry.

Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R.

Nat Rev Mol Cell Biol. 2010 Nov;11(11):789-801. doi: 10.1038/nrm2973. Epub 2010 Oct 14. Review.

PMID:
20944666
35.

Model organism proteomics.

Ahrens CH, Schrimpf SP, Brunner E, Aebersold R.

J Proteomics. 2010 Oct 10;73(11):2051-3. doi: 10.1016/j.jprot.2010.09.001. Epub 2010 Sep 9. No abstract available.

PMID:
20832510
36.

PeptideClassifier for protein inference and targeted quantitative proteomics.

Qeli E, Ahrens CH.

Nat Biotechnol. 2010 Jul;28(7):647-50. doi: 10.1038/nbt0710-647. No abstract available.

PMID:
20622826
37.

Protein and gene model inference based on statistical modeling in k-partite graphs.

Gerster S, Qeli E, Ahrens CH, Bühlmann P.

Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12101-6. doi: 10.1073/pnas.0907654107. Epub 2010 Jun 18.

38.

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules.

Delmotte N, Ahrens CH, Knief C, Qeli E, Koch M, Fischer HM, Vorholt JA, Hennecke H, Pessi G.

Proteomics. 2010 Apr;10(7):1391-400. doi: 10.1002/pmic.200900710.

PMID:
20104621
39.

Quantitative proteomics: a central technology for systems biology.

Ahrens CH, Brunner E, Basler K.

J Proteomics. 2010 Feb 10;73(4):820-7. doi: 10.1016/j.jprot.2009.12.007. Epub 2009 Dec 21. No abstract available.

PMID:
20026292
40.

Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.

Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E.

PLoS Biol. 2009 Nov;7(11):e1000236. doi: 10.1371/journal.pbio.1000236. Epub 2009 Nov 3.

41.

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function.

Grobei MA, Qeli E, Brunner E, Rehrauer H, Zhang R, Roschitzki B, Basler K, Ahrens CH, Grossniklaus U.

Genome Res. 2009 Oct;19(10):1786-800. doi: 10.1101/gr.089060.108. Epub 2009 Jun 22.

42.

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.

Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO.

PLoS Biol. 2009 Mar 3;7(3):e48. doi: 10.1371/journal.pbio.1000048.

43.

A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics.

Ahrens CH, Brunner E, Hafen E, Aebersold R, Basler K.

Fly (Austin). 2007 May-Jun;1(3):182-6. Epub 2007 May 4.

PMID:
18820430
44.

Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules.

Pessi G, Ahrens CH, Rehrauer H, Lindemann A, Hauser F, Fischer HM, Hennecke H.

Mol Plant Microbe Interact. 2007 Nov;20(11):1353-63.

45.

The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry.

Potthast F, Gerrits B, Häkkinen J, Rutishauser D, Ahrens CH, Roschitzki B, Baerenfaller K, Munton RP, Walther P, Gehrig P, Seif P, Seeberger PH, Schlapbach R.

J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Jul 1;854(1-2):173-82. Epub 2007 Apr 25.

PMID:
17513179
46.

A high-quality catalog of the Drosophila melanogaster proteome.

Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R.

Nat Biotechnol. 2007 May;25(5):576-83. Epub 2007 Apr 22.

PMID:
17450130
47.

Current challenges and approaches for the synergistic use of systems biology data in the scientific community.

Ahrens CH, Wagner U, Rehrauer HK, Türker C, Schlapbach R.

EXS. 2007;97:277-307. Review.

PMID:
17432272
48.

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data.

Kristensen DB, Brønd JC, Nielsen PA, Andersen JR, Sørensen OT, Jørgensen V, Budin K, Matthiesen J, Venø P, Jespersen HM, Ahrens CH, Schandorff S, Ruhoff PT, Wisniewski JR, Bennett KL, Podtelejnikov AV.

Mol Cell Proteomics. 2004 Oct;3(10):1023-38. Epub 2004 Jul 29.

49.

WNT1 inducible signaling pathway protein 3, WISP-3, a novel target gene in colorectal carcinomas with microsatellite instability.

Thorstensen L, Diep CB, Meling GI, Aagesen TH, Ahrens CH, Rognum TO, Lothe RA.

Gastroenterology. 2001 Dec;121(6):1275-80.

PMID:
11729105
50.

The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome.

Ahrens CH, Russell RL, Funk CJ, Evans JT, Harwood SH, Rohrmann GF.

Virology. 1997 Mar 17;229(2):381-99.

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