Publications


Refereed papers

2014
Orfanoudaki, G. and Economou, A. (2014)
Proteome-wide Sub-cellular Topologies of E.coli polypeptides database (STEPdb)
Molecular and Cellular Proteomics (in press)
[Abstract]

 

2013
Papanastasiou, M., Orfanoudaki, G., Koukaki, M., Kountourakis, N., Sardis, M.F., Aivaliotis, M., Karamanou, S., Economou, A. (2013) The Escherichia coli Peripheral Inner Membrane Proteome.
Molecular and Cellular Proteomics 12: 599-610 
[Abstract]


2012
Schlesner, M., Miller, A., Besir, H., Aivaliotis, M., Streif, J., Scheffer, B., Siedler, F., Oesterhelt, D. (2012)  The Protein Interaction Network  of a Taxis Signal Transduction System in a Halophilic Archaeon. Proteomics BMC Microbiology 12: 272
[Abstract]

Zerefos, P. G., Aivaliotis, M., Baumann, M., Vlahou, A. (2012) Analysis of the  urine proteome via a combination of multi-dimensional approaches.
Proteomics 12:
391-400
[Abstract]


2011
Kapellios, E. A., Karamanou, S., Sardis, M. F., Aivaliotis, M., Economou, A., Pergantis, S. A. (2011)   Using Nanoelectrospray Ion Mobility Spectrometry (GEMMA) to Determine the Size and Relative Molecular Mass of Proteins and Protein Assemblies: A Comparison with MALLS and QELS.
Analytical and Bioanalytical Chemistry 399: 2421-33  
[Abstract]


2010
Mischak, H., Kolch, W., Aivaliotis, M., Bouyssie, D., Court, M., Dihazi, H., Dihazi, G. H., Franke, J., Garin, J., Gonzalez de Peredo, A., Iphofer, A., Jansch, L., Lacroix, C., Makridakis, M., Masselon, C., Metzger, J., Monsarrat, B., Mrug, M., Norling, M., Novak, J., Pich, A., Pitt, A., Bongcam-Rudloff, E., Siwy, J., Suzuki, H., Thongboonkerd, V., Wang, L.-S., Zoidakis, J. , Zurbig, P., Schanstra, J. P., Vlahou, A. (2010) Comprehensive  human urine standards for comparability and standardization in  clinical proteome analysis. Proteomics Clinical applications 4: 464-478
[Abstract]

Kouyianou, K., Aivaliotis, M., Gevaert, K., Karas, M., Tsiotis, G. (2010) Membrane proteome of the green sulfur bacterium Chlorobium tepidum  (syn. Chlorobaculum tepidum) analyzed by gel-based and gel-free  methods.
Photosynth Res. 104: 153-62
[Abstract]

Samoilis, G., Aivaliotis, M., Vranakis, I., Papadioti, A., Tselentis, Y., Tsiotis, G., Psaroulaki, A. (2010) Proteomic screening for possible effector  molecules secreted by the obligate intracellular pathogen Coxiella  burnetii.
J Proteome Res. 9: 1619-26
[Abstract]

Lionaki, E, Aivaliotis M., Pozidis C. and Tokatlidis K. (2010) The N-terminal shuttle domain of Erv1 determines the affinity for Mia40 and mediates electron transfer to the catalytic Erv1 core in yeast mitochondria.
Antioxidants and Redox Signalling 13: 1327-39
[Abstract]

 

Refereed Conference Papers

2014
Papanastasiou, M., Trelle, M.B., Tsirigotaki, A., Karamanou, S., Jorgensen, T.J.D., Economou, A. (2014) Investigation of the dynamics of the translocase motor SecA by hydrogen deuterium-exchange mass spectrometry.
ASMS 2014 Conference on Mass Spectrometry and Allied Topics

Tsirigotaki, A., Papanastasiou, M., Konijnenberg, A., Chatzi, K., Trelle,M.B., Jørgensen, T.J.D., Sobott,F., Karamanou, S., and Economou, A. (2014) The non-native code of secreted preproteins investigated by HDX-MS and Native IM/MS.
ASMS 2014 Conference on Mass Spectrometry and Allied Topics


2013
Tzerpos, P., Savvidis, T., Aivaliotis, M., Benos P., Spilianakis, C. (2013) Bioinformatic and proteomic analysis of transcription factor binding  sites in interacting regulatory elements in mouse T cells.
FEBS  Journal, Special Issue: 38th FEBS Congress, Saint Petersburg, Russia,  (July 6-11, 2013, 280, s1, 1-661)

2012
Papanastasiou, M., Trelle, M.B., Gouridis, G., Karamanou, S., Famelis, N., Jorgensen, T.J.D., Economou, A. (2012) Unraveling the Translocon Machinery at Work by Hydrogen-Deuterium Exchange Mass Spectrometry.
60th ASMS Conference on Mass Spectrometry and Allied Topics (May 20-24, 2012)

2011
Mylona, E.A., Savelonas, M.A., Maroulis, D., Aivaliotis, M. (2011) 2D-GE Image  Segmentation based on Level-Sets in Proc.
IEEE International  Conference on Image Processing (ICIP), Brussesls, Belgium

Kapellios, E. A., Karamanou, S., Sardis, M. F., Papanastasiou, M., Aivaliotis, M., Pergantis, S. A. and Economou, A. (2011) A Multiplexed Approach for the Determination of Intact Protein Mass, Dimension and Oligomerization Using Nanoelectrospray Ion Mobility Spectrometry (GEMMA), LTQ-Orbitrap MS, MALLS and QELS.
59th ASMS Conference on Mass Spectrometry (June 5-9, 2011)

Papanastasiou, M., Orfanoudaki, G., Sardis, M. F., Mavroudis, P., Aivaliotis, M., Karamanou, S. and Economou, A. (2011) Deciphering the Cell Envelope Proteome of Escherichia coli.
59th ASMS Conference on Mass Spectrometry  (June 5-9, 2011)

Aivaliotis, M., Portaliou, A., Balabanidou, V., Karamanou, S. and Economou, A. (2011) Complexome dynamics during Type III protein secretion.
Omics Meets Cell Biology, Keystone Symposia on Molecular and Cellular Biology (May 8-13, 2011)


2010
Papanastasiou, M., Sardis, M. F., Aivaliotis, M., Karamanou, S. and Economou, A. (2010) Comprehensive Characterization of the Inner Membrane Proteome of Escherichia coli Using a nanoLC-LTQ Orbitrap MS. 58th ASMS Conference on Mass Spectrometry and Allied Topics (May 23-27, 2010)
[Abstract]

Aivaliotis, M., Papanastasiou, M. and Economou, A. (2011) Study of non-covalent protein complexes using a top-down approach on a hybrid LTQ-Orbitrap mass spectrometer.
58th ASMS Conference on Mass Spectrometry and Allied Topics (May 23-27, 2010)
[Abstract]

Balabanidou, V., Aivaliotis, M., Papanastasiou, M., Karamanou, S. and Economou, A. (2010) Global and targeted complexome analysis of the cytosolic proteome of Enteropathogenic Escherichia coli using Native-PAGE combined with nLC-LTQ Orbitrap MS.
58th ASMS Conference on Mass Spectrometry and Allied Topics (May 23-27, 2010)
[Abstract]


2009
Kapellios, E. A., Karamanou, S., Sardis, M. F., Aivaliotis, M., Pergantis, S. A. and Economou, A. (2009) Nanoelectrospray Differential Ion Mobility Spectrometry for Protein Sizing and Molecular Mass Determination: Method Development and Validation.
18th International Mass Spectrometry Conference, Bremen, Germany (Aug 30-Sep 04, 2009)
[Abstract]

 

Conference abstracts/Posters

2012
Aivaliotis, M., Portaliou, A., Balabanidou, V., Kountourakis, N., Chronaki, D., Orfanoudaki, G., Karamanou, S., and Economou, A. (2012) Determination of Complexes formed during protein secretion through Type III secretion system in Enteropathogenic E. coli.
[Abstract]

Famelis, N., Gouridis, G., Karamanou, S., Martin, S., Papanastasiou, M., Trelle, M.B., Kapelios, E., Aivaliotis, M., Pergantis S., , Capitani, G., Jorgensen, T.J.D., Economou, A. (2012) Structure and dynamics of chaperone-preprotein recognition in the secretory pathway.
[Abstract]

Aivaliotis, M., Portaliou, A., Balabanidou, V., Kountourakis, N., Chronaki, D., Orfanoudaki, G., Karamanou, S., Economou, A. (2012) Dynamic complexome and secretome analysis for the study of type III protein translocation and secretion mechanism.
[Abstract]

2011
Aivaliotis, M., Portaliou, A., Balabanidou, V., Kountourakis, N., Orfanoudaki, G., Karamanou, S. and Economou, A. (2011) Dissecting Type III Protein Secretion Mechanism in Enteropathogenic Escherichia coli by Dynamic Complexome and Secretome Analysis.
EMBO practical workshop on Protein-Protein and Protein-Nucleic Acid Cross-linking and Mass Spectrometry  (October 23-29, 2011)

Stratigi, C., Aivaliotis, M. and Spilianakis, C. (2011) Homologous Association in the TNF- α Locus.
International workshop on Functional and Structural Proteomics, Athens 2011 (FunSPA, October 6-7, 2011)

Portaliou, A., Aivaliotis, M., Kountourakis, N., Balabanidou, V., Karamanou, S. and Economou, A. (2011) Global analysis of the Type III protein secretion system of enteropathogenic Escherichia coli.
International workshop on Functional and Structural Proteomics, Athens 2011 (FunSPA, October 6-7, 2011)

Papanastasiou, M., Orfanoudaki, G., Sardis, M. F., Aivaliotis, M., Karamanou, S. and Economou, A. (2011) Comprehensive Characterization of the Cell Envelope Proteome of Escherichia coli.
International workshop on Functional and Structural Proteomics, Athens 2011 (FunSPA, October 6-7, 2011)

Aivaliotis, M., Portaliou, A., Balabanidou, V., Orfanoudaki, G., Kountourakis, N., Karamanou, S. and Economou, A. (2011) Elucidating Type III Protein Secretion Mechanism in Enteropathogenic Escherichia coli by Dynamic Complexome Analysis.
International workshop on Functional and Structural Proteomics, Athens 2011 (FunSPA, October 6-7, 2011)

Aivaliotis, M., Portaliou, A., Balabanidou, V., Kountourakis, N., Karamanou, S. and Economou A. (2011) Complexome dynamics during Type III protein secretion.
Summer school on Computational Mass Spectrometry Based Proteomics, Max Planck Institute Munich (May 22-27, 2011) 

Aivaliotis, M., Portaliou, A., Balabanidou, V., Karamanou, S. and Economou A. (2011) Complexome dynamics during type III protein secretion by Enteropathogenic Escherichia coli.
44th Annual Meeting of the German Society for Mass Spectrometry (DGMS,  February 27 – March 2, 2011)

 

2010
Portaliou, A., Kountourakis, N., Aivaliotis, M., Balabanidou, V., Karamanou, S. and Economou A. (2010) Analysis of the secretome of enteropathogenic Escherichia coli.
4th Protein Biotechnology Summer School on Crete (May 26-27, 2010)

Tzerpos, P., Savvidis, T., Aivaliotis, M. and Spilianakis C. (2010) Affinity Capture and Mass Spectrometric Identification of Specific DNA Binding Proteins.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Balabanidou, V., Portaliou, A., Karamanou, S., Aivaliotis, M. and Economou, A. (2010) Chaperone/Secreted protein native complexes mediate protein export.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Kallergi, E., Kritsiligou, P., Lionaki, E., Aivaliotis, M., Katrakili, N., Pozidis, C. and Tokatlidis, K. (2010) Function and molecular interactions of mitochondrial sulfhydryl oxidase Erv1.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Kapellios, E. A., Karamanou, S., Sardis, M. F., Aivaliotis, M., Economou A. and Pergantis S. A. (2010) Using Nanoelectrospray Ion Mobility Spectrometry (GEMMA) to Determine the Size and Relative Molecular Mass of Proteins and Protein Assemblies: A Comparison with MALLS and QELS.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Papanastasiou, M., Sardis, M. F., Orfanoudaki, G., Giapitzaki, J., Aivaliotis, M., Karamanou, S. and Economou, A. (2010) Comprehensive Characterization of the E. coli Cell Envelope Using a nanoLC-LTQ Orbitrap MS.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Aivaliotis, M., Papanastasiou, M. and Economou, a. (2010) Study of non-covalent protein complexes using a Top-Down approach on a hybrid LTQ-Orbitrap mass spectrometer.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

Aivaliotis, M., Balabanidou, V., Portaliou, A., Kountourakis, N., Karamanou, S. and Economou, A. (2010) Global and targeted complexome analysis of the cytosolic proteome of Enteropathogenic Escherichia coli using Native-PAGE combined with nLC-LTQ Orbitrap MS.
1st International Proteomics Conference on Crete- IPCC01 (October 7-8, 2010)

 

Papers acknowledging ProFI services

Bariotaki, A., Kalaitzakis, D. and Smonou, I. (2012) Enzymatic Reductions for the Regio- and Stereoselective Synthesis of Hydroxyketo Esters and Dihydroxy Esters.
Organic Letters : DOI 10.1021
[Abstract]

Kamileri, I., Karakasilioti, I., Sideri, A., Kosteas, T., Tatarakis, A., Talianidis, I. and Garinis, G. A. (2012) Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria.
PNAS doi: 10.1073/pnas.1114941109
[Abstract]

Gryparis, C., Lykakis, I. N., Efe, C., Zaravinos, I. P., Vidali, T., Kladou, E. and Stratakis, M. (2011) Functionalized 3(2H)-furanones via photooxygenation of (b-keto)-2-substituted furans: Application to the biomimetic synthesis of merrekentrone C.
Organic and  Biomolecular  Chemistry 9:5655–5658
[Abstract]

Lykakis, I. N., Psyllaki, A. and Stratakis, M. (2011) Oxidative Cycloaddition of 1,1,3,3-Tetramethyldisiloxane to Alkynes Catalyzed by Supported Gold Nanoparticles.
Journal of the American Chemical Society 133:10426–10429
[Abstract]

Lykakis, I. N., Efe, C., Gryparis, C. and Stratakis, M. (2011) Ph3PAuNTf2 as a Superior Catalyst for the Selective Synthesis of 2H-Chromenes: Application to the Concise Synthesis of Benzopyran Natural Products.
European Journal of Organic Chemistry 2334–2338
[Abstract]

Kalaitzakis, D. and Smonou, I. (2010) A two-step, one-pot enzymatic synthesis of 2-substituted-1,3-diols.
J. Org. Chem. 75:8658-8661  
[Abstract]

Kalaitzakis, D. and Smonou, I. (2010) Highly diastereoselective synthesis of 2-substituted-1,3-diols catalyzed by Ketoreductases.
Tetrahedron 66:9431-9439
[Abstract]