2018

Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J,  Eisenacher M, Marcus  K. Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry. J Prot Res. 2018 Sep 12. doi: 10.1021/acs.jproteome.8b00308. [Epub ahead of print]

Winter L, Unger A, Berwanger C, Spörrer M, Wellhausen M, Türk M, Chevessier F, Strucksberg KH, Schlötzer-Schrehardt U, Wittig I, Goldmann WH, Marcus K, Linke WA, Clemen CS, Schröder R. Imbalances in protein homeostasis caused by mutant desmin. Neuropathol Appl Neurobiol. 2018 Sep 4. doi: 10.1111/nan.12516. [Epub ahead of print]

Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W. Proceedings of the EuBIC developer's meeting 2018. J proteomics 2018 Jun 2. doi: 10.1016/j.jprot.2018.05.015

Niedieker D, Großerüschkamp F, Schreiner A, Barkovits K, Kötting C, Marcus K, Gerwert K, Vorgerd M. Label-free identification of myopathological features with coherent anti-Stokes Raman scattering. Muscle Nerve. 2018 Apr 16. doi: 10.1002/mus.26140. [Epub ahead of print]

Cortese-Krott MM, Mergia E, Kramer CM, Lückstädt W, Yang J, Wolff G, Panknin C, Bracht T, Sitek B, Pernow J, Stasch JP, Feelisch M, Koesling D, Kelm M. Identification of a soluble guanylate cyclase in RBCs: preserved activity in patients with coronary artery disease. Redox Biol. 2018 Apr;14:328-337. doi: 10.1016/j.redox.2017.08.020. Epub 2017 Sep 8.

Duarte M., Subedi P,  Yilmaz E, Marcus K,  Laurell T, Ekström S. Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides. J Mol Recognit. 2018 Mar;31(3). doi: 10.1002/jmr.2677. Epub 2017 Oct 12.

Lollies A, Hartmann S, Schneider M, Bracht T, Weiß A, Arnolds J, Klein-Hitpass L, Sitek B, Hansmann ML, Küppers R, Weniger MA. An oncogenic axis of STAT-mediated BATF3 upregulation causing MYC activity in classical Hodgkin lymphoma and anaplastic large cell lymphoma. Leukemia. 2018 Jan;32(1):92-101. doi: 10.1038/leu.2017.203. Epub 2017 Jun 29.

Megger DA, Lax PM, Paauwe J, Fonseca Guerra C, Lippert B. Mixed guanine, adenine base quartets: possible roles of protons and metal ions in their stabilization. J Biol Inorg Chem. 2018 Jan;23(1):41-49. doi: 10.1007/s00775-017-1507-7. Epub 2017 Dec 7.

Baraniskin A, Chomiak M, Ahle G, Gress T, Buchholz M, Turewicz M, Eisenacher M, Margold M, Schlegel U, Schmiegel W, Hahn S, Schroers R. MicroRNA-30c as a novel diagnostic biomarker for primary and secondary B-cell lymphoma of the CNS. J Neurooncol. 2018 Jan 11. doi: 10.1007/s11060-018-2749-0. [Epub ahead of print]

2017

Eckl J, Sima S, Marcus K, Lindemann C, Richter K. Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes. PLoS One. 2017 Oct 27;12(10):e0186386. doi: 10.1371/journal.pone.0186386. eCollection 2017.

Seddigh P, Bracht T, Molinier-Frenkel V, Castellano F, Kniemeyer O, Schuster M, Weski J, Hasenberg A, Kraus A, Poschet G, Hager T, Theegarte D, Opitz C, Brakhage AA, Sitek B, Hasenberg M, Gunzer M. Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection. Mol Cell Proteomics. 2017 Dec;16(12):2184-2198. doi: 10.1074/mcp.RA117.000072. Epub 2017 Sep 26. 

Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T. Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma.  Proteomics Clin Appl. 2017 Dec;11(11-12). doi: 10.1002/prca.201700014. Epub 2017 Jul 10.

Megger DA, Pott LL, Rosowski K, Zülch B, Tautges S, Bracht T, Sitek B. NHS-based Tandem Mass Tagging of Proteins at the Level of Whole Cells: A Critical Evaluation in Comparison to Conventional TMT-Labeling Approaches for Quantitative Proteome Analysis. Anal Sci. 2017;33(12):1387-1394. doi: 10.2116/analsci.33.1387.

Minakaki G, Menges S, Kittel A, Emmanouilidou E, Schaeffner I, Barkovits K, Bergmann A, Rockenstein E, Adame A, Marxreiter F, Mollenhauer B, Galasko D, Irén Buzá E, Schlötzer-Schrehardt U, Marcus K, Xiang W, Chichung Lie D, Vekrellis K, Masliah E, Winkler J, Klucken J. Autophagy inhibition promotes alpha-synuclein release and transfer via extracellular vesicles with a hybrid autophago/exosome-like phenotype. Autophagy. 2017 Dec 4:1-61. doi: 10.1080/15548627.2017.1395992. [Epub ahead of print]

Mora MI, Molina M, Odriozola L, Elortza F, Mato JM, Sitek B, Zhang P, He F, Latasa MU, Avila M, Corrales F. Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. J Proteome Res. 2017 Dec 1;16(12):4506-4514. doi: 10.1021/acs.jproteome.7b00390. Epub 2017 Oct 2.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

Turewicz M, Kohl M, Ahrens M, Mayer G, Uszkoreit J, Naboulsi W, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. BioInfra.Prot: A Comprehensive Proteomics Workflow Including Data Standardization, Protein Inference, Expression Analysis and Data Publication. J Biotechnol. 2017 Nov 10;261:116-125. doi: 10.1016/j.jbiotec.2017.06.005. Epub 2017 Jun 9.

Rieder V, Schork KU, Kerschke L, Blank-Landeshammer B, Sickmann A, Rahnenführer J. Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra. J. Proteome Res. 2017 16 (11), 4035-4044. doi: 10.1021/acs.jproteome.7b00427. Epub 2017 Sep 29.

Drees SL, Klinkert B, Helling S, Beyer DF, Marcus K, Narberhaus F, Lübben M. One Gene, two proteins: Coordinated production of a copper chaperone by differential transcript formation and translational frameshifting in Escherichia coli. Mol Microbiol. 2017 Nov;106(4):635-645. doi: 10.1111/mmi.13841. Epub 2017 Oct 6.

Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]

Trezzi JP, Galozzi S, Jaeger C, Barkovits K, Brockmann K, Maetzler W, Berg D, Marcus K, Betsou F, Hiller K, Mollenhauer B. Distinct metabolomic signature in cerebrospinal fluid in early parkinson's disease. Mov Disord. 2017 Oct;32(10):1401-1408. doi: 10.1002/mds.27132. Epub 2017 Aug 26.

Megger DA, Philipp J, Le-Trilling VTK, Sitek B, Trilling M. Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression. Front. Immunol. 2017 Sept 14. doi: 10.3389/fimmu.2017.01139.

Nwosu ZC, Megger DA, Hammad S, Sitek B, Roessler S, Ebert MP, Meyer C, Dooley S. Identification of the Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol. 2017 May 31;4(2):303-323.e1. doi: 10.1016/j.jcmgh.2017.05.004. eCollection 2017 Sept.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

Renner M, Reinhard J, Theiss C, May C, Lohmann S, Reinehr S, Stute G, Faissner A, Marcus K, Dick HB. Protective effects on the retina after ranibizumab treatment in an ischemia model. PLoS One. 2017 Aug 11;12(8):e0182407. doi: 10.1371/journal.pone.0182407. eCollection 2017.

Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.

Kälsch J, Padden J, Bertram S, Pott LL, Reis H, Westerwick D, Schaefer CM, Sowa JP, Möllmann D, Fingas C, Dechȇne A, Sitek B, Eisenacher M, Canbay A, Ahrens M, Baba HA. Annexin A10 optimally differentiates between intrahepatic cholangiocarcinoma and hepatic metastases of pancreatic ductal adenocarcinoma: a comparative study of immunohistochemical markers and panels. Virchows Arch. 2017 May;470(5):537-543. doi: 10.1007/s00428-017-2114-2. Epub 2017 Mar 29.

Willems S, Bouyssié D, David M, Locard-Paulet M, Mechtler K, Schwämmle V, Uszkoreit J, Vaudel M, Dorfer V. Proceedings of the EuBIC Winter School 2017. J Proteomics. 2017 May 24;161:78-80. doi: 10.1016/j.jprot.2017.04.001. Epub 2017 Apr 4.

Lindemann C, Thomanek N, Hundt FC, Lerari T, Meyer HE, Wolters D, Marcus K. Strategies in relative and absolute quantitative mass spectrometry based proteomics. Biol Chem. 2017 May 1;398(5-6):687-699. doi: 10.1515/hsz-2017-0104.

Sydor S, Sowa JP, Megger DA, Schlattjan M, Jafoui S, Wingerter L, Carpinteiro A, Baba HA, Bechmann LP, Sitek B, Gerken G, Gulbins E, Canbay A. Acid sphingomyelinase deficiency in Western diet-fed mice protects against adipocyte hypertrophy and diet-induced liver steatosis. Mol Metab. 2017 Mar 12;6(5):416-427. doi: 10.1016/j.molmet.2017.03.002. eCollection 2017 May

Nöbauer K, Hummel K, Mayrhofer C, Ahrens M, Setyabudi FMC, Schmidt-Heydt M, Eisenacher M, Razzazi-Fazeli E. Comprehensive proteomic analysis of Penicillium verrucosum. Proteomics. 2017 May;17(9). doi: 10.1002/pmic.201600467.

Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL. The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry. Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.

Megger DA, Rosowski K, Radunsky C, Kösters J, Sitek B, Müller J. Structurally related hydrazone-based metal complexes with different antitumor activities variably induce apoptotic cell death. Dalton Trans. 2017 Apr 5;46(14):4759-4767. doi: 10.1039/c6dt04613d.

Großerueschkamp F, Bracht T, Diehl HC, Kuepper C, Ahrens M, Kallenbach-Thieltges A, Mosig A, Eisenacher M, Marcus K, Behrens T, Brüning T, Theegarten D, Sitek B, Gerwert K. Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics. Sci Rep. 2017 Mar 30;7:44829. doi: 10.1038/srep44829.

Jia X, Chen J, Megger DA, Zhang X, Kozlowski M, Zhang L, Fang Z, Li J, Chu Q, Wu M, Li Y, Sitek B, Yuan Z. Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line. Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S144-S160. doi: 10.1074/mcp.M116.063503. Epub 2017 Feb 27.

Kälsch J, Pott LL, Takeda A, Kumamoto H, Möllmann D, Canbay A, Sitek B, Baba HA. Bathing in carbon dioxide-enriched water alters protein expression in keratinocytes of skin tissue in rats. Int J Biometeorol. 2017 Apr;61(4):739-746. doi: 10.1007/s00484-016-1252-6. Epub 2016 Oct 5.

Megger DA, Rosowski K, Ahrens M, Bracht T, Eisenacher M, Schlaak JF, Weber F, Hoffmann AC, Meyer HE, Baba HA, Sitek B. Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags. Biomarkers. Biomarkers. 2017 Mar;22(2):113-122. doi: 10.1080/1354750X.2016.1210678. Epub 2016 Jul 28.

Lindemann C, Thomanek N, Kuhlmann K, Meyer HE, Marcus K, Narberhaus F. Next-generation trapping of protease substrates by label-free proteomics. Microbial Proteomics, Methods and Protocolls. in press

Trezzi JP, Jäger C, Galozzi S, Barkovits K, Marcus K, Mollenhauer B, Hiller K. Metabolic profiling of body fluids and multivariate data analysis. MethodsX. 2017 Feb 20;4:95-103. doi: 10.1016/j.mex.2017.02.004. eCollection 2017.

Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger DA, Müller J. A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem. Sci., 2017,8, 1337-1343  doi: 10.1039/C6SC03482A. Epub 2016 Oct 10.

Pott LL, Hagemann S, Reis H, Lorenz K, Bracht T, Herold T, Skryabin BV, Megger DA, Kälsch J, Weber F, Sitek B, Baba HA. Eukaryotic elongation factor 2 is a prognostic marker and its kinase a potential therapeutic target in HCC. Oncotarget. 2017 Feb 14;8(7):11950-11962. doi: 10.18632/oncotarget.14447.

Güttsches AK, Brady S, Krause K, Maerkens A, Uszkoreit J, Eisenacher M, Schreiner A, Galozzi S, Mertens-Rill J, Tegenthoff M, Holton JL, Harms MB, Lloyd TE, Vorgerd M, Weihl CC, Marcus K, Kley R. Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis. Ann Neurol. 2017 Feb;81(2):227-239. doi: 10.1002/ana.24847. Epub 2017 Jan 27.

Herrfurth L, Theis V, Matschke V, May C, Marcus K, Theiss C. Morphological plasticity of emerging Purkinje cells in response to exogenous VEGF. Front Mol Neurosci. 2017 Jan 30;10:2. doi: 10.3389/fnmol.2017.00002. eCollection 2017.

Megger DA, Padden J, Rosowski K, Uszkoreit J, Bracht T, Eisenacher M, Gerges C, Neuhaus H, Schumacher B, Schlaak JF, Sitek B. One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation. Journal of Proteomics. 2017 Jan 10. doi.org/10.1016/j.jprot.2016.11.021

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

Witzke K, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch A, Bracht T, Sitek B. Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins. J Proteome Res. 2017 Jan 6;16(1):137-146. doi: 10.1021/acs.jproteome.6b00575. Epub 2016 Oct 19.

Nieser M, Henopp T, Brix J, Stoß L, Sitek B, Naboulsi W, Anlauf M, Schlitter AM, Klöppel G, Gress T, Moll R, Bartsch DK, Heverhagen AE, Knoefel WT, Kaemmerer D, Haybaeck J, Fend F, Sperveslage J, Sipos B. Loss of Chromosome 18 in Neuroendocrine Tumors of the Small Intestine: The Enigma Remains. Neuroendocrinology. 2017;104(3):302-312. doi: 10.1159/000446917. Epub 2016 May 25.

2016

Arends J, Thomanek N, Kuhlmann K, Marcus K, Narberhaus F. In vivo trapping of FtsH substrates by label-free quantitative proteomics. Proteomics. 2016 Dec;16(24):3161-3172. doi: 10.1002/pmic.201600316.

Kolbe K, Bukhari H, Loosse C, Leonhardt G, Glotzbach A, Pawlas M, Hess K, Theiss C, Müller T. Extensive nuclear sphere generation in the human Alzheimer's brain. Neurobiol Aging. 2016 Dec;48:103-113. doi: 10.1016/j.neurobiolaging.2016.08.016. Epub 2016 Aug 26.

Stratmann B, Engelbrecht B, Espelage BC, Klusmeier N, Tiemann J, Gawlowski T, Mattern Y, Eisenacher M, Meyer HE, Rabbani N, Thornalley PJ, Tschoepe D, Poschmann G, Stühler K. Glyoxalase 1-knockdown in human aortic endothelial cells - effect on the proteome and endothelial function estimates. Sci Rep. 2016 Nov 29;6:37737. doi: 10.1038/srep37737.

Plum S, Steinbach S, Attems J, Keers S, Riederer P, Gerlach M, May C, Marcus K. Proteomic characterization of neuromelanin granules isolated from human substantia nigra by laser-microdissection. Sci Rep. 2016 Nov 14;6:37139. doi: 10.1038/srep37139.

Chen J, Shinde S, Subedi P, Wierzbicka C, Sellergren B, Helling S, Marcus K. Validation of molecularly imprinted polymers for side chain selective phosphopeptide enrichment. J Chromatogr A. 2016 Nov 4;1471:45-50. doi: 10.1016/j.chroma.2016.10.018. Epub 2016 Oct 11.

Pattky M, Barkovits K, Marcus K, Weiergräber OH, Huhn C. Statically Adsorbed Coatings for High Separation Efficiency and Resolution in CE-MS Peptide Analysis: Strategies and Implementation. Methods Mol Biol. 2016;1483:53-75. doi: 10.1007/978-1-4939-6403-1_4.

Kumar G, Hummel K, Ahrens M, Menanteau-Ledouble S, Welch TJ, Eisenacher M, Razzazi-Fazeli E, El-Matbouli M. Shotgun proteomic analysis of Yersinia ruckeri strains under normal and iron-limited conditions. Vet Res. 2016 Oct 6;47(1):100.

Winter L, Wittig I, Peeva V, Eggers B, Heidler J, Chevessier F, Kley RA, Barkovits K, Strecker V, Berwanger C, Herrmann H, Marcus K, Kornblum C, Kunz WS, Schröder R, Clemen CS. Mutant desmin substantially perturbs mitochondrial morphology, function and maintenance in skeletal muscle tissue. Acta Neuropathol. 2016 Sep;132(3):453-73. doi: 10.1007/s00401-016-1592-7. Epub 2016 Jul 8.

Dinter E, Saridaki T, Nippold M, Plum S, Diederichs L, Komnig D, Fensky L, May C, Marcus K, Voigt, A, Schulz J.B, Falkenburger B.H. Rab7 induces clearance of α-synuclein aggregates. J Neurochem. 2016 Sep;138(5):758-74. doi: 10.1111/jnc.13712. Epub 2016 Aug 4.

Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B. Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation. Biochim Biophys Acta. 2016 Nov;1864(11):1579-85. doi: 10.1016/j.bbapap.2016.08.005. Epub 2016 Aug 9

Bukhari H, Kolbe K, Leonhardt G, Loosse C, Schröder E, Knauer S, Marcus K, Müller T. Membrane tethering of APP c-terminal fragments is a prerequisite for T668 phosphorylation preventing nuclear sphere generation. Cell Signal. 2016 Nov;28(11):1725-34. doi: 10.1016/j.cellsig.2016.08.007. Epub 2016 Aug 14.

Recke A, Oei A, Hübner F, Fechner K, Graf J, Hagenah J, May C, Woitalla D, Salmen A, Zillikens D, Gold R, Schlumberger W, Schmidt E. Parkinson's disease and multiple sclerosis are not associated with autoantibodies against structural proteins of the dermal-epidermal junction. Br J Dermatol. 2016 Aug;175(2):407-9. doi: 10.1111/bjd.14538. Epub 2016 May 18.

Henriques AG, Müller T, Oliveira JM, Cova M, da Cruz E Silva CB, da Cruz E Silva OA. Altered protein phosphorylation as a resource for potential AD biomarkers. Sci Rep. 2016 Jul 28;6:30319. doi: 10.1038/srep30319.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, da Veiga Leprevost F, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA. Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput Biol 12(7): e1004947. 14 July 2016; doi:10.1371/journal.pcbi.1004947. PMID: 27415786

Bracht T, Molleken C, Ahrens M, Poschmann G, Schlosser A, Eisenacher M, Stühler K, Meyer HE, Schmiegel WH, Holmskov U, Sorensen GL, Sitek B. Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients. Journal of Translational Medicine. 2016 Jul 4. doi: 10.1186/s12967-016-0952-3.

Bertram S, Padden J, Kälsch J, Ahrens M, Pott L, Canbay A, Weber F, Fingas C, Hoffmann AC, Vietor A, Schlaak JF, Eisenacher M, Reis H, Sitek B, Baba HA. Novel immunohistochemical markers differentiate intrahepatic cholangiocarcinoma from benign bile duct lesions. J Clin Pathol. 2016 Jul;69(7):619-26. doi: 10.1136/jclinpath-2015-203418. Epub 2016 Jan 4.

Broering R, Trippler M, Werner M, Real CI, Megger DA, Bracht T, Schweinsberg V, Sitek B, Eisenacher M, Meyer HE, Baba HA, Weber F, Hoffmann AC, Gerken G, Schlaak JF. Hepatic expression of proteasome subunit alpha type-6 is upregulated during viral hepatitis and putatively regulates the expression of ISG15 ubiquitin-like modifier, a proviral host gene in hepatitis C virus infection. J Viral Hepat. 2016 May;23(5):375-86. doi: 10.1111/jvh.12508. Epub 2016 Feb 1.

Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M. PAA: an R/bioconductor package for biomarker discovery with protein microarrays. Bioinformatics. 2016 May 15;32(10):1577-9. doi: 10.1093/bioinformatics/btw037. Epub 2016 Jan 22.

Mayer G, Marcus K, Eisenacher M, Kohl M. Boolean modeling techniques for protein co-expression networks in systems medicine. Expert Rev Proteomics. 2016 Jun;13(6):555-69. doi: 10.1080/14789450.2016.1181546. Epub 2016 May 6.

Schrötter A, Park YM, Marcus K, Martins-de-Souza D, Nilsson P, Magraoui FE, Meyer HE, Grinberg LT. Key players in neurodegenerative disorders in focus-New insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS, and multiple sclerosis-24th HUPO BPP Workshop: September 29, 2015, Vancouver, Canada. Proteomics. 2016 Apr;16(7):1047-50. doi: 10.1002/pmic.201600047.

Köhler J, Schuler M, Gauler TC, Nöpel-Dünnebacke S, Ahrens M, Hoffmann AC, Kasper S, Nensa F, Gomez B, Hahnemann M, Breitenbuecher F, Cheufou D, Özkan F, Darwiche K, Hoiczyk M, Reis H, Welter S, Eberhardt WEE, Martin Eisenacher, Teschler H, Stamatis G, Schmiegel W, Hahn SA, Baraniskin A. ‘Circulating U2 Small Nuclear RNA Fragments as a Diagnostic and Prognostic Biomarker in Lung Cancer Patients’. J Cancer Res Clin Oncol. 2016 Apr;142(4):795-805. doi: 10.1007/s00432-015-2095-y. Epub 2015 Dec 19.

Manitz MP, Plümper J, Demir S, Ahrens M, Eßlinger M, Wachholz S, Eisenacher M, Juckel G, Friebe A.
Flow cytometric characterization of microglia in the offspring of PolyI:C treated mice.
Brain Res. Brain Res 2016 Apr 1;1636:172-82. doi: 10.1016/j.brainres.2016.02.004. Epub 2016 Feb 10.

Mölleken C, Poschmann G, Bonella F, Costabel U, Sitek B, Stühler K, Meyer HE, Schmiegel WH, Marcussen N, Helmer M, Nielsen O, Hansen S, Schlosser A, Holmskov U, Sorensen GL. MFAP4: a candidate biomarker for hepatic and pulmonary fibrosis? Sarcoidosis Vasc Diffuse Lung Dis. 2016 Mar 29;33(1):41-50.

Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B. Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma from Pancreatic Ductal Adenocarcinoma Discovered by Proteomic Analysis of Microdissected Cells. Mol Cell Proteomics. 2016 Mar;15(3):1072-82. doi: 10.1074/mcp.M115.054585. Epub 2015 Dec 7.

Peters M, Guidato PM, Peters K, Megger DA, Sitek B, Classen B, Heise EM, Bufe A. Allergy-Protective Arabinogalactan Modulates Human Dendritic Cells via C-Type Lectins and Inhibition of NF-κB. J Immunol. 2016 Feb 15;196(4):1626-35. doi: 10.4049/jimmunol.1502178. Epub 2016 Jan 8.

Maerkens A, Olivé M, Schreiner A, Feldkirchner S, Schessl J, Uszkoreit J, Barkovits K, Güttsches AK, Theis V, Eisenacher M, Tegenthoff M, Goldfarb LG, Schröder R, Schoser B, van der Ven PF, Fürst DO, Vorgerd M, Marcus K, Kley RA  New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses. 2016 Feb 3;4(1):8. doi: 10.1186/s40478-016-0280-0.

Casadei N, Sood P, Ulrich T, Fallier-Becker P, Kieper N, Helling S, May C, Glaab E, Chen J, Nuber S, Marcus K, Rapaport D, Ott T, Riess O, Krüger R, Fitzgerald JC. Mitochondrial defects and neurodegeneration in mice overexpressing wild-type or G399S mutant HtrA2. Hum Mol Genet. 2016 Feb 1;25(3):459-71. doi: 10.1093/hmg/ddv485. Epub 2015 Nov 24.

Le-Trilling VT, Megger DA, Katschinski B, Landsberg CD, Rückborn MU, Tao S, Krawczyk A, Bayer W, Drexler I, Tenbusch M, Sitek B, Trilling M. Broad and potent antiviral activity of the NAE inhibitor MLN4924. Sci Rep. 2016 Feb 1;6:19977. doi: 10.1038/srep19977.

Loosse C., Pawlas M., Bukhari H.S., Maghnouj A., Hahn S., Marcus K., Müller T. 'Nuclear spheres modulate the expression of BEST1 and GADD45G.' Cell Signal. 2016 Jan;28(1):100-9. doi: 10.1016/j.cellsig.2015.10.019. Epub 2015 Oct 28.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaino JA. PRIDE Inspector Toolsuite: moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets.  Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

Naboulsi W, Megger DA, Bracht T, Kohl M, Turewicz M, Eisenacher M, Voss DM, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B. Quantitative tissue proteomics analysis reveals versican as potential biomarker for early-stage hepatocellular carcinoma. J Proteome Res. 2016 Jan 4;15(1):38-47.doi:10.1021/acs.jproteome.5b00420. Epub 2015 Dec 18.

Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools, Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2.

Henkel S, Wellhausen R, Woitalla D, Marcus K, May C. Epitope Mapping Using Peptide Microarray in Autoantibody Profiling. Methods Mol Biol. 2016;1368:209-24. doi: 10.1007/978-1-4939-3136-1_15.

2015

Mayer G., Stephan C., Meyer H.E., Kohl M., Marcus K., Eisenacher M. 'ProCon- PROteomics CONversion tool', J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015. Epub 2015 Jul 13.

Montesinos-Rongen M., Purschke F.G., Brunn A., May C., Nordhoff E., Marcus K., Deckert M. 'Primary Central Nervous System (CNS) Lymphoma B Cell Receptors Recognize CNS Proteins.' J Immunol. 2015, 195(3):1312-9.

Chevessier F., Schuld J., Orfanos Z., Plank A.C., Wolf L., Maerkens A., Unger A., Schlötzer-Schrehardt U., Kley R.A., von Hörsten S., Marcus K., Linke W.A., Vorgerd M., van der Ven P.F., Fürst D.O., Schröder R. 'Myofibrillar instability exacerbated by acute exercise in filaminopathy.' Hum Mol Genet. 2015 pii: ddv421.

Haghikia A., Jörg S., Duscha A., Berg J. Manzel A., Waschbisch A., Hammer A.2, Lee D.H., May C., Wilck N., Balogh A., Ostermann A.I., Schebb N.H., Akkad D.A., Grohme D.A., Kleinewietfeld M., Kempa S., Thöne J., Demir S., Müller D.N., Gold R., Linker R.A. 'Dietary Fatty Acids Directly Impact Central Nervous System Autoimmunity via the Small Intestine.' Immunity. 2015 Oct 20;43(4):817-29. doi: 10.1016/j.immuni.2015.09.007.

Plum S, Steinbach S, Abel L, Marcus K, Helling S, May C. Proteomics in neurodegenerative diseases: Methods for obtaining a closer look at the neuronal proteome. Proteomics Clin Appl. 2015 Oct;9(9-10):848-71. doi: 10.1002/prca.201400030. Epub 2014 Nov 10.

Walker A., Skibbe K., Steinmann E., Pfaender S., Kuntzen T., Megger D.A., Groten S., Sitek B., Lauer G.M., Kim A.Y., Pietschmann T., Allen T.M., Timm J. 'Distinct escape pathway by HCV genotype 1a from a dominant CD8+ T cell response by selection of altered epitope processing.'  J Virol. 2015 Oct 7;90(1):33-42. doi: 10.1128/JVI.01993-15.

Rattay S, Trilling M, Megger DA,Sitek, B, Meyer HE, Hengel H, Le-Trilling VT. 'The Canonical Immediate-Early 3 Gene Product pIE611 of Mouse Cytomegalovirus Is Dispensable for Viral Replication, but Mediates Transcriptional and Post-transcriptional Regulation of Viral Gene Products.' J Virol. 2015 Aug;89(16):8590-8. doi: 10.1128/JVI.01234-15. Epub 2015 Jun 10.

Chen J, Shinde S, Koch MH, Eisenacher M, Galozzi S, Lerari T, Barkovits K, Subedi P, Krüger R, Kuhlmann K, Sellergren B, Helling S, Marcus K (2015) Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies. Sci Rep. 2015 Jul 1;5:11438. doi: 10.1038/srep11438.

Reis H., Padden J., Ahrens M., Pütter C., Bertram S., Pott L.L., Reis A.C., Weber F., Juntermanns B., Hoffmann A.C., Eisenacher M., Schlaak J.F., Canbay A., Meyer H.E., Sitek B., Baba H.A. 'Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenecarcinomas' Pathology. 2015 Oct;47(6):543-50. doi: 10.1097/PAT.0000000000000298.

Galozzi S., Marcus K., Barkovits K. 'Amyloid-β as a biomarker for Alzheimer's disease: quantification methods in body fluids', Expert Rev. o Proteomics, August 2015, Vol.12, No. 4 : Pages 343-354; doi:10.1586/14789450.2015.1065183.

Peng J., Alam S., Radhakrishnan K., Mariappan M., Rudolph M.G., May C., Dierks T., von Figura K., and Schmidt B. 'Eukaryotic Formylglycine-Generating Enzyme Catalyzes a Monooxygenase Type of Reaction', FEBS J, 2015 Sep;282(17):3262-74. doi: 10.1111/febs.13347. Epub 2015 Jul 7.

Molina M., Steinbach Y., Park M., Yun S.Y., Di Lorenzo alho A.T., Heinsen H., Grinberg L.T., Marcus K., Leite R.E., and May C. 'Enrichment of Single Neurons and Defined Brain Regions from Human Brain Tissue Samples for Subsequent Proteome Analysis', J Neural Transm, 2015 Jul;122(7):993-1005. doi: 10.1007/s00702-015-1414-4. Epub 2015 Jun 30.

Reis H, Pütter C, Megger DA, Bracht T, Weber F, Hoffmann AC, Bertram S, Wohlschläger J, Hagemann S, Eisenacher M, Scherag A, Schlaak JF, Canbay A, Meyer HE, Sitek B, Baba HA. A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors. Biochim Biophys 2015 Jun;1854(6):641-50. doi: 10.1016/j.bbapap.2014.10.024. Epub 2014 Nov 5.

Uszkoreit J., Maerkens A., Perez-Riverol Y., Meyer H.E., Marcus K., Stephan C., Kohlbacher O., Eisenacher M. 'PIA - An intuitive protein inference engine with a web-based user interface.' J. Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.

Brosseron F1, Marcus K, May C. Isolating peripheral lymphocytes by density gradient centrifugation and magnetic cell sorting. Methods Mol Biol. 2015;1295:33-42. doi: 10.1007/978-1-4939-2550-6_3.

Sitek B., Meyer HE., Kondo T. Editorial Medical Proteomics. Biochim Biophys Acta. 2015 Feb 18. pii: S1570-9639(15)00042-4. doi: 10.1016/j.bbapap.2015.02.006. Epub 2015 Feb 18.

Deutsch E.W., Albar J.P., Binz P.A., Eisenacher M., Jones A.R., Mayer G., Omenn G.S., Orchard S., Vizcaíno J.A., Hermjakob H. Development of Data Representation Standards by the Human Proteome Organization Proteomics Standards Initiative. J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28.

Pienimaeki-Roemer A, Kuhlmann K, Böttcher A, Konovalova T, Black A, Orsó E, Liebisch G, Ahrens M, Eisenacher M, Meyer HE, Schmitz G (2014). Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets. Transfusion 2015 Mar;55(3):507-21. doi: 10.1111/trf.12874. Epub 2014 Oct 21.

Barkovits K., Helling S., Marcus K. MS-based methods for biomarkers of Parkinson's disease: what is the future? Bioanalysis 2015, 7(2):149-51. doi: 10.4155/bio.14.273.

Schoenebeck B. & May C., Mollenhauer B., Meyer H.E., Güldner C., Respondek G., Höglinger G., Marcus K. Improved preparation of nasal lavage fluid (NLF) as a noninvasive sample for proteomic biomarker discovery. BBA – Proteins and Proteomics 2015 Feb 10. doi: 10.1016/j.bbapap.2015.01.015. Epub 2015 Feb 10.

Weiß F., Schnabel A., Planatscher H., van den Berg B.H., Serschnitzki B., Nuessler A.K., Thasler W.E., Weiss T.S., Reuss M., Stoll D., Templin M.F., Joos T.O., Marcus K., Poetz O. Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry. Sci Rep. 2015 Mar 4;5:8759. doi: 10.1038/srep08759.

Schrötter A., Magraoui F.E., Marcus K., Park Y.M., Meyer H.E., Grinberg L.T. New Milestones in the Development of Characterization Tools for Neurodegenerative Diseases in Proteomics: 22nd HUPO BPP Workshop 7 October 2014, Madrid, Spain. Proteomics 2015, 15(4), 627-629. doi: 10.1002/pmic.201570035.

Looße C., Galozzi S., Debor L., Julsing M.K., Bühler B., Schmid A., Barkovits K., Müller T., Marcus K. Direct infusion-SIM for absolute protein quantification in complex samples: simple, fast, robust. EuPA Open Proteomics 2015

Bracht T, Schweinsberg V, Trippler M, Kohl M, Ahrens M, Padden J, Naboulsi W, Barkovits K, Megger DA, Eisenacher M, Borchers CH, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B. Analysis of disease-associated protein expression using quantitative proteomics - Fibulin-5 is expressed in association with hepatic fibrosis. J Proteome Res. 2015 Mar 25. doi: 10.1021/acs.jproteome.5b00053. Epub 2015 Apr 6

Diehl H, Beine B, Elm J, Ahrens M, Trede D, Eisenacher M, Marcus K, Meyer HE, Henkel C. The challenge of on-tissue digestion for MALDI-MSI – a comparison of different protocols to improve imaging experiments. Anal Bioanal Chem. 2015 Mar;407(8):2223-43. doi: 10.1007/s00216-014-8345-z. Epub 2015 Feb 17.

Geisler, C. Gaisa, N. T. Pfister, D. Fuessel, S. Kristiansen, G. Braunschweig, T. Gostek, S. Beine, B. Diehl, H. C. Jackson, A. M. Borchers, C. Heidenreich, A. Meyer, H. E. Knüchel, R. Henkel, C. Identification and Validation of Potential New Biomarkers for Prostate Cancer Diagnosis and Prognosis Using 2D-DIGE and MS. Biomed Research International 2015(-) (2015) 1-23. DOI: 10.1155/2015/454256. Epub 2015 Jan 15.

Reidick, C. El Magraoui, F. Meyer, H. E. Stenmark, H. Platta, H. Regulation of the Tumor-suppressor function of the Class III phosphatidylinositol 3-kinase complex by Ubiquitin and SUMO. Cancers 7(1) (2015) 1-29. DOI: 10.3390/cancers7010001

Ahrens M, Turewicz M, Marcus K, Meyer HE, May C, Eisenacher M, and Rahnenführer J FSOL - a workflow for the detection of patient subgroups and affected molecular features in high-throughput omics data. (accepted on pre-print server of PeerJ group as Proceedings of the German Conference on Bioinformatics, Dortmund, Germany 2015)

2014

2013