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Items: 1 to 50 of 138

1.

Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation.

Mika T, Baraniskin A, Ladigan S, Wulf G, Dierks S, Haase D, Schork K, Turewicz M, Eisenacher M, Schmiegel W, Schroers R, Klein-Scory S.

Int J Lab Hematol. 2019 Jun 21. doi: 10.1111/ijlh.13073. [Epub ahead of print]

PMID:
31225701
2.

Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

J Proteome Res. 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.

PMID:
31081335
3.

Monocytes-neutrophils-ratio as predictive marker for failure of first induction therapy in AML.

Mika T, Ladigan S, Schork K, Turewicz M, Eisenacher M, Schmiegel W, Schroers R, Baraniskin A.

Blood Cells Mol Dis. 2019 Jul;77:103-108. doi: 10.1016/j.bcmd.2019.04.008. Epub 2019 Apr 18.

PMID:
31029023
4.

Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters.

Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T.

Int J Cancer. 2019 Apr 22. doi: 10.1002/ijc.32356. [Epub ahead of print]

PMID:
31008534
5.

Protein Biomarker Discovery Using Human Blood Plasma Microparticles.

Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T.

Methods Mol Biol. 2019;1959:51-64. doi: 10.1007/978-1-4939-9164-8_4.

PMID:
30852815
6.

Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer.

Witzke KE, Großerueschkamp F, Jütte H, Horn M, Roghmann F, von Landenberg N, Bracht T, Kallenbach-Thieltges A, Käfferlein H, Brüning T, Schork K, Eisenacher M, Marcus K, Noldus J, Tannapfel A, Sitek B, Gerwert K.

Am J Pathol. 2019 Mar;189(3):619-631. doi: 10.1016/j.ajpath.2018.11.018. Epub 2019 Feb 12.

PMID:
30770125
7.

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR.

Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13.

PMID:
30688441
8.

Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research.

Schilde LM, Kösters S, Steinbach S, Schork K, Eisenacher M, Galozzi S, Turewicz M, Barkovits K, Mollenhauer B, Marcus K, May C.

PLoS One. 2018 Nov 29;13(11):e0206478. doi: 10.1371/journal.pone.0206478. eCollection 2018.

9.

Protein Inference Using PIA Workflows and PSI Standard File Formats.

Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M.

J Proteome Res. 2019 Feb 1;18(2):741-747. doi: 10.1021/acs.jproteome.8b00723. Epub 2018 Dec 5.

PMID:
30474983
10.

Direct-acting antivirals-based therapy decreases hepatic fibrosis serum biomarker microfibrillar-associated protein 4 in hepatitis C patients.

Mölleken C, Ahrens M, Schlosser A, Dietz J, Eisenacher M, Meyer HE, Schmiegel W, Holmskov U, Sarrazin C, Sorensen GL, Sitek B, Bracht T.

Clin Mol Hepatol. 2019 Mar;25(1):42-51. doi: 10.3350/cmh.2018.0029. Epub 2018 Nov 19.

11.

The PRIDE database and related tools and resources in 2019: improving support for quantification data.

Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106.

12.

Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry.

Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K.

J Proteome Res. 2018 Oct 5;17(10):3418-3430. doi: 10.1021/acs.jproteome.8b00308. Epub 2018 Sep 12.

PMID:
30207155
13.

MicroRNA-30c as a novel diagnostic biomarker for primary and secondary B-cell lymphoma of the CNS.

Baraniskin A, Chomiak M, Ahle G, Gress T, Buchholz M, Turewicz M, Eisenacher M, Margold M, Schlegel U, Schmiegel W, Hahn S, Schroers R.

J Neurooncol. 2018 May;137(3):463-468. doi: 10.1007/s11060-018-2749-0. Epub 2018 Jan 11.

PMID:
29327175
14.

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M.

Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]

PMID:
29092005
15.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

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.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

16.

A community proposal to integrate proteomics activities in ELIXIR.

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.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.

17.

Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma.

Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T.

Proteomics Clin Appl. 2017 Dec;11(11-12). doi: 10.1002/prca.201700014. Epub 2017 Jul 10.

PMID:
28626882
18.

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

Turewicz M, Kohl M, Ahrens M, Mayer G, Uszkoreit J, Naboulsi W, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M.

J Biotechnol. 2017 Nov 10;261:116-125. doi: 10.1016/j.jbiotec.2017.06.005. Epub 2017 Jun 9. Review.

19.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

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.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.

20.

Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics.

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.

Sci Rep. 2017 Mar 30;7:44829. doi: 10.1038/srep44829.

21.

Annexin A10 optimally differentiates between intrahepatic cholangiocarcinoma and hepatic metastases of pancreatic ductal adenocarcinoma: a comparative study of immunohistochemical markers and panels.

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.

Virchows Arch. 2017 May;470(5):537-543. doi: 10.1007/s00428-017-2114-2. Epub 2017 Mar 29.

PMID:
28357490
22.

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL.

Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.

PMID:
28318237
23.

Comprehensive proteomic analysis of Penicillium verrucosum.

Nöbauer K, Hummel K, Mayrhofer C, Ahrens M, Setyabudi FMC, Schmidt-Heydt M, Eisenacher M, Razzazi-Fazeli E.

Proteomics. 2017 May;17(9). doi: 10.1002/pmic.201600467.

PMID:
28267294
24.

Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis.

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 RA.

Ann Neurol. 2017 Feb;81(2):227-239. doi: 10.1002/ana.24847. Epub 2017 Jan 27.

25.

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

Megger DA, Padden J, Rosowski K, Uszkoreit J, Bracht T, Eisenacher M, Gerges C, Neuhaus H, Schumacher B, Schlaak JF, Sitek B.

J Proteomics. 2017 Feb 10;154:13-21. doi: 10.1016/j.jprot.2016.11.021. Epub 2016 Dec 5.

PMID:
27932303
26.

Glyoxalase 1-knockdown in human aortic endothelial cells - effect on the proteome and endothelial function estimates.

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.

Sci Rep. 2016 Nov 29;6:37737. doi: 10.1038/srep37737.

27.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

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.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
28.

Shotgun proteomic analysis of Yersinia ruckeri strains under normal and iron-limited conditions.

Kumar G, Hummel K, Ahrens M, Menanteau-Ledouble S, Welch TJ, Eisenacher M, Razzazi-Fazeli E, El-Matbouli M.

Vet Res. 2016 Oct 6;47(1):100.

29.

Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins.

Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch A, Bracht T, Sitek B.

J Proteome Res. 2017 Jan 6;16(1):137-146. doi: 10.1021/acs.jproteome.6b00575. Epub 2016 Oct 19.

PMID:
27696881
30.

Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation.

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.

Biochim Biophys Acta. 2016 Nov;1864(11):1579-85. doi: 10.1016/j.bbapap.2016.08.005. Epub 2016 Aug 9.

PMID:
27519163
31.

Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags.

Megger DA, Rosowski K, Ahrens M, Bracht T, Eisenacher M, Schlaak JF, Weber F, Hoffmann AC, Meyer HE, Baba HA, Sitek B.

Biomarkers. 2017 Mar;22(2):113-122. doi: 10.1080/1354750X.2016.1210678. Epub 2016 Jul 28.

PMID:
27467182
32.

Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients.

Bracht T, Mölleken C, Ahrens M, Poschmann G, Schlosser A, Eisenacher M, Stühler K, Meyer HE, Schmiegel WH, Holmskov U, Sorensen GL, Sitek B.

J Transl Med. 2016 Jul 4;14(1):201. doi: 10.1186/s12967-016-0952-3.

33.

Boolean modeling techniques for protein co-expression networks in systems medicine.

Mayer G, Marcus K, Eisenacher M, Kohl M.

Expert Rev Proteomics. 2016 Jun;13(6):555-69. doi: 10.1080/14789450.2016.1181546. Epub 2016 May 6. Review.

PMID:
27105325
34.

Flow cytometric characterization of microglia in the offspring of PolyI:C treated mice.

Manitz MP, Plümper J, Demir S, Ahrens M, Eßlinger M, Wachholz S, Eisenacher M, Juckel G, Friebe A.

Brain Res. 2016 Apr 1;1636:172-182. doi: 10.1016/j.brainres.2016.02.004. Epub 2016 Feb 10.

PMID:
26872595
35.

New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses.

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.

Acta Neuropathol Commun. 2016 Feb 3;4:8. doi: 10.1186/s40478-016-0280-0.

36.

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.

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.

J Viral Hepat. 2016 May;23(5):375-86. doi: 10.1111/jvh.12508. Epub 2016 Feb 1.

PMID:
26833585
37.

PAA: an R/bioconductor package for biomarker discovery with protein microarrays.

Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M.

Bioinformatics. 2016 May 15;32(10):1577-9. doi: 10.1093/bioinformatics/btw037. Epub 2016 Jan 22.

38.

Novel immunohistochemical markers differentiate intrahepatic cholangiocarcinoma from benign bile duct lesions.

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.

J Clin Pathol. 2016 Jul;69(7):619-26. doi: 10.1136/jclinpath-2015-203418. Epub 2016 Jan 4.

PMID:
26729014
39.

Circulating U2 small nuclear RNA fragments as a diagnostic and prognostic biomarker in lung cancer patients.

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 WE, Eisenacher M, Teschler H, Stamatis G, Schmiegel W, Hahn SA, Baraniskin A.

J Cancer Res Clin Oncol. 2016 Apr;142(4):795-805. doi: 10.1007/s00432-015-2095-y. Epub 2015 Dec 19.

PMID:
26687686
40.

Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells.

Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B.

Mol Cell Proteomics. 2016 Mar;15(3):1072-82. doi: 10.1074/mcp.M115.054585. Epub 2015 Dec 7.

41.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

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.

J Proteome Res. 2016 Jan 4;15(1):38-47. doi: 10.1021/acs.jproteome.5b00420. Epub 2015 Dec 18.

PMID:
26626371
42.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

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, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

43.

Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenocarcinomas.

Reis H, Padden J, Ahrens M, Pütter C, Bertram S, Pott LL, Reis AC, Weber F, Juntermanns B, Hoffmann AC, Eisenacher M, Schlaak JF, Canbay A, Meyer HE, Sitek B, Baba HA.

Pathology. 2015 Oct;47(6):543-50. doi: 10.1097/PAT.0000000000000298.

PMID:
26308133
44.

ProCon - PROteomics CONversion tool.

Mayer G, Stephan C, Meyer HE, Kohl M, Marcus K, Eisenacher M.

J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015. Epub 2015 Jul 13.

PMID:
26182917
45.

Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies.

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.

Sci Rep. 2015 Jul 1;5:11438. doi: 10.1038/srep11438.

46.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.

J Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.

PMID:
25938255
47.

Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis.

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.

J Proteome Res. 2015 May 1;14(5):2278-86. doi: 10.1021/acs.jproteome.5b00053. Epub 2015 Apr 6.

PMID:
25807371
48.

Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28. Review.

49.

The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments.

Diehl HC, Beine B, Elm J, Trede D, Ahrens M, Eisenacher M, Marcus K, Meyer HE, Henkel C.

Anal Bioanal Chem. 2015 Mar;407(8):2223-43. doi: 10.1007/s00216-014-8345-z. Epub 2015 Feb 17.

PMID:
25687681
50.

The bacterial proteogenomic pipeline.

Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M.

BMC Genomics. 2014;15 Suppl 9:S19. doi: 10.1186/1471-2164-15-S9-S19. Epub 2014 Dec 8.

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