PD Dr. rer. medic. Martin Eisenacher, 12th May 1973

Medizinische Bioinformatik am Medizinischen Proteom-Center (MPC)
Ruhr-University Bochum
building ProDi, room E2.269, Gesundheitscampus 4
D-44801 Bochum, Germany
Telefon: +49 / 234 / 32 - 18104
Email: martin.eisenacher@rub.de
Webpage: http://www.ruhr-uni-bochum.de/mpc/


Department leader of the “Medical Bioinformatics” at Medizinisches Proteom-Center, RUB
personnel responsibility for PostDocs, PhD / Master / Bachelor students, technical staff

Consortium speaker and project leader of several running projects funded by BMBF, federal ministry for research and innovation, Deutsche Gesetzliche Unfallversicheung (DGUV);
Consortium speaker of the service center “Bioinformatics for Proteomics – BioInfra.Prot” within the BMBF funded “German Network for Bioinformatics Infrastructure – de.NBI”

Habilitation (German qualification for higher education) in the medical faculty, RUB
Cumulative habilitation thesis: “Standard data formats, algorithms and analysis strategies for the bioinformatics of proteomics“
Habilitation colloquium at the faculty council: „Big data – chances and risks of personalised medicine“

Project leader and coordination of several finished projects funded by EU, BMBF, federal ministry for research and innovation, Deutsche Gesetzliche Unfallversicheung (DGUV), Cluster Industrielle Biotechnologie (CLIB), medical faculty RUB (FoRUM)

Group leader of the work group “Bioinformatics / Biostatistics” at Medizinisches Proteom-Center, RUB
personnel responsibility for PostDocs, PhD / Master / Bachelor students, technical staff

PostDoc at Medizinisches Proteom-Center, Ruhr-University Bochum (RUB), Germany

PhD studies at the medical faculty, Westfälische Wilhelms-University Münster, Germany
PhD thesis: “intensity based quality control and scaling of gene expression data“

Studies in computer science, university Dortmund, Germany
Degree: diploma in computer science


Member of Ethics Committee, RUB

Faculty coordinator for IT security and data privacy of the medical faculty, RUB

Organisation, supervision of and lecturer at the de.NBI summer school „ From Big Data to Big Insights - Computational Methods for the analysis and interpretation of mass-spectrometric high-throughput data”, Leibniz-Zentrum für Informatik, Castle Dagstuhl, Germany

Member of the extended user council for the IT.Services department, RUB

Reviewer for conferences and funding institutions, e.g. DFG, German Conference for Bioinformatics (GCB), French Institute of Bioinformatics (IFB)

Editor of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO): execution of the review process (“PSI document process”) for suggested standardisation documents

Member of the editorial board of the journal “BBA – Proteins and Proteomics”

Peer reviewer for scientific journals, e.g. Bioinformatics, BMC Bioinformatics, Molecular and Cellular Proteomics, Proteomics, J Proteome Research, J Proteomics, BBA Proteins and Proteomics


DGPF (German Society for Proteome Research)
GI (Society for Informatics / Computer Science)
Common work group of scientific societies “Bioinformatics” (FaBi, www.bioinformatik.de)
Research Department Protein (Ruhr-University Bochum)


1. Turewicz M, Kohl M, Ahrens M, Mayer G, Uszkoreit J, Naboulsi W, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M (2017) BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication. J Biotechnol. 2017 Nov 10;261:116-125 (IF 2.6)

2. Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M (2017) A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. Brief Bioinform 2017 Oct 30 (IF 2016: 5.1)

3. 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 (2017) Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis. Ann Neurol 2017 Feb;81(2):227-239 (IF 9.9)

4. Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M (2016) PAA: an R/bioconductor package for biomarker discovery with protein microarrays. Bioinformatics 2016 May 15;32(10):1577-9 (IF 7.3)

5. Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M (2015) PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface. J Proteome Res. 2015 Jul 2;14(7):2988-97 (IF 4.2)

6. Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2014 Mar 10;32(3):223-6 (IF 41.5)

7. Kohl M, Megger DA, Trippler M, Meckel H, Ahrens M, Bracht T, Weber F, Hoffmann AC, Baba HA, Sitek B, Schlaak JF, Meyer HE, Stephan C, Eisenacher M (2014) A practical data processing workflow for multi-OMICS projects. Biochim Biophys Acta – Proteins and Proteomics 2014 Jan;1844(1 Pt A):52-62 (IF 2.7)

8. Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Antonio Vizcaíno J, Hermjakob H, Stephan C, Meyer HE, Eisenacher M on behalf of the HUPO-PSI Group (2013) The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) – The Journal of Biological Databases and Curation 2013 Mar 12;2013(0):bat009 (IF 4.5)

9. Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard S, Selley J, Searle B, Shofstahl J, Seymour S, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaino JA, Chambers M, Pizarro A, Creasy D (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics 2012 Jul;11(7):M111.014381 (IF 7.3)

10. Bell AW, Deutsch EW, Au CE, …, Eisenacher M, Marcus K, Langenfeld E, May C, …, Falkner JA, Martens L, Vizcaíno JA (2009) A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 2009 Jun;6(6):423-30 (IF 16.8)