Integrated OMICS and Bioinformatics Platform

Abstract:

Z01 provides the members of the CRC with an experienced infrastructure for high throughput proteomics, transcriptomics, genomics and bioinformatics. Z01 will support the optimization of experimental setups and sample preparation, which is critical to obtain reproducible and statistically significant results. Z01 will also provide the required expertise for data processing, analysis and interpretation. Additionally, Z01 provides dedicated training in the application of OMICS-technologies and their bioinformatics evaluation to the PhD students in the CRC.

Principal investigators:

Univ.-Prof. Dr. rer. nat. Stefan Tenzer
Institut für Immunologie
Universitätsmedizin der Johannes Gutenberg-Universität Mainz
Langenbeckstraße 1, 55131 Mainz
Phone: +49 (0)6131 17-6199
E-mail: tenzer@uni-mainz.de
Web: http://www.unimedizin-mainz.de/immunologie/arbeitsgruppen/ag-tenzer.html

Dr. rer. nat. Valesca Bukur (née Boisguérin),
TRON – Translationale Onkologie an der Universitätsmedizin gGmbH
der Johannes Gutenberg-Universität Mainz
Freiligrathstraße 12, 55131 Mainz
Phone: +49 (0)6131 2161-340
E-mail: Valesca.bukur@tron-mainz.de
Web: http://tron-mainz.de/de/tron-abteilungen/genomics/
https://www.researchgate.net/scientific-contributions/2053471550_Valesca_Bukur

Postdoc:

Dr. Mateusz Lacki

 

Project-related publications:

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. (2016). A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol. 34:1130-1136

Distler U, Schmeisser MJ, Pelosi A, Reim D, Kuharev J, Weiczner R, Baumgart J, Boeckers TM, Nitsch R, Vogt J, Tenzer S. (2014) In-depth protein profiling of the postsynaptic density from mouse hippocampus using data-independent acquisition proteomics. Proteomics 14:2607-13

Distler U, Kuharev J, Navarro P, Levin Y, Schild H, Tenzer S. (2014) Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat Methods 11:167-70

Tenzer S*§, Docter D*, Kuharev J, Musyanovych A, Fetz V, Hecht R, Schlenk F, Fischer D, Kiouptsi K, Reinhardt C, Landfester K, Schild H, Maskos M, Knauer SK, Stauber RH§ (2013) Rapid formation of plasma protein corona critically affects nanoparticle pathophysiology. Nat Nanotechnol 8:772-81 (*joint first authors, §corresponding authors)

Tenzer S, Moro A, Kuharev J, Francis AC, Vidalino L, Provenzani A, Macchi P (2013) Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach. J Proteome Res 12:2869-84 (*joint first authors)

Sahin U, Derhovanessian E, Miller M, Kloke B, Simon P, Löwer M, Bukur V, Tadmor A, Luxemburger U, Schrörs B, Omokoko T, Vormehr M, Albrecht C, Paruzynski A, Kuhn A, Buck J, Heesch S, Schreeb K, Müller F, Ortseifer I, Vogler I, Godehardt E, Attig S, Rae R, Breitkreuz A, Tolliver C, Suchan M, Martic G, Hohberger A, Sorn P, Diekmann J, Ciesla J, Waksmann O, Kemmer-Brück A, Witt M, Zillgen M, Rothermel A, Kasemann B, Langer D, Bolte S, Diken M, Kreiter S, Nemecek R, Gebhardt C, Grabbe S, Höller C, Utikal J, Huber C, Loquai C*, Türeci Ö* (2017) A personalized neo-epitope RNA vaccine mobilizes potent, poly-specific T-cell immunity against cancer. Nature 10.1038/nature23003 (*contributed equally)

Boisguérin V, Castle JC, Loewer M, Diekmann J, Mueller F, Britten CM, Kreiter S, Türeci Ö, Sahin U (2014) Translation of genomics-guided RNA-based personalised cancer vaccines: towards the bedside. Br J Cancer. 111(8):1469-75

Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, Stade B, Franke A, Mayer J, Spangler J, McLaughlin S, Shah M, Lee C, Harkins TT, Sartori A, Moreno-Estrada A, Henn B, Sikora M, Semino O, Chiaroni J, Rootsi S, Myres NM, Cabrera VM, Underhill PA, Bustamante CD, Vigl EE, Samadelli M, Cipollini G, Haas J, Katus H, O'Connor BD, Carlson MR, Meder B, Blin N, Meese E, Pusch CM, Zink A. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun, 3:698

Keller A, Leidinger P, Bauer A, Elsharawy A, Haas J, Backes C, Wendschlag A, Giese N, Tjaden C, Ott K, Werner J, Hackert T, Ruprecht K, Huwer H, Huebers J, Jacobs G, Rosenstiel P, Dommisch H, Schaefer A, Müller-Quernheim J, Wullich B, Keck B, Graf N, Reichrath J, Vogel B, Nebel A, Jager SU, Staehler P, Amarantos I, Boisguerin V, Staehler C, Beier M, Scheffler M, Büchler MW, Wischhusen J, Haeusler SF, Dietl J, Hofmann S, Lenhof HP, Schreiber S, Katus HA, Rottbauer W, Meder B, Hoheisel JD, Franke A, Meese E. (2011) Toward the blood-borne miRNome of human diseases. Nature Methods 841-3

Matzas M, Kefer N, Siebelt N, Boisguérin V, Leonard JT, Stähler PF, Keller A, Stähler CF, Häberle P, Gharizadeh B, Babrzadeh F, Church G (2010) High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nature Biotechnology 1291-4