I worked for 15 years in molecular genetics and cancer research.
During this time I (co-)authored several publications ...
Schütte, M., Risch, T., Abdavi-Azar, N., Boehnke, K., Schumacher, D., Keil, M., Yildirimman, R., Jandrasits, C., Borodina, T., Amstislavskiy, V., Worth, C.L., Schweiger, C., Liebs, S., Lange, M., Warnatz, H.J., Butcher, L.M., Barrett, J.E., Sultan, M., Wierling, C., Golob-Schwarzl, N., Lax, S., Uranitsch, S., Becker, M., Welte, Y., Regan, J.L., Silvestrov, M., Kehler, I., Fusi, A., Kessler, T., Herwig, R., Landegren, U., Wienke, D., Nilsson, M., Velasco, J.A., Garin-Chesa, P., Reinhard, C., Beck, S., Schäfer, R., Regenbrecht, C.R., Henderson, D., Lange, B., Haybaeck, J., Keilholz, U., Hoffmann, J., Lehrach, H., Yaspo, M.L.
Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors
Nature Communications 8, 14262 doi: 10.1038/ncomms14262
Herwig, R., Gmuender, H., Corvi, R., Bloch, K.M.,, Brandenburg, A., Castell, J.5, Ceelen, L., Chesne, C., Doktorova, T.Y., Jennen, D., Jennings, P., Limoncie,l A., Lock, E.A., McMorrow, T., Phrakonkham, P., Radford, R., Slattery, C., Stierum, R., Vilardell, M., Wittenberger, T., Yildirimman, R., Ryan, M., Rogiers, V., Kleinjans, J.
Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective
Archives of Toxicology, 2016 Sep;90(9):2215-29. doi: 10.1007/s00204-015-1617-3
Doktorova, T.Y., Yildirimman, R., Ceelen, L., Vilardell, M., Vanhaecke, T., Vinken, M., Ates, G., Heymans, A., Gmuender, H., Bort, R., Corvi, R., Phrakonkham, P., Li, R., Mouchet, N., Chesne, C., van Delft, J., Kleinjans, J., Castell, J., Herwig, R., Rogiers, V.
Testing Chemical Carcino Genicity By Using A Transcriptomics Heparg-Based Model
EXCLI Journal, 2014;13:623-637
Doktorova, T.Y., Yildirimman, R., Vinken, M., Vilardell, M., Vanhaecke, T., Gmuender, H., Bort, R., Brolen, G., Holmgren, G., Li, R., Chesne, C., van Delft, J., Kleinjans, J., Castell, J., Bjorquist, P., Herwig, R., Rogiers, V.
Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models
Carcinogenesis, 2013 Jun;34(6):1393-402
Suter, B., Fontaine, J.F., Yildirimman, R., Raskó, T., Schaefer, M.H., Rasche, A., Porras, P., Vázquez-Álvarez, B.M., Russ, J., Rau, K., Foulle, R., Zenkner, M., Saar, K., Herwig, R., Andrade-Navarro, M.A., Wanker, E.E.
Development and application of a DNA microarray-based yeast two-hybrid system
Nucleic Acids Res., 2013 Feb 1;41(3):1496-507
Dreher, F., Kreitler, T., Hardt, C., Kamburov, A., Yildirimman, R., Schellander, K., Lehrach, H., Lange, B., Herwig, H.
DIPSBC - Data Integration Platform for Systems Biology Collaborations
BMC Bioinformatics, 2012, 13:85, DOI: 10.1186/1471-2105-13-85
Yildirimman, R., Brolén, G., Vilardell, M., Eriksson, G., Synnergren, J., Gmuender, H., Kamburov, A., Ingelman-Sundberg, M., Castell, J., Lahoz, A., Kleinjans, J., van Delft, J., Björquist, P., Herwig, R.
Human Embryonic Stem Cell Derived Hepatocyte-Like Cells as a Tool for In Vitro Hazard Assessment of Chemical Carcinogenicity
ToxSci, 2011 Dec; 124(2): 278–290
Meinel, T., Mueller, M. S., Ahmed, J., Yildirimman, R., Dunkel, M., Herwig, R., and Preissner, R.
SOAP/WSDL-Based Web Services for Biomedicine: Demonstrating the Technique with the CancerResource
Proceedings of the MEDICON, 2010, 29(5):835-838
Rasche, A., Yildirimman, R. and Herwig, R.
Integrative Analysis of microarray data - a path for systems toxicology
Handbook of Systems Toxicology (Eds. D. A. Casciano and S. C. Sahu), John Wiley & Sons Ltd. 2010, ISBN-13: 978-0-470-68401-6, DOI: 10.1002/9780470744307.gat207
Yildirimman, R.
The GenomeMatrix : data mining from biological databases and data sources for building integrated functional genomics information
TU Berlin, 2005
The HSA21 expression map initiative
A gene expression map of human chromosome 21 orthologues in the mouse
Nature, 2002, 420:586-590, doi:10.1038/nature01270
... and presented on several topics ...
OncoTrack DB - a cancer genomics data integration platform
EMBL Conference: Cancer Genomics, Poster presenation, Heidelberg 2013.
PREDICT - Wiki-based data integration platform for collaborative research in systems biology
Evaluation conference, Poster presenation, BMBF funding priority Medical Systems Biology, Freiburg 2010.
PREDICT – network-based analysis of tumour variability in in vivo models of non-small cell lung cancers
Evaluation conference, Poster presenation, BMBF funding priority Medical Systems Biology, Freiburg 2010.
Carcinogenesis induced by chemical compounds - a case study on Benzo[a]Pyrene
15th International AEK Cancer Congress, Poster presenation, Berlin 2009.
Meta-analysis pipeline for identifying discriminative patterns of chemicals in liver models
carcinoGENOMICS annual meeting, Bioinformatics workshop, Barcelona 2009.
The GenomeMatrix Information Retrieval System
HUGO Human-Genome-Meeting, Poster presenation, Berlin 2004.
... and was involved in several funded large-scale research projects ...
CanPathPro addresses the challenge of predictive modelling of biological data by developing and refining bioinformatic and experimental tools for the evaluation and control of systems biology modelling predictions. Components comprise highly defined mouse and organotypic experimental systems, next generation sequencing, quantitative proteomics and a systems biology computational model for data integration, visualisation and predictive modelling.
CANCER-ID is a newly formed European consortium funded by the Innovative Medicines Initiative (IMI) with currently 33 partners from 13 countries aiming at the establishment of standard protocols for and clinical validation of blood-based biomarkers. It brings together experts from academic and clinical research, innovative Small-to-Medium sized Enterprises (SMEs), diagnostics companies and the pharmaceutical industry thus providing a unique setting for establishing clinical utility of “liquid biopsies”.
OncoTrack, “Methods for systematic next generation oncology biomarker development”, is an international consortium of over 100 scientists, that has launched one of Europe’s largest collaborative academic-industry research projects to develop and assess novel approaches for identification of new markers for colon cancer. This unique six year project brings together top scientists from European academic institutions offering a wide range of expertise, and partners them with pharmaceutical companies.
Recent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animal experimentation. The Sixth Framework Program project carcinoGENOMICS was specifically raised to develop omics-based in vitro screens for testing the carcinogenic potential of chemical compounds in a pan-European context.
PREDICT - a systems biology approach to pre-clinical testing in cancer
The main goal of the project is to implement a systematic experimental and computational approach (PREDICT) and to develop computer models able to accelerate and improve the pre-clinical testing phase by prediction of diagnostic potential of marker genes, therapeutic decisions based on the individual status of the tumours and the individual effects of drug treatments in different tumour entities (with an initial focus on lung cancer).