Description of organisation
Fraunhofer Society is the largest research organisation devoted exclusively to the advancement for applied and industrial research and development in Europe.
Fraunhofer for Biomedical Egineering (IBMT), Dahlem Center (DC) and Potsdam (P), Berlin, Germany
The Fraunhofer Institute for Biomedical Engineering has a central focus on translating research in the biomedical field into applications and industrial products and services, thereby cooperating closely with companies of various size and on national, European and global scale. The spectrum of applications comprises nanobiotechnology, material sciences, biomarker development, molecular tools for the life sciences, automated cellular systems and tools for stem cell research and application, cell‑free bioproduction systems, medical and diagnostic devices, sensors, cryobiophysics, biobanking, telemedicine and (bio)informatics development and includes also the enabling via development of integrating platforms.
The IBMT branch Berlin (IBMT‑DC, Dahlem Centre for Genome Research and Medical Systems Biology) was established by Prof. Hans Lehrach with the aim of realisation and funding of Genome Research and Medical Systems Biology in particular the analysis, characterisation and modelling of diseases (e.g. tumour patients). Publication and access of the research results for other research institutions and the interested public through publications, organisation of seminars, lectures and the implementation of results in professional databases.
Profile of staff members
Prof. Dr. Hans Lehrach is one of Germany’s foremost molecular biologists.
Dr. Lehrach obtained his Ph.D. at the Max Planck Institute for Experimental Medicine and the Max Planck Institute for Biophysical Chemistry in 1974. Next he moved on to Harvard University, Boston (1974‑1978) for a postdoc and then became group leader at EMBL, Heidelberg (1978‑1987). He then moved to the Imperial Cancer Research Fund, London (1987‑1994) to become head of the Genome Analysis Department. He then returned to Germany to become Director and Scientific Member at the Max Planck Institute for Molecular Genetics (since 1994) and joined the Fraunhofer IBMT since 2012. His scientific achievements are many. Highlights include his key involvement in several genome sequencing projects, such as the human, rat, and Schizosaccharomyces. His group also was part of the team which identified the Huntington’s disease gene. Dr. Lehrach also performed key work on technologies such as protein microarrays, protein interactome analysis, yeast artificial chromosomes and RNAseq.
For his work, Dr. Lehrach has received several awards such as the Ján Jessenius SAS Medal of Honour for outstanding achievements in medical sciences of the Slovak Academy of Sciences and the Karl Heinz Beckurts Award for achievements in genome research. Dr. Lehrach has co‑founded several biotechnology companies such as Sequana Therapeutics, GPC Biotech, Scienion, Prot@gen, PSF Biotech, Atlas Biolabs, Alacris Theranostics
Prof. Dr. Günter Fuhr is director of the Fraunhofer Institute for Biomedical Engineering in St. Ingbert since 2001 with branches in Sulzbach/Saar, Potsdam, Berlin, China and USA, and since 2008 he is also CEO of the Fraunhofer institution of Marine Biotechnology in Lübeck. He gained world‑wide recognised expertise in many areas of the life sciences and biophysics including cryo technology and biobanking, medical technology, cellular biotechnology and biochips, nanobiotechnology and nanomedicine, computer‑assisted simulations and bioelectronics. Prof. Fuhr is founding director of the research Cryobank with the Center for Cryobiotechnology »EUROCRYOSaar« and also central coordinator of the Integrated EU‑Project »CellPROM« with 27 European partners. He won the Humboldt‑Award and the Michael‑Widmer‑Award of the Swiss Chemical Society. Prof. Fuhr is also very active in the process of translating innovation into market applications – he holds more than 200 registered patents–and won several prices in this field.
Prof. Dr. Frank Bier is the director of the IBMT institute branch in Potsdam. He started as a physicist, but moved into biochemistry in the frame of his habilitation. Being group leader in projects dedicated to molecular bioanalytics with special focus on biosensors and chip technology. Since 2003 Frank Bier is also full professor at the University of Potsdam with a chair for Molecular Bioanalytics. He was successfully initiating large‑scale projects on biosensors and lab‑on‑a‑chip technologies and on in vitro bioproduction systems. His institute was coordinator of several EU projects like NUCAN and participated in numerous other projects. Also on the national level Frank Bier initiated and coordinated large‑scale projects like the Center for integrated Bioanalysis or the joint initiative of the Fraunhofer‑Gesellschaft on development of in vitro Diagnostics (ivD platform) and “in vitro Bioproduction Systems”. Prof. Frank Bier is member of several advisory boards and networks, he is e.g. head of the advisory board of the national network “DiagnosticNet Berlin‑Brandenburg”.
Recent publications relevant to the project
1 Wierling C, Kühn A, Hache H, Daskalaki A, Maschke‑Dutz E, Peycheva S, Li J, Herwig R, Lehrach H. (2012) Prediction in the face of uncertainty: a Monte Carlo‑based approach for systems biology of cancer treatment. Mutat Res. Aug 15;746(2):163‑70.
2 Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson‑Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 30(3):224‑6.
3 1000 Genomes Project Consortium (2012) A map of human genome variation from population‑scale sequencing. Nature 467(7319):1061‑73.
4 Schumacher S, Nestler J, Otto T, Wegener M, Ehrentreich‑Förster E, Michel D, Wunderlich K, Palzer S, Sohn K, Weber A, Burgard M, Grzesiak A, Teichert A, Brandenburg A, Koger B, Albers J, Nebling E, Bier FF (2012) Highly‑integrated lab‑on‑chip system for point‑of‑care multiparameter analysis. Lab Chip. 12, 464‑473.
5 Lermen D, Blömeke B, Browne R, Clarke A, Dyce PW, Fixemer T, Fuhr GR, Holt WV, Jewgenow K, Lloyd RE, Lötters S, Paulus M, Reid GM, Rapoport DH, Rawson D, Ringleb J, Ryder OA, Spörl G, Schmitt T, Veith M, Müller P (2009) Cryobanking of viable biomaterials: implementation of new strategies for conservation purposes. Mol Ecol. 18(6):1030‑3.
Description of organisation
Information Extraction / Semantic Text Analysis, Applied Chemoinformatics, Grid and Cloud Middleware, Mathematical Modelling of Neurodegenerative Diseases
In compliance with the general mission of a Fraunhofer Institute, the Department of Bioinformatics is working closely with industrial partners – including small and medium size enterprises–to enhance their competitiveness through mediating knowledge and technology transfer from academic research to industrial application. Collaborative research and development projects of the Department of Bioinformatics deliver solutions to the pharmaceutical industry, the biotech industry and to the life science software industry. Positioned at the boundary between pure commercial and pure academic research we maintain strong links to both communities. As an organisation dedicated to applied research we take part in the education of students of the Life Science Informatics curriculum of the Bonn‑Aachen International Centre for Information Technology (B‑IT) and we participate actively in various national and European research initiatives.
Profile of staff members
Martin Hofmann‑Apitius has always worked in applied, translational research. He has experience with industrial as well as academic research and development and with his current position he is right in the middle between the two worlds. In compliance with the general mission of a Fraunhofer Department, all research and development done in the Department of Bioinformatics at Fraunhofer SCAI is aimed at solving realworld problems.
Shahid Mohammad is a PhD student experienced in applied chemoinformatics; his particular expertise is in the area of design and implementation of intelligent approaches to model complex pharmacological systems such as the Human Brain Pharmacome.
Wolfgang Ziegler is an experienced scientist in the area of eInfrastructures, eScience and Grid‑/Cloud‑Middleware. He is and was involved in major international grid‑ and cloud‑projects, including activities aimed at providing the necessary standardisation (OGF etc.) for grids and clouds.
Recent publications relevant to the project
1 Gurulingappa, Harsha; Rajput, Abdul‑Mateen; Roberts, Angus; Fluck, Juliane; Hofmann‑Apitius, Martin; Toldo, Luca: Development of a benchmark corpus to support the automatic extraction of drug‑related adverse effects from medical case reports. Journal of biomedical informatics : JBI, Vol.45 (2012), No.5, pp.885‑892 info:doi/10.1016/j.jbi.2012.04.008
2 Juan Ferrer, A.; Hernández, F.; Tordsson, J.; Elmroth, E.; Ali‑Eldin, A.; Zsigri, C.; Sirvent, R.; Guitart, J.; Badia, R.M.; Djemame, K.; Ziegler, W.; Dimitrakos, T.; Nair, S.K.; Kousiouris, G.; Konstanteli, K.; Varvarigou, T.; Hudzia, B.; Kipp, A.; Wesner, S.; Corrales, M.; Forgo, N.; Sharif, T.; Sheridan, C.: OPTIMIS: A holistic approach to cloud service provisioning. Future generation computer systems : FGCS, Vol.28 (2012), No.1, pp.66‑77 info:doi/10.1016/j.future.2011.05.022
3 Holl, S.; Zimmermann, O.; Hofmann‑Apitius, M.: A UNICORE plugin for HPC‑enabled scientific workflows in Taverna 2.2. (World Congress on Services (SERVICES) <7, 2011, Washington/DC>). Institute of Electrical and Electronics Engineers ‑IEEE‑: 2011 IEEE World Congress on Services, SERVICES 2011. Proceedings: Washington, DC, USA, 4–9 July 2011. Piscataway, NJ: IEEE, 2011, pp. 220‑223 info:doi/10.1109/SERVICES.2011.46
4 Ivchenko, O.; Younesi, E.; Shahid, M.; Wolf, A.; Müller, B.; Hofmann‑Apitius, M.:PLIO: An ontology for formal description of protein‑ligand interactions. Bioinformatics, Vol.27 (2011), No.12, pp.1684‑1690 info:doi/10.1093/bioinformatics/btr256
5 Mohammad Shahid, Vinod Kasam and Martin Hofmann‑Apitius An Improved Weighted‑Residue Profile Based Method of Using Protein–Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists (pages 781–791) Article first published online: 27 OCT 2010 | DOI: 10.1002/minf.201000068