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An Integrated Project financially supported by a grant from the European Commission (PL037712)

Publications by the EU commission

• Booklets on alternative testing strategies
  
  This booklet has been published by DG Research in 2006. It gives a good overview of FP6 and FP7 projects.

  Alternative Testing Strategies 2006

• Alternative Testing Strategies – Progress Report 2009

  Alternative Testing Strategies - Progress Report 2009

Full Papers

• The metabolomics standards initiative
  
  Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. (2007). The metabolomics standards initiative. Nat Biotechnol. 25(8):846-8.

  http://www.nature.com/nbt/journal/v25/n8/pdf/nbt0807-846b.pdf

• The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
  
  Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg JL, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Shah N, Whetzel PL, Suzanna L. (2007). The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 25(11):1251-5.

  http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf

• The First MGED RSBI (ISA-TAB) Workshop: "can a simple format work for complex studies?"
  
  Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S. (2008). The First MGED RSBI (ISA-TAB) Workshop: "can a simple format work for complex studies?". OMICS. 12(2):143-9.

  http://www.liebertonline.com/doi/pdfplus/10.1089/omi.2008.0019

• Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
  
  Taylor CF*, Field D*, Sansone SA*, Apweiler R, Ashburner M, Ball CA, Binz PA, Brazma A, Brinkman R, Bruskiewich R, Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Grimes G, Hardy NW, Hermjakob H, Julian RK, Kane M, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, McNally R, Mehrle A, Morrison N, Paton NW, Quackenbush J, Robertson DG, Rocca- Serra P, Smith B, Snape J, Sterk P, Weimann S. (2008). Promoting coherent minimum reporting requirements for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 26(8):889-896.

  http://isatab.sourceforge.net/docs/Field-Sansone-Science-OmicsDataSharing.pdf

• ’Omics Data Sharing
  
  Field D*, Sansone SA*, Collis A*, Booth T, Millard S, Dukes P, Gregurick SK, Kennedy K, Kolar P, Maxon M, Mugabushaka AM, Perrin N, Remacle JE, Remington K, Rocca-Serra P, Taylor CF, Thorley M, Tiwari B, Wilbanks J. (2009). ‘Omics data sharing. Science 326(5950):234-6.

  http://isatab.sourceforge.net/docs/Field-Sansone-Science-OmicsDataSharing.pdf

• ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (in press)
  
  Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W and Sansone SA.

• Hepatocyte-like cells derived from human embryonic stem cells specifically via definitive endoderm and a progenitor stage
  
  Brolén G, Sivertsson L, Björquist P, Eriksson G, Ek M, Semb H, Johansson I, Andersson TB, Ingelman-Sundberg M, Heins N.
  J Biotechnol. 2010 Feb 1;145(3):284-94. Epub 2009 Nov 20.PMID: 19932139 [PubMed - indexed for MEDLINE]

  http://www.ncbi.nlm.nih.gov/pubmed/19932139

• Transcriptional profiling of human embryonic stem cells differentiating to definitive and primitive endoderm and further towards the hepatic lineage
  
  Synnergren J, Heins N, Brolén G, Eriksson G, Lindahl A, Hyllner J, Olsson B, Sartipy P, Björquist P.
  Stem Cells Dev. 2009 Sep 16. [Epub ahead of print] PMID: 19757991 [PubMed - as supplied by publisher]

  http://www.ncbi.nlm.nih.gov/pubmed/19757991

• Handbook of Systems Toxicology, ch. Integrative Analysis of microarray data - a path for systems toxicology.
  
  Rasche, A., Yildirimman, R. and Herwig, R. (2010). ed. D.A. Casciano and S.C. Sahu. John Wiley & Sons Ltd./, *in press*.

• Integrative Analysis of Microarray Data: A Path for Systems Toxicology
  
  Axel Rasche, Reha Yildirimman, and Ralf Herwig

  hst017.pdf (200 kb)

• Comparison of HepG2 and HepaRG by Whole-Genome Gene Expression Analysis for the Purpose of Chemical Hazard Identification
  
  http://toxsci.oxfordjournals.org/cgi/reprint/115/1/66
  
  Danyel G. J. Jennen, Christina Magkoufopoulou, Hans B. Ketelslegers, Marcel H. M. van Herwijnen, Jos C. S. Kleinjans, and Joost H. M. van Delft

  Jennen_et_al._2010.pdf (1.2 MB)

• Gap junctional intercellular communication as a target for liver toxicity and carcinogenicity
  
  Mathieu Vinken, Tatyana Doktorova, Elke Decrock, Luc Leybaert, Tamara Vanhaecke, and Vera Rogiers

  critical_reviews_paper.pdf (894 kb)

• Biochemical Characterisation of an In VitroModel of Hepatocellular Apoptotic Cell Death
  
  Mathieu Vinken, Elke Decrock, Elke De Vuyst, Luc Leybaert, Tamara Vanhaecke and Vera Rogiers

  ATLA.pdf (340 kb)

• Inter-laboratory comparison of human renal proximal tubule (HK-2) transcriptome alterations due to Cyclosporine A exposure and medium exhaustion
  
  Paul Jennings, Sonia Aydin, Jason Bennett, Rachael McBride, Christina Weiland, Niamh Tuite, Leonhard N. Gruber, Paul Perco, Peadar Ó Gaora, Heidrun Ellinger-Ziegelbauer, Hans-Juergen Ahr, Cees Van Kooten, Mohamed R. Daha, Pilar Prieto, Michael P. Ryan, Walter Pfaller, Tara McMorrow

  Jennings_2009_CsA_ILC.pdf (1.4 MB)

• Genetic algorithms for simultaneous variable and sample selection in metabonomics
  
  Rachel Cavill, Hector C. Keun, Elaine Holmes, John C. Lindon, Jeremy K. Nicholson and Timothy M. D. Ebbels

  http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/1/112

• Epigenetic regulation of gap junctional intercellular communication: More than a way to keep cells quiet?
  
  Mathieu Vinken, Evelien De Rop, Elke Decrock, Elke De Vuyst, Luc Leybaert,Tamara Vanhaecke, Vera Rogiers

  biochimica_et_biophysica_acta_reviews_on_cancer.pdf (426 kb)

• hTERT alone immortalizes epithelial cells of renal proximal tubules without changing their functional characteristics.
  
  Wieser M, Stadler G, Jennings P, Streubel B, Pfaller W, Ambros P, Riedl C, Katinger H, Grillari J, and Grillari R. Am J Physiol Renal Physiol, 2008.
  
  PMID 18715936

  Weiser_et_al_hTERT_2008.pdf (2.1 MB)

• Influence of microvascular endothelial cells on transcriptional regulation of proximal tubular epithelial cells.
  
  Aydin S, Signorelli S, Lechleitner T, Joannidis M, Pleban C, Perco P, Pfaller W, and Jennings P. Am J Physiol Cell Physiol 294: C543-554, 2008.
  
  PMID 18057119

  Aydin_et_al_co-culture_2008.pdf (532 kb)

• New publication of MPIMG within carcinogenomics
  
  In this paper we describe the ConsensusPathDB that was developed for integrating heterogeneous human interaction data. The database is used within Carcinogenomics in order to identify functional modules.
  
  Kamburov A, Wierling C, Lehrach H, Herwig R (2008) ConsensusPathDB - a database for matching human functional interaction networks. Nucleic Acids Res, in press.
  
  Early online access:
  http://nar.oxfordjournals.org/cgi/content/full/gkn698v1

• Publications of MPIMG which acknowledge Carcinogenomics funding
  
  In this paper we give a review on different pathway database resources and modelling tools that are useful for network-based analysis of carcinogenomics data.
  
  Wierling C, Herwig R, Lehrach H (2007) Brief Funct Genom Proteom 6(3):240-51.
  
  Link to the abstract:
  http://bfgp.oxfordjournals.org/cgi/content/abstract/6/3/240

Congresses / Abstracts

• Characterisation of a new human renal proximal tubular cell line (RPTEC/TERT1), generated by the introduction of telomerase activity.
  
  Guber L, Prajczer S, Boei J, Wieser M, Voglauer R, Pfaller W and Jennings P.
  15th Congress on Alternatives to Animal Testing – Linz 2008. [Bo Holmstedt Memorial Foundation Poster Award]