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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at MDC Berlin (Helmholz Consortium)

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	1.	Review Epigallocatechin-3-gallate: a useful, effective and safe clinical approach for targeted prevention and individualised treatment of neurological diseases? Anja Mähler, Silvia Mandel, Mario Lorenz, Urs Ruegg, Erich E Wanker, Michael Boschmann, Friedemann Paul EPMA Journal 2013, 4:5 (18 February 2013) Abstract \| Full text \| PDF \| PubMed
	2.	Workshop presentation *High spatial and temporal myocardial CINE T2 mapping at 7.0 T: a feasibility study** F Hezel, C Thalhammer, S Waiczies, J Schulz-Menger, T Niendorf Journal of Cardiovascular Magnetic Resonance 2013, 15(Suppl 1):W29 (30 January 2013) Full text \| PDF
	3.	Hypothesis Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis Jordi Solana EvoDevo 2013, 4:2 (8 January 2013) Abstract \| Provisional PDF \| PubMed
	4.	Research highlight Mining the literature: new methods to exploit keyword profiles Miguel A Andrade-Navarro Genome Medicine 2012, 4:81 (30 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Miguel Andrade-Navarro highlights two recent publications by Wasserman et al. demonstrating that keyword profiles can be used to detect new associations between genes and inherited diseases.
	5.	Research Peer2ref: a peer-reviewer finding web tool that uses author disambiguation Miguel A Andrade-Navarro, Gareth A Palidwor, Carol Perez-Iratxeta BioData Mining 2012, 5:14 (7 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new web tool which uses author disambiguation and usage based keywords is shown to enhance the automated search of peer reviewers, particularly those who operate in narrow areas of research.
	6.	Research article *Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1* expression in mouse limb buds** Aimée Zuniga, Frédéric Laurent, Javier Lopez-Rios, Christian Klasen, Nicolas Matt, Rolf Zeller BMC Developmental Biology 2012, 12:23 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Distant cis-regulatory regions scattered through a larger genome region control the highly dynamic expression of Gremlin1 (GREM1), a Bone Morphogenetic Protein (BMP) antagonist, which is key to normal progression of mouse limb bud development.
	7.	Research SNPs in the coding region of the metastasis-inducing gene MACC1 and clinical outcome in colorectal cancer Felicitas Schmid, Susen Burock, Konrad Klockmeier, Peter M Schlag, Ulrike Stein Molecular Cancer 2012, 11:49 (29 July 2012) Abstract \| Full text \| PDF \| PubMed
	8.	Research article Multi-compartmental modeling of SORLA’s influence on amyloidogenic processing in Alzheimer’s disease Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E Willnow, Olaf Wolkenhauer BMC Systems Biology 2012, 6:74 (22 June 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Research article Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans Amit Sinha, Ralf J Sommer, Christoph Dieterich BMC Genomics 2012, 13:254 (19 June 2012) Abstract \| Full text \| PDF \| PubMed
	10.	Research article MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells Lea H Gregersen, Anders Jacobsen, Lisa B Frankel, Jiayu Wen, Anders Krogh, Anders H Lund BMC Cancer 2012, 12:232 (12 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	11.	Research article Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii Guido Mastrobuoni, Susann Irgang, Matthias Pietzke, Heike E Aßmus, Markus Wenzel, Waltraud X Schulze, Stefan Kempa BMC Genomics 2012, 13:215 (31 May 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Research Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach Jordi Solana, Damian Kao, Yuliana Mihaylova, Farah Jaber-Hijazi, Sunir Malla, Ray Wilson, Aziz Aboobaker Genome Biology 2012, 13:R19 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Planarian stem cells are ablated by RNAi against histone 2B and the neoblast-specific transcriptome is determined
	13.	Research Insights into the structure and activity of prototype foamy virus RNase H Berit Leo, Maximilian J Hartl, Kristian Schweimer, Florian Mayr, Birgitta M Wöhrl Retrovirology 2012, 9:14 (10 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This paper demonstrates that the independent PFV RNase H domain is structured and active. The presence of the C-helix in PFV RNase H could be confirmed by assigning the protein backbone and calculating the chemical shift index using NMR spectroscopy.
	14.	Software article Caipirini: using gene sets to rank literature Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Wanderley-Nogueira, Nina Soares-Cavalcanti, Reinhard Schneider BioData Mining 2012, 5:1 (1 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed.
	15.	Research article Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis Sven Knüppel, Jorge Esparza-Gordillo, Ingo Marenholz, Hermann-Georg Holzhütter, Anja Bauerfeind, Andreas Ruether, Stephan Weidinger, Young-Ae Lee, Klaus Rohde BMC Medical Genetics 2012, 13:8 (27 January 2012) Abstract \| Full text \| PDF \| PubMed
	16.	Research article Sonic hedgehog lineage in the mouse hypothalamus: from progenitor domains to hypothalamic regions Gonzalo Alvarez-Bolado, Fabian A Paul, Sandra Blaess Neural Development 2012, 7:4 (20 January 2012) Abstract \| Full text \| PDF \| PubMed
	17.	Proceedings Preimplantation development regulatory pathway construction through a text-mining approach Elisa Donnard, Adriano Barbosa-Silva, Rafael LM Guedes, Gabriel R Fernandes, Henrique Velloso, Matthew J Kohn, Miguel A Andrade-Navarro, J Ortega BMC Genomics 2011, 12(Suppl 4):S3 (22 December 2011) Abstract \| Full text \| PDF \| PubMed
	18.	Software PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries Adriano Barbosa-Silva, Jean-Fred Fontaine, Elisa R Donnard, Fernanda Stussi, J Ortega, Miguel A Andrade-Navarro BMC Bioinformatics 2011, 12:435 (9 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19.	Research The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu et al. BMC Bioinformatics 2011, 12(Suppl 8):S3 (3 October 2011) Abstract \| Full text \| PDF \| PubMed
	20.	Technical Note QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards Jean F Fontaine, Bernhard Suter, Miguel A Andrade-Navarro BMC Research Notes 2011, 4:57 (9 March 2011) Abstract \| Full text \| PDF \| PubMed
	21.	Methodology *Reliable transgene-independent method for determining Sleeping Beauty* transposon copy numbers** Orsolya Kolacsek, Virág Krízsik, Anita Schamberger, Zsuzsa Erdei, Ágota Apáti, György Várady, Lajos Mátés, Zsuzsanna Izsvák, Zoltán Ivics, Balázs Sarkadi, Tamás I Orbán Mobile DNA 2011, 2:5 (3 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22.	Research Identification of early molecular markers for breast cancer Céline Kretschmer, Anja Sterner-Kock, Friederike Siedentopf, Winfried Schoenegg, Peter M Schlag, Wolfgang Kemmner Molecular Cancer 2011, 10:15 (11 February 2011) Abstract \| Full text \| PDF \| PubMed
	23.	Research article Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover Werner E Mayer, Lisa N Schuster, Gabi Bartelmes, Christoph Dieterich, Ralf J Sommer BMC Evolutionary Biology 2011, 11:13 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cellulases have been acquired by nematodes following horizontal gene transfer and analysis of their functional assimilation, gene turnover and selection provides further evidence to support models of horizontal gene transfer in eukaryotes.
	24.	Review The expanding universe of transposon technologies for gene and cell engineering Zoltán Ivics, Zsuzsanna Izsvák Mobile DNA 2010, 1:25 (7 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25.	Methodology article Improved Tet-responsive promoters with minimized background expression Rainer Loew, Niels Heinz , Mathias Hampf, Hermann Bujard, Manfred Gossen BMC Biotechnology 2010, 10:81 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central