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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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Subscription

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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

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