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Member - DKFZ Heidelberg (Helmholtz Consortium)

Research staff and students at DKFZ Heidelberg:

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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at DKFZ Heidelberg (Helmholtz Consortium)

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	1.	Method Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
	2.	Forum What does the concept of the stem cell niche really mean today? Arthur D Lander, Judith Kimble, Hans Clevers, Elaine Fuchs, Didier Montarras, Margaret Buckingham, Anne L Calof, Andreas Trumpp, Thordur Oskarsson BMC Biology 2012, 10:19 (9 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How do current researchers view the stem cell niche? Eight experts from different fields provide their perspective, and ask how stem cells evolve in such an environment, launching a new Forum article type within the cross-journal collection on stem cells.
	3.	Research article Coffee consumption modifies risk of estrogen-receptor negative breast cancer Jingmei Li, Petra Seibold, Jenny Chang-Claude, Dieter Flesch-Janys, Jianjun Liu, Kamila Czene, Keith Humphreys, Per Hall Breast Cancer Research 2011, 13:R49 (14 May 2011) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A Swedish study finds that a high daily intake of coffee is associated with a statistically significant decrease in estrogen receptor-negative breast cancer among postmenopausal women.
	4.	Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
	5.	Review Serum microRNAs as non-invasive biomarkers for cancer Jan C Brase, Daniela Wuttig, Ruprecht Kuner, Holger Sültmann Molecular Cancer 2010, 9:306 (26 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6.	Research article *The Drosophila* methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2** Joachim Marhold, Alexander Brehm, Katja Kramer BMC Molecular Biology 2004, 5:20 (29 October 2004) Abstract \| Full text \| PDF \| PubMed
	7.	Research article Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3 Ramona Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel-Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast BMC Genomics 2010, 11:349 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	8.	Research The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
	9.	Research article Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker, Hans Lehrach, Michal R Schweiger BMC Medical Genomics 2011, 4:68 (29 September 2011) Abstract \| Full text \| PDF \| PubMed
	10.	Methodology RNAi-based validation of antibodies for reverse phase protein arrays Heiko A Mannsperger, Stefan Uhlmann, Christian Schmidt, Stefan Wiemann, Özgür Sahin, Ulrike Korf Proteome Science 2010, 8:69 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	11.	Methodology article Conditional gene expression systems in the transgenic rat brain Kai Schönig, Tillmann Weber, Ariana Frömmig, Lena Wendler, Brigitte Pesold, Dominik Djandji, Hermann Bujard, Dusan Bartsch BMC Biology 2012, 10:77 (3 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The advantages of rats over mice for biomedical research have to date been offset by a dearth of proven methods for their genetic manipulation. Addressing this deficit, Bartsch and coauthors develop transgenic rats with inducible reporter gene expression in forebrain neurons.
	12.	Methodology article Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy Phillip Hundeshagen, Anne Hamacher-Brady, Roland Eils, Nathan R Brady BMC Biology 2011, 9:38 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is much interest in activating autophagy, by which cells deliver their own contents to the lysosomal system, in cancer therapy. Nathan Brady and colleagues report a flow cytometric method whereby drug candidates may be screened for effects on separate steps in the process.
	13.	Methodology Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification Jan C Brase, Heiko Mannsperger, Holger Fröhlich, Stephan Gade, Christian Schmidt, Stefan Wiemann, Tim Beissbarth, Thorsten Schlomm, Holger Sültmann, Ulrike Korf Proteome Science 2010, 8:36 (22 June 2010) Abstract \| Full text \| PDF \| PubMed
	14.	Research article Adiposity, hormone replacement therapy use and breast cancer risk by age and hormone receptor status: a large prospective cohort study Rebecca Ritte, Annekatrin Lukanova, Franco Berrino, Laure Dossus, Anne Tjønneland, Anja Olsen, Thure Overvad, Kim Overvad, Françoise Clavel-Chapelon, Agnès Fournier, Guy Fagherazzi, Sabine Rohrmann, Birgit Teucher, Heiner Boeing, Krasimira Aleksandrova, Antonia Trichopoulou, Pagona Lagiou, Dimitrios Trichopoulos, Domenico Palli, Sabina Sieri, Salvatore Panico, Rosario Tumino, Paolo Vineis, José Quirós, Genevieve Buckland, Maria-José Sánchez, Pilar Amiano, María-Dolores Chirlaque, Eva Ardanaz, Malin Sund et al. Breast Cancer Research 2012, 14:R76 (14 May 2012) Abstract \| Full text \| PDF \| PubMed
	15.	Research Body fluid derived exosomes as a novel template for clinical diagnostics Sascha Keller, Johannes Ridinger, Anne-Kathleen Rupp, Johannes WG Janssen, Peter Altevogt Journal of Translational Medicine 2011, 9:86 (8 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16.	Review The receptor RAGE: Bridging inflammation and cancer Astrid Riehl, Julia Németh, Peter Angel, Jochen Hess Cell Communication and Signaling 2009, 7:12 (8 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	17.	Review Molecular biology of cantharidin in cancer cells Rolf Rauh, Stefan Kahl, Herbert Boechzelt, Rudolf Bauer, Bernd Kaina, Thomas Efferth Chinese Medicine 2007, 2:8 (4 July 2007) Abstract \| Full text \| PDF \| PubMed
	18.	Research article Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2 Anna Mulligan, Fergus J Couch, Daniel Barrowdale, Susan M Domchek, Diana Eccles, Heli Nevanlinna, Susan J Ramus, Mark Robson, Mark Sherman, Amanda B Spurdle, Barbara Wappenschmidt, Andrew Lee, Lesley McGuffog, Sue Healey, Olga M Sinilnikova, Ramunas Janavicius, Thomas vO Hansen, Finn C Nielsen, Bent Ejlertsen, Ana Osorio, Iván Muñoz-Repeto, Mercedes Durán, Javier Godino, Maroulio Pertesi, Javier Benítez, Paolo Peterlongo, Siranoush Manoukian, Bernard Peissel, Daniela Zaffaroni, Elisa Cattaneo et al. Breast Cancer Research 2011, 13:R110 (2 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19.	Research article *Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365* are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers** Antonis C Antoniou, Karoline B Kuchenbaecker, Penny Soucy, Jonathan Beesley, Xiaoqing Chen, Lesley McGuffog, Andrew Lee, Daniel Barrowdale, Sue Healey, Olga M Sinilnikova, Maria A Caligo, Niklas Loman, Katja Harbst, Annika Lindblom, Brita Arver, Richard Rosenquist, Per Karlsson, Kate Nathanson, Susan Domchek, Tim Rebbeck, Anna Jakubowska, Jan Lubinski, Katarzyna Jaworska, Katarzyna Durda, Elżbieta Złowowcka-Perłowska, Ana Osorio, Mercedes Durán, Raquel Andrés, Javier Benítez, Ute Hamann et al. Breast Cancer Research 2012, 14:R33 (20 February 2012) Abstract \| Full text \| PDF \| PubMed
	20.	Research article *Exploring the link between MORF4L1* and risk of breast cancer** Griselda Martrat, Christopher A Maxwell, Emiko Tominaga, Montserrat Porta-de-la-Riva, Núria Bonifaci, Laia Gómez-Baldó, Massimo Bogliolo, Conxi Lázaro, Ignacio Blanco, Joan Brunet, Helena Aguilar, Juana Fernández-Rodríguez, Sheila Seal, Anthony Renwick, Nazneen Rahman, Julia Kühl, Kornelia Neveling, Detlev Schindler, María J Ramírez, María Castellà, Gonzalo Hernández, Douglas F Easton, Susan Peock, Margaret Cook, Clare T Oliver, Debra Frost, Radka Platte, D Gareth Evans, Fiona Lalloo et al. Breast Cancer Research 2011, 13:R40 (5 April 2011) Abstract \| Full text \| PDF \| PubMed
	21.	Short paper DNA-vaccination via tattooing induces stronger humoral and cellular immune responses than intramuscular delivery supported by molecular adjuvants Dana Pokorna, Ivonne Rubio, Martin Müller Genetic Vaccines and Therapy 2008, 6:4 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tattoo delivery of DNA vaccines is cost effective, induces a greater immune response, and is a more efficient delivery strategy for laboratory studies than intramuscular injection.
	22.	Research *Global expression analysis of the brown alga Ectocarpus siliculosus* (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress** Simon M Dittami, Delphine Scornet, Jean-Louis Petit, Béatrice Ségurens, Corinne Da Silva, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, Lieven Sterck, Pierre Rouzé, Yves Van de Peer, J Mark Cock, Catherine Boyen, Thierry Tonon Genome Biology 2009, 10:R66 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
	23.	Research article Serum 25-hydroxyvitamin D and postmenopausal breast cancer survival: a prospective patient cohort study Alina Vrieling, Rebecca Hein, Sascha Abbas, Andreas Schneeweiss, Dieter Flesch-Janys, Jenny Chang-Claude Breast Cancer Research 2011, 13:R74 (26 July 2011) Abstract \| Full text \| PDF \| PubMed
	24.	Question and Answer Video Q&A: Excess body weight and cancer Rudolf Kaaks BMC Medicine 2013, 11:2 (3 January 2013) Full text \| PDF \| PubMed \| Editor’s summary Rudolf Kaaks talks about types of cancers linked to the overweight and obesity epidemic, and advises that although weight loss may decrease the risk of developing cancer, ultimately prevention is better than the cure.
	25.	Research Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer Laura D Nelson, Christian Bender, Heiko Mannsperger, Daniel Buergy, Patryk Kambakamba, Giridhar Mudduluru, Ulrike Korf, Dennis Hughes, Michael W Van Dyke, Heike Allgayer Molecular Cancer 2012, 11:38 (8 June 2012) Abstract \| Full text \| PDF \| PubMed