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MPI-INF D3 Publications

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Your search returned the following 47 documents:

  1. A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
    Juan Sandoval, Jesus Mendez-Gonzales, Ernest Nadal, Guoan Chen, F. Javier Carmona, Sergi Sayols, Sebastian Moran, Holger Heyn, Miguel Vizoso, Antonio Gomez, Montse Sanchez-Cespedes, Yassen Assenov, Fabian Müller, Christoph Bock, Miquel Taron, Josefina Mora, Lucia A. Muscarella, Triantafillos Liloglou, Michael Davies, Marina Pollan, Maria J. Pajares, Wenceslao Torre, Luis M. Montuenga, Elisabeth Brambilla, John K. Field, Luca Roz, Marco Lo Iacono, Giorgio V. Scagliotti, Rafael Rosell, David G. Beer, and Manel Esteller
    Journal of Clinical Oncology 31 (32): 4140-4147, 2013
  2. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
    F. Simmer, A.B. Brinkmann, Yassen Assenov, F. Matarese, A. Kaan, Thomas Lengauer, Christoph Bock, V. Colantuoni, L. Altucci, and H.G. Stunnenberg
    Epigenetics 7 (12): 1355-1367, 2013
  3. Interactive exploration of large genome and epigenome datasets in real time
    Konstantin Halachev, H. Bast, Thomas Lengauer, and Christoph Bock
    Genome Biology 13 (10), 2013
  4. A promoter DNA demethylation landscape of human hematopoietic differentiation
    Vincenzo Calvanese, Agustín F. Fernandez, Rocío G. Urdinguio, Beatriz Suarez-Álvarez, Cristina Mangas, Vicente Pérez-García, Clara Bueno, Rosa Montes, Verónica Ramos-Mejía, Pablo Martínez-Camblor, Cecilia Ferrero, Yassen Assenov, Christoph Bock, Pablo Menendez, Ana Clara Carrera, Carlos Lopez-Larrea, and Mario F. Fraga
    Nucleic Acids Research 40 (1): 116-131, 2012
  5. A DNA methylation fingerprint of 1628 human samples
    Agustin F. Fernandez, Yassen Assenov, Jose Ignacio Martin-Subero, Balazs Balint, Reiner Siebert, Hiroaki Taniguchi, Hiroyuki Yamamoto, Manuel Hidalgo, Aik-Choon Tan, Oliver Galm, Isidre Ferrer, Montse Sanchez-Cespedes, Alberto Villanueva, Javier Carmona, Jose V. Sanchez-Mut, Maria Berdasco, Victor Moreno, Gabriel Capella, David Monk, Esteban Ballestar, Santiago Ropero, Ramon Martinez, Marta Sanchez-Carbayo, Felipe Prosper, Xabier Agirre, Mario F. Fraga, Osvaldo Gran˜a, Luis Perez-Jurado, Jaume Mora, Susana Puig, Jaime Prat, Lina Badimon, Annibale A. Puca, Stephen J. Meltzer, Thomas Lengauer, John Bridgewater, Christoph Bock, and Manel Esteller
    Genome Research 22 (2): 407-419, 2012. Note: PMID: 21613409
  6. Analysing and interpreting DNA methylation data
    Christoph Bock
    Nature Reviews Genetics 13 (10): 705-719, 2012
  7. Analyzing epigenome data in context of genome evolution and human diseases
    Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Mueller, Christoph Bock, and Thomas Lengauer
    In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, 2012, 431-467
  8. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
    Femke Simmer, Arie B. Brinkman, Yassen Assenov, Filomena Matarese, Anita Kaan, Lina Sabatino, Alberto Villanueva, Dori Huertas, Manel Esteller, Thomas Lengauer, Christoph Bock, Vittorio Colantuoni, Lucia Altucci, and Henk G. Stunnenberg
    Epigenetics 7 (12): 1355-1367, 2012
  9. EpiExplorer: live exploration and global analysis of large epigenomic datasets
    K. Halachev, H. Bast, F. Albrecht, Thomas Lengauer, and Christoph Bock
    Genome Biology 13: R96,1-R96,14, 2012
  10. EpiExplorer: live exploration and global analysis of large epigenomic datasets
    Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, and Christoph Bock
    Genome Biology 13 (10): R96,1-R96,14, 2012

  11. Epigenom-Karten erstellen und nutzen
    Christoph Bock and Thomas Lengauer
    BIOspektrum 18 (2): 138-141, 2012
  12. Erosion of dosage compensation impacts human iPSC disease modeling
    Shila Mekhubad, Christoph Bock, A. Sophie de Boer, Evangelos Kiskinis, Alexander Meissner, and Kevin Eggan
    Cell Stem Cell 10 (5): 595-609, 2012
  13. Managing drug resistance in cancer: lessons from HIV therapy
    Thomas Lengauer and Christoph Bock
    Nature Reviews Cancer 12 (7): 494-501, 2012
  14. Managing drug resistance in cancer: lessons from HIV therapy
    Christoph Bock and Thomas Lengauer
    Nature Reviews Cancer 12 (7): 494-501, 2012
  15. RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    Yuanxin Xi, Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, and Wei Li
    Bioinformatics 28 (3): 430-432, 2012
  16. BLUEPRINT to decode the epigenetic signature written in blood
    David Adams, Lucia Altucci, Stylianos E Antonarakis, Juan Ballesteros, Stephan Beck, Adrian Bird, Christoph Bock, Bernhard Boehm, Elias Campo, Andrea Caricasole, Fredrik Dahl, Emmanouil T Dermitzakis, Tariq Enver, Manel Esteller, Xavier Estivill, Anne Ferguson-Smith, Jude Fitzgibbon, Paul Flicek, Claudia Giehl, Thomas Graf, Frank Grosveld, Roderic Guigó, Ivo Gut, Kristian Helin, Jonas Jarvius, Ralf Küppers, Hans Lehrach, Thomas Lengauer, Åke Lernmark, David Leslie, Markus Loeffler, Elizabeth Macintyre, Antonello Mai, Joost H A Martens, Saverio Minucci, Willem H Ouwehand, Pier Giuseppe Pelicci, Hèléne Pendeville, Bo Porse, Vardhman Rakyan, Wolf Reik, Martin Schrappe, Dirk Schübeler, Martin Seifert, Reiner Siebert, David Simmons, Nicole Soranzo, Salvatore Spicuglia, Michael Stratton, Hendrik G Stunnenberg, Amos Tanay, David Torrents, Alfonso Valencia, Edo Vellenga, Martin Vingron, Jörn Walter, and Spike Willcocks
    Nature Biotechnology 30 (3): 224-226, 2012
  17. DNA methylation biomarkers in cancer: Progress towards clinical implementation
    Thomas Mikeska, Christoph Bock, Hongdo Do, and Alexander Dobrovic
    Expert Reviews of Molecular Diagnostics 12 (5): 473-487, 2012
  18. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
    Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter, and Christoph Bock
    Nucleic Acids Research 39 (Suppl. 2): W551-W556, 2011
  19. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J. Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B. Epstein, Bradley E. Bernstein, Thomas Lengauer, Andreas Gnirke, and Alexander Meissner
    PLoS Genetics 17 (12): e1002389,1-e1002389,15, 2011
  20. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
    Sima J. Zacharek, Christine M. Fillmore, Allison N. Lau, David W. Gludish, alan Chou, Joshua W. K. Ho, Raffaella Zamponi, Roi Gazit, Christoph Bock, Natalie Jäger, Zachary D. Smith, Tae-min Kim, Arven H. Saunders, Janice Wong, Joo-Hyeon Lee, Rebecca R. Roach, Derrick J. Rossi, Alex Meissner, Alexander A. Gimelbrant, Peter J. Park, and Carla F. Kim
    Cell Stem Cell 9 (3): 272-280, 2011
  21. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    Hongcang Gu, Zachary D. Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, and Alexander Meissner
    Nature Protocols 6 (4): 468-481, 2011
  22. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
    Christoph Bock, Evangelos Kiskinis, Griet Verstappen, Hongcang Gu, Gabriella Boulting, Zachary D. Smith, Michael Ziller, Gist F. Croft, MacKenzie W. Amoroso, Derek H. Oakley, Andreas Gnirke, Kevin Eggan, and Alexander Meissner
    Cell 144 (3): 439-452, 2011
  23. RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
    Yuanxin Xi, Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, and Wei Li
    Bioinformatics 28 (3): 430-432, 2011
  24. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R. Alan Harris, Ting Wang, Cristian Coarfa, Raman P. Nagarajan, Chibo Hong, Sara L. Downey, Brett E. Johnson, Shaun D. Fouse, Allen Delaney, Yongjun Zhao, Adam Olshen, Tracy Ballinger, Xin Zhou, Kevin J. Forsberg, Junchen Gu, Lorigail Echipare, Heriette O'Geen, Ryan Lister, Mattia Pelizzola, Yuanxin Xi, Charles B. Epstein, Bradley E. Bernstein, R. David Hawkins, Bing Ren, Wen-Yu Chung, Hongcang Gu, Christoph Bock, Andreas Gnirke, Michael Q. Zhang, David Haussler, Joseph R. Ecker, Wei Li, Peggy J. Farnham, Robert a. Waterland, Alexander Meissner, Marco A. Marra, Martin Hirst, Aleksandar Milosavljevic, and Joseph F. Costello
    Nature Biotechnology 28 (10): 1097-1105, 2010
  25. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    Hongcang Gu, Christoph Bock, Tarjei S. Mikkelsen, Natalie Jäger, Zachary D. Smith, Eleni Tomazou, Andreas Gnirke, Eric S. Lander, and Alexander Meissner
    Nature Methods 7 (2): 133-136, 2010
    [PDF: Download: Manuscript - DNA methylation mapping of clinical samples.pdf]
  26. Quantitative comparison of genome-wide DNA methylation mapping technologies
    Christoph Bock, Eleni M. Tomazou, Arie B. Brinkman, Fabian Müller, Femke Simmer, Hongcang Gu, Natalie Jäger, Andreas Gnirke, Hendrik G. Stunnenberg, and Alexander Meissner
    Nature Biotechnology 28 (10): 1106-1114, 2010
    [PDF: Download: Genome-wide mapping of DNA methylation - a quantitative technology comparison.pdf]
  27. Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
    Christoph Bock, Greg Von Kuster, Konstantin Halachev, James Taylor, Anton Nekrutenko, and Thomas Lengauer
    In: Genetic Variation : Methods and Protocols, 2010, 275-296
  28. An exhaustive methode for CpG island annotation
    Lars Feuerbach, Konstantin Halachev, Thomas Lengauer, and Christoph Bock
    In: Special Issue: Abstracts of the 3rd MC-GARD Meeting, Pollock Halls of Residence, 18 Holyrood Park Road, Edinburgh, Scotland, 2009, 146-146, paper no. P77.
  29. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution
    Yingying Zhang, Christian Rohde, Sascha Tierling, Tomasz P. Jurkowski, Christoph Bock, Diana Santacruz, Sergey Ragozin, Richard Reinhardt, Marco Groth, Jörn Walter, and Albert Jeltsch
    PLoS Genetics 5 (3): e1000438:1-e1000438:15, 2009
    [PDF: Download: DNA Methylation Analysis of Chromosome 21 Gene Promoters.pdf]
  30. Epigenetic biomarker development
    Christoph Bock
    Epigenomics 1 (1): 99-110, 2009
    [PDF: Download: Epigenetic biomarker development - postprint.pdf]
  31. Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
    Dirk Moser, Savira Ekawardhani, Robert Kumsta, Haukur Palmason, Christoph Bock, Zoi Athanassiadou, Klaus-Peter Lesch, and Jobst Meyer
    Neuropsychopharmacology 34 (2): 458-467, 2009

  32. MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
    Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, and Christoph Bock
    Genome Biology 10 (10): R105:1-R105:10, 2009
    [PDF: Download: MethMarker - user-friendly design and optimization of gene-specific DNA methylation assays.pdf]
  33. EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
    Christoph Bock, Konstantin Halachev, Joachim Büch, and Thomas Lengauer
    Genome Biology 10: R14.1-R14.14, 2009
    [PDF: Download: EpiGRAPH - User-friendly software for statistical analysis and prediction of (epi-) genomic data.pdf]
  34. Computational epigenetics
    Christoph Bock and Thomas Lengauer
    Bioinformatics 24 (1): 1-10, 2008
    [PDF: Download: Review on Computational Epigenetics - Advanced Access.pdf]
  35. Computational Epigenetics - Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics
    Christoph Bock
    Doctoral dissertation, Universität des Saarlandes, 2008
  36. Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
    Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer
    Nucleic Acids Research 36 (10): e55 p., 2008
    [PDF: Download: Bock et al. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.pdf]
  37. Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
    Martin Kircher, Christoph Bock, and Martina Paulsen
    BMC Genomics 9: 346 p., 2008
    [PDF: Download: Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1-Gtl2 imprinting region.pdf]
  38. IVF: stars may have to consider the risk of stolen parenthood
    Christoph Bock
    Nature 454 (7207): 938 p., 2008
  39. Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung
    Christoph Bock and Thomas Lengauer
    In: Jahrbuch 2007, 2007, 271-277
    [PDF: Download: Reprint - Computational Epigenetics - Bioinformatik für neue Wege in der Krebsforschung.pdf]
  40. Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
    Thomas Mikeska, Christoph Bock, Osman El-Maarri, Anika Hübner, Denise Ehrentraut, Johannes Schramm, Jörg Felsberg, Philip Kahl, Reinhard Büttner, Torsten Pietsch, and Andreas Waha
    Journal of Molecular Diagnostics 9 (3): 368-381, 2007

  41. The human genomic melting map
    Fang Liu, Eivind Tostesen, Jostein K. Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G. Thilly, and Eivind Hovig
    PLoS Computational Biology 3 (5): e93 p., 2007
    [PDF: Download: The Human Genomic Melting Map.pdf]
  42. CpG Island Mapping by Epigenome Prediction
    Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer
    PLoS Computational Biology 3 (6): 1055-1070, 2007
    [PDF: Download: C. Bock et al. (2007) CpG island mapping by epigenome prediction.pdf] [PDF: Download: BockWalter.pdf]
  43. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
    Christoph Bock, Thomas Lengauer, Sabine Reither, Thomas Mikeska, Martina Paulsen, and Jörn Walter
    Bioinformatics 21 (21): 4067-4068, 2005

  44. Analysis and Prediction of Helix Shift Errors in Homology Modeling
    Christoph Bock and Jürgen Hesser
    In Silico Biology 6 (1-2): 131-145, 2006

  45. Bioinformatik: Neue Strategien gegen Krebs
    Christoph Bock
    Deutsches Ärzteblatt PRAXiS 103 (36): 10-11, 2006
  46. Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs
    Christoph Bock, Konstantin Halachev, and Thomas Lengauer
    In: Aktuelle Trends in der Softwareforschung, 2006, 91-99
  47. CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
    Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, and Jörn Walter
    PLoS Genetics 2 (3): 0243-0252, 2006
    [PDF: Download: Bock et al. (2006) - CpG Island Methylation in Human Lymphocytes.pdf]