Ausgewählte Publikationen

Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function

Epigenetics & Chromatin

July 2017

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

Nucleic Acids Research

January 2017

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

Immunity

November 2016

reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

Nature Communications

August 2016

Epigenetic dynamics of monocyte-to-macrophage differentiation

Epigenetics & Chromatin

July 2016

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets

Nucleic Acids Research

April 2016

deepTools2: a next generation web server for deep-sequencing data analysis

Nucleic Acids Research Advance Access

April 2016

Standardizing chromatin research: a simple and universal method for ChIP-seq

Nucleic Acids Research Advance Access

December 2015

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

Genome Biology

July 2015

Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling

Nucleic Acids Research

November 2014

Weitere ausgewählte Publikationen

• Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T:
  High-resolution TADs reveal DNA sequences underlying genome organization in flies
  Nature Communications, January 15, 2018
• Schultheiss CS, Laggai S, Czepukojc B, Hussein UK, List M, Barghash A, Tierling S, Hosseini K, Golob-Schwarzl N, Pokorny J, Schulz M, Helms V, Walter J, Zimmer V, Lammert F, Bohle RM, Dandolo L, Haybaeck J, Kiemer AK, Kessler SM:
  The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma
  Cell Stress, 1(1), 2017
• Szilagyi B A, Triebus J, Kressler C, de Almeida M, Tierling S, Durek P, Mardahl M, Szilagyi A, Floess S, Huehn J, Syrbe U, Walter J, Polansky J K, Hamann A:
  Gut memories do not fade: epigenetic regulation of lasting gut homing receptor expression in CD4+ memory T cells
  Mucosal Immunology, February 15, 2017
• Kessler SM, Haybaeck J, Kiemer AK:
  Insulin-like growth factor 2 – the oncogene and its accomplices
  Current Pharmaceutical Design, 22(39), 2016
• Pink M, Ratsch BA, Mardahl M, Durek P, Polansky JK, Karl M, Baumgrass R, Wallner S, Cadenas C, Gianmoena K, Floess S, Chen W, Nordstroem K, Tierling S, Olek S, Walter J, Hamann A, Syrbe U:
  Imprinting of Skin/Inflammation Homing in CD4+ T Cells Is Controlled by DNA Methylation within the Fucosyltransferase 7 Gene
  The Journal of Immunology, October 15, 2016
• Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt MT, Krawczak M, Schreiber S, Rosenstiel P.:
  Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease
  Gut, September 30, 2016
• Dembek A, Laggai S, Kessler SM, Czepukojc B, Simon Y, Kiemer AK, Hoppstädter J:
  Hepatic interleukin-6 production is maintained during endotoxin tolerance and facilitates lipid accumulation
  Immunobiology, June 2016
• Fengler VHI, Macheiner T, Kessler SM, Czepukojc B, Gemperlein K, Müller R, Kiemer AK, Magnes C, Haybaeck J, Lackner C, Sargsyan K:
  Susceptibility of different mouse wild type strains to develop diet-induced NAFLD/AFLD-associated liver disease
  PLoS One, May 11, 2016
• Grothaus K, Kanber D, Gellhaus A, Mikat B, Kolarova J, Siebert R, Wieczorek D, Horsthemke B:
  Genome-wide methylation analysis of retrocopy associated CpG islands and their genomic environment
  Epigenetics, March 28, 2016
• Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, Buonomo SC:
  Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program
  Molecular Cell, January 21, 2016
• Ebert P, Muller F, Nordstrom K, Lengauer T, Schulz MH:
  A general concept for consistent documentation of computational analyses
  Database, June 8, 2015
• Berulava T, Rahmann S, Rademacher K, Klein-Hitpass L, Horsthemke B:
  N6-adenosine methylation in miRNAs
  PLoS One, February 27, 2015
• Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F:
  histoneHMM: Differential analysis of histone modifications with broad genomic footprints
  BMC Bioinformatics, February 22, 2015
• Pink M, Ratsch BA, Mardahl M, Schroter MF, Engelbert D, Triebus J, Hamann A, and Syrbe U:
  Identification of two regulatory elements controlling Fucosyltransferase 7 transcription in murine CD4⁺ T cells
  Molecular Immunology, November 2014
• PLuetke-Eversloh M, Hammer Q, Durek P, Nordstrom K, Gasparoni G, Pink M, Hamann A, Walter J, Chang HD, Dong J, and Romagnani C:
  Human cytomegalovirus drives epigenetic imprinting of the IFNG locus in NKG2C^hi natural killer cells
  PLOS Pathogens, October 15, 2014
• Bulut-Karslioglu A, De La Rosa-Velázquez IA, Ramirez F, Barenboim M, Onishi-Seebacher M, Arand J, Galán C, Winter GE, Engist B, Gerle B, O'Sullivan RJ, Martens JH, Walter J, Manke T, Lachner M, Jenuwein T.:
  Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells
  Molecular Cell, July 17, 2014
• Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J:
  BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.
  Nucleic Acids Research, July 2014
• Luetke-Eversloh M, Cicek BB, Siracusa F, Thom JT, Hamann A, Frischbutter S, Baumgrass R, Chang HD, Thiel A, Dong J, and Romagnani C:
  NK cells gain higher IFN-gamma competence during terminal differentiation
  European Journal of Immunology, July 2014
• Rademacher K, Schröder C, Kanber D, Klein-Hitpass L, Wallner S, Zeschnigk M, Horsthemke B:
  Evolutionary origin and methylation status of human intronic CpG islands that are not present in mouse
  Genome Biology and Evolution, June 12, 2014
• Wallner S, Grandl M, Konovalova T, Sigrüner A, Kopf T, Peer M, Orsó E, Liebisch G, Schmitz G:
  Monocyte to Macrophage Differentiation Goes along with Modulation of the Plasmalogen Pattern through Transcriptional Regulation
  PLoS One, April 8, 2014
• Kessler SM, Simon Y, Gemperlein K, Gianmoena K, Cadenas C, Zimmer V, Pokorny J, Barghash A, Helms V, van Rooijen N, Bohle RM, Lammert F, Hengstler JG, Müller R, Haybaeck J, Kiemer AK:
  Fatty acid elongation in non-alcoholic steatohepatitis and hepatocellular carcinoma
  International Journal of Molecular Science, April 4, 2014
• Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K, Wahl S, Hoffmann C, Qian K, Rönn T, Riess L, Müller-Nurasyid M, Bretschneider N, Skurk T, Horsthemke B, DIAGRAM+ Consortium, Spieler D, Klingenspor M, Seifert M, Kern MJ, Mejhert N, Dahlman I, Hansson O, Hauck SM, Blüher M, Arner P, Groop L, Illig T, Suhre K, Hsu Y, Mellgren G, Hauner H, and Laumen H:
  Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms
  Cell 156, 343–358, January 16, 2014
• Rahmann S, Beygo J, Kanber D, Martin M, Horsthemke B, and Buiting K:
  Amplikyzer: Automated Methylation Analysis of Amplicons from Bisulfite Flowgram Sequencing
  PeerJ PrePrints, November 29, 2013
• Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET:
  Transcriptome and genome sequencing uncovers functional variation in humans
  Nature, September 26, 2013
• Mammana A, Vingron M, and Chung, HR:
  Inferring nucleosome positions with their histone mark annotation from ChIP data
  Bioinformatics, August 26, 2013
• Barann M, Esser D, Klostermeier UC, Lappalainen T, Luzius A, Kuiper JW, Ammerpohl O, Vater I, Siebert R, Amstislavskiy V, Sudbrak R, Lehrach H, Schreiber S, Rosenstiel P:
  Janus--a comprehensive tool investigating the two faces of transcription
  Bioinformatics, July 1, 2013
• Toker A, Engelbert D, Garg G, Polansky JK, Floess S, Miyao T, Baron U, Duber S, Geffers R, Giehr P, Schallenberg S, Kretschmer K, Olek S, Walter J, Weiss S, Hori S, Hamann A, Huehn J:
  Active Demethylation of the Foxp3 Locus Leads to the Generation of Stable Regulatory T Cells within the Thymus
  The Journal of immunology, April 2013, prepublished online February 18, 2013