Below is a list of publications from the last few years that have been produced by members of IMB's Core Facilities.

Fröhlich D, Kuo WP, Frühbeis C, Sun JJ, Zehendner CM, Luhmann HJ, Pinto S, Toedling J, Trotter J and Krämer-Albers EM. (2014). Multifaceted effects of oligodendroglial exosomes on neurons: impact on neuronal firing rate, signal transduction and gene regulation. Philos Trans R Soc Lond B Biol Sci, 369: 1652.

Malone CD, Mestdagh C, Akhtar J, Kreim N, Deinhard P, Sachidanandam R, Treisman J and Roignant JY. (2014). The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript. Genes Dev, 28: 1786-1799.

Simonetti M, Agarwal N, Stösser S, Bali KK, Karaulanov E, Kamble R, Pospisilova B, Kurejova M, Birchmeier W, Niehrs C, Heppenstall P and Kuner R (2014). Wnt-Fzd signaling sensitizes peripheral sensory neurons via distinct noncanonical pathways. Neuron, 83: 104-121.

Acebron SP,Karaulanov E, Berger BS, Huang YL, Niehrs C. (2014). Mitotic Wnt signaling promotes protein stabilization and regulates cell size.Mol Cell, 54: 663–674.

de Albuquerque BF, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJ, Klein H, Boxem M and Ketting RF. (2014). PID-1 is a novel factor that operates  during 21U-RNA biogenesis in Caenorhabditis elegans. Genes Dev, 28: 683-688. 

Holloschi A, Ritz S, Schäfer Iand Kioschis P. (2014). Analysis of huntingtin aggregation by fluorescence and FRET microscopy. In: Microscopy: Advances in scientific research and education.Volume 1.Ed. Méndez-Vilas A. Badajoz, Formatex: 217-225.

Schäfer A,Karaulanov E,Stapf U, Döderlein G and Niehrs C. (2013). Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3. Genes Dev, 27: 261-273.

Wiench B, Chen YR, Paulsen M, Hamm R, Schröder S, Yang NS and Efferth T. (2013). Integration of different "-omics" technologies identifies inhibition of the IGF1R-Akt-mTOR signaling cascade involved in the cytotoxic effect of shikonin against leukemia cells. Evid Based Complement Alternat Med, 818709.

Meyer P, Siwo G, Zeevi D, Sharon E,Norel R; DREAM6 Promoter Prediction Consortium: Siwo G, Rider AK, Tan A, Pinapati RS, Emrich S, Chawla N, Ferdig MT, Tung YA, Chen YS, Chen MJ, Chen CY, Knight JM, Sahraeian SM, Esfahani MS, Dreos R, Bucher P, Maier E, Saeys Y, Szczurek E, Mysicková A, Vingron M, Klein H, Kielbasa SM, Knisley J, Bonnell J, Knisley D, Kursa MB, Rudnicki WR, Bhattacharjee M, Sillanpää MJ, Yeung J, Meysman P, Rodríguez AS, Engelen K, Marchal K, Huang Y, Mordelet F, Hartemink A, Pinello L, Yuan GC; Segal E and Stolovitzky G. (2013). Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Research, 23: 1928-1937.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Agius P, Arvey A, Bucher P, Callan CG Jr, Chang CW, Chen CY, Chen YS, Chu YW, Grau J, Grosse I, Jagannathan V, Keilwagen J, Kiełbasa SM, Kinney JB, Klein H, Kursa MB, Lähdesmäki H, Laurila K, Lei C, Leslie C, Linhart C, Murugan A, Myšičková A, Noble WS, Nykter M, Orenstein Y, Posch S, Ruan J, Rudnicki WR, Schmid CD, Shamir R, Sung WK, Vingron M, Zhang Z, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G and Hughes TR. (2013). Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology,  31: 126-134.

Klusch A, Ponce L, Gorzelanny C, Schäfer I, Schneider SW, Ringkamp M, Holloschi A, Schmelz M, Hafner M and Petersen M. (2012). Coculture model of sensory neurites and keratinocytes to investigate functional interaction: Chemical stimulation and atomic force microscope–transmitted mechanical stimulation combined with live-cell imaging. Journal of Investigative Dermatology, 133: 1387-1390.

Abba M, Laufs S, Aghajany M, Korn B, Benner A and Allgayer H. (2012). Look who‘s talking: Deregulated signaling in colorectal cancer. Cancer Genomics Proteomics, 9: 15-25.

Ammerpohl O, Haake A, Pellissery S, Giefing M, Richter J, Balint B, Kulis M, Le J, Bibikova M, Drexler HG, Seifert M, Shaknovic R, Korn B, Küppers R, Martín-Subero JI and Siebert R. (2012). Array-based DNA methylation analysis in classical Hodgkin lymphoma reveals new insights into the mechanisms underlying silencing of B cell-specific genes. Leukemia, 26: 185-188.

Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Berthet ED, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C and Barillot E. (2012). NcPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics, 28: 3147-3149.

Gierl MS, Gruhn WH, von Seggern A, Maltry N and Niehrs C. (2012). GADD45G functions in male sex determination by promoting p38 signaling and sry expression. Dev Cell, 23: 1032-1042.

Spaich S, Will RD, Just S, Spaich S, Kuhn C, Frank D, Berger I, Wiemann S, Korn B, Koegl M, Backs J, Katus HA, Rottbauer W and Frey N. (2012). Fbxl22, a cardiac-enriched F-Box protein, regulates sarcomeric protein turnover and is essential for maintenance of contractile function in vivo. Circ Res, 111: 1504-1516.

Stumm M, Entezami M, Trunk N, Beck M, Löcherbach J, Wegner RD, Hagen A, Becker R, and Hofmann W. (2012). Noninvasive prenatal detection of chromosomal aneuploidies using different next generation sequencing strategies and algorithms. Prenatal Diagnosis, 32: 569-577.

Teufel A, Becker D, Weber SN, Dooley S, Breitkopf-Heinlein K, Maass T, Hochrath K, Krupp M, Marquardt JU, Kolb M, Korn B,Niehrs C, Zimmermann T, Godoy P, Galle PR and Lammert F. (2012). Identification of RARRES1 as a core regulator in liver fibrosis. J Mol Med (Berl), 90: 1439-1447.

Toedling J, Servant N, Ciaudo C, Farinelli L, Voinnet O, Heard E  and Barillot E. (2012). Deep-Sequencing Protocols Influence the Results Obtained in Small-RNA Sequencing. PLoS ONE, 7: e32724.

Wiench B, Eichhorn T, Korn B, Paulsen M and Efferth T. (2012). Utilizing inherent fluorescence of therapeutics to analyze real-time uptake and multi-parametric effector kinetics. Methods, 57: 376-382.

Wiench B, Eichhorn T, Paulsen M and Efferth T. (2012). Shikonin directly targets mitochondria and causes mitochondrial dysfunction in cancer cells. Evid Based Complement Alternat Med, 2012: 726025.

Roepcke S, Stahlberg S, Klein H, Schulz MH, Theobald L, Gohlke S, Vingron M and Walther DJ. (2011). A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ. BMC Genomics, 12: 624.

Kaufmann LT, Gierl MS and Niehrs C. (2011). Gadd45a, Gadd45b and Gadd45g expression during mouse embryonic development. Gene Expr Patterns, 8: 465-470.

Paulsen M*, Legewie S*, Eils R, Karaulanov E and Niehrs C. (2011). Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development. PNAS, 108: 10202-10207. (* indicates equal contribution)

Meder B, Haas J, Keller A, Heid C, Just S, Borries A, Boisguerin V, Scharfenberger-Schmeer M, Staehler P, Beier M, Weichenhan D, Strom TM, Pfeufer A, Korn B, Katus HA and Rottbauer W. (2011). Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circulation-Cardiovascular Genetics, 4: 110-122.

Hallen L, Klein H, Stoschek C, Wehrmeyer S, Nonhoff U, Ralser M, Wilde J, Roehr C, Schweiger MR, Zatloukal K, Vingron M, Lehrach H, Konthur Z and Krobitsch S. (2011). The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. Hum Mol Genet, 20: 104-114.

Corpet A, De Koning L, Toedling J, Savignoni A, Berger F, Lemaitre C, O'Sullivan RJ, Karlseder J, Barillot E, Asselain B, Sastre-Garau X and Almouzni G. (2011). Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer. EMBO Journal, 30: 480-493.

Breitling LP, Yang R, Korn B, Burwinkel B and Brenner H. (2011). Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. American Journal of Human Genetics, 88: 450-457.

Bartholomae CC, Arens A, Balaggan KS, Yanez-Munoz RJ, Montini E, Howe SJ, Paruzynski A, Korn B, Appelt JU, MacNeil A, Cesana D, Abel U, Glimm H, Naldini L, Ali RR, Thrasher AJ, von Kalle C and Schmidt M. (2011). Lentiviral vector integration profiles differ in rodent postmitotic tissues. Molecular Therapy, 19: 703-710.

Ammerpohl O, Haake A, Pellissery S, Giefing M, Richter J, Balint B, Kulis M, Le J, Bibikova M, Drexler HG, Seifert M, Shaknovic R, Korn B, Kuppers R, Martin-Subero JI and Siebert R. (2011). Array-based DNA methylation analysis in classical Hodgkin lymphoma reveals new insights into the mechanisms underlying silencing of B cell-specific genes. Leukemia, 26: 185–188.

Amann PM, Schadendorf D, Owen RW, Korn B, Eichmueller SB and Bazhin AV. (2011). Retinal and retinol are potential regulators of gene expression in the keratinocyte cell line HaCaT. Experimental Dermatology, 20: 373-375.

Will RD, Eden M, Just S, Hansen A, Eder A, Frank D, Kuhn C, Seeger TS, Oehl U, Wiemann S, Korn B, Koegl M, Rottbauer W, Eschenhagen T, Katus HA and Frey N. (2010). Myomasp/LRRC39, a heart- and muscle-specific protein, is a novel component of the sarcomeric M-band and is involved in stretch sensing. Circulation Research, 107: 1253-1264.

Toedling J, Ciaudo C, Voinnet O, Heard E and Barillot E. (2010). girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics, 26: 2902-2903.

Kielbasa SM,Klein H, Roider HG, Vingron M and Bluethgen N. (2010). TransFind-predicting transcriptional regulators for gene sets. Nucleic Acids Research, 38: 275-280.

Groenniger E, Weber B, Heil O, Peters N, Staeb F, Wenck H, Korn B, Winnefeld M and Lyko F. (2010). Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet, 6: e1000971.

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W and Steinmetz LM. (2010). High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biology, 11: R24.

Gloriam DE, Orchard S, Bertinetti D, Bjorling E, Bongcam-Rudloff E, Borrebaeck CAK, Bourbeillon J, Bradbury ARM, de Daruvar A, Duebel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlen M, van der Maarel S, Wingren C, Woollard P, Sherman DJ and Hermjakob H. (2010). A community standard format for the representation of protein affinity reagents. Molecular & Cellular Proteomics, 9: 1-10.

Kawaguchi J, Nichols J, Gierl MS, Faial T and Smith A. (2010). Isolation and propagation of enteric neural crest progenitor cells from mouse embryonic stem cells and embryos. Development, 137: 693-704.

Cruciat CM, Ohkawara B, Acebron SP, Karaulanov E, Reinhard C, Ingelfinger D, Boutros M and Niehrs C. (2010). Requirement of prorenin receptor and vacuolar H(+)-ATPase-mediated acidification for Wnt signaling. Science, 327: 459-463.

Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Duebel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren P-A, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H and Sherman D. (2010). Minimum information about a protein affinity reagent (MIAPAR). Nature Biotechnology, 28: 650-653.

Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD and Wagner W. (2010). DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells. Aging Cell, 9: 54-63.

Waldeck W, Pipkorn R, Korn B, Mueller G, Schick M, Toth K, Wiessler M, Didinger B and Braun K. (2009). Transporter molecules influence the gene expression in HeLa cells. International Journal of Medical Sciences, 6: 18-27.

Sakai M, Vonderheit A, Wei X, Kuttel C and Stemmer A. (2009). A novel biofuel cell harvesting energy from activated human macrophages. Biosens Bioelectron, 25: 68-75.

Riedel A, End C, Christiansen H, Renner M, Bender C, Schmidt S, Korn B, Sueltmann H and Mollenhauer J. (2009). Construction of biosensor systems for determining the pathophysiological potential of carrageenan variants. Molecular Biosystems, 5: 973-979.

Pape UJ, Klein H and Vingron M. (2009). Statistical detection of cooperative transcription factors with similarity adjustment. Bioinformatics, 25: 2103-2109.

Martin-Subero JI, Kreuz M, Bibikova M, Bentink S, Ammerpohl O, Wickham-Garcia E, Rosolowski M, Richter J, Lopez-Serra L, Ballestar E, Berger H, Agirre X, Bernd H-W, Calvanese V, Cogliatti SB, Drexler HG, Fan J-B, Fraga MF, Hansmann ML, Hummel M, Klapper W, Korn B, Kueppers R, MacLeod RAF, Moeller P, Ott G, Pott C, Prosper F, Rosenwald A, Schwaenen C, Schuebeler D, Seifert M, Stuerzenhofecker B, Weber M, Wessendorf S, Loeffler M, Truemper L, Stein H, Spang R, Esteller M, Barker D, Hasenclever D, Siebert R and Mol Mech Malignant Lymphomas N. (2009). New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood, 113: 2488-2497.

Karaulanov E, Boettcher RT, Stannek P, Wu W, Rau M, Ogata S, Cho KWY and Niehrs C. (2009). Unc5B interacts with FLRT3 and Rnd1 to modulate cell adhesion in Xenopus embryos. PLoS One, 4: e5742.

Elias A, Siegelin MD, Steinmueller A, von Deimling A, Lass U, Korn B and Mueller W. (2009). Epigenetic silencing of death receptor 4 mediates tumor necrosis factor-related apoptosis-inducing ligand resistance in gliomas. Clinical Cancer Research, 15: 5457-5465.

Davidson G, Shen J, Huang Y-L, Su Y, Karaulanov E, Bartscherer K, Hassler C, Stannek P, Boutros M and Niehrs C. (2009). Cell cycle control of Wnt receptor activation. Developmental Cell, 17: 788-799.

Bolat O, Zipper P, Wolter M, Korn B and Reifenberger G. (2009). Characterization of differential microRNA expression in medulloblastoma. Acta Neuropathologica, 118: 436-436.

Toedling J and Huber W. (2008). Analyzing ChIP-chip data using bioconductor. PLoS Computational Biology, 4: e1000227.

Rolfs A, Hu Y, Ebert L, Hoffmann D, Zuo D, Ramachandran N, Raphael J, Kelley F, McCarron S, Jepson DA, Shen B, Baqui MMA, Pearlberg J, Taycher E, DeLoughery C, Hoerlein A, Korn B and LaBaer J. (2008). A biomedically enriched collection of 7000 human ORF clones. PLos One, 3: 1-8.          

Konkimalla VB, Blunder M, Korn B, Soomro SA, Jansen H, Change W, Posner GH, Bauer R and Efferth T. (2008). Effect of artemisinins and other endoperoxides on nitric oxide-related signaling pathway in RAW 264.7 mouse macrophage cells. Nitric Oxide-Biology and Chemistry, 19: 184-191.

Fischer JJ, Toedling J, Krueger T, Schueler M, Huber W and Sperling S. (2008). Combinatorial effects of four histone modifications in transcription and differentiation. Genomics, 91: 41-51.

Wildner H*, Gierl MS*, Strehle M, Pla P and Birchmeier C. (2008). Insm1 (IA-1) is a crucial component of the transcriptional network that controls the differentiation of sympatho-adrenergic precursor cells. Development, 135: 473-481. (* indicates equal contribution)

Toedling J, Sklyar O, Krueger T, Fischer JJ,  Sperling S and Huber W. (2007). Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8: 221.

Taussig MJ, Stoevesandt O, Borrebaeck CAK, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Duebel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren P-A, Palcy S, Plueckthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M and Uhlen M. (2007). ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nature Methods, 4: 126-126.

Schneider A, Nowrouzi A, Krenzer N, Schmidt M,Korn B and von Kalle C. (2007). Evaluation of a highly sensitive integration site assay to monitor the influence of vector integration on gene expression. Human Gene Therapy, 18: 1036.

Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W and Sperling S. (2007). Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics, 89, 580-587.

Lottaz C, Toedling J and Spang R. (2007). Annotation-based distance measures for patient subgroup discovery in clinical microarray studies. Bioinformatics, 23: 2256-2264.

Langlais C, Guilleaume B, Wermke N, Scheuermann T, Ebert L, LaBaer J andKorn B. (2007). A systematic approach for testing expression of human full-length proteins in cell-free expression systems. BMC Biotechnology, 7: 64.     

Klein H and Vingron M. (2007). Using transcription factor binding site co-occurrence to predict regulatory regionsGenome Informatics, 18: 109-18.

Kittler R, Surendranath V, Heninger A-K, Slabicki M, Theis M, Putz G, Franke K, Caldarelli A, Grabner H, Kozak K, Wagner J, Rees E, Korn B, Frenzel C, Sachse C, Soennichsen B, Guo J, Schelter J, Burchard J, Linsley PS, Jackson AL, Habermann B and Buchholz F. (2007). Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nature Methods, 4: 337-344.

Jakobs A, Koehnke J, Himstedt F, Funk M, Korn B, Gaestel M and Niedenthal R. (2007). Ubc9 fusion-directed SUMOylation (UFDS): a method to analyze function of protein SUMOylation. Nature Methods, 4: 245-250.

Jakobs A, Himstedt F, Funk M, Korn B, Gaestel M and Niedenthal R. (2007). Ubc9 fusion-directed SUMOylation identifies constitutive and inducible SUMOylationl. Nucleic Acids Research, 35: 1-8.

Toedling J, Rhein P, Ratei R, Karawajew L and Spang R. (2006). Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring. BMC Bioinformatics. 7: 282.  

Gierl MS*, Karoulias N*, Wende H, Strehle M and Birchmeier C. (2006). The zinc-finger factor Insm1 (IA-1) is essential for the development of pancreatic beta cells and intestinal endocrine cells. Genes Dev, 20: 2465-2478. (* indicates equal contribution)   

Mendrzyk F, Korshunov A, Toedt G, Schwarz F, Korn B, Joos S, Hochhaus A, Schoch C, Lichter P and Radlwimmer B. (2006). Isochromosome breakpoints on 17p in medulloblastoma are flanked by different classes of DNA sequence repeats. Genes Chromosomes & Cancer, 45: 401-410.

Kuryshev VY, Vorobyov E, Zink D, Schmitz J, Rozhdestvensky TS, Muenstermann E, Ernst U, Wellenreuther R, Moosmayer P, Bechtel S, Schupp I, Horst J, Korn B, Poustka A and Wiemann S. (2006). An anthropoid-specific segmental duplication on human chromosome 1q22. Genomics, 88: 143-151.

Kirschner-Schwabe R, Lottaz C, Toedling J, Rhein P, Karawajew L, Eckert C, von Stackelberg A, Ungethuem U, Kostka D, Kulozik AE, Ludwig W-D, Henze G, Spang R, Hagemeier C and Seeger K. (2006). Expression of late cell cycle genes and an increased proliferative capacity characterize very early relapse of childhood acute lymphoblastic leukemia. Clinical Cancer Research, 12: 4553-4561.

Karaulanov E, Bottcher RT and Niehrs C. (2006). A role for fibronectin-leucine-rich transmembrane cell-surface proteins in homotypic cell adhesion. EMBO Reports, 7: 283-290.

Huber W, Toedling J and Steinmetz LM. (2006). Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics, 22: 1963-1970.

David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW and Steinmetz LM. (2006). A high-resolution map of transcription in the yeast genome. PNAS, 103: 5320-5325.