Publications

(Only peer-reviewed publications are listed. The more relevant publications are marked in red, group members are marked in bold print)

• 2012

• C. Schmidt, S. Bultmann, D. Meilinger, B. Zacher, A. Tresch, K. Maier, C. Peter, D. Martin, H. Leonhardt1, F. Spada. Global DNA hypomethylation prevents consolidation of differentiation programs and allows reversion to the embryonic stem cell state, submitted.
• A. Johnson, K. Akman, S. Calimport, D. Wuttke, A. Stolzing, J. de Magalhães. The Role of DNA Methylation in Aging, Rejuvenation, and Age-related Disease, Rejuvenation Res. 2012, accepted.
• T. Niederberger, S. Etzold, M. Lidschreiber, K. Maier, D. Martin, H. Fröhlich, P. Cramer, A. Tresch 
  EMiNEM maps the Interaction Landscape of the Mediator, in revision.
• S. Dümcke, M. Seizl, S. Etzold, N. Pirkl, D. Martin, P. Cramer, A. Tresch 
  OneHandClapping: Detection of condition-specific transcription factor interactions from genome-wide gene activity Data, in revision.
• S. Esslinger, B. Schwalb, S. Helfer, K. Maier, D. Martin, B. Michalke, A. Tresch, P. Cramer, K. Förstemann K 
  Drosophila miR-277 controls TOR activity and lifespan via tuning of branched-chain amino acid metabolism, under review.
• B. Zacher, K. Abnaof, S. Gade, E. Younesi, A. Tresch, H. Fröhlich 
  Joint Bayesian Inference of Condition Specific miRNA and Transcription Factor Activities from Combined Gene and microRNA Expression Data, under review.
• R. Norousi, S. Wickles, T. Becker, R. Beckmann, V. Schmid, A. Tresch 
  Automatic post-picking improves particle image detection from Cryo-EM micrographs, under review. [preprint]
• B. Schwalb, D. Schulz, M. Sun, B. Zacher, S. Dümcke, D. Martin, P. Cramer, A. Tresch
  Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). Bioinformatics [abstract, article].
• A. Hoffman, O. Korczynski, A. Tresch, F. Rahman, M. Goetz, P.R. Galle, R. Kiesslich  Acetic acid guided biopsies compared with high definition endoscopy and i-scan guided biopsies in the detection of Barrett`s esophagus - A prospective randomized trial. submitted.
• M. Sun, B. Schwalb, D. Schulz, N. Pirkl, S. Etzold, L. Larivière, K. Maier, M. Seizl, A. Tresch*, P. Cramer* (* co-correspondence)  Comparative Dynamic Transcriptome Analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Research (2012) [abstract, article].
• A. May, M. Linke, N. El Hajj, A. Tresch, A. Daser, K. Reifenberg, T. Haaf, U. Zechner. Ovarian stimulation leads to a loss of maternal Snrpn methylation and downregulation of developmentally important candidate reprogramming genes in individual mouse preimplantation embryos, submitted.
• C. Miller, I. Matic, K. Maier, S. Roether, B. Schwalb, K. Straesser, A. Tresch, M. Mann, P. Cramer. 
  Mediator phosphorylation is involved in stress response. under review.

• 2011

• J. Gagneur, M. Elze, A. Tresch 
  Selective phenotyping, Entropy Reduction and the Mastermind Game. BMC Bioinformatics (2011). [abstract, full text]
• B. Zacher, P. Torkler, A. Tresch 
  Analysis of Affymetrix ChIP-chip data using Starr and Bioconductor. Cold Spring Harbor Protocols (2011) [abstract, full text, preprint]
• C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Dümcke, B. Zacher, A. Mayer, J. Sydow, L. Marcinowski, L. Dölken, D. Martin, A. Tresch*, P. Cramer* (* co-correspondence) 
  Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Molecular Systems Biology 7; Article number 458 (2011) [abstract, article, supplements, online supplements, Cell Leading Edge Select]
• N. Beerenwinkel, P. Knupfer, A. Tresch 
  Learning monotonic genotype-phenotype maps. Statistical Applications in Genetics and Molecular Biology (2011) [abstract, full text]
• N. El Hajj, U. Zechner, E. Schneider, A. Tresch, J. Gromoll, T. Hahn, M. Schorsch, T. Haaf.  
  Methylation Status of Imprinted Genes and Repetitive Elements in Sperm DNA from Infertile Males. , in Sex. Dev. (2011) [abstract, full text]
• T. Niederberger, S. Hartung, K. Hopfner, A. Tresch 
  Processive RNA decay by the Exosome: Merits of a quantitative Bayesian Sampling approach. RNA Biology (2011) [abstract, full text, supplementary material].
• M. Krupp, T. Maass, F. Staib, T. Bauer, S. Biesterfeld, P. Galle, A. Tresch, A. Teufel.  
  The functional cancer map: A systems-level synopsis of dysregulation in cancer. BMC Medical Genomics (2011) [abstract, provisional pdf]

• 2010

• H. Fröhlich, P. Praveen, A. Tresch 
  Fast and efficient dynamic Nested Effects Models. Bioinformatics (2010) [abstract, full text]
• A. Joecker, J. Sonntag, F. Henjes, F. Goetschel, A. Tresch, T. Beissbarth, S. Wiemann, U. Korf.  QuantProReloaded: Quantitative analysis of Microspot Immunoassays. Bioinformatics (2010), [abstract, full text].
• A. Hoffman, F.Sar, M. Goetz, A. Tresch, J. Mudter, S. Biesterfeld, P. Galle, M.F. Neurath, R. Kiesslich.  High definition colonoscopy combined with i-Scan is superior in the detection of colorectal neoplasias compared to standard video colonoscopy – a prospective randomized controlled trial. submitted.
• J. Stritzker, S. Weibel, C. Seubert, A. Götz, A. Tresch, N. van Rooijen, T. Oelschlaeger, P. Hill, I. Gentschevl, A. Szalayl. Enterobacterial tumor colonization in mice depends on bacterial metabolism and macrophages but is independent of chemotaxis and motility. Int J Med Microbiol (2010) [abstract, full text].
• A. Hoffman A, C. Kagel, M. Goetz, A. Tresch, J. Mudter, S. Biesterfeld, P. Galle, M. Neurath, R. Kiesslich.  Recognition and characterization of small colonic neoplasia with high-definition colonoscopy using i-Scan is as precise as chromoendoscopy. Dig Liver Dis. (2010) [abstract, full text].
• E. Schneider, G. Pliushch, N. El Hajj, D. Galetzka, A. Puhl, M. Schorsch, K. Frauenknecht, T. Riepert, A. Tresch, A. Müller, W. Coerdt, U. Zechner, T. Haaf.  Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Research (2010) [abstract, full text].
• S. Hartung, T. Niederberger M. Hartung, A. Tresch, K.P. Hopfner 
  Mechanisms of processivity in RNA degradation by the archaeal RNA exosome. Nucleic Acids Research (2010) Featured Article. [abstract, full text, supplementary material]
• B. Zacher, P.F. Kuan, A. Tresch 
  Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. BMC Bioinformatics (2010).
  [abstract, full text, Bioconductor link, vignette,Bioconductor link, supplements page].
• W. Siggelkow, M. Schmidt, C. Skala, D. Boehm, S. von Forstner, H. Koelbl, A. Tresch. A new algorithm for improving fetal weight estimation from ultrasound data at term. Archives of Gynecology and Obstetrics (2010). [abstract, full text, supplementary material].

• 2009

• A. Buness, M. Ruschhaupt, R. Kuner, A. Tresch. Classification across gene expression microarray studies.
  BMC Bioinformatics (2009), [abstract, full text].
• U. Zechner, G. Pliushch, E. Schneider, N. El Hajj, A. Tresch, Y. Shufaro, L. Seidmann, A. Müller, W. Coerdt, T. Haaf.  Quantitative methylation analysis of developmentally important genes in human pregnancy losses after ART and spontaneous conception. Molecular Human Reproduction (2009), [abstract, full text].
• G. Pliusch , E. Schneider, D. Weise, N. El Hajj, A. Tresch, L. Seidmann, W. Coerdt, A. Müller, U. Zechner, T. Haaf.  Extreme Methylation Values of Imprinted Genes in Human Abortions and Stillbirths. The American Journal of Pathology (2009), [abstract, full text].
• K. Klein, M. Glaser, R. Reisch, A. Tresch, C. Werner, K. Engelhard. Intraoperative Monitoring of Cerebral Microcirculation and Oxygenation - A Feasibility Study using a novel Photo-Spectrometric Laser Doppler Flowmetry. J Neurosurgical Anesthesiology (2009), [abstract, full text].
• N. Radde, N. Bar, A. Tresch. A comparison of likelihoods for dynamic stochastic models of biological networks. Proceedings of the WCSB (2009), [full text].
• A. Hoffman, N. Basting, M. Goetz, A. Tresch, J. Mudter, S. Biesterfeld, P. Galle, M. Neurath, R. Kiesslich. High-definition endoscopy with i-Scan and Lugol's solution for more precise detection of mucosal breaks in patients with reflux symptoms. Endoscopy (2009). [abstract, full text].
• T. Haaf, A. Tresch, A. Lambrecht, B. Grossmann, E. Schwaab, O. Khanaga, T. Hahn, M. Schorsch.  
  Outcome of intracytoplasmatic sperm injection with and without polar body diagnosis of oocytes. Fertil. Steril. (2009), [abstract, full text].
• B. Anchang, M. Sadeh, J. Jacob, A. Tresch, M. Vlad, P. Oefner, R. Spang.  
  Modelling the temporal interplay of molecular signalling and gene expression using dynamic nested effects models. PNAS (2009), [abstract, full text].
• K. Klein, M. Glaser, R. Reisch, A. Tresch, C. Werner, K. Engelhard.  
  Effects of PaCO2 and Sevoflurane on Simultaneous Measurements of Cortical Blood Flow and Oxygen Saturation during Craniotomy. Anesth Analg (2009), [abstract, full text].
• H. Fröhlich, A. Tresch , T. Beissbarth. Nested Effects Models for Learning Signalling Networks from Perturbation Data. Biometrical Journal (2009), [abstract, full text].
• I. Lasarzik, U. Winkelheide, S. Stallmann, C. Orth, A. Schneider, A. Tresch , C. Werner, K. Engelhard  
  Assessment of Postischemic Neurogenesis in Rats with Cerebral Ischemia and Propofol Anesthesia. Anesthesiology (2009), [abstract, full text]

• 2008

• A. May, R. Kirchner, H. Müller, P. Hartmann, N. El Hajj, A. Tresch. , U. Zechner, W. Mann, T. Haaf.  
  Multiplex RT-PCR Expression Analysis of Developmentally Important Genes in Individual Mouse Preimplantation Embryos and Blastomeres.
  Biology of Reproduction (2008) [abstract, full text]
• C. Zeller , H. Fröhlich, A. Tresch.  
  A Bayesian Network View on Nested Effects Models.
  EURASIP Journal on Bioinformatics and Systems Biology (2008) [abstract, full text]
• H. Fröhlich, T. Beißbarth, A. Tresch , D. Kostka, J. Jacob, R. Spang, F. Markowetz. 
  Analyzing Gene Perturbation Screens With Nested Effects Models in R and Bioconductor.
  Bioinformatics Applications Notes (2008) [abstract, full text]
• J. Fassunke, M. Majores, A. Tresch , P. Niehusmann, A. Grote, S. Schoch, A.J. Becker.  
  Array analysis of epilepsy-associated gangliogliomas reveals expression patterns related to aberrant development of neuronal precursors.
  Brain (2008) [abstract, full text]
• U. Korf, F. Henjes, C. Schmidt, A. Tresch, H. Mannsperger, C. Löbke, T. Beissbarth, A. Poustka. Quantitative protein microarrays for time-resolved measurements of protein phosphorylation.
  Proteomics (2008) [abstract, full text]
• U. Korf, F. Henjes, C. Schmidt, A. Tresch, H. Mannsperger, C. Löbke, T. Beissbarth, A. Poustka. Antibody Microarrays as an Experimental Platform for the Analysis of Signal Transduction Networks.
  Advances in Biochemical Engineering/Biotechnology. Springer Berlin/Heidelberg (2008). ISSN 0724-6145 [abstract, full text]
• A. Tresch and F. Markowetz 
  Structure Learning in Nested Effects Models.
  Statistical Applications in Genetics and Molecular Biology (2008) [abstract, full text]
• T. Haaf, A. Hahn, A. Lambrecht, B. Grossmann, E. Schwaab, O. Khanaga, T. Hahn, A. Tresch, M. Schorsch. A high oocyte yield for A high oocyte yield for intracytoplasmic sperm injection treatment is associated with an increased chromosome error rate.
  Fertility and Sterility (2008) [abstract, full text]
• A. Hofmann, U. Ritz, M.H. Hessmann, C. Schmid, A. Tresch, J.D. Rompe, A. Meurer, P.M. Rommens. Cell viability, osteoblast differentiation, and gene expression are altered in human osteoblasts from hypertrophic fracture non-unions.
  Bone (2008) [abstract, full text]

• 2007

• A. Tresch, T. Beissbarth, H. Sueltmann, R. Kuner, A. Poustka, A. Buness.
  Discrimination of direct and indirect effects in a network of regulatory effects.
  Jounal of Computational Biology 14 Vol.9 (2007), 1217–1228. [abstract, full text, Supplements]
• A. Buness, R. Kuner, M. Ruschhaupt, A. Poustka, H. Sueltmann, A. Tresch
  Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer.
  Bioinformatics (2007) 23(17):2273-2280. [abstract, full text]
• A. Tresch. Soluble groups with their centralizer factor groups of bounded rank.
  Journal of  Pure and Applied Algebra 208 (2007), 331-338. [abstract, full text]
• K. U. Klein, K. Engelhard, M. Glaser, R. Reisch, A. Tresch, C. Werner. Monitoring of Cerebral Blood Flow and Oxygen Saturation during Craniotomies.
  J. Neurosurg Anesthesiol 2007; 19(4): 321-322

• Earlier Publications

• A. Tresch, K. Samol. On a conjecture on algebras that are locally embeddable into finite dimensional algebras.
  Illinois Journal of Mathematics 48 (2005), 941-944. [abstract, full text]
• A. Tresch. Hyperabelian groups with finite co-central rank.
  Journal of  Algebra 276 (2005), 103-116. [abstract, full text]
• A. Tresch, Y.P. Sysak. Groups with finite co-central rank.
  Journal of Group Theory 4 (2001), 325-340. [full text]