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Benefits of a factorial design focusing on inclusion of female and male animals in one experiment.

Buch T, Moos K, Ferreira FM, Fröhlich H, Gebhard C, Tresch A.

J Mol Med (Berl). 2019 Jun;97(6):871-877. doi: 10.1007/s00109-019-01774-0. Epub 2019 Apr 13.


Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging.

Failmezger H, Dursun E, Dümcke S, Endele M, Poron D, Schroeder T, Krug A, Tresch A.

Bioinformatics. 2019 Jul 1;35(13):2291-2299. doi: 10.1093/bioinformatics/bty939.


MowJoe: a method for automated-high throughput dissected leaf phenotyping.

Failmezger H, Lempe J, Khadem N, Cartolano M, Tsiantis M, Tresch A.

Plant Methods. 2018 Mar 26;14:27. doi: 10.1186/s13007-018-0290-y. eCollection 2018.


G-EYE advanced colonoscopy for improved polyp detection rates - a randomized tandem pilot study with different endoscopists.

Rey JW, Dümcke S, Haschemi J, Tresch A, Borger D, Kirchner AC, Teubner D, Kiesslich R, Hoffman A.

Z Gastroenterol. 2018 Feb 9. doi: 10.1055/s-0043-124089. [Epub ahead of print]


The Manchester Triage System (MTS): a score for emergency management of patients with acute gastrointestinal bleeding.

Nguyen-Tat M, Cornelius C, Hoffman A, Tresch A, Krey J, Kiesslich R, Galle PR, Rey JW.

Z Gastroenterol. 2018 Feb 9. doi: 10.1055/s-0043-124194. [Epub ahead of print]


Efficient Maximum Likelihood Estimation for Pedigree Data with the Sum-Product Algorithm.

Engelhardt A, Rieger A, Tresch A, Mansmann U.

Hum Hered. 2016;82(1-2):1-15. doi: 10.1159/000475465. Epub 2017 Jul 21.


GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

Stricker G, Engelhardt A, Schulz D, Schmid M, Tresch A, Gagneur J.

Bioinformatics. 2017 Aug 1;33(15):2258-2265. doi: 10.1093/bioinformatics/btx150.


Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues.

Kiefer C, Severing E, Karl R, Bergonzi S, Koch M, Tresch A, Coupland G.

Mol Ecol. 2017 Jul;26(13):3437-3457. doi: 10.1111/mec.14084. Epub 2017 Mar 22.


Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.

Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J.

PLoS One. 2017 Jan 5;12(1):e0169249. doi: 10.1371/journal.pone.0169249. eCollection 2017.


Continuous single cell imaging reveals sequential steps of plasmacytoid dendritic cell development from common dendritic cell progenitors.

Dursun E, Endele M, Musumeci A, Failmezger H, Wang SH, Tresch A, Schroeder T, Krug AB.

Sci Rep. 2016 Nov 28;6:37462. doi: 10.1038/srep37462.


Non-invasive lung cancer diagnosis by detection of GATA6 and NKX2-1 isoforms in exhaled breath condensate.

Mehta A, Cordero J, Dobersch S, Romero-Olmedo AJ, Savai R, Bodner J, Chao CM, Fink L, Guzmán-Díaz E, Singh I, Dobreva G, Rapp UR, Günther S, Ilinskaya ON, Bellusci S, Dammann RH, Braun T, Seeger W, Gattenlöhner S, Tresch A, Günther A, Barreto G.

EMBO Mol Med. 2016 Dec 1;8(12):1380-1389. doi: 10.15252/emmm.201606382. Print 2016 Dec.


TT-seq maps the human transient transcriptome.

Schwalb B, Michel M, Zacher B, Frühauf K, Demel C, Tresch A, Gagneur J, Cramer P.

Science. 2016 Jun 3;352(6290):1225-8. doi: 10.1126/science.aad9841.


T cell-specific inactivation of mouse CD2 by CRISPR/Cas9.

Beil-Wagner J, Dössinger G, Schober K, vom Berg J, Tresch A, Grandl M, Palle P, Mair F, Gerhard M, Becher B, Busch DH, Buch T.

Sci Rep. 2016 Feb 23;6:21377. doi: 10.1038/srep21377.


Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.

Glas J, Dümcke S, Zacher B, Poron D, Gagneur J, Tresch A.

Nucleic Acids Res. 2016 Mar 18;44(5):e44. doi: 10.1093/nar/gkv1184. Epub 2015 Nov 17.


Heterochrony underpins natural variation in Cardamine hirsuta leaf form.

Cartolano M, Pieper B, Lempe J, Tattersall A, Huijser P, Tresch A, Darrah PR, Hay A, Tsiantis M.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10539-44. doi: 10.1073/pnas.1419791112. Epub 2015 Aug 4.


Intraprocedural bowel cleansing with the JetPrep cleansing system improves adenoma detection.

Hoffman A, Murthy S, Pompetzki L, Rey JW, Goetz M, Tresch A, Galle PR, Kiesslich R.

World J Gastroenterol. 2015 Jul 14;21(26):8184-94. doi: 10.3748/wjg.v21.i26.8184.


Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions.

Niederberger T, Failmezger H, Uskat D, Poron D, Glauche I, Scherf N, Roeder I, Schroeder T, Tresch A.

Bioinformatics. 2015 Jun 1;31(11):1816-23. doi: 10.1093/bioinformatics/btv040. Epub 2015 Jan 31.


Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A.

Mol Syst Biol. 2014 Dec 19;10:768. doi: 10.15252/msb.20145654.


High-definition endoscopy with iScan and Lugol's solution for the detection of inflammation in patients with nonerosive reflux disease: histologic evaluation in comparison with a control group.

Rey JW, Deris N, Marquardt JU, Thomaidis T, Moehler M, Kittner JM, Nguyen-Tat M, Dümcke S, Tresch A, Biesterfeld S, Goetz M, Mudter J, Neurath MF, Galle PR, Kiesslich R, Hoffman A.

Dis Esophagus. 2016 Feb-Mar;29(2):185-91. doi: 10.1111/dote.12308. Epub 2014 Dec 17.


A novel test for independence derived from an exact distribution of ith nearest neighbours.

Dümcke S, Mansmann U, Tresch A.

PLoS One. 2014 Oct 2;9(9):e107955. doi: 10.1371/journal.pone.0107955. eCollection 2014.


High definition plus colonoscopy combined with i-scan tone enhancement vs. high definition colonoscopy for colorectal neoplasia: A randomized trial.

Hoffman A, Loth L, Rey JW, Rahman F, Goetz M, Hansen T, Tresch A, Niederberger T, Galle PR, Kiesslich R.

Dig Liver Dis. 2014 Nov;46(11):991-6. doi: 10.1016/j.dld.2014.07.169. Epub 2014 Aug 20.


Efficacy of SpyGlass(TM)-directed biopsy compared to brush cytology in obtaining adequate tissue for diagnosis in patients with biliary strictures.

Rey JW, Hansen T, Dümcke S, Tresch A, Kramer K, Galle PR, Goetz M, Schuchmann M, Kiesslich R, Hoffman A.

World J Gastrointest Endosc. 2014 Apr 16;6(4):137-43. doi: 10.4253/wjge.v6.i4.137.


Selection of higher order regression models in the analysis of multi-factorial transcription data.

Prazeres da Costa O, Hoffman A, Rey JW, Mansmann U, Buch T, Tresch A.

PLoS One. 2014 Mar 21;9(3):e91840. doi: 10.1371/journal.pone.0091840. eCollection 2014.


Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Akman K, Haaf T, Gravina S, Vijg J, Tresch A.

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.


Processing-body movement in Arabidopsis depends on an interaction between myosins and DECAPPING PROTEIN1.

Steffens A, Jaegle B, Tresch A, Hülskamp M, Jakoby M.

Plant Physiol. 2014 Apr;164(4):1879-92. doi: 10.1104/pp.113.233031. Epub 2014 Feb 13.


Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression.

Eser P, Demel C, Maier KC, Schwalb B, Pirkl N, Martin DE, Cramer P, Tresch A.

Mol Syst Biol. 2014 Jan 30;10:717. doi: 10.1002/msb.134886. Print 2014. Erratum in: Mol Syst Biol. 2014;10:726.


Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.

Dümcke S, Bräuer J, Anchang B, Spang R, Beerenwinkel N, Tresch A.

Bioinformatics. 2014 Feb 1;30(3):414-9. doi: 10.1093/bioinformatics/btt696. Epub 2013 Nov 30.


Analysis of interobserver variability for endomicroscopy of the gastrointestinal tract.

Hoffman A, Rey JW, Mueller L, Hansen T, Goetz M, Tresch A, Galle PR, Kiesslich R.

Dig Liver Dis. 2014 Feb;46(2):140-5. doi: 10.1016/j.dld.2013.09.004. Epub 2013 Nov 7.


Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels.

Sun M, Schwalb B, Pirkl N, Maier KC, Schenk A, Failmezger H, Tresch A, Cramer P.

Mol Cell. 2013 Oct 10;52(1):52-62. doi: 10.1016/j.molcel.2013.09.010.


Unsupervised automated high throughput phenotyping of RNAi time-lapse movies.

Failmezger H, Fröhlich H, Tresch A.

BMC Bioinformatics. 2013 Oct 4;14:292. doi: 10.1186/1471-2105-14-292.


Acetic acid compared with i-scan imaging for detecting Barrett's esophagus: a randomized, comparative trial.

Hoffman A, Korczynski O, Tresch A, Hansen T, Rahman F, Goetz M, Murthy S, Galle PR, Kiesslich R.

Gastrointest Endosc. 2014 Jan;79(1):46-54. doi: 10.1016/j.gie.2013.07.013. Epub 2013 Aug 14.


Drosophila miR-277 controls branched-chain amino acid catabolism and affects lifespan.

Esslinger SM, Schwalb B, Helfer S, Michalik KM, Witte H, Maier KC, Martin D, Michalke B, Tresch A, Cramer P, Förstemann K.

RNA Biol. 2013 Jun;10(6):1042-56. doi: 10.4161/rna.24810. Epub 2013 Apr 30.


Semi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.

Failmezger H, Jaegle B, Schrader A, Hülskamp M, Tresch A.

PLoS Comput Biol. 2013 Apr;9(4):e1003029. doi: 10.1371/journal.pcbi.1003029. Epub 2013 Apr 18.


Learning gene network structure from time laps cell imaging in RNAi Knock downs.

Failmezger H, Praveen P, Tresch A, Fröhlich H.

Bioinformatics. 2013 Jun 15;29(12):1534-40. doi: 10.1093/bioinformatics/btt179. Epub 2013 Apr 17.


Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs.

Norousi R, Wickles S, Leidig C, Becker T, Schmid VJ, Beckmann R, Tresch A.

J Struct Biol. 2013 May;182(2):59-66. doi: 10.1016/j.jsb.2013.02.008. Epub 2013 Feb 21.


Global DNA hypomethylation prevents consolidation of differentiation programs and allows reversion to the embryonic stem cell state.

Schmidt CS, Bultmann S, Meilinger D, Zacher B, Tresch A, Maier KC, Peter C, Martin DE, Leonhardt H, Spada F.

PLoS One. 2012;7(12):e52629. doi: 10.1371/journal.pone.0052629. Epub 2012 Dec 27.


Mediator phosphorylation prevents stress response transcription during non-stress conditions.

Miller C, Matic I, Maier KC, Schwalb B, Roether S, Strässer K, Tresch A, Mann M, Cramer P.

J Biol Chem. 2012 Dec 28;287(53):44017-26. doi: 10.1074/jbc.M112.430140. Epub 2012 Nov 7.


One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.

Dümcke S, Seizl M, Etzold S, Pirkl N, Martin DE, Cramer P, Tresch A.

Nucleic Acids Res. 2012 Oct;40(18):8883-92. doi: 10.1093/nar/gks695. Epub 2012 Jul 25.


MC EMiNEM maps the interaction landscape of the Mediator.

Niederberger T, Etzold S, Lidschreiber M, Maier KC, Martin DE, Fröhlich H, Cramer P, Tresch A.

PLoS Comput Biol. 2012;8(6):e1002568. doi: 10.1371/journal.pcbi.1002568. Epub 2012 Jun 21.


Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.

Zacher B, Abnaof K, Gade S, Younesi E, Tresch A, Fröhlich H.

Bioinformatics. 2012 Jul 1;28(13):1714-20. doi: 10.1093/bioinformatics/bts257. Epub 2012 May 4.


Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation.

Sun M, Schwalb B, Schulz D, Pirkl N, Etzold S, Larivière L, Maier KC, Seizl M, Tresch A, Cramer P.

Genome Res. 2012 Jul;22(7):1350-9. doi: 10.1101/gr.130161.111. Epub 2012 Mar 30.


Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA).

Schwalb B, Schulz D, Sun M, Zacher B, Dümcke S, Martin DE, Cramer P, Tresch A.

Bioinformatics. 2012 Mar 15;28(6):884-5. doi: 10.1093/bioinformatics/bts052. Epub 2012 Jan 28.


Selective phenotyping, entropy reduction, and the mastermind game.

Gagneur J, Elze MC, Tresch A.

BMC Bioinformatics. 2011 Oct 20;12:406. doi: 10.1186/1471-2105-12-406.


The functional cancer map: a systems-level synopsis of genetic deregulation in cancer.

Krupp M, Maass T, Marquardt JU, Staib F, Bauer T, König R, Biesterfeld S, Galle PR, Tresch A, Teufel A.

BMC Med Genomics. 2011 Jun 30;4:53. doi: 10.1186/1755-8794-4-53.


Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor.

Zacher B, Torkler P, Tresch A.

Cold Spring Harb Protoc. 2011 May 1;2011(5):pdb.top110. doi: 10.1101/pdb.top110.


Methylation status of imprinted genes and repetitive elements in sperm DNA from infertile males.

El Hajj N, Zechner U, Schneider E, Tresch A, Gromoll J, Hahn T, Schorsch M, Haaf T.

Sex Dev. 2011;5(2):60-9. doi: 10.1159/000323806. Epub 2011 Feb 4.


Learning monotonic genotype-phenotype maps.

Beerenwinkel N, Knupfer P, Tresch A.

Stat Appl Genet Mol Biol. 2011;10:Article 3. doi: 10.2202/1544-6115.1603. Epub 2011 Jan 6.


Processive RNA decay by the exosome: merits of a quantitative Bayesian sampling approach.

Niederberger T, Hartung S, Hopfner KP, Tresch A.

RNA Biol. 2011 Jan-Feb;8(1):55-60. Epub 2011 Jan 1.


Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.

Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, Martin DE, Tresch A, Cramer P.

Mol Syst Biol. 2011 Jan 4;7:458. doi: 10.1038/msb.2010.112.


Fast and efficient dynamic nested effects models.

Fröhlich H, Praveen P, Tresch A.

Bioinformatics. 2011 Jan 15;27(2):238-44. doi: 10.1093/bioinformatics/btq631. Epub 2010 Nov 10.


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