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Testicular expression of long non-coding RNAs is affected by curative GnRHa treatment of cryptorchidism.

Hadziselimovic F, Verkauskas G, Vincel B, Stadler MB.

Basic Clin Androl. 2019 Dec 27;29:18. doi: 10.1186/s12610-019-0097-3. eCollection 2019.


Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2.

Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J.

EMBO J. 2020 Jan 15;39(2):e102591. doi: 10.15252/embj.2019102591. Epub 2019 Nov 29.


Genes located in Y-chromosomal regions important for male fertility show altered transcript levels in cryptorchidism and respond to curative hormone treatment.

Gegenschatz-Schmid K, Verkauskas G, Stadler MB, Hadziselimovic F.

Basic Clin Androl. 2019 Jun 3;29:8. doi: 10.1186/s12610-019-0089-3. eCollection 2019.


Self-organization and symmetry breaking in intestinal organoid development.

Serra D, Mayr U, Boni A, Lukonin I, Rempfler M, Challet Meylan L, Stadler MB, Strnad P, Papasaikas P, Vischi D, Waldt A, Roma G, Liberali P.

Nature. 2019 May;569(7754):66-72. doi: 10.1038/s41586-019-1146-y. Epub 2019 Apr 24.


Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.

Barisic D, Stadler MB, Iurlaro M, Schübeler D.

Nature. 2019 May;569(7754):136-140. doi: 10.1038/s41586-019-1115-5. Epub 2019 Apr 17.


Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3.

Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Geneviève D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Rivière JB, Faivre L, Betschinger J.

Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8. doi: 10.1016/j.stem.2018.11.021. Epub 2018 Dec 27.


PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility.

Hadziselimovic F, Cathomas G, Verkauskas G, Dasevicius D, Stadler MB.

Genes (Basel). 2018 Aug 1;9(8). pii: E391. doi: 10.3390/genes9080391.


A Novel Inducible Mouse Model of MLL-ENL-driven Mixed-lineage Acute Leukemia.

Stavropoulou V, Almosailleakh M, Royo H, Spetz JF, Juge S, Brault L, Kopp P, Iacovino M, Kyba M, Tzankov A, Stadler MB, Cazzaniga G, Peters AHFM, Schwaller J.

Hemasphere. 2018 Jun 12;2(4):e51. doi: 10.1097/HS9.0000000000000051. eCollection 2018 Aug.


The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans.

Fassnacht C, Tocchini C, Kumari P, Gaidatzis D, Stadler MB, Ciosk R.

PLoS Genet. 2018 Mar 26;14(3):e1007252. doi: 10.1371/journal.pgen.1007252. eCollection 2018 Mar.


Cell-autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells.

Bellazzo A, Di Minin G, Valentino E, Sicari D, Torre D, Marchionni L, Serpi F, Stadler MB, Taverna D, Zuccolotto G, Montagner IM, Rosato A, Tonon F, Zennaro C, Agostinis C, Bulla R, Mano M, Del Sal G, Collavin L.

Cell Death Differ. 2018 Jul;25(7):1224-1238. doi: 10.1038/s41418-018-0088-5. Epub 2018 Mar 22.


Curative GnRHa treatment has an unexpected repressive effect on Sertoli cell specific genes.

Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB, Hadziselimovic F.

Basic Clin Androl. 2018 Feb 9;28:2. doi: 10.1186/s12610-018-0067-1. eCollection 2018.


The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells.

Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, Eglinger J, Stadler MB, Giorgetti L, Chao JA.

Mol Cell. 2017 Nov 2;68(3):615-625.e9. doi: 10.1016/j.molcel.2017.09.030. Epub 2017 Oct 19.


DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility.

Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB, Hadziselimovic F.

Genes (Basel). 2017 Oct 11;8(10). pii: E267. doi: 10.3390/genes8100267.


Genes Involved in Long-Term Memory Are Expressed in Testis of Cryptorchid Boys and Respond to GnRHa Treatment.

Hadziselimovic F, Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB.

Cytogenet Genome Res. 2017;152(1):9-15. doi: 10.1159/000477522. Epub 2017 Jul 13.


MicroRNAs-143 and -145 induce epithelial to mesenchymal transition and modulate the expression of junction proteins.

Avalle L, Incarnato D, Savino A, Gai M, Marino F, Pensa S, Barbieri I, Stadler MB, Provero P, Oliviero S, Poli V.

Cell Death Differ. 2017 Oct;24(10):1750-1760. doi: 10.1038/cdd.2017.103. Epub 2017 Jun 23.


pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase.

An J, Ponthier CM, Sack R, Seebacher J, Stadler MB, Donovan KA, Fischer ES.

Nat Commun. 2017 May 22;8:15398. doi: 10.1038/ncomms15398.


GnRHa Treatment of Cryptorchid Boys Affects Genes Involved in Hormonal Control of the HPG Axis and Fertility.

Hadziselimovic F, Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB.

Sex Dev. 2017;11(3):126-136. doi: 10.1159/000471937. Epub 2017 May 16.


An Immune Atlas of Clear Cell Renal Cell Carcinoma.

Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B.

Cell. 2017 May 4;169(4):736-749.e18. doi: 10.1016/j.cell.2017.04.016.


Gene bivalency at Polycomb domains regulates cranial neural crest positional identity.

Minoux M, Holwerda S, Vitobello A, Kitazawa T, Kohler H, Stadler MB, Rijli FM.

Science. 2017 Mar 31;355(6332). pii: eaal2913. doi: 10.1126/science.aal2913.


The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERα.

Britschgi A, Duss S, Kim S, Couto JP, Brinkhaus H, Koren S, De Silva D, Mertz KD, Kaup D, Varga Z, Voshol H, Vissieres A, Leroy C, Roloff T, Stadler MB, Scheel CH, Miraglia LJ, Orth AP, Bonamy GM, Reddy VA, Bentires-Alj M.

Nature. 2017 Jan 26;541(7638):541-545. doi: 10.1038/nature20829. Epub 2017 Jan 9.


XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans.

Miki TS, Carl SH, Stadler MB, Großhans H.

PLoS Genet. 2016 Sep 15;12(9):e1006313. doi: 10.1371/journal.pgen.1006313. eCollection 2016 Sep.


miR-214 and miR-148b Targeting Inhibits Dissemination of Melanoma and Breast Cancer.

Orso F, Quirico L, Virga F, Penna E, Dettori D, Cimino D, Coppo R, Grassi E, Elia AR, Brusa D, Deaglio S, Brizzi MF, Stadler MB, Provero P, Caselle M, Taverna D.

Cancer Res. 2016 Sep 1;76(17):5151-62. doi: 10.1158/0008-5472.CAN-15-1322. Epub 2016 Jun 21.


The methyltransferase Setdb1 is essential for meiosis and mitosis in mouse oocytes and early embryos.

Eymery A, Liu Z, Ozonov EA, Stadler MB, Peters AH.

Development. 2016 Aug 1;143(15):2767-79. doi: 10.1242/dev.132746. Epub 2016 Jun 17.


miR-146a Exerts Differential Effects on Melanoma Growth and Metastatization.

Raimo M, Orso F, Grassi E, Cimino D, Penna E, De Pittà C, Stadler MB, Primo L, Calautti E, Quaglino P, Provero P, Taverna D.

Mol Cancer Res. 2016 Jun;14(6):548-62. doi: 10.1158/1541-7786.MCR-15-0425-T.


Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa.

Royo H, Stadler MB, Peters AHFM.

Dev Cell. 2016 Apr 4;37(1):98-104. doi: 10.1016/j.devcel.2016.03.010.


Erratum: Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation.

Gaidatzis D, Burger L, Florescu M, Stadler MB.

Nat Biotechnol. 2016 Feb;34(2):210. doi: 10.1038/nbt0216-210a. No abstract available.


Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation.

Royo H, Seitz H, ElInati E, Peters AH, Stadler MB, Turner JM.

PLoS Genet. 2015 Oct 28;11(10):e1005461. doi: 10.1371/journal.pgen.1005461. eCollection 2015 Oct.


Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function.

Avrahami D, Li C, Zhang J, Schug J, Avrahami R, Rao S, Stadler MB, Burger L, Schübeler D, Glaser B, Kaestner KH.

Cell Metab. 2015 Oct 6;22(4):619-32. doi: 10.1016/j.cmet.2015.07.025. Epub 2015 Aug 27.


NDR Kinases Are Essential for Somitogenesis and Cardiac Looping during Mouse Embryonic Development.

Schmitz-Rohmer D, Probst S, Yang ZZ, Laurent F, Stadler MB, Zuniga A, Zeller R, Hynx D, Hemmings BA, Hergovich A.

PLoS One. 2015 Aug 25;10(8):e0136566. doi: 10.1371/journal.pone.0136566. eCollection 2015.


PIK3CA(H1047R) induces multipotency and multi-lineage mammary tumours.

Koren S, Reavie L, Couto JP, De Silva D, Stadler MB, Roloff T, Britschgi A, Eichlisberger T, Kohler H, Aina O, Cardiff RD, Bentires-Alj M.

Nature. 2015 Sep 3;525(7567):114-8. doi: 10.1038/nature14669. Epub 2015 Aug 12.


Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation.

Gaidatzis D, Burger L, Florescu M, Stadler MB.

Nat Biotechnol. 2015 Jul;33(7):722-9. doi: 10.1038/nbt.3269. Epub 2015 Jun 22. Erratum in: Nat Biotechnol. 2016 Feb;34(2):210. Florescu, Maria [Deleted].


The Paf1 complex represses small-RNA-mediated epigenetic gene silencing.

Kowalik KM, Shimada Y, Flury V, Stadler MB, Batki J, Bühler M.

Nature. 2015 Apr 9;520(7546):248-252. doi: 10.1038/nature14337. Epub 2015 Mar 25.


Potent degradation of neuronal miRNAs induced by highly complementary targets.

de la Mata M, Gaidatzis D, Vitanescu M, Stadler MB, Wentzel C, Scheiffele P, Filipowicz W, Großhans H.

EMBO Rep. 2015 Apr;16(4):500-11. doi: 10.15252/embr.201540078. Epub 2015 Feb 27.


QuasR: quantification and annotation of short reads in R.

Gaidatzis D, Lerch A, Hahne F, Stadler MB.

Bioinformatics. 2015 Apr 1;31(7):1130-2. doi: 10.1093/bioinformatics/btu781. Epub 2014 Nov 21.


The TRIM-NHL protein LIN-41 controls the onset of developmental plasticity in Caenorhabditis elegans.

Tocchini C, Keusch JJ, Miller SB, Finger S, Gut H, Stadler MB, Ciosk R.

PLoS Genet. 2014 Aug 28;10(8):e1004533. doi: 10.1371/journal.pgen.1004533. eCollection 2014 Aug.


Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide.

Fischer ES, Böhm K, Lydeard JR, Yang H, Stadler MB, Cavadini S, Nagel J, Serluca F, Acker V, Lingaraju GM, Tichkule RB, Schebesta M, Forrester WC, Schirle M, Hassiepen U, Ottl J, Hild M, Beckwith RE, Harper JW, Jenkins JL, Thomä NH.

Nature. 2014 Aug 7;512(7512):49-53. doi: 10.1038/nature13527. Epub 2014 Jul 16.


Tyrosine phosphatase SHP2 increases cell motility in triple-negative breast cancer through the activation of SRC-family kinases.

Sausgruber N, Coissieux MM, Britschgi A, Wyckoff J, Aceto N, Leroy C, Stadler MB, Voshol H, Bonenfant D, Bentires-Alj M.

Oncogene. 2015 Apr 23;34(17):2272-8. doi: 10.1038/onc.2014.170. Epub 2014 Jun 16.


DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

Gaidatzis D, Burger L, Murr R, Lerch A, Dessus-Babus S, Schübeler D, Stadler MB.

PLoS Genet. 2014 Feb 13;10(2):e1004143. doi: 10.1371/journal.pgen.1004143. eCollection 2014 Feb.


Engineering of a conditional allele reveals multiple roles of XRN2 in Caenorhabditis elegans development and substrate specificity in microRNA turnover.

Miki TS, Rüegger S, Gaidatzis D, Stadler MB, Großhans H.

Nucleic Acids Res. 2014 Apr;42(6):4056-67. doi: 10.1093/nar/gkt1418. Epub 2014 Jan 20.


Genome-wide chromatin analysis in mature mouse and human spermatozoa.

Hisano M, Erkek S, Dessus-Babus S, Ramos L, Stadler MB, Peters AH.

Nat Protoc. 2013 Dec;8(12):2449-70. doi: 10.1038/nprot.2013.145. Epub 2013 Nov 14. Erratum in: Nat Protoc. 2014 Mar;9(3):741.


Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J.

BMC Genomics. 2013 Jul 29;14:514. doi: 10.1186/1471-2164-14-514.


Identification of active regulatory regions from DNA methylation data.

Burger L, Gaidatzis D, Schübeler D, Stadler MB.

Nucleic Acids Res. 2013 Sep;41(16):e155. doi: 10.1093/nar/gkt599. Epub 2013 Jul 4.


Analysis of gene expression in wild-type and Notch1 mutant retinal cells by single cell profiling.

Mizeracka K, Trimarchi JM, Stadler MB, Cepko CL.

Dev Dyn. 2013 Oct;242(10):1147-59. doi: 10.1002/dvdy.24006. Epub 2013 Sep 2.


Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa.

Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AH.

Nat Struct Mol Biol. 2013 Jul;20(7):868-75. doi: 10.1038/nsmb.2599. Epub 2013 Jun 16. Erratum in: Nat Struct Mol Biol. 2013 Oct;20(10):1236.


Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D.

Genome Res. 2013 Jan;23(1):60-73. doi: 10.1101/gr.142661.112. Epub 2012 Sep 10.


Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels.

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D.

Mol Syst Biol. 2012 Jul 17;8:593. doi: 10.1038/msb.2012.23.


Gene expression changes within Müller glial cells in retinitis pigmentosa.

Roesch K, Stadler MB, Cepko CL.

Mol Vis. 2012;18:1197-214. Epub 2012 May 9.


Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop.

Aceto N, Sausgruber N, Brinkhaus H, Gaidatzis D, Martiny-Baron G, Mazzarol G, Confalonieri S, Quarto M, Hu G, Balwierz PJ, Pachkov M, Elledge SJ, van Nimwegen E, Stadler MB, Bentires-Alj M.

Nat Med. 2012 Mar 4;18(4):529-37. doi: 10.1038/nm.2645.


Transcriptional code and disease map for adult retinal cell types.

Siegert S, Cabuy E, Scherf BG, Kohler H, Panda S, Le YZ, Fehling HJ, Gaidatzis D, Stadler MB, Roska B.

Nat Neurosci. 2012 Jan 22;15(3):487-95, S1-2. doi: 10.1038/nn.3032.


A chromatin-modifying function of JNK during stem cell differentiation.

Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C.

Nat Genet. 2011 Dec 18;44(1):94-100. doi: 10.1038/ng.1036.


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