Publications

Scientific publications

Scientific and academic publications of our team members. For a most recent list, please see our publications in PubMed or pubget.

2016

    • Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O, Ferg M, Strahle U, Sanges R, Müller F. The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.
      Sci Rep. 2016; 6: 33210.Published online 2016 Sep 15. doi: 10.1038/srep33210.

2015

    • Wittmann C, Reischl M, Shah A H, Kronfuss E, Mikut R, Liebel U, Grabher C.
      A Zebrafish Drug-Repurposing Screen Reveals sGC-Dependent and sGC-Independent Pro-Inflammatory Activities of Nitric Oxide.
      PloS one 10 (10): e0137286. doi:10.1371.

2014

      • Wittbrodt JN, Liebel U, Gehrig, J.
        Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing.
        BMC Biotechnology. 2014 14:36, doi:10.1186/1472-6750-14-36.
      • Streichan SJ, Hoerner CR, Schneidt T, Holzer D, Hufnagel L.
        Spatial constraints control cell proliferation in tissues.
        Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5586-91. doi: 10.1073/pnas.1323016111. Epub 2014 Mar 31. PubMed PMID: 24706777.
      • Revenu C, Streichan S, Donà E, Lecaudey V, Hufnagel L, Gilmour D.
        Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation.
        Development. 2014 Mar;141(6):1282-91. doi: 10.1242/dev.101675. PubMed PMID: 24595289.
      • Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van Ijcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B.
        Two independent transcription initiation codes overlap on vertebrate core promoters.
        Nature. 2014 Feb 16. doi:10.1038/nature12974. [Epub ahead of print] PubMed PMID: 24531765.
      • Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE.
        Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer’s Activity.
        PLoS Genet. 2014 Jan;10(1):e1004060. doi:10.1371/journal.pgen.1004060. Epub 2014 Jan 2. PubMed PMID: 4391522.

2013

      • Westhoff JH, Giselbrecht S, Schmidts M, Schindler S, Beales PL, Tönshoff B, Liebel U, Gehrig J.
        Development of an automated imaging pipeline for the analysis of the zebrafish larval kidney.
        PLoS One. 2013 Dec 4;8(12):e82137. doi: 10.1371/journal.pone.0082137. PubMed PMID: 24324758.
      • Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B, Müller F.
        Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
        Genome Res. 2013 Nov;23(11):1938-50. doi: 10.1101/gr.153692.112. Epub 2013 Sep 3. PMID: 24002785.

2012

      • Wittmann C, Reischl M, Shah AH, Mikut R, Liebel U, Grabher C.
        Facilitating drug discovery: an automated high-content inflammation assay in zebrafish.
        J Vis Exp. 2012 Jul 16;(65):e4203. doi: 10.3791/4203. PubMed PMID: 22825322.
      • Krzic U, Gunther S, Saunders TE, Streichan SJ, Hufnagel L.
        Multiview light-sheet microscope for rapid in toto imaging.
        Nat Methods. 2012 Jun 3;9(7):730-3. doi: 10.1038/nmeth.2064. PubMed PMID: 22660739.
      • Kokel D, Rennekamp AJ, Shah AH, Liebel U, Peterson RT.
        Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology.
        Trends Biotechnol. 2012 Aug;30(8):421-5. doi: 10.1016/j.tibtech.2012.05.001. Epub 2012 May 29. Review. PubMed PMID: 22652049.
      • Chiou KK, Hufnagel L, Shraiman BI.
        Mechanical stress inference for two dimensional cell arrays.
        PLoS Comput Biol. 2012;8(5):e1002512. doi: 10.1371/journal.pcbi.1002512. Epub 2012 May 17. PubMed PMID: 22615550.
      • Donauer J, Schreck I, Liebel U, Weiss C.
        Role and interaction of p53, BAX and the stress-activated protein kinases p38 and JNK in benzo(a)pyrene-diolepoxide induced apoptosis in human colon carcinoma cells.
        Arch Toxicol. 2012 Feb;86(2):329-37. doi: 10.1007/s00204-011-0757-3. Epub 2011 Oct 9. PubMed PMID: 21983885.
      • Puliafito A, Hufnagel L, Neveu P, Streichan S, Sigal A, Fygenson DK, Shraiman BI.
        Collective and single cell behavior in epithelial contact inhibition.
        Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):739-44. doi: 10.1073/pnas.1007809109. Epub 2012 Jan 6. PubMed PMID: 22228306.

2011

      • Capoulade J, Wachsmuth M, Hufnagel L, Knop M.
        Quantitative fluorescence imaging of protein diffusion and interaction in living cells.
        Nat Biotechnol. 2011 Aug 7;29(9):835-9. doi: 10.1038/nbt.1928. PubMed PMID: 21822256.
      • Streichan SJ, Valentin G, Gilmour D, Hufnagel L.
        Collective cell migration guided by dynamically maintained gradients.
        Phys Biol. 2011 Aug;8(4):045004. doi: 10.1088/1478-3975/8/4/045004. Epub 2011 Jul 12. PubMed PMID: 21750360.
      • Geyer FL, Ueda E, Liebel U, Grau N, Levkin PA.
        Superhydrophobic-superhydrophilic micropatterning: towards genome-on-a-chip cell microarrays.
        Angew Chem Int Ed Engl. 2011 Aug 29;50(36):8424-7. doi: 10.1002/anie.201102545. Epub 2011 Jul 12. PubMed PMID: 21751312.
      • Peravali R, Gehrig J, Giselbrecht S, Lütjohann DS, Hadzhiev Y, Müller F, Liebel U.
        Automated feature detection and imaging for high-resolution screening of zebrafish embryos.
        Biotechniques. 2011 May;50(5):319-24. doi: 10.2144/000113669. PubMed PMID: 21548893.
      • Lütjohann DS, Shah AH, Christen MP, Richter F, Knese K, Liebel U.
        ‘Sciencenet’–towards a global search and share engine for all scientific knowledge.
        Bioinformatics. 2011 Jun 15;27(12):1734-5. doi: 10.1093/bioinformatics/btr181. Epub 2011 Apr 14. PubMed PMID: 21493657.
      • Graf SF, Hötzel S, Liebel U, Stemmer A, Knapp HF.
        Image-based fluidic sorting system for automated Zebrafish egg sorting into multiwell plates.
        J Lab Autom. 2011 Apr;16(2):105-11. doi: 10.1016/j.jala.2010.11.002. PubMed PMID: 21609691.
      • Conrad C, Wünsche A, Tan TH, Bulkescher J, Sieckmann F, Verissimo F, Edelstein A, Walter T, Liebel U, Pepperkok R, Ellenberg J.
        Micropilot: automation of fluorescence microscopy-based imaging for systems biology.
        Nat Methods. 2011 Mar;8(3):246-9. doi: 10.1038/nmeth.1558. Epub 2011 Jan 23. PubMed PMID: 21258339.

2010

      • d’Alençon CA, Peña OA, Wittmann C, Gallardo VE, Jones RA, Loosli F, Liebel U, Grabher C, Allende ML.
        A high-throughput chemically induced inflammation assay in zebrafish. BMC Biol. 2010 Dec 22;8:151. doi: 10.1186/1741-7007-8-151. PubMed PMID: 21176202.
      • Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V,
        Schmitz MH, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J.
        Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010 Apr 1;464(7289):721-7. doi: 10.1038/nature08869. PubMed PMID: 20360735.

2002-2009

    • Gehrig J, Reischl M, Kalmár E, Ferg M, Hadzhiev Y, Zaucker A, Song C, Schindler S, Liebel U, Müller F.
      Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nat Methods. 2009 Dec;6(12):911-6. doi: 10.1038/nmeth.1396. Epub 2009 Nov 8. PubMed PMID: 19898487.
    • Yang L, Ho NY, Alshut R, Legradi J, Weiss C, Reischl M, Mikut R, Liebel U, Müller F, Strähle U.
      Zebrafish embryos as models for embryotoxic and teratological effects of chemicals. Reprod Toxicol. 2009 Sep;28(2):245-53. doi: 10.1016/j.reprotox.2009.04.013. Epub 2009 May 4. Review. PubMed PMID: 19406227.
    • Michelsen K, Schmid V, Metz J, Heusser K, Liebel U, Schwede T, Spang A, Schwappach B.
      Novel cargo-binding site in the beta and delta subunits of coatomer. J Cell Biol. 2007 Oct 22;179(2):209-17. PubMed PMID: 17954604.
    • Ferg M, Sanges R, Gehrig J, Kiss J, Bauer M, Lovas A, Szabo M, Yang L, Straehle U, Pankratz MJ, Olasz F, Stupka E, Müller F.
      The TATA-binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish. EMBO J. 2007 Sep 5;26(17):3945-56. Epub 2007 Aug 16. PubMed PMID: 17703193.
    • Liebel U, Link W.
      Meeting report: trends and challenges in high content analysis. Biotechnol J. 2007 Aug;2(8):938-40. PubMed PMID: 17680709.
    • Simpson JC, Cetin C, Erfle H, Joggerst B, Liebel U, Ellenberg J, Pepperkok R.
      A RNAi screening platform to identify secretion machinery in mammalian cells. J Biotechnol. 2007 Apr 30;129(2):352-65. Epub 2007 Jan 14. PubMed PMID: 17275941.
    • Hufnagel L, Teleman AA, Rouault H, Cohen SM, Shraiman BI.
      On the mechanism of wing size determination in fly development. Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3835-40. Epub 2007 Feb 28. PubMed PMID: 17360439.
    • Erfle H, Neumann B, Liebel U, Rogers P, Held M, Walter T, Ellenberg J, Pepperkok R.
      Reverse transfection on cell arrays for high content screening microscopy. Nat Protoc. 2007;2(2):392-9. PubMed PMID: 17406600.
    • Hufnagel L, Kreuger J, Cohen SM, Shraiman BI.
      On the role of glypicans in the process of morphogen gradient formation. Dev Biol. 2006 Dec 15;300(2):512-22. Epub 2006 Sep 19. PubMed PMID: 17074313.
    • Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellenberg J.
      High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods. 2006 May;3(5):385-90. PubMed PMID: 16628209.
    • Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S. Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Cancer Res. 2005 Sep 1;65(17):7733-42. PubMed PMID: 16140941.
    • Knauer SK, Moodt S, Berg T, Liebel U, Pepperkok R, Stauber RH.
      Translocation biosensors to study signal-specific nucleo-cytoplasmic transport, protease activity and protein-protein interactions. Traffic. 2005 Jul;6(7):594-606. PubMed PMID: 15941410.
    • Liebel U, Kindler B, Pepperkok R.
      Bioinformatic “Harvester”: a search engine for genome-wide human, mouse, and rat protein resources. Methods Enzymol. 2005;404:19-26. PubMed PMID: 16413254.
    • Pepperkok R, Simpson JC, Rietdorf J, Cetin C, Liebel U, Terjung S, Zimmermann T.
      Imaging platforms for measurement of membrane trafficking. Methods Enzymol. 2005;404:8-18. PubMed PMID: 16413253.
    • Starkuviene V, Liebel U, Simpson JC, Erfle H, Poustka A, Wiemann S, Pepperkok R.
      High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. Genome Res. 2004 Oct;14(10A):1948-56. PubMed PMID: 15466293.
    • Liebel U, Kindler B, Pepperkok R.
      ‘Harvester’: a fast meta search engine of human protein resources. Bioinformatics. 2004 Aug 12;20(12):1962-3. Epub 2004 Feb 26. PubMed PMID: 14988114.
    • Liebel U, Starkuviene V, Erfle H, Simpson JC, Poustka A, Wiemann S, Pepperkok R.
      A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett. 2003 Nov 20;554(3):394-8. PubMed PMID: 14623100.
    • Hufnagel L, Ketzmerick R, Otto MF, Schanz H.
      Eigenstates ignoring regular and chaotic phase-space structures. Phys Rev Lett. 2002 Oct 7;89(15):154101. Epub 2002 Sep 18. PubMed PMID: 12365989.