AG WittbrodtVeröffentlichungen

All of my papers are now open access.

All manuscripts that I sign as corresponding author are pre-print submissions at the point of review.

Aktuelle Pre-Print Submissions

Instantaneous isotropic volumetric imaging of fast biological processes

Nils Wagner, Nils Norlin, Jakob Gierten, Gustavo de Medeiros, Bálint Balázs, Joachim Wittbrodt, Lars Hufnagel, Robert Prevedel
bioRxiv 459370; doi:

Automated high troughput heart rate measurement in medaka and zebrafish embryos under physiological conditions

Jakob Gierten, Christian Pylatiuk, Omar T Hammouda, Christian Schock, Johannes Stegmaier, Joachim Wittbrodt, Jochen Gehrig, Felix Loosli.

bioRxiv 548594; doi:


*Equal contribution

  • Weinhardt V, Shkarin R, Wernet TWittbrodt J, Baumbach T, Loosli F. (2018). Quantitative morphometric analysis of adult teleost fish by X-ray computed tomography. Sci Rep. 8(1):16531.

Abstract: Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.

  • Gutierrez-Triana JA*, Tavhelidse T*, Thumberger T*, Thomas I, Wittbrodt B, Kellner T, Anlas K, Tsingos E, Wittbrodt J. (2018). Efficient single-copy HDR by 5' modified long dsDNA donors. Elife. 7. pii: e39468.
  • Lust K, Wittbrodt J. (2018). Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. eLife. 7. pii: e32319.
  • Inoue D*, Stemmer M, Thumberger T, Ruppert T, Bärenz F, Wittbrodt J*, Gruss OJ*. (2017). Expression of the novel maternal centrosome assembly factor Wdr8 is required for vertebrate embryonic mitoses. Nat Commun. 8:14090. DOI:


  • Tsingos E, Höckendorf B, Sütterlin T, Kirchmaier S, Grabe N, Centanin L, Wittbrodt J. (2019). Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish. Elife. 8. pii: e42646.
  • Eckert P, Knickmeyer MD, Schütz L, Wittbrodt J, Heermann S. (2019). Morphogenesis and axis specification occur in parallel during optic cup and optic fissure formation, differentially modulated by BMP and Wnt. Open Biol. 9(2):180179.
  • Lischik CQ, Adelmann L, Wittbrodt J. (2019) Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One. 14(3):e0212956.

    doi: 10.1371/journal.pone.0212956

    . eCollection 2019.
  • Hammouda OT, Boettger F, Wittbrodt J, Thumberger T. (2019) Swift Large-scale Examination of Directed Genome Editing. PLoS One. 14(3):e0213317.

    doi: 10.1371/journal.pone.0213317

    . eCollection 2019.
  • Kikuchi M, Nishimura T, Saito D, Shigenobu S, Takada R, Gutierrez-Triana JA, Cerdán JLM, Takada S, Wittbrodt J, Suyama M, Tanaka M. (2019). Novel components of germline sex determination acting downstream of foxl3 in medaka. Dev Biol. pii: S0012-1606(18)30516-5.


  • Weinhardt V, Shkarin R, Wernet T, Wittbrodt J, Baumbach T, Loosli F. (2018). Quantitative morphometric analysis of adult teleost fish by X-ray computed tomography. Sci Rep. 8(1):16531.
  • Saturnino AP, Lust K, Wittbrodt J. (2018). Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth. Development. 2018 Oct 18. pii: dev.169698.
    Abstract: Patterning of a continuously growing naive field in the context of a life-long growing organ such as the teleost eye is of highest functional relevance. Intrinsic and extrinsic signals were proposed to regulate lineage specification in progenitors that exit the stem cell niche in the ciliary marginal zone (CMZ). The proper cell type composition arising from those progenitors is prerequisite for retinal function. Our findings in the teleost medaka (Oryzias latipes) uncover that the Notch-Atoh7 axis continuously patterns the CMZ. The complement of cell-types originating from the two juxtaposed progenitors marked by Notch or Atoh7 activity contains all constituents of a retinal column. Modulation of Notch signalling specifically in Atoh7-expressing cells demonstrates the crucial role of this axis in generating the correct cell type proportions. After transiently blocking Notch signalling, retinal patterning and differentiation is reinitiated de novo Taken together we show that Notch activity in the CMZ continuously structures the growing retina by juxtaposing Notch and Atoh7 progenitors giving rise to distinct, complementary lineages, revealing a coupling of de novo patterning and cell-type specification in the respective lineages.

    Article has an altmetric score of 4

  • Roussigné M, Wei L, Tsingos E, Kuchling F, Alkobtawi M, Tsalavouta M, Wittbrodt J, Carl M, Blader P, Wilson SW. (2018). Left/right asymmetric collective migration of parapineal cells is mediated by focal FGF signaling activity in leading cells. Proc Natl Acad Sci U S A. 115(42):E9812-E9821.
    Abstract: The ability of cells to collectively interpret surrounding environmental signals underpins their capacity to coordinate their migration in various contexts, including embryonic development and cancer metastasis. One tractable model for studying collective migration is the parapineal, a left-sided group of neurons that arises from bilaterally positioned precursors that undergo a collective migration to the left side of the brain. In zebrafish, the migration of these cells requires Fgf8 and, in this study, we resolve how FGF signaling correlates with-and impacts the migratory dynamics of-the parapineal cell collective. The temporal and spatial dynamics of an FGF reporter transgene reveal that FGF signaling is activated in only few parapineal cells usually located at the leading edge of the parapineal during its migration. Overexpressing a constitutively active Fgf receptor compromises parapineal migration in wild-type embryos, while it partially restores both parapineal migration and mosaic expression of the FGF reporter transgene in fgf8 -/- mutant embryos. Focal activation of FGF signaling in few parapineal cells is sufficient to promote the migration of the whole parapineal collective. Finally, we show that asymmetric Nodal signaling contributes to the restriction and leftwards bias of FGF pathway activation. Our data indicate that the first overt morphological asymmetry in the zebrafish brain is promoted by FGF pathway activation in cells that lead the collective migration of the parapineal to the left. This study shows that cell-state differences in FGF signaling in front versus rear cells is required to promote migration in a model of FGF-dependent collective migration.
  • Gutierrez-Triana JA*, Tavhelidse T*, Thumberger T*, Thomas I, Wittbrodt B, Kellner T, Anlas K, Tsingos E, Wittbrodt J. (2018). Efficient single-copy HDR by 5' modified long dsDNA donors. Elife. 7. pii: e39468.

    * Equal contribution

    Article has an altmetric score of 82

  • Knickmeyer MD(1)(2), Mateo JL(3), Eckert P(1)(2), Roussa E(1), Rahhal B(1), Zuniga A(4), Krieglstein K(1), Wittbrodt J(5), Heermann S(6). TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism.
  • Inoue D, Wittbrodt J, Gruss OJ. (2018). Loss and Rebirth of the Animal Microtubule Organizing Center: How Maternal Expression of Centrosomal Proteins Cooperates with the Sperm Centriole in Zygotic Centrosome Reformation. Bioessays. 40(4):e1700135.
  • Europe PMC Pubmed
  • Lust K, Wittbrodt J. (2018). Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. eLife. 7. pii: e32319.

    doi: 10.7554/eLife.32319

  • Europe PMC

    Article has an altmetric score of 7


  • Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. (2017). Correction: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One. 12(4):e0176619.
  • [This corrects the article

    doi: 10.1371/journal.pone.0124633

    . ].
  • Pereiro L, Loosli F, Fernández J, Härtel S, Wittbrodt J, Concha ML. (2017). Gastrulation in an annual killifish: Molecular and cellular events during germ layer formation in Austrolebias. 2. Dev Dyn. 2017 Mar 1.
  • Shi D*, Tavhelidse T*, Thumberger T, Wittbrodt J, Greb T. (2017). Bifacial stem cell niches in fish and plants. Curr Opin Genet Dev. 45:28-33.
  • Inoue D*, Stemmer M, Thumberger T, Ruppert T, Bärenz F, Wittbrodt J*, Gruss OJ*. (2017). Expression of the novel maternal centrosome assembly factor Wdr8 is required for vertebrate embryonic mitoses. Nat Commun. 8:14090.

    doi: 10.1038/ncomms14090

    Article has an altmetric score of 3

  • Kirchmaier S, Lust K, Wittbrodt J. (5. Methods Mol Biol. 2017;1472:157-68.

    doi: 10.1007/978-1-4939-6343-0_12

    . ). Generation of DNA Constructs Using the Golden GATEway Cloning Method. 5. Methods Mol Biol. 2017;1472:157-68.

    Article has an altmetric score of 17


  • Gutierrez-Triana JA, Mateo JL, Ibberson D, Ryu S, Wittbrodt J. (2016). iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. Development. 143(22):4272-4278.

    doi: 10.1242/dev.139261

    Article has an altmetric score of 17

  • Nicolás-Pérez M, Kuchling F, Letelier J, Polvillo R, Wittbrodt J, Martínez-Morales JR. (2016). Analysis of cellular behavior and cytoskeletal dynamics reveal a constriction mechanism driving optic cup morphogenesis. Elife. 5. pii: e15797.

    Article has an altmetric score of 26

  • Aghaallaei N, Gruhl F, Schaefer CQ, Wernet T, Weinhardt V, Centanin L, Loosli F, Baumbach T, Wittbrodt J. (2016). Identification, visualization and clonal analysis of intestinal stem cells in fish. Development. 143(19):3470-3480.

    Article has an altmetric score of 8

  • Kromm D, Thumberger T, Wittbrodt J. (2016). An eye on light-sheet microscopy. 4. Methods Cell Biol. 2016;133:105-23.
  • Lust K, Sinn R, Pérez Saturnino A, Centanin L, Wittbrodt J. (2016). De novo neurogenesis by targeted expression of atoh7 to Müller glia cells. Development. 143(11):1874-83.

    Article has an altmetric score of 53

  • Friedrich J, Sorge S, Bujupi F, Eichenlaub MP, Schulz NG, Wittbrodt J, Lohmann I. (2016). Hox Function Is Required for the Development and Maintenance of the Drosophila Feeding Motor Unit. Cell Rep. 14(4):850-60.

    Article has an altmetric score of 70

  • Alonso-Barba JI, Rahman RU, Wittbrodt J, Mateo JL. (2016). MEPD: medaka expression pattern database, genes and more. Nucleic Acids Res. 2016 Jan 4;44(D1):D819-21.

    doi: 10.1093/nar/gkv1029


    Article has an altmetric score of 3


  • Lust K, Wittbrodt J. (2015) Hold your breath. Elife. 2015 Dec 16;4:e12523.

    doi: 10.7554/eLife.12523


    Article has an altmetric score of 5

  • Zhang P, Kratz AS, Salama M, Elabd S, Heinrich T, Wittbrodt J, Blattner C, Davidson G. (2015). Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway. BMC Biotechnol. 15(1):92.
  • Beccari L, Marco-Ferreres R, Tabanera N, Manfredi A, Souren M, Wittbrodt B, Conte I, Wittbrodt J, Bovolenta P. (2015). A trans-regulatory code for the forebrain expression of Six3.2 in the medaka fish. J Biol Chem. 2015 Sep 16. pii: jbc.M115.681254. [

    Article has an altmetric score of 1

  • Bajoghli B, Kuri P, Inoue D, Aghaallaei N, Hanelt M, Thumberger T, Rauzi M, Wittbrodt J, Leptin M. (2015). Noninvasive In Toto Imaging of the Thymus Reveals Heterogeneous Migratory Behavior of Developing T Cells. J Immunol. 195(5):2177-86.

    Article has an altmetric score of 6

  • Auer TO, Xiao T, Bercier V, Gebhardt V, Duroure K, Concordet J-P, Wyart C, Suster M, Kawakami K, Wittbrodt J, Baier H, Del Bene F. (2015). Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3. eLIFE. 4:e05061.

    Article has an altmetric score of 3

  • Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. (2015). CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One. 10(4):e0124633.

    Article has an altmetric score of 16

  • Reinhardt R, Centanin L, Tavhelidse T, Inoue D, Wittbrodt B, Concordet JP, Martinez-Morales JR, Wittbrodt J. (2015). Sox2, Tlx, Gli3, and Her9 converge on Rx2 to define retinal stem cells in vivo. EMBO J. 2015 Apr 23. pii: e201490706.

    Article has an altmetric score of 1

  • Kirchmaier S, Naruse K, Wittbrodt J, Loosli F. (2015). The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes). Genetics. 199(4):905-918.

    Article has an altmetric score of 18

  • Zhang P, Elabd S, Hammer S, Solozobova V, Yan H, Bartel F, Inoue S, Henrich T, Wittbrodt J, Loosli F, Davidson G, Blattner C. (2015). TRIM25 has a dual function in the p53/Mdm2 circuit. 1. Oncogene. 2015 Mar 2.
  • Heermann S, Schütz L, Lemke S, Krieglstein K, Wittbrodt J. (2015). Eye morphogenesis driven by epithelial flow into the optic cup facilitated by modulation of bone morphogenetic protein. eLIFE. 4:e05216.

    Article has an altmetric score of 69

  • Stemmer M, Schuhmacher LN, Foulkes NS, Bertolucci C, Wittbrodt J. (2015). Cavefish eye loss in response to an early block in retinal differentiation progression. Development. 142:743-752.

    Article has an altmetric score of 20


  • Chen Q, Su Y, Wesslowski J, Hagemann AI, Ramialison M, Wittbrodt J, Scholpp S, Davidson G. (2014). Tyrosine phosphorylation of LRP6 by Src and Fer inhibits Wnt/β-catenin signalling. 1. EMBO Rep. 2014 Nov 12. pii: e201439644.

    Article has an altmetric score of 1

  • Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. (2014). Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multi-functional regulator of self-renewal. 2. Genome Res. 2014 Oct 7. pii: gr.173435.114.

    Article has an altmetric score of 9

  • Crespo CL, Vernieri C, Keller PJ, Garrè M, Bender JR, Wittbrodt J, Pardi R. (2014). The PAR complex controls the spatiotemporal dynamics of F-actin and the MTOC in directionally migrating leukocytes. J Cell Sci. 127(20): 4381-4395.

    Article has an altmetric score of 1

  • Sinn R, Peravali R, Heermann S, Wittbrodt J. (2014). Differential responsiveness of distinct retinal domains to Atoh7. 2. Mech Dev. 2014 Aug 21. pii: S0925-4773(14)00038-0.

    Article has an altmetric score of 1

  • Centanin L, Ander JJ, Hoeckendorf B, Lust K, Kellner T, Kraemer I, Urbany C, Hasel E, Harris WA, Simons BD, Wittbrodt J. (2014). Exclusive multipotency and preferential asymmetric divisions in post-embryonic neural stem cells of the fish retina. Development. 141(18):3472-82.

    Article has an altmetric score of 10

  • Mazaheri F, Breus O, Durdu S, Haas P, Wittbrodt J, Gilmour D, Peri F. (2014). Distinct roles for BAI1 and TIM-4 in the engulfment of dying neurons by microglia. Nat Commun. 5:4046.

    Article has an altmetric score of 2

  • Tena JJ, González-Aguilera C, Fernández-Miñán A, Vázquez-Marín J, Parra-Acero H, Cross JW, Rigby PW, Carvajal JJ, Wittbrodt J, Gómez-Skarmeta JL, Martínez-Morales JR. (2014). Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome Res. 24(7):1075-85.

    Article has an altmetric score of 3

  • Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J. (2014). Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish. 1. G3 (Bethesda). 2014 Jan 9. pii: g3.113.008722v1.

    Article has an altmetric score of 16

  • Centanin L, Wittbrodt J. (2014). Retinal neurogenesis. Development. 141(2):241-4.

    Article has an altmetric score of 3


  • Müller C, Maeso I, Wittbrodt J, Martínez-Morales JR. (2013). The medaka mutation tintachina sheds light on the evolution of V-ATPase B subunits in vertebrates. Sci Rep. 3:3217.
  • Kirchmaier S, Lust K, Wittbrodt J. (2013). Golden GATEway Cloning - A Combinatorial Approach to Generate Fusion and Recombination Constructs. PLoS One. 8(10):e76117.
  • Kirchmaier S, Höckendorf B, Möller EK, Bornhorst D, Spitz F, Wittbrodt J. (2013). Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase. Development. 140(20):4287-95.
  • Martynoga B, Mateo JL, Zhou B, Andersen J, Achimastou A, Urbán N, van den Berg D, Georgopoulou D, Hadjur S, Wittbrodt J, Ettwiller L, Piper M, Gronostajski RM, Guillemot F. (2013). Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence. Genes Dev. 27(16):1769-86.
  • Schaafhausen MK, Yang WJ, Centanin L, Wittbrodt J, Bosserhoff A, Fischer A, Schartl M, Meierjohann S. (2013). Tumor angiogenesis is caused by single melanoma cells in a manner dependent on reactive oxygen species and NF-κB. J Cell Sci. 126(Pt 17):3862-72.
  • Bärenz F, Inoue D, Yokoyama H, Tegha-Dunghu J, Freiss S, Draeger S, Mayilo D, Cado I, Merker S, Klinger M, Hoeckendorf B, Pilz S, Hupfeld K, Steinbeisser H, Lorenz H, Ruppert T, Wittbrodt J, Gruss OJ. (2013). The centriolar satellite protein SSX2IP promotes centrosome maturation. J Cell Biol. 202(1):81-95.
  • Herder C, Swiercz JM, Müller C, Peravali R, Quiring R, Offermanns S, Wittbrodt J, Loosli F. (2013). ArhGEF18 regulates RhoA-Rock2 signaling to maintain neuro-epithelial apico-basal polarity and proliferation. Development. 140(13):2787-97.
  • Sinn R, Wittbrodt J. (2013). An eye on eye development. Mech Dev. 130(6-8):347-58.


  • Höckendorf B, Thumberger T, Wittbrodt J. (2012). Quantitative analysis of embryogenesis: a perspective for light sheet microscopy. Dev Cell. 23(6):1111-20.
  • Alten L, Schuster-Gossler K, Eichenlaub MP, Wittbrodt B, Wittbrodt J, Gossler A. (2012). A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. PLoS One. 2012;7(10):e47785.
  • Bogdanovic O, Delfino-Machín M, Nicolás-Pérez M, Gavilán MP, Gago-Rodrigues I, Fernández-Miñán A, Lillo C, Ríos RM, Wittbrodt J, Martínez-Morales JR. (2012). Numb/Numbl-Opo antagonism controls retinal epithelium morphogenesis by regulating integrin endocytosis. Dev Cell. 23(4):782-95.
  • ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassmann T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanari E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature. 489(7414):57-74.

    Article has an altmetric score of 750

  • Schulz S, Chachami G, Kozaczkiewicz L, Winter U, Stankovic-Valentin N, Haas P, Hofmann K, Urlaub H, Ovaa H, Wittbrodt J, Meulmeester E, Melchior F. (2012). Ubiquitin-specific protease-like 1 (USPL1) is a SUMO isopeptidase with essential, non-catalytic functions. EMBO Rep. 13(10):930-8.
  • Harden MV, Pereiro L, Ramialison M, Wittbrodt J, Prasad MK, McCallion AS, Whitlock KE. (2012). Close association of olfactory placode precursors and cranial neural crest cells does not predestine cell mixing. Dev Dyn. 241(7):1143-54.
  • Ramialison M, Reinhardt R, Henrich T, Wittbrodt B, Kellner T, Lowy CM, Wittbrodt J. (2012). Cis-regulatory properties of medaka synexpression groups. Development. 139(5):917-28.


  • Centanin L, Hoeckendorf B, Wittbrodt J. (2011). Fate restriction and multipotency in retinal stem cells. Cell Stem Cell. 9(6):553-62.
  • Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EH. (2011). Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development. Cold Spring Harb Protoc. 2011(10):1235-43.
  • Mongin E, Auer TO, Bourrat F, Gruhl F, Dewar K, Blanchette M, Wittbrodt J, Ettwiller L. (2011). Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One. 2011;6(5):e19747.
  • Inoue D, Wittbrodt J. (2011). One for all--a highly efficient and versatile method for fluorescent immunostaining in fish embryos. PLoS One. 2011;6(5):e19713.
  • Maurya AK, Tan H, Souren M, Wang X, Wittbrodt J, Ingham PW. (2011). Integration of Hedgehog and BMP signalling by the engrailed2a gene in the zebrafish myotome. Development. 138(4):755-65.


  • Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EH. (2010). Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat Methods. 7(8):637-42.
  • Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L. (2010). Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Nat Protoc. 5(2):323-34.


  • Brown KE, Keller PJ, Ramialison M, Rembold M, Stelzer EH, Loosli F, Wittbrodt J. (2009). Nlcam modulates midline convergence during anterior neural plate morphogenesis. Dev Biol. 339(1):14-25.
  • Martinez-Morales JR, Wittbrodt J. (2009). Shaping the vertebrate eye. Curr Opin Genet Dev. 19(5):511-7.
  • Bajoghli B, Ramialison M, Aghaallaei N, Czerny T, Wittbrodt J. (2009). Identification of starmaker-like in medaka as a putative target gene of Pax2 in the otic vesicle. Dev Dyn.238(11):2860-6.
  • Mertes F, Martinez-Morales JR, Nolden T, Spörle R, Wittbrodt J, Lehrach H, Himmelbauer H. (2009). Cloning of mouse ojoplano, a reticular cytoplasmic protein expressed during embryonic development. Gene Expr Patterns.9(8):562-7.
  • Souren M, Martinez-Morales JR, Makri P, Wittbrodt B, Wittbrodt J. (2009). A global survey identifies novel upstream components of the Ath5 neurogenic network. Genome Biol. 2009;10(9):R92.
  • Martinez-Morales JR, Rembold M, Greger K, Simpson JC, Brown KE, Quiring R, Pepperkok R, Martin-Bermudo MD, Himmelbauer H, Wittbrodt J. (2009). ojoplano-mediated basal constriction is essential for optic cup morphogenesis. Development. 136(13):2165-75.
  • Sano S, Takashima S, Niwa H, Yokoi H, Shimada A, Arenz A, Wittbrodt J, Takeda H. (2009). Characterization of teleost Mdga1 using a gene-trap approach in medaka (Oryzias latipes). Genesis. 47(8):505-13.
  • Signore IA, Guerrero N, Loosli F, Colombo A, Villalón A, Wittbrodt J, Concha ML. (2009). Zebrafish and medaka: model organisms for a comparative developmental approach of brain asymmetry. Philos Trans R Soc Lond B Biol Sci. 364(1519):991-1003.


  • Ettwiller L, Budd A, Spitz F, Wittbrodt J. (2008). Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. Genome Biol. 9(12):R172.
  • Grabher C, Wittbrodt J.(2008). Recent advances in meganuclease-and transposon-mediated transgenesis of medaka and zebrafish. Methods Mol Biol. 461:521-39.
  • Keller PJ*, Schmidt AD, Wittbrodt J*, Stelzer EH. (2008). Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science. 322(5904):1065-9. * corresponding authors
  • Ramialison M, Bajoghli B, Aghaallaei N, Ettwiller L, Gaudan S, Wittbrodt B, Czerny T, Wittbrodt J. (2008). Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools. Genome Biol. 9(10):R145.


  • Grabher C, Wittbrodt J. (2007). Meganuclease and transposon mediated transgenesis in medaka. Genome Biol. 8 Suppl 1:S10.
  • Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. (2007). 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res.36(Database issue):D847-53.
  • Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J. (2007). In vivo validation of a computationally predicted conserved Ath5 target gene set. PLoS Genet. 3(9):1661-71.
  • Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. (2007). Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods. 4(7):563-5.
  • Rembold M, Lahiri K, Foulkes NS, Wittbrodt J. (2006). Transgenesis in fish: efficient selection of transgenic fish by co-injection with a fluorescent reporter construct. Nat Protoc. 1(3):1133-9.
  • Martinez-Morales JR, Henrich T, Ramialison M, Wittbrodt J. (2007). New genes in the evolution of the neural crest differentiation program. Genome Biol. 8(3):R36.
  • Steinmetz PR, Zelada-Gonzáles F, Burgtorf C, Wittbrodt J, Arendt D. (2007). Polychaete trunk neuroectoderm converges and extends by mediolateral cell intercalation. Proc Natl Acad Sci U S A. 104(8):2727-32.


  • Yokoi H, Shimada A, Carl M, Takashima S, Kobayashi D, Narita T, Jindo T, Kimura T, Kitagawa T, Kage T, Sawada A, Naruse K, Asakawa S, Shimizu N, Mitani H, Shima A, Tsutsumi M, Hori H, Wittbrodt J, Saga Y, Ishikawa Y, Araki K, Takeda H. (2006). Mutant analyses reveal different functions of fgfr1 in medaka and zebrafish despite conserved ligand-receptor relationships. Dev Biol.304(1):326-37.
  • Grabher C, Cliffe A, Miura K, Hayflick J, Pepperkok R, Rørth P, Wittbrodt J. (2007). Birth and life of tissue macrophages and their migration in embryogenesis and inflammation in medaka. J Leukoc Biol.81(1):263-71.
  • Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH. (2006). Differences in vertebrate microRNA expression. Proc Natl Acad Sci U S A.103(39):14385-9.
  • Rembold M, Loosli F, Adams RJ, Wittbrodt J. (2006). Individual cell migration serves as the driving force for optic vesicle evagination. Science. 313(5790):1130-4.
  • Swindell EC, Bailey TJ, Loosli F, Liu C, Amaya-Manzanares F, Mahon KA, Wittbrodt J, Jamrich M. (2006). Rx-Cre, a tool for inactivation of gene expression in the developing retina. Genesis.44(8):361-3.
  • Nakamura S, Kobayashi D, Aoki Y, Yokoi H, Ebe Y, Wittbrodt J, Tanaka M. (2006). Identification and lineage tracing of two populations of somatic gonadal precursors in medaka embryos. Dev Biol.295(2):678-88.
  • publications before 2006
  • Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. (2005). The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 6(12):R104.
  • Wichmann O, Wittbrodt J, Schultz C. (2006). A small-molecule FRET probe to monitor phospholipase A2 activity in cells and organisms. Angew Chem Int Ed Engl.45(3):508-12.
  • Fritzsch B, Piatigorsky J, Tessmar-Raible K, Jékely G, Guy K, Raible F, Wittbrodt J, Arendt D. (2005). Ancestry of Photic and Mechanic Sensation? Science. 308(5725):1113-1114.
  • Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, Wittbrodt J. (2005). MEPD: a resource for medaka gene expression patterns. Bioinformatics.21(14):3195-7.
  • Del Bene F, Wittbrodt J. (2005). Cell cycle control by homeobox genes in development and disease. Semin Cell Dev Biol. 16(3):449-60.
  • Schäfer M, Rembold M, Wittbrodt J, Schartl M, Winkler C. (2005). Medial floor plate formation in zebrafish consists of two phases and requires trunk-derived Midkine-a. Genes Dev. 19(8):897-902.
  • Martinez-Morales JR, Del Bene F, Nica G, Hammerschmidt M, Bovolenta P, Wittbrodt J. (2005). Differentiation of the vertebrate retina is coordinated by an FGF signaling center. Dev Cell. 8(4):565-74.
  • Grabher C(1), Joly JS, Wittbrodt J. ( 65. Methods Cell Biol. 2004;77:381-401. ). Highly efficient zebrafish transgenesis mediated by the meganuclease I-SceI. 65. Methods Cell Biol. 2004;77:381-401.
  • Schartl M(1), Nanda I, Kondo M, Schmid M, Asakawa S, Sasaki T, Shimizu N, Henrich T, Wittbrodt J, Furutani-Seiki M, Kondoh H, Himmelbauer H, Hong Y, Koga A, Nonaka M, Mitani H, Shima A. ( 66. Methods Cell Biol. 2004;77:173-99. ). Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI). 66. Methods Cell Biol. 2004;77:173-99.
  • Arendt D(1), Tessmar-Raible K, Snyman H, Dorresteijn AW, Wittbrodt J. (2004). Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science. 306(5697):869-71.
  • Grabher C(1), Wittbrodt J. (2004). Efficient activation of gene expression using a heat-shock inducible Gal4/Vp16-UAS system in medaka. BMC Biotechnol. 4:26.
  • Huisken J(1), Swoger J, Del Bene F, Wittbrodt J, Stelzer EH. (2004). Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science. 305(5686):1007-9.
  • Quiring R(1), Wittbrodt B, Henrich T, Ramialison M, Burgtorf C, Lehrach H, Wittbrodt J. (2004). Large-scale expression screening by automated whole-mount in situ hybridization. Mech Dev. 121(7-8):971-6.
  • Rembold M(1), Wittbrodt J. (2004). In vivo time-lapse imaging in medaka--n-heptanol blocks contractile rhythmical movements. Mech Dev. 121(7-8):965-70.
  • Henrich T(1), Ramialison M, Segerdell E, Westerfield M, Furutani-Seiki M, Wittbrodt J, Kondoh H. (2004). GSD: a genetic screen database. Mech Dev. 121(7-8):959-63.
  • Khorasani MZ(1), Hennig S, Imre G, Asakawa S, Palczewski S, Berger A, Hori H, Naruse K, Mitani H, Shima A, Lehrach H, Wittbrodt J, Kondoh H, Shimizu N, Himmelbauer H. (2004). A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing. Mech Dev. 121(7-8):903-13.
  • Watanabe T(1), Asaka S, Kitagawa D, Saito K, Kurashige R, Sasado T, Morinaga C, Suwa H, Niwa K, Henrich T, Hirose Y, Yasuoka A, Yoda H, Deguchi T, Iwanami N, Kunimatsu S, Osakada M, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Wittbrodt J, Abe K, Takahama Y, Takahashi K, Katada T, Nishina H, Kondoh H, Furutani-Seiki M. (2004). Mutations affecting liver development and function in Medaka, Oryzias latipes, screened by multiple criteria. Mech Dev. 121(7-8):791-802.
  • Yoda H(1), Hirose Y, Yasuoka A, Sasado T, Morinaga C, Deguchi T, Henrich T, Iwanami N, Watanabe T, Osakada M, Kunimatsu S, Wittbrodt J, Suwa H, Niwa K, Okamoto Y, Yamanaka T, Kondoh H, Furutani-Seiki M. (2004). Mutations affecting retinotectal axonal pathfinding in Medaka, Oryzias latipes. Mech Dev. 121(7-8):715-28.
  • Loosli F(1), Del Bene F, Quiring R, Rembold M, Martinez-Morales JR, Carl M, Grabher C, Iquel C, Krone A, Wittbrodt B, Winkler S, Sasado T, Morinaga C, Suwa H, Niwa K, Henrich T, Deguchi T, Hirose Y, Iwanami N, Kunimatsu S, Osakada M, Watanabe T, Yasuoka A, Yoda H, Winkler C, Elmasri H, Kondoh H, Furutani-Seiki M, Wittbrodt J. (2004). Mutations affecting retina development in Medaka. Mech Dev. 121(7-8):703-14.
  • Kitagawa D(1), Watanabe T, Saito K, Asaka S, Sasado T, Morinaga C, Suwa H, Niwa K, Yasuoka A, Deguchi T, Yoda H, Hirose Y, Henrich T, Iwanami N, Kunimatsu S, Osakada M, Winkler C, Elmasri H, Wittbrodt J, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Momoi A, Katada T, Nishina H, Kondoh H, Furutani-Seiki M. (2004). Genetic dissection of the formation of the forebrain in Medaka, Oryzias latipes. Mech Dev. 121(7-8):673-85.
  • Elmasri H(1), Winkler C, Liedtke D, Sasado T, Morinaga C, Suwa H, Niwa K, Henrich T, Hirose Y, Yasuoka A, Yoda H, Watanabe T, Deguchi T, Iwanami N, Kunimatsu S, Osakada M, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Wittbrodt J, Abe K, Takahama Y, Takahashi K, Katada T, Nishina H, Kondoh H, Furutani-Seiki M. (2004). Mutations affecting somite formation in the Medaka (Oryzias latipes). Mech Dev. 121(7-8):659-71.
  • Furutani-Seiki M(1), Sasado T, Morinaga C, Suwa H, Niwa K, Yoda H, Deguchi T, Hirose Y, Yasuoka A, Henrich T, Watanabe T, Iwanami N, Kitagawa D, Saito K, Asaka S, Osakada M, Kunimatsu S, Momoi A, Elmasri H, Winkler C, Ramialison M, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Shinomiya A, Kota Y, Yamanaka T, Okamoto Y, Takahashi K, Todo T, Abe K, Takahama Y, Tanaka M, Mitani H, Katada T, Nishina H, Nakajima N, Wittbrodt J, Kondoh H. (2004). A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech Dev. 121(7-8):647-58.
  • Furutani-Seiki M(1), Wittbrodt J. (2004). Medaka and zebrafish, an evolutionary twin study. Mech Dev. 121(7-8):629-37.
  • Poggi L(1), Vottari T, Barsacchi G, Wittbrodt J, Vignali R. (2004). The homeobox gene Xbh1 cooperates with proneural genes to specify ganglion cell fate within the Xenopus neural retina. Development. 131(10):2305-15.
  • Martinez-Morales JR(1), Naruse K, Mitani H, Shima A, Wittbrodt J. (2004). Rapid chromosomal assignment of medaka mutants by bulked segregant analysis. Gene. 329:159-65.
  • Del Bene F(1), Tessmar-Raible K, Wittbrodt J. (2004). Direct interaction of geminin and Six3 in eye development. Nature. 427(6976):745-9.
  • Grabher C(1), Henrich T, Sasado T, Arenz A, Wittbrodt J, Furutani-Seiki M. (2003). Transposon-mediated enhancer trapping in medaka. Gene. 322:57-66.
  • Prud'homme B(1), de Rosa R, Arendt D, Julien JF, Pajaziti R, Dorresteijn AW, Adoutte A, Wittbrodt J, Balavoine G. (2003). Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation. Curr Biol. 13(21):1876-81.
  • Loosli F(1), Staub W, Finger-Baier KC, Ober EA, Verkade H, Wittbrodt J, Baier H. (2003). Loss of eyes in zebrafish caused by mutation of chokh/rx3. EMBO Rep. 4(9):894-9.
  • Hammerschmidt M(1), Kramer C, Nowak M, Herzog W, Wittbrodt J. (2003). Loss of maternal Smad5 in zebrafish embryos affects patterning and morphogenesis of optic primordia. Dev Dyn. 227(1):128-33.
  • Shima A(1), Himmelbauer H, Mitani H, Furutani-Seiki M, Wittbrodt J, Schartl M. (2003). Fish genomes flying. Symposium on Medaka Genomics. EMBO Rep. 4(2):121-5.
  • Henrich T(1), Ramialison M, Quiring R, Wittbrodt B, Furutani-Seiki M, Wittbrodt J, Kondoh H; Medaka Expression Pattern Database. (2003). MEPD: a Medaka gene expression pattern database. Nucleic Acids Res. 31(1):72-4.
  • López-Ríos J(1), Tessmar K, Loosli F, Wittbrodt J, Bovolenta P. (2003). Six3 and Six6 activity is modulated by members of the groucho family. Development. 130(1):185-95.
  • Thermes V(1), Grabher C, Ristoratore F, Bourrat F, Choulika A, Wittbrodt J, Joly JS. (2002). I-SceI meganuclease mediates highly efficient transgenesis in fish. Mech Dev. 118(1-2):91-8.
  • Tessmar K(1), Loosli F, Wittbrodt J. (2002). A screen for co-factors of Six3. Mech Dev. 117(1-2):103-13.
  • Poggi L(1), Carl M, Vignali R, Barsacchi G, Wittbrodt J. (2002). Expression of a medaka (Oryzias latipes) Bar homologue in the differentiating central nervous system and retina. Mech Dev. 114(1-2):193-6.
  • Carl M(1), Loosli F, Wittbrodt J. (2002). Six3 inactivation reveals its essential role for the formation and patterning of the vertebrate eye. Development. 129(17):4057-63.
  • Arendt D(1), Tessmar K, de Campos-Baptista MI, Dorresteijn A, Wittbrodt J. (2002). Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria. Development. 129(5):1143-54.
  • Loosli F(1), Mardon G, Wittbrodt J. (2002). Cloning and expression of medaka Dachshund. Mech Dev. 112(1-2):203-6.
  • Wittbrodt J(1), Shima A, Schartl M. (2002). Medaka--a model organism from the far East. Nat Rev Genet. 3(1):53-64.
  • Loosli F(1), Winkler S, Burgtorf C, Wurmbach E, Ansorge W, Henrich T, Grabher C, Arendt D, Carl M, Krone A, Grzebisz E, Wittbrodt J. (2001). Medaka eyeless is the key factor linking retinal determination and eye growth. Development. 128(20):4035-44.
  • Arendt D(1), Wittbrodt J. (2001). Reconstructing the eyes of Urbilateria. Philos Trans R Soc Lond B Biol Sci. 356(1414):1545-63.
  • Adamska M(1), Wolff A, Kreusler M, Wittbrodt J, Braun T, Bober E. (2001). Five Nkx5 genes show differential expression patterns in anlagen of sensory organs in medaka: insight into the evolution of the gene family. Dev Genes Evol. 211(7):338-49.
  • Loosli F(1), Köster RW, Carl M, Kühnlein R, Henrich T, Mücke M, Krone A, Wittbrodt J. (2000). A genetic screen for mutations affecting embryonic development in medaka fish (Oryzias latipes). Mech Dev. 97(1-2):133-9.
  • Köster RW(1), Kühnlein RP, Wittbrodt J. (2000). Ectopic Sox3 activity elicits sensory placode formation. Mech Dev. 95(1-2):175-87.
  • Henrich T(1), Wittbrodt J. (2000). An in situ hybridization screen for the rapid isolation of differentially expressed genes. Dev Genes Evol. 210(1):28-33.
  • Loosli F(1), Winkler S, Wittbrodt J. (1999). Six3 overexpression initiates the formation of ectopic retina. Genes Dev. 13(6):649-54.
  • Loosli F(1), Köster RW, Carl M, Krone A, Wittbrodt J. (1998). Six3, a medaka homologue of the Drosophila homeobox gene sine oculis is expressed in the anterior embryonic shield and the developing eye. Mech Dev. 74(1-2):159-64.
  • Koster R(1), Stick R, Loosli F, Wittbrodt J. (1997). Medaka spalt acts as a target gene of hedgehog signaling. Development. 124(16):3147-56.
  • Oliver G(1), Loosli F, Köster R, Wittbrodt J, Gruss P. (1996). Ectopic lens induction in fish in response to the murine homeobox gene Six3. Mech Dev. 60(2):233-9.
  • Rissi M(1), Wittbrodt J, Délot E, Naegeli M, Rosa FM. (1995). Zebrafish Radar: a new member of the TGF-beta superfamily defines dorsal regions of the neural plate and the embryonic retina. Mech Dev. 49(3):223-34.
  • Wittbrodt J(1), Rosa FM. (1994). Disruption of mesoderm and axis formation in fish by ectopic expression of activin variants: the role of maternal activin. Genes Dev. 8(12):1448-62.
  • Wittbrodt J(1), Lammers R, Malitschek B, Ullrich A, Schartl M. (1992). The Xmrk receptor tyrosine kinase is activated in Xiphophorus malignant melanoma. EMBO J. 11(11):4239-46.
  • Winkler C(1), Hong Y, Wittbrodt J, Schartl M. (1992). Analysis of heterologous and homologous promoters and enhancers in vitro and in vivo by gene transfer into Japanese medaka (Oryzias latipes) Xiphophorus. Mol Mar Biol Biotechnol. 1(4-5):326-37.
  • Förnzler D(1), Wittbrodt J, Schartl M. (1991). Analysis of an esterase linked to a locus involved in the regulation of the melanoma oncogene and isolation of polymorphic marker sequences in Xiphophorus. Biochem Genet. 29(11-12):509-24.
  • Wiesmüller L(1), Wittbrodt J, Noegel AA, Schleicher M. (1991). Purification and cDNA-derived sequence of adenylosuccinate synthetase from Dictyostelium discoideum. J Biol Chem. 266(4):2480-5.
  • Wittbrodt J, Erhardt W. (1989). An inexpensive and versatile computer-controlled PCR machine using a Peltier Element as a thermoelectric heat pump. Trends Genet. 5(7):202-3.
  • Wittbrodt J(1), Adam D, Malitschek B, Mäueler W, Raulf F, Telling A, Robertson SM, Schartl M. (1989). Novel putative receptor tyrosine kinase encoded by the melanoma-inducing Tu locus in Xiphophorus. Nature. 341(6241):415-21.
  • Adam D(1), Wittbrodt J, Telling A, Schartl M. (1988). RFLP for an EGF-receptor related gene associated with the melanoma oncogene locus of Xiphophorus maculatus. Nucleic Acids Res. 16(14B):7212.