• Leesch, F.#, Lorenzo-Orts, L.#, Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A., Matzinger, M., Roitinger, E., Belacic, K., Kandolf, S., Lin, TY., Mechtler, K., Meinhart, A., Haselbach, D.#, Pauli, A.# (2023). A molecular network of conserved factors keeps ribosomes dormant in the egg. Nature. Jan;613(7945):712-720 (bioRxiv: 10.1101/2021.11.03.467131). doi:10.1038/s41586-022-05623-y

  • Bhat, P., Cabrera Quio, LE., Herzog, VA., Fasching, N., Pauli, A.#, Ameres, SL.# (2023). SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. Cell Reports Feb 8;42(2):112070 (bioRxiv: 10.1101/2022.06.01.494399). doi:10.1016/j.celrep.2023.112070


  • Gert, KR., Panser, K., Surm, J., Steinmetz, BS., Schleiffer, A., Moran, Y., Kondrashov, F., Pauli, A. (2022). Distinct features in fish Bouncer proteins determine sperm-egg compatibility. bioRxiv . doi:10.1101/2022.09.01.506233

  • Binner, MI.#, Kogan, A.#, Panser, K., Schleiffer, A., Deneke, VE.#, Pauli, A.# (2022). The sperm protein Spaca6 is essential for fertilization in zebrafish. Frontiers in Cell and Developmental Biology (bioRxiv: 10.1101/2021.11.19.469324). doi:10.3389/fcell.2021.806982

  • Huth, M., Santini, L., Galimberti, E., Ramesmayer, J., Titz-Teixeira, F., Sehlke, R., Oberhuemer, M., Stummer, S., Herzog, V., Garmhausen, M., Romeike, M., Chugunova, A., Leesch, F., Holcik, L., Weipoltshammer, K., Lackner, A., Schoefer, C., von Haeseler, A., Bücker, C., Pauli, A., Ameres, SL., Smith, A., Beyer, A., Leeb, M. (2022). NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes & Development. 1-20 (bioRxiv: 10.1101/2020.07.07.180133). doi:10.1101/gad.347690.120

  • Kellner, MJ.#, Ross, JJ., Schnabl, J., Dekens, MPS., Matl M., Heinen, R., Grishkovskaya, I., Bauer, B., Stadlmann, J., Menéndez-Arias, L., Straw, AD., Fritsche-Polanz, R., Traugott, M., Seitz, T., Zoufaly, A., Födinger, M., Wenisch, C., Zuber, J., Vienna Covid-19 Detection Initiative (VCDI), Pauli, A.#, Brennecke, J.# (2022). A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. Frontiers in Molecular Biosciences. Volume 9 Article 801309 (bioRxiv: 10.1101/2020.06.23.166397). doi:10.3389/fmolb.2022.801309

  • Noda, T., Blaha, A., Fujihara, Y., Gert, KR., Emori, C., Deneke, VE., Oura, S., Panser, K., Lu, Y., Berent, S., Kodani, M., Cabrera-Quio, LE., Pauli, A.#, Ikawa, M.# (2022). Sperm membrane proteins DCST1 and DCST2 are required for the sperm-egg interaction in mice and fish. Communications Biology (bioRxiv: 10.1101/2021.04.18.440256). doi:10.1038/s42003-022-03289-w

  • Stock, J., Kazmar, T., Schlumm, F., Hannezo, E.#, Pauli, A.# (2022). A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. Sep 16;8(37):eadd2488 (bioRxiv: 10.1101/2021.12.16.472981). doi:10.1126/sciadv.add2488

  • Wu, S-HS., Lee, H., Szep-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, J-H., Kim, J., Zhu, Y., Pilat-Carotta, S., Hohenstein, P., Theussl, HC., Pauli, A., Koo, BK. (2022). SCON - a Short Conditional intrON for conditional knockout with one-step zygote injection. Exp Mol Med (bioRxiv 2021: 10.1101/2021.05.09.443220). doi:10.1101/2021.05.09.443220


  • Gert, KR., Cabrera Quio, LE, Novatchkova, M., Guo, Y., Cairns, BR., Pauli, A.# (2021). Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing. bioRxiv . doi:10.1101/2021.11.03.467109

  • Guo, Y., Gert, KR., Lebedeva, S., Potok, ME., Wike, CL., Grow, EJ., Ketting, RF., Pauli, A., Cairns, BR. (2021). Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos. bioRxiv . doi:10.1101/2021.11.03.467172

  • Kellner, MJ.#, Matl, M., Ross, JJ., Schnabl, J., Handler, D., Heinen, R., Schaeffer, J., Hufnagl, P., Indra, A., Dekens, MPS., Fritsche-Polanz, R., Födinger, M., Zuber, J., Vienna Covid-19 Detection Initiative (VCDI), Allerberger, F., Pauli, A.#, Brennecke, J.# (2021). Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics. medRxiv . doi:2021.01.19.21250079

  • Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL. (2021). Systematic refinement of gene annotations by parsing mRNA 3′ end sequencing datasets. Methods in Enzymology, pages 1-19. doi:10.1016/bs.mie.2021.03.016

  • Cabrera-Quio, LE., Schleiffer, A., Mechtler, K., Pauli, A.# (2021). Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition. PlosGenetics 17(2): e1009390 (bioRxiv: 10.1101/2020.03.19.998716). doi:10.1371/journal.pgen.1009390

  • Deneke, VE.#, Pauli, A.# (2021). The Fertilization Enigma: How Sperm and Egg Fuse. Annual Review of Cell and Developmental Biology, 37:1. doi:10.1146/annurev-cellbio-120219-021751

  • Fujihara, Y.#, Herberg, S.#, Blaha, A., Panser, K., Kobayashi, K., Larasati, T., Novatchkova, M., Theussl, HC., Olszanska, O., Ikawa, M.#, Pauli, A.# (2021). The conserved fertility factor SPACA4/Bouncer has divergent modes of action in vertebrate fertilization. PNAS 118 (39) e2108777118 (bioRxiv: 10.1101/2021.05.02.442348). doi:10.1073/pnas.2108777118

  • Stock, J., Pauli, A.# (2021). Self-organized cell migration across scales – from single cell movement to tissue formation. Development, pages 1-13. doi:10.1242/dev.191767


  • Gert, KR., Pauli, A.# (2020). Species-specific mechanisms during fertilization. Current Topics in Developmental Biology, Volume 140, pages 121-144. doi:10.1016/bs.ctdb.2019.10.005


  • Kamieniarz-Gdula, K.#, Gdula, MR., Panser, K., Nojima, T., Monks, J., Wisniewski, JR., Riepsaame, J., Brockdorff, N., Pauli, A.#, Proudfoot, NJ.# (2019). Selective roles of vertebrate PCF11 in premature and full-length transcript termination. Molecular Cell Apr 4;74(1):158-172.e9. doi:10.1016/j.molcel.2019.01.027


  • Herberg, S., Gert, KR., Schleiffer, A., Pauli, A.# (2018). The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization. Science 361(6406), 1029–1033. doi:10.1126/science.aat7113


  • Rogers, KW., Lord, ND., Gagnon, JA., Pauli, A., Zimmerman, S., Aksel, DC., Reyon, D., Tsai, SQ., Joung, JK., Schier, AF. (2017). Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 6, e28785. doi:10.7554/eLife.28785

  • Freyer, L., Hsu, CW., Nowotschin, S., Pauli, A., Ishida, J., Kuba, K., Fukamizu, A., Schier, AF., Hoodless, PA., Dickinson, ME., Hadjantonakis, AK. (2017). Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives. Cell Reports 20, 2116–2130. doi:10.1016/j.celrep.2017.08.014

  • Norris, ML., Pauli, A., Gagnon, JA., Lord, ND., Rogers, KW., Mosimann, C., Zon, LI., Schier, AF. (2017). Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling. eLife 6, e22626. doi:10.7554/eLife.22626



  • Pauli, A.#, Valen, E.#, Schier, AF#. (2015). Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays 37(1):103-12. doi:10.1002/bies.201400103

  • Pauli, A.#, Montague, TG., Lennox, KA., Behlke, MA., Schier, AF#. (2015). Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One 10(10):e0139504. doi:10.1371/journal.pone.0139504 | Pubmed:26436892


  • Pauli, A.#, Norris, ML., Valen, E., Chew, GL., Gagnon, JA., Zimmerman, S., Mitchell, A., Ma, J., Dubrulle, J., Reyon, D., Tsai, SQ., Joung, JK., Saghatelian, A., Schier, AF.# (2014). Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343(6172):1248636. doi:10.1126/science.1248636 | Pubmed:24407481

  • Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, DJ., Pauli, A., Hacohen, N., Schier, AF., Blackshear, PJ., Friedman, N., Amit, I., Regev, A. (2014). High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell 159(7):1698-710. doi:10.1016/j.cell.2014.11.015 | Pubmed:25497548

  • Zhang, Y., Vastenhouw, NL., Feng, J., Fu, K., Wang, C., Ge, Y., Pauli, A., van Hummelen, P., Schier, AF., Liu, XS. (2014). Canonical nucleosome organization at promoters forms during genome activation. Genome Res 24(2):260-6. doi:10.1101/gr.157750.113 | Pubmed:24285721

  • Gagnon, JA., Valen, E., Thyme, SB., Huang, P., Akhmetova, L., Ahkmetova, L., Pauli, A., Montague, TG., Zimmerman, S., Richter, C., Schier, AF. (2014). Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9(5):e98186. doi:10.1371/journal.pone.0098186 | Pubmed:24873830


  • Chew, GL., Pauli, A., Rinn, JL., Regev, A., Schier, AF., Valen, E. (2013). Ribosome profiling reveals resemblance between long non-coding RNAs and 5’ leaders of coding RNAs. Development 140(13):2828-34. doi:10.1242/dev.098343 | Pubmed:23698349


  • Pauli, A.#, Valen, E., Lin, MF., Garber, M., Vastenhouw, NL., Levin, JZ., Fan, L., Sandelin, A., Rinn, JL., Regev, A., Schier, AF#. (2012). Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22(3):577-91. doi:10.1101/gr.133009.111 | Pubmed:22110045


  • Pauli, A.#, Rinn, JL., Schier, AF#. (2011). Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12(2):136-49. doi:10.1038/nrg2904 | Pubmed:21245830

  • Strübbe, G., Popp, C., Schmidt, A., Pauli, A., Ringrose, L., Beisel, C., Paro, R. (2011). Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci U S A 108(14):5572-7. doi:10.1073/pnas.1007916108 | Pubmed:21415365


  • Pauli, A.#, van Bemmel, JG., Oliveira, RA., Itoh, T., Shirahige, K., van Steensel, B., Nasmyth, K#. (2010). A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol 20(20):1787-98. doi:10.1016/j.cub.2010.09.006 | Pubmed:20933422

  • Oliveira, RA., Hamilton, RS., Pauli, A., Davis, I., Nasmyth, K. (2010). Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei. Nat Cell Biol 12(2):185-92. doi:10.1038/ncb2018 | Pubmed:20081838


  • Pauli, A., Althoff, F., Oliveira, RA., Heidmann, S., Schuldiner, O., Lehner, CF., Dickson, BJ., Nasmyth, K. (2008). Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev Cell 14(2):239-51. doi:10.1016/j.devcel.2007.12.009 | Pubmed:18267092


  • Panse, VG., Kressler, D., Pauli, A., Petfalski, E., Gnädig, M., Tollervey, D., Hurt, E. (2006). Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway. Traffic 7(10):1311-21. doi:10.1111/j.1600-0854.2006.00471.x | Pubmed:16978391