• Binner, M.I.#, Kogan, A.#, Panser, K., Schleiffer, A., Deneke, V.E.#, Pauli, A.# (2021). The sperm protein Spaca6 is essential for fertilization in zebrafish. bioRxiv . doi:10.1101/2021.11.19.469324

  • Gert, K.R., Cabrera Quio, L.E, Novatchkova, M., Guo, Y., Cairns, B.R., 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, K.R., Lebedeva, S., Potok, M.E., Wike, C.L., Grow, E.J., Ketting, R.F., Pauli, A., Cairns, B.R. (2021). Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos. bioRxiv . doi:10.1101/2021.11.03.467172

  • Kellner, M.J.#, Matl, M., Ross, J.J., Schnabl, J., Handler, D., Heinen, R., Schaeffer, J., Hufnagl, P., Indra, A., Dekens, M.P.S., 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

  • Leesch, K.F.#, Lorenzo-Orts, L.#, Pribitzer, C., Grishkovskaya, I., Matzinger, M., Roitinger, E., Belacic, K., Kandolf, S., Lin, T.-Y., Mechtler, K., Meinhart, A., Haselbach, D.#, Pauli, A.# (2021). A molecular network of conserved factors keeps ribosomes dormant in the egg. bioRxiv . doi:10.1101/2021.11.03.467131

  • Noda, T., Blaha, A., Fujihara, Y., Gert, K.R., Emori, C., Deneke, V.E., Oura, S., Berent, S., Kodani, M., Panser, K., Cabrera-Quio, L.E., Pauli, A.#, Ikawa. M.# (2021). Sperm membrane proteins DCST1 and DCST2 are required for the sperm-egg fusion process in mice and fish. bioRxiv . doi:10.1101/2021.04.18.440256

  • Wu, S.-H.S., Szep-Bakonyi, R., Lee, H., Colozza, G., Boese, A., Gert, K.R., Hallay, N., Kim, J., Zhu, Y., Pilat-Carotta, S., Theussl, H.-C., Pauli, A., Koo, B.-K. (2021). SCON - A Short Conditional intrON for conditional knockout with one-step zygote injection. bioRxiv . doi:10.1101/2021.05.09.443220

  • Bhat, P., Burkard, T.R., Herzog, V.A., Pauli, A., Ameres, S.L. (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, L.E., 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, V.E.#, 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, H.-C., 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, K.R., 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

  • Galimberti, E., Sehlke, R., Huth, M., Garmhausen, M., Romeike, M., Ramesmayer, J., Stummer, S., Titz-Teixeira, F., Herzog, V., Chugunova, A., Leesch, K.F., Holcik, L., Weipoltshammer, K., Santini, L., Lackner, A., von Haeseler, A., Bücker, C., Pauli, A., Schoefer, C., Ameres, S.L., Smith, A., Beyer, A., Leeb, M. (2020). NMD is required for timely cell fate transitions by fine-tuning gene expression and controlling translation. bioRxiv . doi:10.1101/2020.07.07.180133

  • Kellner, M.J.#, Ross, J.J., Schnabl, J., Dekens, M.P.S., Heinen, R., Grishkovskaya, I., Bauer, B., Stadlmann, J., Menéndez-Arias, L., 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.# (2020). A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. bioRxiv . doi:10.1101/2020.06.23.166397


  • Kamieniarz-Gdula, K.#, Gdula, M.R., Panser, K., Nojima, T., Monks, J., Wisniewski, J.R., Riepsaame, J., Brockdorff, N., Pauli, A.#, Proudfoot, N.J.# (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, K. R., 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