2023
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
2022
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
2021
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
2020
- 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
2019
- 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
2018
- 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
2017
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
2016
Chew, GL., Pauli, A., Schier, AF. (2016). Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 7:11663. doi:10.1038/ncomms11663 | Pubmed:27216465
Cabrera-Quio, LE., Herberg, S., Pauli, A.# (2016). Decoding sORF translation - from small proteins to gene regulation. RNA Biol 13(11):1051-1059. doi:10.1080/15476286.2016.1218589 | Pubmed:27653973
2015
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
2014
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
2013
- 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
2012
- 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
2011
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
2010
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
2008
- 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
2006
- 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
2004
- Marhold, J., Rothe, N., Pauli, A., Mund, C., Kuehle, K., Brueckner, B., Lyko, F. (2004). Conservation of DNA methylation in dipteran insects. Insect Mol Biol 13(2):117-23. doi:10.1111/j.0962-1075.2004.00466.x | Pubmed:15056358