Publications Andrea Pauli | Scientific Papers Pauli Lab

Márquez-Oller, D., Pauli, A., Fallmann, J. (2026)

BRIDGE: an interactive application for multi-omics data analysis, visualization and integration.

Bioinformatics. 42(7)

Chugunova, A., Schütz, I., Keresztes, H., Kobylinska, R., Novatchkova, M., Lendl, T., Strobl, M., Fallmann, J., Oller, DM., Schutzbier, M., Dürnberger, G., Imre, R., Roitinger, E., Kidd, P., Pasierbek, P., Cencerrado, AM., Brandstetter, M., Köcher, T., Agerer, B., Genger, JW., Bergthaler, A., Pauli, A. (2026)

ER-mitochondria contacts and mitochondrial fusion correlate with increased mitochondrial activity during vertebrate embryogenesis.

Cell Rep. 45(7):117615

Pre-printDeneke, VE., Suwita, JP., Wang, H., Tonai, S., Lu, Y., Panser, K., Schleiffer, A., Hollis, JA., Novatchkova, M., Dürnberger, G., Stejskal, K., Krssakova, G., Blaha, A., Andresan, AAR., Mirus, M., Marvanova, H., Chang, HY., Noda, T., Burga, A., Roitinger, E., Ikawa, M., Pauli, A. (2026)

The SPARK complex forms the molecular basis of vertebrate fertilization

bioRxiv. 10.64898/2026.05.13.724128

Heizler, K., Chugunova, A., Hofmann, M., Prochazkova, M., Procházka, J., Ho-Xuan, H., Fallmann, J., Stejskal, K., Krssakova, G., Bader, S., Kocak, E., Yasar, D., Luckner, P., Lehmann, G., Köngeter, J., Riester, M., Roitinger, E., Wetzel, C., Diederichs, S., Sedlacek, R., Bruckmann, A., Gebhardt, JCM., Pauli, A., Meister, G. (2026)

The microprotein SMIM26 connects metabolite transporters of the outer and inner mitochondrial membranes and is essential for respiratory chain function.

Genes Dev.

Calderón, L., Schäfer, M., Rončević, M., Rauschmeier, R., Jaritz, M., Schwickert, TA., Sun, Q., Pauli, A., Zuber, J., Busslinger, M. (2026)

In vivo CRISPR/Cas9 screens identify new regulators of B cell activation and plasma cell differentiation.

J Exp Med. 223(3)

Matl, M., Kellner, MJ., Ansah, F., Grishkovskaya, I., Handler, D., Heinen, R., Bauer, B., Menéndez-Arias, L., Auer, TO., Prieto-Godino, LL., Penninger, JM., Awandare, GA., Brennecke, J., Pauli, A. (2025)

A lyophilized open-source RT-LAMP assay for molecular diagnostics in resource-limited settings.

Life Sci Alliance. 8(10)

Blaha, A., Schleiffer, A., Pauli, A. (2025)

Conservation and divergence of the molecular regulators of the vertebrate fertilization synapse.

Curr Opin Genet Dev. 93:102352

Pre-printBlaha, A., Pauli, A. (2024)

Bouncer’s receptor on sperm: Investigating sperm-egg compatibility in fish

bioRxiv. 2024.12.13.628393

Deneke, VE., Blaha, A., Lu, Y., Suwita, JP., Draper, JM., Phan, CS., Panser, K., Schleiffer, A., Jacob, L., Humer, T., Stejskal, K., Krssakova, G., Roitinger, E., Handler, D., Kamoshita, M., Vance, TDR., Wang, X., Surm, JM., Moran, Y., Lee, JE., Ikawa, M., Pauli, A. (2024)

A conserved fertilization complex bridges sperm and egg in vertebrates.

Corresponding preprint Cell. 187(25):7066-7078.e22

Pre-printAmann SJ, Dong K, Roehsner J, Krall D, Grishkovskaya I, Kotisch H, Schleiffer A, Roitinger E, Pauli A, Martin A, Haselbach D (2024)

PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy

bioRxiv. 2024.12.04.626795

Pre-printShah, AN., Leesch, F., Lorenzo-Orts, L., Grundmann, L., Novatchkova, M., Haselbach, D., Calo, E., Pauli, A. (2024)

A dual ribosomal system in the zebrafish soma and germline

bioRxiv. doi:10.1101/2024.08.29.610041

Rappol, T., Waldl, M., Chugunova, A., Hofacker, IL., Pauli, A., Vilardo, E. (2024)

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.

Corresponding preprint Nucleic Acids Res.

Pre-printChugunova, A., Keresztes, H., Kobylinska, R., Novatchkova, M., Lendl, T., Strobl, M., Schutzbier, M., Dürnberger, G., Imre, R., Roitinger, E., Pasierbek, P., Moreno Cencerrado, A., Brandstetter, M., Köcher, T., Agerer, B., Genger, J-W., Bergthaler, A., Pauli, A. (2024)

Increase in ER-mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis

bioRxiv. 10.1101/2024.06.11.598492v1

Lorenzo-Orts, L., Pauli, A. (2024)

The molecular mechanisms underpinning maternal mRNA dormancy.

Biochem Soc Trans.

Pre-printBriedis-Gert, KR., Schulze, G., Novatchkova, M., Panser, K., Cabrera Quio, LE., Koller, A., Guo, Y., Cairns, BR., Valen, E., Pauli, A (2026)

Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

bioRxiv. 10.1101/2021.11.03.467109

Lorenzo-Orts, L., Strobl, M., Steinmetz, B., Leesch, F., Pribitzer, C., Roehsner, J., Schutzbier, M., Dürnberger, G., Pauli, A. (2024)

eIF4E1b is a non-canonical eIF4E protecting maternal dormant mRNAs.

Corresponding preprint EMBO Rep. 25(1):404-427

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.

Corresponding preprint Cell Rep. 42(2):112070

Ross, SE., Vázquez-Marín, J., Gert, KRB., González-Rajal, Á., Dinger, ME., Pauli, A., Martínez-Morales, JR., Bogdanovic, O. (2023)

Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species.

Corresponding preprint Nucleic Acids Res.

Gert, KRB., Panser, K., Surm, J., Steinmetz, BS., Schleiffer, A., Jovine, L., Moran, Y., Kondrashov, F., Pauli, A. (2023)

Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries.

Corresponding preprint Nat Commun. 14(1):3506

Leesch, F., Lorenzo-Orts, L., Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A., Matzinger, M., Roitinger, E., Belačić, 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.

Corresponding preprint Nature.

Wu, SS., Lee, H., Szép-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, JH., Kim, J., Zhu, Y., Linssen, MM., 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.

Corresponding preprint Exp Mol Med.

Stock, J., Kazmar, T., Schlumm, F., Hannezo, E., Pauli, A. (2022)

A self-generated Toddler gradient guides mesodermal cell migration.

Corresponding preprint Sci Adv. 8(37):eadd2488

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., Buecker, 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.

Corresponding preprint Genes Dev. 36(5-6):348-367

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., Pauli, A., Brennecke, J. (2022)

A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing.

Corresponding preprint Front Mol Biosci. 9:801309

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 sperm-egg interaction in mice and fish.

Corresponding preprint Commun Biol. 5(1):332

Binner, MI., Kogan, A., Panser, K., Schleiffer, A., Deneke, VE., Pauli, A. (2022)

The Sperm Protein Spaca6 is Essential for Fertilization in Zebrafish.

Corresponding preprint Front Cell Dev Biol. 9:806982

Pre-printGuo,Y., Gert,KR., Lebedeva,S., Potok,ME., Wike,CL., Grow,EJ., Ketting,RF., Pauli,A., Cairns,B. (2021)

Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos

bioRxiv. 2021.11.03.467172

Pre-printGert,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. 2021.11.03.467109

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.

Corresponding preprint Proc Natl Acad Sci U S A. 118(39)

Deneke, VE., Pauli, A. (2021)

The Fertilization Enigma: How Sperm and Egg Fuse.

Annu Rev Cell Dev Biol.

Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL. (2021)

Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.

Methods Enzymol. 655:205-223

Cabrera-Quio, LE., Schleiffer, A., Mechtler, K., Pauli, A. (2021)

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition.

PLoS Genet. 17(2):e1009390

Stock, J., Pauli, A. (2021)

Self-organized cell migration across scales - from single cell movement to tissue formation.

Development. 148(7)

Pre-printKellner 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. 2021.01.19.21250079

Gert, KR., Pauli, A. (2020)

Species-specific mechanisms during fertilization.

Curr Top Dev Biol. 140:121-144

Kamieniarz-Gdula, K., Gdula, MR., Panser, K., Nojima, T., Monks, J., Wiśniewski, JR., Riepsaame, J., Brockdorff, N., Pauli, A., Proudfoot, NJ. (2019)

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.

Mol Cell. 74(1):158-172.e9

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

Chew, GL., Pauli, A., Schier, AF. (2016)

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.

Nat Commun. 7:11663

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

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

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 Rep. 20(9):2116-2130

Cabrera-Quio, LE., Herberg, S., Pauli, A. (2016)

Decoding sORF translation - from small proteins to gene regulation.

RNA Biol. 13(11):1051-1059

Pauli, A., Montague, TG., Lennox, KA., Behlke, MA., Schier, AF. (2015)

Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish.

PLoS One. 10(10):e0139504

Pauli, A., Valen, E., Schier, AF. (2015)

Identifying (non-)coding RNAs and small peptides: challenges and opportunities.

Bioessays. 37(1):103-12

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

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

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

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

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

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

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

Pauli, A., Rinn, JL., Schier, AF. (2011)

Non-coding RNAs as regulators of embryogenesis.

Nat Rev Genet. 12(2):136-49

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

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

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

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

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

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