Publications | IMP Scientific Papers | Research Institute of Molecular Pathology (IMP)

Chen, S., Loubiere, V., Hollingsworth, EW., Murakami, K., Mandlburger, N., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A. (2026)

Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.

Nat Genet. 58(9):2129-2133

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

Bugai, A., Hohmann, U., Lorenzo, A., Graf, M., Fin, L., Rouvière, JO., Tirian, L., Dou, Y., Le Rest, M., Polák, P., Johnsen, D., Jakobsen, L., Andersen, JS., Brennecke, J., Plaschka, C., Jensen, TH. (2026)

Molecular basis of polyadenylated RNA fate determination in the nucleus.

Nature. 655(8124):1070-1078

Wutz, G., Davidson, IF., Banigan, EJ., Stocsits, RR., Kawasumi, R., Tang, W., Nagasaka, K., Costantino, L., Jansen, R., Hirota, K., Branzei, D., Mirny, LA., Peters, JM. (2026)

PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes.

Mol Cell.

Junker, S., Clausen, T. (2026)

BacPROTAC-induced protein degradation as a new antibiotic concept.

Trends Biochem Sci. 51(3):249-260

Brunner, HL., Kalis, RW., Grundmann, L., Hodáková, Z., Koskova, Z., Grishkovskaya, I., de Almeida, M., Hinterndorfer, M., Knaudt, H., Höfflin, S., Andersch, F., Kotisch, H., Dickmanns, A., Cuylen-Haering, S., Zuber, J., Haselbach, D. (2026)

A multivalent adaptor mechanism drives the nuclear import of proteasomes.

Nat Commun.

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)

Kordic, D., Williams, TL., Deszcz, L., Ehrmann, JF., Arnese, R., Schleiffer, A., Clausen, T., Meinhart, A. (2025)

Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2/E3 hybrid enzyme UBE2O.

J Biol Chem. 302(2):111073

Chen, S., Loubiere, V., Hollingsworth, EW., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A. (2025)

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo.

bioRxiv.

Hohmann, U., Graf, M., Tirián, L., Pacheco-Fiallos, B., Schellhaas, U., Fin, L., Handler, D., Phillips, AW., Riabov-Bassat, D., Faraway, R., Pühringer, T., Szalay, MF., Roitinger, E., Brennecke, J., Plaschka, C. (2025)

An ATP-gated molecular switch orchestrates human mRNA export

Nature. 649(8098):1042-1050

Groessl, S., Kalis, R., Snaebjornsson, MT., Wambach, L., Haider, J., Andersch, F., Schulze, A., Palm, W., Zuber, J. (2025)

Acidosis orchestrates adaptations of energy metabolism in tumors.

Science. 390(6769):eadp7603

Faraway, R., Costello Heaven, N., Digby, H., Kuret Hodnik, K., Rebselj, J., Wilkins, OG., Chakrabarti, AM., Iosub, IA., Vadnjal, N., Dore, R., Knez, L., Ameres, SL., Plaschka, C., Ule, J. (2025)

Collective homeostasis of condensation-prone proteins via their mRNAs.

Nature.

Faraway, R., Zenklusen, D., Plaschka, C. (2025)

Mechanisms of Messenger RNA Packaging and Export.

Annu Rev Cell Dev Biol. 41(1):479-504

Estivill, G., Obenauf, AC. (2025)

Trio fatale: Neutrophils, NETs, and necrosis.

Immunity. 58(9):2154-2156

Grabarczyk, DB., Ehrmann, JF., Murphy, P., Yang, WS., Kurzbauer, R., Bell, LE., Deszcz, L., Neuhold, J., Schleiffer, A., Shulkina, A., Lee, J., Shin, JS., Meinhart, A., Versteeg, GA., Zavodszky, E., Song, HK., Hegde, RS., Clausen, T. (2025)

Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.

Science. 389(6763):909-914

Grabarczyk, DB., Aird, EJ., Reznikow, V., Kirchgatterer, PC., Ehrmann, JF., Kurzbauer, R., Bell, LE., Kellner, MJ., Aggarwal, R., Schleiffer, A., Faas, V., Deszcz, L., Meinhart, A., Versteeg, GA., Penninger, JM., Stelzl, LS., Gaidt, MM., Tessmer, I., Corn, JE., Clausen, T. (2025)

A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles.

Cell.

Tsai, TY., Pinheiro, D. (2025)

Coping with uncertainty: Challenges for robust pattern formation in dynamical tissues.

Semin Cell Dev Biol. 173:103629

Valeri, E., Gaidt, MM. (2025)

DIY innate immune sensing: Crafting fresh DNA to detect viruses.

Mol Cell. 85(15):2818-2820

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)

Estivill, G., Elewaut, A., Obenauf, AC. (2025)

Unlocking Immunity Within: Inflammatory Monocytes Stimulate T Cells at Immune Hubs in the Tumor Microenvironment.

J Invest Dermatol.

Nemčko, F., Stark, A. (2025)

A tighter grip on gene expression.

Science. 389(6755):31-32

Schoeberl, UE., Fitz, J., von der Linde, M., Valieris, R., Bauer, B., Malzl, D., Froussios, K., Costea, J., Schmidt, F., Pflaum, J., Bartl, B., Albrecht, J., Wiedemann, EM., Garcia, AC., Peycheva, M., Rizzi, M., Goloborodko, A., Tojal da Silva, I., Pavri, R. (2025)

Regulation of somatic hypermutation by higher-order chromatin structure.

Mol Cell.

Davidson, IF., Barth, R., Nagasaka, K., Tang, W., Wutz, G., Horn, S., Janissen, R., Stocsits, RR., Chlosta, E., Bauer, BW., Dekker, C., Peters, JM. (2025)

Cohesin supercoils DNA during loop extrusion.

Cell Rep. 44(6):115856

Müller, F., Brutiu, BR., Saridakis, I., Leischner, T., Birklbauer, MJ., Matzinger, M., Madalinski, M., Lendl, T., Shaaban, S., Dorfer, V., Maulide, N., Mechtler, K. (2025)

Developing a new cleavable crosslinker reagent for in-cell crosslinking.

Commun Chem. 8(1):191

Jäger, C., Dimitrova, P., Sun, Q., Tennebroek, J., Marchiori, E., Jaritz, M., Rauschmeier, R., Estivill, G., Obenauf, A., Busslinger, M., van der Veeken, J. (2025)

Inducible protein degradation reveals inflammation-dependent function of the Treg cell lineage-defining transcription factor Foxp3.

Sci Immunol. 10(108):eadr7057

Ventura, G., Pinheiro, D. (2025)

Gastrulation: Lessons from the quail embryo.

Curr Biol. 35(10):R384-R386

Umkehrer, C., Obenauf, A. (2025)

Functional Lineage Tracing Using CaTCH.

Methods Mol Biol. 2905:95-120

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

Harar, P., Herrmann, L., Grohs, P., Haselbach, D. (2025)

FakET: Simulating cryo-electron tomograms with neural style transfer.

Structure. 33(4):820-827.e4

Elewaut, A., Estivill, G., Bayerl, F., Castillon, L., Novatchkova, M., Pottendorfer, E., Hoffmann-Haas, L., Schönlein, M., Nguyen, TV., Lauss, M., Andreatta, F., Vulin, M., Krecioch, I., Bayerl, J., Pedde, AM., Fabre, N., Holstein, F., Cronin, SM., Rieser, S., Laniti, DD., Barras, D., Coukos, G., Quek, C., Bai, X., Muñoz I Ordoño, M., Wiesner, T., Zuber, J., Jönsson, G., Böttcher, JP., Vanharanta, S., Obenauf, AC. (2025)

Cancer cells impair monocyte-mediated T cell stimulation to evade immunity.

Nature. 637(8046):716-725

Tang, W., Costantino, L., Stocsits, R., Wutz, G., Ladurner, R., Hudecz, O., Mechtler, K., Peters, JM. (2025)

Cohesin positions the epigenetic reader Phf2 within the genome.

EMBO J. 44(3):736-766

Birklbauer, MJ., Müller, F., Geetha, SS., Matzinger, M., Mechtler, K., Dorfer, V. (2024)

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.

Commun Chem. 7(1):300

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

Hofbauer, L., Pleyer, LM., Reiter, F., Schleiffer, A., Vlasova, A., Serebreni, L., Huang, A., Stark, A. (2024)

A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression.

Mol Cell. 84(23):4503-4521.e14

Arbanas, LI., Cura Costa, E., Chara, O., Otsuki, L., Tanaka, EM. (2024)

Lineage tracing of Shh+ floor plate cells and dynamics of dorsal-ventral gene expression in the regenerating axolotl spinal cord.

Dev Growth Differ. 66(8):414-425

Loubiere, V., de Almeida, BP., Pagani, M., Stark, A. (2024)

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.

Nat Commun. 15(1):8584

Hornung, V., Gaidt, MM. (2024)

Friendly fire: recognition of self by the innate immune system.

Curr Opin Immunol. 90:102457

Fedl, AS., Tagoh, H., Gruenbacher, S., Sun, Q., Schenk, RL., Froussios, K., Jaritz, M., Busslinger, M., Schwickert, TA. (2024)

Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development.

Nat Immunol. 25(9):1663-1677

Kawaguchi, A., Wang, J., Knapp, D., Murawala, P., Nowoshilow, S., Masselink, W., Taniguchi-Sugiura, Y., Fei, JF., Tanaka, EM. (2024)

A chromatin code for limb segment identity in axolotl limb regeneration.

Dev Cell. 59(16):2239-2253.e9

Vorländer, MK., Rothe, P., Kleifeld, J., Cormack, ED., Veleti, L., Riabov-Bassat, D., Fin, L., Phillips, AW., Cochella, L., Plaschka, C. (2024)

Mechanism for the initiation of spliceosome disassembly.

Nature. 632(8024):443-450

Krammer, T., Stuart, HT., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., Becerril Perez, F., Wang, J., Costantini, E., Lehr, S., Arbanas, L., Hörmann, A., Neumüller, RA., Elvassore, N., Siggia, E., Briscoe, J., Kicheva, A., Tanaka, EM. (2024)

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

Dev Cell. 59(15):1940-1953.e10

Vogel, A., Arnese, R., Gudino Carrillo, RM., Sehr, D., Deszcz, L., Bylicki, A., Meinhart, A., Clausen, T. (2024)

UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome.

Nat Commun. 15(1):6272

Nemčko, F., Himmelsbach, M., Loubiere, V., Yelagandula, R., Pagani, M., Fasching, N., Brennecke, J., Elling, U., Stark, A., Ameres, SL. (2024)

Proteome-scale tagging and functional screening in mammalian cells by ORFtag.

Nat Methods.

Riabov Bassat, D., Visanpattanasin, S., Vorländer, MK., Fin, L., Phillips, AW., Plaschka, C. (2024)

Structural basis of human U5 snRNP late biogenesis and recycling.

Nat Struct Mol Biol.

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

Pinheiro, D., Mitchel, J. (2024)

Pulling the strings on solid-to-liquid phase transitions in cell collectives.

Curr Opin Cell Biol. 86:102310

de Almeida, BP., Schaub, C., Pagani, M., Secchia, S., Furlong, EEM., Stark, A. (2024)

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.

Nature. 626(7997):207-211

Matzinger, M., Schmücker, A., Yelagandula, R., Stejskal, K., Krššáková, G., Berger, F., Mechtler, K., Mayer, RL. (2024)

Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.

Nat Commun. 15(1):1019

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

Ciriello, G., Magnani, L., Aitken, SJ., Akkari, L., Behjati, S., Hanahan, D., Landau, DA., Lopez-Bigas, N., Lupiáñez, DG., Marine, JC., Martin-Villalba, A., Natoli, G., Obenauf, AC., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., Vanharanta, S., Zuber, J. (2024)

Cancer Evolution: A Multifaceted Affair.

Cancer Discov. 14(1):36-48

Jessberger, G., Várnai, C., Stocsits, RR., Tang, W., Stary, G., Peters, JM. (2023)

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei.

Genome Res. 33(12):2094-107

Pinheiro, D. (2023)

How embryos sort themselves out.

Nat Rev Mol Cell Biol. 24(12):856

Gruenbacher, S., Jaritz, M., Hill, L., Schäfer, M., Busslinger, M. (2023)

Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development.

J Exp Med. 220(12)

Falcon, F., Tanaka, EM., Rodriguez-Terrones, D. (2023)

Transposon waves at the water-to-land transition.

Curr Opin Genet Dev. 81:102059

Hodáková, Z., Grishkovskaya, I., Brunner, HL., Bolhuis, DL., Belačić, K., Schleiffer, A., Kotisch, H., Brown, NG., Haselbach, D. (2023)

Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5.

EMBO J. 42(16):e113348

Hill, L., Jaritz, M., Tagoh, H., Schindler, K., Kostanova-Poliakova, D., Sun, Q., Schwickert, TA., Leeb, M., Busslinger, M. (2023)

Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus.

EMBO J. 42(15):e112741

Jacobs, J., Pagani, M., Wenzl, C., Stark, A. (2023)

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila.

Science. 381(6654):198-204

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

Hoi, DM., Junker, S., Junk, L., Schwechel, K., Fischel, K., Podlesainski, D., Hawkins, PME., van Geelen, L., Kaschani, F., Leodolter, J., Morreale, FE., Kleine, S., Guha, S., Rumpel, K., Schmiedel, VM., Weinstabl, H., Meinhart, A., Payne, RJ., Kaiser, M., Hartl, M., Boehmelt, G., Kazmaier, U., Kalscheuer, R., Clausen, T. (2023)

Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.

Cell. 186(10):2176-2192.e22

Davidson, IF., Barth, R., Zaczek, M., van der Torre, J., Tang, W., Nagasaka, K., Janissen, R., Kerssemakers, J., Wutz, G., Dekker, C., Peters, JM. (2023)

CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion.

Corresponding preprint Nature. 616(7958):822-827

Pacheco-Fiallos, B., Vorländer, MK., Riabov-Bassat, D., Fin, L., O'Reilly, FJ., Ayala, FI., Schellhaas, U., Rappsilber, J., Plaschka, C. (2023)

mRNA recognition and packaging by the human transcription-export complex.

Nature.

Reiter, F., de Almeida, BP., Stark, A. (2023)

Enhancers display constrained sequence flexibility and context-specific modulation of motif function.

Genome Res.

Ishihara, K., Mukherjee, A., Gromberg, E., Brugués, J., Tanaka, EM., Jülicher, F. (2023)

Topological morphogenesis of neuroepithelial organoids.

Nat Phys. 19(2):177-183

Schmoellerl, J., Barbosa, IAM., Minnich, M., Andersch, F., Smeenk, L., Havermans, M., Eder, T., Neumann, T., Jude, J., Fellner, M., Ebert, A., Steininger, M., Delwel, R., Grebien, F., Zuber, J. (2023)

EVI1 drives leukemogenesis through aberrant ERG activation.

Blood. 141(5):453-466

Klaus, L., de Almeida, BP., Vlasova, A., Nemčko, F., Schleiffer, A., Bergauer, K., Hofbauer, L., Rath, M., Stark, A. (2023)

Systematic identification and characterization of repressive domains in Drosophila transcription factors.

EMBO J. 42(3):e112100

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.

Wöhner, M., Pinter, T., Bönelt, P., Hagelkruys, A., Kostanova-Poliakova, D., Stadlmann, J., Konieczny, SF., Fischer, M., Jaritz, M., Busslinger, M. (2022)

The Xbp1-regulated transcription factor Mist1 restricts antibody secretion by restraining Blimp1 expression in plasma cells.

Front Immunol. 13:859598

Amann, SJ., Keihsler, D., Bodrug, T., Brown, NG., Haselbach, D. (2023)

Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM.

Structure. 31(1):4-19

Leiendecker, L., Neumann, T., Jung, PS., Cronin, SM., Steinacker, TL., Schleiffer, A., Schutzbier, M., Mechtler, K., Kervarrec, T., Laurent, E., Bachiri, K., Coyaud, E., Murali, R., Busam, KJ., Itzinger-Monshi, B., Kirnbauer, R., Cerroni, L., Calonje, E., Rütten, A., Stubenrauch, F., Griewank, KG., Wiesner, T., Obenauf, AC. (2023)

Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers.

Cancer Discov. 13(1):70-84

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.

Kawaguchi, A., Tanaka, EM. (2023)

Chromosome Conformation Capture for Large Genomes.

Methods Mol Biol. 2562:291-318

Taniguchi-Sugiura, Y., Tanaka, EM. (2023)

Artificial Insemination in Axolotl.

Methods Mol Biol. 2562:417-423

Masselink, W., Tanaka, EM. (2023)

Ethyl Cinnamate-Based Tissue Clearing Strategies.

Methods Mol Biol. 2562:123-133

Nowoshilow, S., Tanaka, EM. (2023)

Navigation and Use of Custom Tracks within the Axolotl Genome Browser.

Methods Mol Biol. 2562:273-289

Murawala, P., Oliveira, CR., Okulski, H., Yun, MH., Tanaka, EM. (2023)

Baculovirus Production and Infection in Axolotls.

Methods Mol Biol. 2562:369-387

Hendy, O., Serebreni, L., Bergauer, K., Muerdter, F., Huber, L., Nemčko, F., Stark, A. (2022)

Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers.

Mol Cell. 82(19):3598-3612.e7

Pinter, T., Fischer, M., Schäfer, M., Fellner, M., Jude, J., Zuber, J., Busslinger, M., Wöhner, M. (2022)

Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development.

Front Immunol. 13:979606

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

Peycheva, M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, UE., Pavri, R. (2022)

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations.

Science. 377(6612):eabj5502

Lust, K., Maynard, A., Gomes, T., Fleck, JS., Camp, JG., Tanaka, EM., Treutlein, B. (2022)

Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration.

Science. 377(6610):eabp9262

Vorländer, MK., Pacheco-Fiallos, B., Plaschka, C. (2022)

Structural basis of mRNA maturation: Time to put it together.

Curr Opin Struct Biol. 75:102431

Kaiser, FMP., Gruenbacher, S., Oyaga, MR., Nio, E., Jaritz, M., Sun, Q., van der Zwaag, W., Kreidl, E., Zopf, LM., Dalm, VASH., Pel, J., Gaiser, C., van der Vliet, R., Wahl, L., Rietman, A., Hill, L., Leca, I., Driessen, G., Laffeber, C., Brooks, A., Katsikis, PD., Lebbink, JHG., Tachibana, K., van der Burg, M., De Zeeuw, CI., Badura, A., Busslinger, M. (2022)

Biallelic PAX5 mutations cause hypogammaglobulinemia, sensorimotor deficits, and autism spectrum disorder.

J Exp Med. 219(9)

Obenauf, AC. (2022)

Mechanism-based combination therapies for metastatic cancer.

Sci Transl Med. 14(655):eadd0887

Polikarpova, A., Ellinghaus, A., Schmidt-Bleek, O., Grosser, L., Bucher, CH., Duda, GN., Tanaka, EM., Schmidt-Bleek, K. (2022)

The specialist in regeneration-the Axolotl-a suitable model to study bone healing?

NPJ Regen Med. 7(1):35

Lin, TY., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Tanaka, EM. (2022)

Inducible and tissue-specific cell labeling in Cre-ERT2 transgenic Xenopus lines.

Dev Growth Differ. 64(5):243-253

Morreale, FE., Kleine, S., Leodolter, J., Junker, S., Hoi, DM., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., Guha, S., Podlesainski, D., Kazmaier, U., Boehmelt, G., Weinstabl, H., Rumpel, K., Schmiedel, VM., Hartl, M., Haselbach, D., Meinhart, A., Kaiser, M., Clausen, T. (2022)

BacPROTACs mediate targeted protein degradation in bacteria.

Corresponding preprint Cell. 185(13):2338-2353.e18

Otsuki, L., Tanaka, EM. (2022)

Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb.

Cold Spring Harb Perspect Biol. 14(6)

Neumayr, C., Haberle, V., Serebreni, L., Karner, K., Hendy, O., Boija, A., Henninger, JE., Li, CH., Stejskal, K., Lin, G., Bergauer, K., Pagani, M., Rath, M., Mechtler, K., Arnold, CD., Stark, A. (2022)

Differential cofactor dependencies define distinct types of human enhancers.

Nature. 606(7913):406-413

Glotzer, GL., Tardivo, P., Tanaka, EM. (2022)

Canonical Wnt signaling and the regulation of divergent mesenchymal Fgf8 expression in axolotl limb development and regeneration.

Elife. 11

de Almeida, BP., Reiter, F., Pagani, M., Stark, A. (2022)

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.

Nat Genet. 54(5):613-624

Echeverri, K., Fei, J., Tanaka, EM. (2022)

The Axolotl's journey to the modern molecular era.

Curr Top Dev Biol. 147:631-658

Jurado, S., Fedl, AS., Jaritz, M., Kostanova-Poliakova, D., Malin, SG., Mullighan, CG., Strehl, S., Fischer, M., Busslinger, M. (2022)

The PAX5-JAK2 translocation acts as dual-hit mutation that promotes aggressive B-cell leukemia via nuclear STAT5 activation.

EMBO J. 41(7):e108397

Nemčko, F., Stark, A. (2022)

Proteome-scale identification of transcriptional activators in human cells.

Mol Cell. 82(3):497-499

Zhong, Y., Walker, SK., Pritykin, Y., Leslie, CS., Rudensky, AY., van der Veeken, J. (2022)

Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families.

Nat Immunol. 23(1):122-134

Rauschmeier, R., Reinhardt, A., Gustafsson, C., Glaros, V., Artemov, AV., Dunst, J., Taneja, R., Adameyko, I., Månsson, R., Busslinger, M., Kreslavsky, T. (2022)

Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.

J Exp Med. 219(2)

Haas, L., Elewaut, A., Gerard, CL., Umkehrer, C., Leiendecker, L., Pedersen, M., Krecioch, I., Hoffmann, D., Novatchkova, M., Kuttke, M., Neumann, T., da Silva, IP., Witthock, H., Cuendet, MA., Carotta, S., Harrington, KJ., Zuber, J., Scolyer, RA., Long, GV., Wilmott, JS., Michielin, O., Vanharanta, S., Wiesner, T., Obenauf, AC. (2021)

Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma.

Nat Cancer. 2(7):693-708

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

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Targeting CD56 with an antibody-drug conjugate in Merkel cell carcinoma.

Br J Dermatol.

de Almeida, M., Hinterndorfer, M., Brunner, H., Grishkovskaya, I., Singh, K., Schleiffer, A., Jude, J., Deswal, S., Kalis, R., Vunjak, M., Lendl, T., Imre, R., Roitinger, E., Neumann, T., Kandolf, S., Schutzbier, M., Mechtler, K., Versteeg, GA., Haselbach, D., Zuber, J. (2021)

AKIRIN2 controls the nuclear import of proteasomes in vertebrates.

Nature. 599(7885):491-496

Bassat, E., Tanaka, EM. (2021)

The cellular and signaling dynamics of salamander limb regeneration.

Curr Opin Cell Biol. 73:117-123

Bauer, BW., Davidson, IF., Canena, D., Wutz, G., Tang, W., Litos, G., Horn, S., Hinterdorfer, P., Peters, JM. (2021)

Cohesin mediates DNA loop extrusion by a "swing and clamp" mechanism.

Cell. 184(21):5448-5464.e22

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Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia.

Cancer Discov. 11(11):2868-2883

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

Gutiérrez-Pérez, P., Santillán, EM., Lendl, T., Wang, J., Schrempf, A., Steinacker, TL., Asparuhova, M., Brandstetter, M., Haselbach, D., Cochella, L. (2021)

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Sci Adv. 7(42):eabh1434

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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)

Hajdusits, B., Suskiewicz, MJ., Hundt, N., Meinhart, A., Kurzbauer, R., Leodolter, J., Kukura, P., Clausen, T. (2021)

McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.

Corresponding preprint Elife. 10

Grabarczyk, DB., Petrova, OA., Deszcz, L., Kurzbauer, R., Murphy, P., Ahel, J., Vogel, A., Gogova, R., Faas, V., Kordic, D., Schleiffer, A., Meinhart, A., Imre, R., Lehner, A., Neuhold, J., Bader, G., Stolt-Bergner, P., Böttcher, J., Wolkerstorfer, B., Fischer, G., Grishkovskaya, I., Haselbach, D., Kessler, D., Clausen, T. (2021)

HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.

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The Fertilization Enigma: How Sperm and Egg Fuse.

Annu Rev Cell Dev Biol.

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Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma

Nature Cancer. 2:693–708

Davidson, IF., Peters, JM. (2021)

Genome folding through loop extrusion by SMC complexes.

Nat Rev Mol Cell Biol. 22(7):445-464

Calderón, L., Schindler, K., Malin, SG., Schebesta, A., Sun, Q., Schwickert, T., Alberti, C., Fischer, M., Jaritz, M., Tagoh, H., Ebert, A., Minnich, M., Liston, A., Cochella, L., Busslinger, M. (2021)

Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.

Sci Immunol. 6(61)

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

Cura Costa, E., Otsuki, L., Rodrigo Albors, A., Tanaka, EM., Chara, O. (2021)

Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration.

Elife. 10

Pre-printAhel J, Fletcher A, Grabarczyk DB, Roitinger E, Deszcz L, Lehner A, Virdee S, Clausen T. (2021)

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

bioRxiv. 2021.05.10.443411

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

Pre-printSchoeberl, U. E., Fitz, J., Froussios, K., Valieris, R., Makharova, M., Ourailidis, I., Bauer, B., Neumann, T., Wiedemann, E., Steininger, M., Garcia, A. C., Mastrovito, M., Mouquet, H., Tojal Da Silva, I., Pavri, R. (2022)

Somatic hypermutation spectra are independent of the local transcriptional and epigenetic landscape

bioRxiv. 2022.05.21.492925

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