Department Biozentrum

Amer Salem, Michèle et al. (2025) ‘Quantitative Proteomic Analysis Reveals Different Functional Subtypes among IDH -Wildtype Glioblastoma’, Journal of Proteome Research [Preprint]. Available at: https://doi.org/10.1021/acs.jproteome.5c00199.

Pereira, Joana et al. (2025) ‘Large-scale protein clustering in the age of deep learning’, Current Opinion in Structural Biology, 94. Available at: https://doi.org/10.1016/j.sbi.2025.103078.

Pignon, Estelle et al. (2025) ‘Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia’, The ISME Journal, p. Online ahead of print. Available at: https://doi.org/10.1093/ismejo/wraf122.

Okur, Zeynep and Scheiffele, Peter (2025) ‘Molecular programs specifying properties and plasticity of parvalbumin interneuron innervation’, Current Opinion in Neurobiology, 93, p. Online ahead of print. Available at: https://doi.org/10.1016/j.conb.2025.103060.

Baumann, Kevin N. et al. (2025) ‘Elucidating the nanoscopic organization and dynamics of the nuclear pore complex’, Nucleus, 16(1). Available at: https://doi.org/10.1080/19491034.2025.2510106.

Mas, Guillaume and Hiller, Sebastian (2025) ‘Mechanism of ATP hydrolysis in the Hsp70 BiP nucleotide-binding domain’, Nature Communications, 16(1). Available at: https://doi.org/10.1038/s41467-025-60343-x.

Petrovic, Ivana et al. (2025) ‘Arrestin recognizes GPCRs independently of the receptor state’, Proceedings of the National Academy of Sciences, 122(20). Available at: https://doi.org/10.1073/pnas.2501487122.

Wu, Feng-Jie et al. (2025) ‘Activation dynamics traced through a G protein–coupled receptor by 81 1 H- 15 N NMR probes’, Science, 388(6748). Available at: https://doi.org/10.1126/science.adq9106.

Roche, Béatrice et al. (2025) ‘A Salmonella subset exploits erythrophagocytosis to subvert SLC11A1-imposed iron deprivation’, Cell Host and Microbe, 33, pp. 632–642.e4. Available at: https://doi.org/10.1016/j.chom.2025.04.013.

Ramesh, Divvya et al. (2025) ‘When less is not more: Limits to the evolution of metabolic dependence in spatially structured microbial communities’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.05.09.651753.

de Groot, Daan Hugo et al. (2025) ‘Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv ). Available at: https://doi.org/10.1101/2025.05.08.652944.

Marone, Romina et al. (2025) ‘Impact of Human Genetic Variation Underlying Resistance to Antigen-Specific Immunotherapy’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.05.02.651174.

Robin, Xavier et al. (2025) ‘Benchmarking of macromolecular complexes with the Continuous Automated Model Evaluation (CAMEO)’, Authorea [Preprint]. Authorea (Authorea). Available at: https://doi.org/10.22541/au.174638718.83117953/v1.

Laman Trip, Diederik S. et al. (2025) ‘A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes’, Nature Biotechnology, p. Online ahead of print. Available at: https://doi.org/10.1038/s41587-025-02659-z.

Furrer, Regula et al. (2025) ‘Metabolic dysregulation contributes to the development of dysferlinopathy’, Life Science Alliance, 8(5), p. e202402991. Available at: https://doi.org/10.26508/lsa.202402991.

McNamara, Harold M. et al. (2025) ‘Optogenetic control of Nodal signaling patterns’, Development (Cambridge), 152(9). Available at: https://doi.org/10.1242/dev.204506.

Papassotiropoulos, Andreas et al. (2025) ‘The effect of fampridine on working memory: a randomized controlled trial based on a genome-guided repurposing approach’, Molecular Psychiatry. 08.11.2024, 30(5), pp. 2085–2094. Available at: https://doi.org/10.1038/s41380-024-02820-1.

Ruiz, Alexis et al. (2025) ‘5-aza-2-deoxycytidine improves skeletal muscle function in a mouse model for recessive RYR1-related congenital myopathy’, Human Molecular Genetics. 13.02.2025, 34(9), pp. 790–805. Available at: https://doi.org/10.1093/hmg/ddaf021.

Sigal, Alex, Neher, Richard A. and Lessells, Richard J. (2025) ‘The consequences of SARS-CoV-2 within-host persistence’, Nature Reviews Microbiology, 23(5), pp. 288–302. Available at: https://doi.org/10.1038/s41579-024-01125-y.

Djermoun, Sarah et al. (2025) ‘Biofilm architecture determines the dissemination of conjugative plasmids’, Proceedings of the National Academy of Sciences, 122(17). Available at: https://doi.org/10.1073/pnas.2417452122.

Giandomenico, Stefano L et al. (2025) ‘The proteasome maturation factor POMP moonlights as a stress-induced transcriptional regulator’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.04.25.650603.

Julou, Thomas et al. (2025) ‘Growth rate controls the sensitivity of gene regulatory circuits’, Science Advances, 11(17). Available at: https://doi.org/10.1126/sciadv.adu9279.

Confavreux, Basile et al. (2025) ‘Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks’, PLOS Computational Biology. Edited by Touboul, Jonathan David, 21(4), p. e1012910. Available at: https://doi.org/10.1371/journal.pcbi.1012910.

Leonte, Radu et al. (2025) ‘IVA Prime: Automated Primer Design for In Vivo Assembly Cloning’, Nucleic Acids Research [Preprint]. Available at: https://doi.org/10.1093/nar/gkaf386.

Sobkowiak, K. et al. (2025) ‘REV7 functions with REV3 as a checkpoint protein delaying mitotic entry until DNA replication is completed’, Cell Reports, 44(4). Available at: https://doi.org/10.1016/j.celrep.2025.115431.

Schneider-Heieck, Konstantin et al. (2025) ‘Krüppel-like factor 5 remodels lipid metabolism in exercised skeletal muscle’, Molecular Metabolism, 96(June). Available at: https://doi.org/10.1016/j.molmet.2025.102154.

Solinger, Jachen A., Ott, Daniel P. and Spang, Anne (2025) ‘ESCRTing the RABs through conversion’, Biochemical Society Transactions, 53(02), pp. 431–445. Available at: https://doi.org/10.1042/bst20253007.

Arber, Silvia, Falasconi, Antonio and Kanodia, Harsh (2025) ‘Dynamic basal ganglia output signals license and suppress forelimb movements’, Research Square [Preprint]. Research Square Company (Research Square). Available at: https://doi.org/10.21203/rs.3.rs-4676122/v1.

Gompper, G. et al. (2025) ‘The 2025 motile active matter roadmap’, Journal of Physics Condensed Matter, 37(14). Available at: https://doi.org/10.1088/1361-648X/adac98.

Lehner,Philippe Alain et al. (2025) ‘Architecture and conformational dynamics of the BAM–SurA insertase holo complex’, Science Advances, 11(14). Available at: https://doi.org/10.1126/sciadv.ads6094.

Ham, Daniel J. et al. (2025) ‘Muscle fiber Myc is dispensable for muscle growth and its forced expression severely perturbs homeostasis’, Nature Communications . 03.04.2025, 16(1). Available at: https://doi.org/10.1038/s41467-025-58542-7.

López-Pagán, Nieves et al. (2025) ‘Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection’, Nature Microbiology, 10(4), pp. 958–972. Available at: https://doi.org/10.1038/s41564-025-01966-0.

Träger, Lena et al. (2025) ‘Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12’, Nucleic Acids Research, 53(5). Available at: https://doi.org/10.1093/nar/gkaf132.

Waltz, Florent et al. (2025) ‘In-cell architecture of the mitochondrial respiratory chain’, Science, 387(6740), pp. 1296–1301. Available at: https://doi.org/10.1126/science.ads8738.

Furrer, Regula and Handschin, Christoph (2025) ‘Biomarkers of aging: from molecules and surrogates to physiology and function’, Physiological Reviews, 105(3), pp. 1609–1694. Available at: https://doi.org/10.1152/physrev.00045.2024.

Heuberger, Lukas et al. (2025) ‘Polymeric Giant Unilamellar Vesicles Support Longevity of Native Nuclei in Protocells’, Small Science. 18.03.2025, 5(6). Available at: https://doi.org/10.1002/smsc.202400622.

Yuping, Li et al. (2025) ‘Jumbo phage killer immune system targets early infection of nucleus-forming phages’, Cell, p. Online ahead of print. Available at: https://doi.org/10.1016/j.cell.2025.02.016.

McGowan, Timothy J. et al. (2025) ‘AAV capsids target muscle resident cells with different efficiencies - a comparative study between AAV8, AAVMYO and AAVMYO2’, Molecular Therapy: Methods & Clinical Development, 33(2). Available at: https://doi.org/10.1016/j.omtm.2025.101451.

Taggi, Valerio et al. (2025) ‘Targeted and Untargeted Proteomics-based Comparison of Adenoviral Infected hCMEC/D3 and hBMEC as a Human Brain Endothelial Cells to Study the OATP2B1 Transporter’, Molecular Neurobiology, p. Online ahead of print. Available at: https://doi.org/10.1007/s12035-025-04807-7.

Podlaski, William F., Agnes, Everton J. and Vogels, Tim P. (2025) ‘High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating’, Physical Review X, 15(1), p. 011057. Available at: https://doi.org/10.1103/PhysRevX.15.011057.

Molodenskiy, Dmitry et al. (2025) ‘AlphaPulldown2 – a general pipeline for high-throughput structural modeling’, Bioinformatics, 41(3). Available at: https://doi.org/10.1093/bioinformatics/btaf115.

Tavano, Stefania et al. (2025) ‘BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation’, Cell Reports, 44(3). Available at: https://doi.org/10.1016/j.celrep.2025.115387.

Brüderlin, Mitchell et al. (2025) ‘Pseudomonas aeruginosa assembles H1-T6SS in response to physical and chemical damage of the outer membrane’, Science Advances , 11(10). Available at: https://doi.org/10.1126/sciadv.adr1713.

Fanous, Joseph et al. (2025) ‘Limited impact of Salmonella stress and persisters on antibiotic clearance’, Nature, 639(8053), pp. 181–189. Available at: https://doi.org/10.1038/s41586-024-08506-6.

Ham, Alexander S. et al. (2025) ‘Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance’, Nature Communications, 16(1). Available at: https://doi.org/10.1038/s41467-025-57487-1.

Furrer, Regula and Handschin, Christoph (2025) ‘Biomarkers of aging: functional aspects still trump molecular parameters’, npj Aging, 11(1). Available at: https://doi.org/10.1038/s41514-025-00207-2.

Lubrano, P. et al. (2025) ‘Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks’, Molecular Systems Biology , 21(3), pp. 274–293. Available at: https://doi.org/10.1038/s44320-024-00084-z.

Alberto, Anthea et al. (2025) ‘Management of Digital Research Data at the End of a Project’. Available at: https://doi.org/10.5281/ZENODO.14925912.

Lehr, S. et al. (2025) ‘Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling’, Developmental Cell, 60(4), pp. 567–580.e14. Available at: https://doi.org/10.1016/j.devcel.2024.10.024.

Wang, Yiqun et al. (2025) ‘Gene module reconstruction identifies cellular differentiation processes and the regulatory logic of specialized secretion in zebrafish’, Developmental Cell. 25.11.2024, 60, pp. 581–598.e9. Available at: https://doi.org/10.1016/j.devcel.2024.10.015.

Henderson, Alyssa et al. (2025) ‘Disentangling the feedback loops driving spatial patterning in microbial communities’, npj Biofilms and Microbiomes, 11(1). Available at: https://doi.org/10.1038/s41522-025-00666-1.

Balajti, Máté et al. (2025) ‘HTSinfer: Inferring metadata from bulk Illumina RNA-Seq libraries’, Bioinformatics, 41(3). Available at: https://doi.org/10.1093/bioinformatics/btaf076.

Schwede, Torsten et al. (2025) ‘Comparing macromolecular complexes - a fully automated benchmarking suite’, Research Square [Preprint]. Springer Science and Business Media LLC (Research Square). Available at: https://doi.org/10.21203/rs.3.rs-5920881/v1.

Pal, Jagriti et al. (2025) ‘Nonstop mutations cause loss of renal tumor suppressor proteins VHL and BAP1 and affect multiple stages of protein translation’, Science Advances, 11(7). Available at: https://doi.org/10.1126/sciadv.adr6375.

Tintignac, Lionel et al. (2025) ‘Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.02.10.636994.

Škrinjar, Peter et al. (2025) ‘Have protein-ligand co-folding methods moved beyond memorisation?’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.02.03.636309.

Ott, Daniel P et al. (2025) ‘Coordination between ESCRT function and Rab conversion during endosome maturation’, The EMBO Journal, p. Online ahead of print. Available at: https://doi.org/10.1038/s44318-025-00367-7.

Erdmann, Joana et al. (2025) ‘Amoxicillin Concentrations in Samples of Musculoskeletal Infections’, Helvetica Chimica Acta, 108(2). Available at: https://doi.org/10.1002/hlca.202400178.

Seelig, Joachim and Seelig, Anna (2025) ‘Pressure Protein Denaturation Compared to Thermal and Chemical Unfolding: Analyses with Cooperative Models’, The Journal of Physical Chemistry B, 129(4), pp. 1229–1236. Available at: https://doi.org/10.1021/acs.jpcb.4c07703.

Gómez-Cabrera, Maria Carmen and Handschin, Christoph (2025) ‘Special Issue: ‘Unlocking Athletic Potential: Exploring Exercise Physiology from Mechanisms to Performance’’, Free Radical Biology and Medicine, 230, pp. 48–49. Available at: https://doi.org/10.1016/j.freeradbiomed.2025.01.036.

Ndinyanka Fabrice, Tohnyui et al. (2025) ‘T cell population size control by coronin 1 uncovered: from a spot identified by two-dimensional gel electrophoresis to quantitative proteomics’, Expert Review of Proteomics, 22(1), pp. 35–44. Available at: https://doi.org/10.1080/14789450.2025.2450812.

Espinoza Miranda, Suyen Solange et al. (2025) ‘Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges’, Microbiology and Molecular Biology Reviews, 89(1). Available at: https://doi.org/10.1128/mmbr.00138-24.

Tejada-Arranz, Alejandro et al. (2025) ‘Mechanisms of Pseudomonas aeruginosa resistance to Type VI Secretion System attacks’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2024.10.26.620397.

Schwayer, C. et al. (2025) ‘Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.01.14.632683.

Smith, William P. J. et al. (2025) ‘Multiplicity of type 6 secretion system toxins limits the evolution of resistance’, Proceedings of the National Academy of Sciences, 122(2). Available at: https://doi.org/10.1073/pnas.2416700122.

Giulia Di Bartolomei et al. (2025) ‘Dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons’, eLife [Preprint]. (eLife). Available at: https://doi.org/10.7554/eLife.104808.1.

Moon, Youngbin et al. (2025) ‘PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data’, Nucleic Acids Research. 12.11.2024, 53(D1), pp. D197–D204. Available at: https://doi.org/10.1093/nar/gkae1043.

Alter, Claudio Luca et al. (2025) ‘Nano Plasma Membrane Vesicle-Lipid Nanoparticle Hybrids for Enhanced Gene Delivery and Expression’, Advanced Healthcare Materials. 10.11.2024, 14(1). Available at: https://doi.org/10.1002/adhm.202401888.

Bayer, Emily A et al. (2025) ‘The mechanosensory DEG/ENaC channel DEGT-1 is a proprioceptor of C. elegans foregut movement’, bioRxiv [Preprint]. bioRxiv: Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2025.01.01.631014.

Agustoni, E. (2025) Molecular mechanisms of hybrid proteins in bacterial signal transduction. Doctoral Thesis.

Alaball Pujol, M.-E. (2025) Quantifying bacterial responses to antibiotics at the single-cell level. Doctoral Thesis.

Battaglioni, S. (2025) Exploring the landscape of mTOR substrates: identification of two novel targets. Doctoral Thesis.

Chaaban, M. (2025) Modulation of human adipose derived stromal cell chondrogenesis for controlled endochondral ossification and efficient bone formation. Doctoral Thesis.

de Smalen, Laura M. (2025) Molecular underpinnings of skeletal muscle plasticity in aging and exercise. Doctoral Thesis. University of Basel.

FARAVELLI, SIMONE (2025) Beyond the array: exploring Vaultrc5 and its association to clustered protocadherin array. Doctoral Thesis. University of Basel.

Garaudé, S. (2025) Engineering an antibody-discernible and functional CD45 variant on hematopoietic stem and progenitor cells via base editing. Doctoral Thesis.

Han, Ji Hoon (2025) Integrative analysis of genetic disorders using NGS, computational approaches and functional assays. Dissertation. University of Basel.

Hasiuk, Marko (2025) Exploring the microRNA-17~92 target network and T cell homeostasis with arrayed CRISPR screening. Doctoral Thesis. University of Basel.

Hernandez-Gonzalez, Hector Arturo (2025) Tales by light: how growth heterogeneity enables Pseudomonas aeruginosa adaptation to nutrient shifts and antibiotic survival. Doctoral Thesis. University of Basel.

Heynisch, A.C.-F. (2025) Protein engineering to modulate dynamics of molecular machines. Doctoral Thesis.

Hu, B. (2025) Function and organization of an autoassociative olfactory memory network. Doctoral Thesis.

Jia, Shichao (2025) Ultrasonic sample handling by acoustic radiation force: applications in acoustic levitation and acoustic tweezing. Doctoral Thesis. University of Basel.

Kolesnikov, M. (2025) Defining the molecular basis of dynamic localization of type VI secretion system assembly in ‘Pseudomonas aeruginosa’. Doctoral Thesis.

Kveim, V.A. (2025) Dissecting the contribution of developmentally-defined neuronal subpopulations to memory functions in the mouse hippocampus. Doctoral Thesis.

Marinucci, Mattia (2025) Molecular and metabolic dynamics in cancer: therapeutic insights for metastatic colorectal cancer and hepatocellular carcinoma. Doctoral Thesis. University of Basel.

Molari, Marco, Shaw, Liam P. and Neher, Richard A. (2025) ‘Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes’, Molecular Biology and Evolution, 42(1). Available at: https://doi.org/10.1093/molbev/msae272.

Morin, Benedict (2025) Human musculoskeletal Staphylococcus aureus infections – characteristics of host-pathogen interactions and treatment failures. Doctoral Thesis. University of Basel.

Pan, Xuya et al. (2025) ‘Coordinated Role of Autophagy and ERAD in Maintaining Neuroendocrine Function by Preventing Prohormone Aggregation’, Advanced Science [Preprint]. Available at: https://doi.org/10.1002/advs.202411662.

Pengue, Simone Raffaello (2025) Diffusion of nucleocytoplasmic transporters in intrinsically disordered proteins enhanced by molecular crowding. Doctoral Thesis. University of Basel.

Pössnecker, Elisabeth (2025) Deciphering B cell dynamics along the gut-brain axis in Multiple Sclerosis. Doctoral Thesis. University of Basel.

Reimão-Pinto, Madalena M. et al. (2025) ‘The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis’, Developmental Cell [Preprint]. Available at: https://doi.org/10.1016/j.devcel.2024.12.038.

Soussi, G. (2025) TBX3 restricts anterior gene expression from the posterior mesenchyme to protect posterior identity that is promoted by HAND2. Doctoral Thesis.

Tauriello, Gerardo et al. (2025) ‘ModelArchive: A Deposition Database for Computational Macromolecular Structural Models’, Journal of Molecular Biology [Preprint]. Available at: https://doi.org/10.1016/j.jmb.2025.168996.

Vaidya, S. et al. (2025) ‘Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation’, Nature Microbiology, 10(1), pp. 144–157. Available at: https://doi.org/10.1038/s41564-024-01886-5.

Yogesh, B. (2025) Neuromodulation of cortex: modulatory signals, computational impact, and evolutionary merit. Doctoral Thesis.

Kelley, Ron et al. (2024) ‘Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2024.12.28.630444.

Barrat-Charlaix, Pierre and Neher, Richard A. (2024) ‘Eco-evolutionary dynamics of adapting pathogens and host immunity’, eLife, 13. Available at: https://doi.org/10.7554/eLife.97350.

Kuwayama, Naohiro et al. (2024) ‘Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation’, Cell Reports, 43(12). Available at: https://doi.org/10.1016/j.celrep.2024.115059.

Chancellor, Andrew et al. (2024) ‘The carbonyl nucleobase adduct M3Ade is a potent antigen for adaptive polyclonal MR1-restricted T cells’, Immunity. 18.12.2024, 58(2), pp. 431–447.e10. Available at: https://doi.org/10.1016/j.immuni.2024.11.019.

Malong, Liza et al. (2024) ‘A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular ASO activity’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory (bioRxiv). Available at: https://doi.org/10.1101/2024.12.17.628665.