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Maffei, E., Burkolter, M., Heyer, Y., Egli, A., Jenal, U. and Harms, A. (2022) ‘Phage Paride hijacks bacterial stress responses to kill dormant, antibiotic-tolerant cells’, bioRxiv, p. 477855. 10.1101/2022.01.26.477855.   edoc | Open Access
Sellner, B., Prakapaitė, R., van Berkum, M., Heinemann, M., Harms, A. and Jenal, U. (2021) ‘A new sugar for an old phage: A c-di-GMP dependent polysaccharide pathway sensitizes E. coli for bacteriophage infection’, bioRxiv. Cold Spring Harbor Laboratory. 10.1101/2021.09.27.461960.   edoc | Open Access
Maffei, E., Shaidullina, A., Burkolter, M., Druelle, V., Willi, L., Estermann, F., Michaelis, S., Hilbi, H., Thaler, D. S. and Harms, A. (2021) ‘Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection’. bioRxiv. 10.1101/2021.03.08.434280.   edoc | Open Access
Maffei, E. and Harms, A. (2021) ‘Messages from the dead protect bacteria from viral attack’, The EMBO Journal, 41(3), p. e110382. 10.15252/embj.2021110382.   edoc
Schirmer, T., de Beer, T. A. P., Tamegger, S., Harms, A., Dietz, N., Dranow, D. M., Edwards, T. E., Myler, P. J., Phan, I. and Dehio, C. (2021) ‘Evolutionary Diversification of Host-Targeted; Bartonella; Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module’, Microorganisms, 9(8), p. 23. 10.3390/microorganisms9081645.   edoc | Open Access
Maffei, E., Fino, C. and Harms, A. (2021) ‘Antibiotic Tolerance and Persistence Studied Throughout Bacterial Growth Phases’, in Verstraeten, N. and Michiels, J. (eds) Bacterial Persistence. Cham: Springer Nature (Methods in Molecular Biology), pp. 23–40. 10.1007/978-1-0716-1621-5.   edoc
Maffei, E., Shaidullina, A., Burkolter, M., Heyer, Y., Estermann, F., Druelle, V., Sauer, P., Willi, L., Michaelis, S., Hilbi, H., Thaler, D. S. and Harms, A. (2021) ‘Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection’, PLoS Biology, 19(11), p. e300142. 10.1371/journal.pbio.3001424.   edoc | Open Access
Reinders, A., Sellner, B., Fadel, F., van Berkum, M., Kaczmarczyk, A., Ozaki, S., Rueher, J., Manfredi, P., Sangermani, M., Harms, A., Perez, C., Schirmer, T. and Jenal, U. (2021) ‘Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity’. bioRxiv. 10.1101/2021.10.01.462762.   edoc
Dietz, N., Huber, M., Sorg, I., Goepfert, A., Harms, A., Schirmer, T. and Dehio, C. (2021) ‘Structural basis for selective AMPylation of Rac-subfamily GTPases by Bartonella effector protein 1 (Bep1)’, Proceedings of the National Academy of Sciences, 118(12), p. e2023245118. 10.1073/pnas.2023245118.   edoc | Open Access
Dietz, N. B., Huber, M., Sorg, I., Goepfert, A., Harms, A., Schirmer, T. and Dehio, C. (2020) ‘Structural basis for selective targeting of Rac subfamily GTPases by a bacterial effector protein’. bioRxiv. 10.1101/2020.06.29.167221.   edoc | Open Access
Righetto, R. D., Anton, L., Adaixo, R., Jakob, R. P., Zivanov, J., Mahi, M.-A., Ringler, P., Schwede, T., Maier, T. and Stahlberg, H. (2020) ‘High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica’, Nature Communications, 11(1), p. 5101. 10.1038/s41467-020-18870-2.   edoc
Fino, C., Vestergaard, M., Ingmer, H., Pierrel, F., Gerdes, K. and Harms, A. (2020) ‘PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10’, MicrobiologyOpen, 9(8), p. e1064. 10.1002/mbo3.1064.   edoc | Open Access
Horesh, G., Fino, C., Harms, A., Dorman, M. J., Parts, L., Gerdes, K., Heinz, E. and Thomson, N. R. (2020) ‘Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population’, Nucleic Acids Research, 48(8), pp. 4357–4370. 10.1093/nar/gkaa198.   edoc
Sorg, I., Schmutz, C., Lu, Y.-Y., Fromm, K., Siewert, L. K., Bögli, A., Strack, K., Harms, A. and Dehio, C. (2020) ‘A Bartonella effector acts as signaling hub for intrinsic STAT3 activation to trigger anti-inflammatory responses’, Cell host & microbe, 27(3), pp. 476–485. 10.1016/j.chom.2020.01.015.   edoc | Open Access
Svenningsen, M. S., Veress, A., Harms, A., Mitarai, N. and Semsey, S. (2019) ‘Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells’, Scientific Reports, 9(1), p. 6056. 10.1038/s41598-019-42403-7.   edoc | Open Access
Harms, A. and Diard, M. (2019) ‘Crowd Controlled-Host Quorum Sensing Drives Phage Decision’, Cell host & microbe, 25(2), pp. 179–181. 10.1016/j.chom.2019.01.016.   edoc
Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A., Collins, J. J., Dehio, C., Fortune, S. M., Ghigo, J.-M., Hardt, W.-D., Harms, A., Heinemann, M., Hung, D. T., Jenal, U., Levin, B. R., Michiels, J., Storz, G., Tan, M.-W., Tenson, T., Van Melderen, L. and Zinkernagel, A. (2019) ‘Definitions and guidelines for research on antibiotic persistence’, Nature Reviews Microbiology, 17(7), pp. 441–448. 10.1038/s41579-019-0196-3.   edoc
Harms, A. (2019) ‘The Biology of Persister Cells in Escherichia coli’, in Lewis, K. (ed.) Persister Cells and Infectious Disease. Cham: Springer Nature, pp. 39–57. 10.1007/978-3-030-25241-0_3.   edoc
Vettiger, A. (2019) Shining light on T6SS mode of action and function within single cells and bacterial communities. 10.5451/unibas-007116201.   edoc | Open Access
Arquint, C., Cubizolles, F., Morand, A., Schmidt, A. and Nigg, E. A. (2018) ‘The SKP1-Cullin-F-box E3 ligase βTrCP and CDK2 cooperate to control STIL abundance and centriole number’, Open biology, 8(2), p. 16. 10.1098/rsob.170253.   edoc
Gruber, A. J., Schmidt, R., Ghosh, S., Martin, G., Gruber, A. R., van Nimwegen, E. and Zavolan, M. (2018) ‘Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC’, Genome biology, 19(1), p. 44. 10.1186/s13059-018-1415-3.   edoc
Rzepiela, A. J., Ghosh, S., Breda, J., Vina-Vilaseca, A., Syed, A. P., Gruber, A. J., Eschbach, K., Beisel, C., van Nimwegen, E. and Zavolan, M. (2018) ‘Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction’, Molecular systems biology, 14(8), p. e8266. 10.15252/msb.20188266.   edoc
Gruber, A. J., Gypas, F., Riba, A., Schmidt, R. and Zavolan, M. (2018) ‘Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms’, Nature methods, 15(10), pp. 832–836. 10.1038/s41592-018-0114-z.   edoc
Harms, A., Brodersen, D. E., Mitarai, N. and Gerdes, K. (2018) ‘Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology’, Molecular cell, 70(5), pp. 768–784. 10.1016/j.molcel.2018.01.003.   edoc
Horesh, G., Harms, A., Fino, C., Parts, L., Gerdes, K., Heinz, E. and Thomson, N. R. (2018) ‘SLING: a tool to search for linked genes in bacterial datasets’, Nucleic Acids Res, 46(21), p. e128. 10.1093/nar/gky738.   edoc
Ferreira-Pinto, M. J., Ruder, L., Capelli, P. and Arber, S. (2018) ‘Connecting Circuits for Supraspinal Control of Locomotion’, Neuron, 100(2), pp. 361–374. 10.1016/j.neuron.2018.09.015.   edoc | Open Access
Hagmann, A. (2018) Regulation of eukaryotic acetyl-CoA carboxylases. 10.5451/unibas-006827378.   edoc | Open Access
Rühl, S. (2018) Effector mechanisms of non-canonical inflammasome activation. 10.5451/unibas-006803410.   edoc | Open Access
Harms, A., Fino, C., Sørensen, M. A., Semsey, S. and Gerdes, K. (2017) ‘Prophages and Growth Dynamics Confound Experimental Results with Antibiotic-Tolerant Persister Cells’, MBio, 8(6), pp. ii:e01964–17. 10.1128/mBio.01964-17.   edoc
Ringel, P. D., Hu, D. and Basler, M. (2017) ‘The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer’, Cell Reports, 21(13), pp. 3927–3940. 10.1016/j.celrep.2017.12.020.   edoc | Open Access
Martin, G., Schmidt, R., Gruber, A. J., Ghosh, S., Keller, W. and Zavolan, M. (2017) ‘3’ End Sequencing Library Preparation with A-seq2’, Journal of Visualized Experiments, (128), p. e56129. 10.3791/56129.   edoc
Herbst, D. A. (2017) Functional architectures of polyketide synthases. 10.5451/unibas-006789988.   edoc | Open Access
Jenal, U., Reinders, A. and Lori, C. (2017) ‘Cyclic di-GMP: second messenger extraordinaire’, Nature Reviews Microbiology, 15(5), pp. 271–284. 10.1038/nrmicro.2016.190.   edoc | Open Access
Storm, P. A., Herbst, D. A., Maier, T. and Townsend, C. A. (2017) ‘Functional and Structural Analysis of Programmed C-Methylation in the Biosynthesis of the Fungal Polyketide Citrinin’, Cell Chemical Biology, 24(3), pp. 316–325. 10.1016/j.chembiol.2017.01.008.   edoc
Vettiger, A., Winter, J., Lin, L. and Basler, M. (2017) ‘The type VI secretion system sheath assembles at the end distal from the membrane anchor’, Nature Communications, 8, p. 16088. 10.1038/ncomms16088.   edoc
Dimitrova, Y., Gruber, A. J., Mittal, N., Ghosh, S., Dimitriades, B., Mathow, D., Grandy, W. A., Christofori, G. and Zavolan, M. (2017) ‘TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition’, Biology Direct, 12(1), p. 8. 10.1186/s13062-017-0180-7.   edoc
Sborgi, L., Rühl, S., Mulvihill, E., Pipercevic, J., Heilig, R., Stahlberg, H., Farady, C. J., Müller, D. J., Broz, P. and Hiller, S. (2016) ‘GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death’, The EMBO Journal, 35(16), pp. 1766–1778. 10.15252/embj.201694696.   edoc | Open Access
Gruber, A. J., Schmidt, R., Gruber, A. R., Martin, G., Ghosh, S., Belmadani, M., Keller, W. and Zavolan, M. (2016) ‘A comprehensive analysis of 3’ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation’, Genome Research, 26(8), pp. 1145–1159. 10.1101/gr.202432.115.   edoc | Open Access
Herbst, D. A., Jakob, R. P., Zähringer, F. and Maier, T. (2016) ‘Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases’, Nature, 531(7595), pp. 533–537. 10.1038/nature16993.   edoc | Open Access
Baron, A. P., von Schubert, C., Cubizolles, F., Siemeister, G., Hitchcock, M., Mengel, A., Schröder, J., Fernández-Montalván, A., von Nussbaum, F., Mumberg, D. and Nigg, E. A. (2016) ‘Probing the catalytic functions of Bub1 kinase using the small molecule inhibitors BAY-320 and BAY-524’, eLife, 5, p. e12187. 10.7554/eLife.12187.   edoc
Renzi, F., Zähringer, U., Chandler, C. E., Ernst, R. K., Cornelis, G. R. and Ittig, S. J. (2016) ‘Modification of the 1-phosphate group during biosynthesis of Capnocytophaga canimorsus lipid A’, Infection and immunity, 84(2), pp. 550–561. 10.1128/IAI.01006-15.   edoc
Matsuda, S., Harmansa, S. and Affolter, M. (2016) ‘BMP morphogen gradients in flies’, Cytokine & Growth Factor Reviews, 27, pp. 119–127. 10.1016/j.cytogfr.2015.11.003.   edoc
Harms, A., Maisonneuve, E. and Gerdes, K. (2016) ‘Mechanisms of bacterial persistence during stress and antibiotic exposure’, Science, 354(6318), p. ii:aaf4268. 10.1126/science.aaf4268.   edoc
Harms, A. and Gerdes, K. (2016) ‘Back to the Roots: Deep View into the Evolutionary History of ADP-Ribosylation Opened by the DNA-Targeting Toxin-Antitoxin Module DarTG’, Molecular cell, 64(6), pp. 1020–1021. 10.1016/j.molcel.2016.11.038.   edoc
Stanger, F. V., Harms, A., Dehio, C. and Schirmer, T. (2016) ‘Crystal Structure of the; Escherichia coli; Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin’, PLoS One, 11(9), p. e0163654. 10.1371/journal.pone.0163654.   edoc
Arquint, C. and Nigg, E. A. (2016) ‘The PLK4-STIL-SAS-6 module at the core of centriole duplication’, Biochemical Society Transactions, 44(5), pp. 1253–1263. 10.1042/BST20160116.   edoc
Harms, A., Stanger, F. V. and Dehio, C. (2016) ‘Biological Diversity and Molecular Plasticity of FIC Domain Proteins’, Annual Reviews of Microbiology. Annual Reviews, pp. 341–360. 10.1146/annurev-micro-102215-095245.   edoc
Hagmann, A., Hunkeler, M., Stuttfeld, E. and Maier, T. (2016) ‘Hybrid Structure of a Dynamic Single-Chain Carboxylase from Deinococcus radiodurans’, Structure, 24(8), pp. 1227–1236. 10.1016/j.str.2016.06.001.   edoc
Vettiger, A. and Basler, M. (2016) ‘Type VI Secretion System Substrates Are Transferred and Reused among Sister Cells’, Cell, 167(1), pp. 99–110.e12. 10.1016/j.cell.2016.08.023.   edoc
Rühl, S. and Broz, P. (2016) ‘The gasdermin-D pore: Executor of pyroptotic cell death’, Oncotarget. Impact Journals LLC, pp. 57481–57482. 10.18632/oncotarget.11421.   edoc
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Ruder, L., Takeoka, A. and Arber, S. (2016) ‘Long-Distance Descending Spinal Neurons Ensure Quadrupedal Locomotor Stability’, Neuron, 92(5), pp. 1063–1078. 10.1016/j.neuron.2016.10.032.   edoc
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Dick, M. S., Sborgi, L., Rühl, S., Hiller, S. and Broz, P. (2016) ‘ASC filament formation serves as a signal amplification mechanism for inflammasomes’, Nature Communications, 7, p. 11929. 10.1038/ncomms11929.   edoc | Open Access
Stanger, F. V., Harms, A., Dehio, C. and Schirmer, T. (2016) ‘Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin’, PLoS ONE, 11(9), p. e0163654. 10.1371/journal.pone.0163654.   edoc | Open Access
Hunkeler, M., Stuttfeld, E., Hagmann, A., Imseng, S. and Maier, T. (2016) ‘The dynamic organization of fungal acetyl-CoA carboxylase’, Nature Communications, 7, p. 11196. 10.1038/ncomms11196.   edoc | Open Access
Stanger, F. V., Burmann, B. M., Harms, A., Aragão, H., Mazur, A., Sharpe, T., Dehio, C., Hiller, S. and Schirmer, T. (2016) ‘Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification’, Proceedings of the National Academy of Sciences of the United States of America, 113(5), pp. E529-E537. 10.1073/pnas.1516930113.   edoc | Open Access
Reinders, A., Hee, C.-S., Ozaki, S., Mazur, A., Boehm, A., Schirmer, T. and Jenal, U. (2016) ‘Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli’, Journal of Bacteriology, 198(3), pp. 448–462. 10.1128/JB.00604-15.   edoc
Bolz, M., Bénard, A., Dreyer, A. M., Kerber, S., Vettiger, A., Oehlmann, W., Singh, M., Duthie, M. S. and Pluschke, G. (2016) ‘Vaccination with the surface proteins MUL_2232 and MUL_3720 of Mycobacterium ulcerans induces antibodies but fails to provide protection against Buruli ulcer’, PLoS neglected tropical diseases, 10(2), p. e0004431. 10.1371/journal.pntd.0004431.   edoc | Open Access
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Rühl, S. and Broz, P. (2015) ‘Caspase-11 activates a canonical NLRP3 inflammasome by promoting K+ efflux’, European journal of immunology, 45(10), pp. 2927–2936. 10.1002/eji.201545772.   edoc
Harms, A., Stanger, F. V., Scheu, P. D., de Jong, I. G., Goepfert, A., Glatter, T., Gerdes, K., Schirmer, T. and Dehio, C. (2015) ‘Adenylylation of Gyrase and Topo IV by FicT Toxins Disrupts Bacterial DNA Topology’, Cell Reports, 12(9), pp. 1497–1507. 10.1016/j.celrep.2015.07.056.   edoc | Open Access
Hollaus, R., Ittig, S. J., Hofinger, A., Haegman, M., Beyaert, R., Kosma, P. and Zamyatina, A. (2015) ‘Chemical synthesis of Burkholderia Lipid A modified with glycosyl phosphodiester-linked 4-amino-4-deoxy-β-L-arabinose and its immunomodulatory potential’, Chemistry, a European journal, 21(10), pp. 4102–4114. 10.1002/chem.201406058.   edoc
Reinders, A. (2015) A moonlighting enzyme imposes second messenger bistability to drive lifestyle decisions in E. coli. 10.5451/unibas-006812280.   edoc | Open Access
Gruber, A. J. (2015) Computational analysis of transcriptional and post-transcriptional regulation of gene expression. 10.5451/unibas-006768410.   edoc | Open Access
Baron, A. (2015) On the regulation of chromosome segregation in human cells : implications of Bub1 Kinase inhibition during cell division. 10.5451/unibas-006624645.   edoc | Open Access
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Gruss, F. (2015) Structural insights into Omp85-mediated protein translocation and insertion in the bacterial outer membrane. 10.5451/unibas-006450358.   edoc | Open Access
Basaldella, E., Takeoka, A., Sigrist, M. and Arber, S. (2015) ‘Multisensory Signaling Shapes Vestibulo-Motor Circuit Specificity’, Cell, Vol. 163, H. 2, pp. 301–312. 10.1016/j.cell.2015.09.023.   edoc
Kanitz, A., Gypas, F., Gruber, A. J., Gruber, A. R., Martin, G. and Zavolan, M. (2015) ‘Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data’, Genome biology, Vol. 16, p. 150. 10.1186/s13059-015-0702-5.   edoc
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Harms, A. (2014) FIC domain toxins are the origin of intra- and inter-kingdom effectors of Bartonella. 10.5451/unibas-006624952.   edoc | Open Access
Gruber, A. R., Martin, G., Müller, P., Schmidt, A., Gruber, A. J., Gumienny, R., Mittal, N., Jayachandran, R., Pieters, J., Keller, W., van Nimwegen, E. and Zavolan, M. (2014) ‘Global 3’ UTR shortening has a limited effect on protein abundance in proliferating T cells’, Nature Communications, 5(5465), pp. 1–10. 10.1038/ncomms6465.   edoc | Open Access
Arquint, C. (2014) On the function and regulation of human STIL - a centrosomal protein implicated in autosomal recessive primary microcephaly. 10.5451/unibas-006331585.   edoc | Open Access
Gruber, A. J., Grandy, W. A., Balwierz, P. J., Dimitrova, Y. A., Pachkov, M., Ciaudo, C., van Nimwegen, E. and Zavolan, M. (2014) ‘Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways’, Nucleic Acids Research, 42(14), pp. 9313–9326. 10.1093/nar/gku544.   edoc | Open Access
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