Publications

ZORA Publication List

Publications

2026
- Journal Article
  - Schimmer, R., Klemm, N., Fullin, J., Topcu, E., Treacy, M., Zielinska, K., Doerdelmann, C., Devesa I Serrano, D., Lock, M., Caiado, F., Koch, C., Dietliker, N., Schwotzer, R., Buehler, M. M., Myllymäki, M., Kurppa, K. J., Manz, M. G., Lopes, M., & Boettcher, S. (2026). Bone marrow failure, somatic rescue by p53 inactivation, and enhanced leukemogenesis in germline ERCC6L2 disease Blood, Epub ahead of print. https://doi.org/10.1182/blood.2025030230
  - Dogan, H., Liptay, M., Barbosa, J. S., Gogola, E., Duarte, A. A., Schmid, J. A., Klebic, I., Mutlu, M., Siffert, M., Francica, P., Salguero, I., van de Ven, M., de Korte-Grimmerink, R., Jackson, S. P., Jonkers, J., Lopes, M., Dibitetto, D., & Rottenberg, S. (2026). MDC1 counteracts replication fork reversal and mediates chemosensitivity in BRCA1/2-deficient tumors Oncogene, 45, 491–504. https://doi.org/10.1038/s41388-025-03659-8
2025
- Journal Article
  - Fullin, J., Topcu, E., Zielińska, K. A., Schimmer, R., Klemm, N., Koch, C., Caiado, F., Lock, M., Doerdelmann, C., Bühler, M., Tchinda, J., Kurppa, K. J., Borsig, L., Jones, P. H., Lopes, M., Manz, M., & Boettcher, S. (2025). The pathogenesis of therapy-related myeloid neoplasms from TP53-mutant clonal hematopoiesis Leukemia, 40, 279–292. https://doi.org/10.1038/s41375-025-02839-5
  - Cherdyntseva, V., Paulson, J., González-Acosta, D., Ubieto-Capella, P., Rodrigues, M., Aouami, M., Adakli, S., Gagné, J.-P., Bakker, C., Poirier, G. G., Taneja, N., & Lopes, M. (2025). Nucleoplasmic Lamin A/C controls replication fork restart upon stress by modulating local H3K9me3 and ADP-ribosylation levels Nature Communications, 16, 11239. https://doi.org/10.1038/s41467-025-66098-9
2024
- Journal Article
  - Merigliano, C., Palumbieri, M. D., Lopes, M., & Chiolo, I. (2024). Replication forks associated with long nuclear actin filaments in mild stress conditions display increased dynamics MicroPublication Biology, 2024, 001259. https://doi.org/10.17912/micropub.biology.001259
  - Dibitetto, D., Liptay, M., Vivalda, F., Dogan, H., Gogola, E., González Fernández, M., Duarte, A., Schmid, J. A., Decollogny, M., Francica, P., Przetocka, S., Durant, S. T., Forment, J. V., Klebic, I., Siffert, M., de Bruijn, R., Kousholt, A. N., Marti, N. A., Dettwiler, M., … Rottenberg, S. (2024). H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours Nature Communications, 15, 4430. https://doi.org/10.1038/s41467-024-48715-1
  - Lynch, J., Troadec, E., Fung, T. K., Gladysz, K., Virely, C., Lau, P. N. I., Cheung, N., Zeisig, B., Wong, J. W. H., Lopes, M., Huang, S., & So, C. W. E. (2024). Hematopoietic stem cell quiescence and DNA replication dynamics maintained by the resilient β-catenin/Hoxa9/Prmt1 axis Blood, 143, 1586–1598. https://doi.org/10.1182/blood.2023022082
  - Ulferts, S., Lopes, M., Miyamoto, K., & Grosse, R. (2024). Nuclear actin dynamics and functions at a glance Journal of Cell Science, 137, jcs261630. https://doi.org/10.1242/jcs.261630
  - González-Acosta, D., & Lopes, M. (2024). DNA replication and replication stress response in the context of nuclear architecture Chromosoma, 133, 57–75. https://doi.org/10.1007/s00412-023-00813-7
  - Muñoz, S., Blanco-Romero, E., González-Acosta, D., Rodriguez-Acebes, S., Megías, D., Lopes, M., & Méndez, J. (2024). RAD51 restricts DNA over-replication from re-activated origins The EMBO Journal, 43, 1043–1064. https://doi.org/10.1038/s44318-024-00038-z
2023
- Journal Article
  - Chanou, A., Weiβ, M., Holler, K., Sajid, A., Straub, T., Krietsch, J., Sanchi, A., Ummethum, H., Lee, C. S. K., Kruse, E., Trauner, M., Werner, M., Lalonde, M., Lopes, M., Scialdone, A., & Hamperl, S. (2023). Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency Nucleic Acids Research, 51, 12303–12324. https://doi.org/10.1093/nar/gkad1022
  - Palumbieri, M. D., Merigliano, C., González-Acosta, D., Kuster, D., Krietsch, J., Stoy, H., von Känel, T., Ulferts, S., Welter, B., Frey, J., Doerdelmann, C., Sanchi, A., Grosse, R., Chiolo, I., & Lopes, M. (2023). Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity Nature Communications, 14, 7819. https://doi.org/10.1038/s41467-023-43183-5
  - Wildschut, M. H. E., Mena, J., Dördelmann, C., van Oostrum, M., Hale, B. D., Settelmeier, J., Festl, Y., Lysenko, V., Schürch, P. M., Ring, A., Severin, Y., Bader, M. S., Pedrioli, P. G. A., Goetze, S., van Drogen, A., Balabanov, S., Skoda, R. C., Lopes, M., Wollscheid, B., … Snijder, B. (2023). Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis Nature Communications, 14, 6414. https://doi.org/10.1038/s41467-023-42101-z
  - Rastokina, A., Cebrián, J., Mozafari, N., Mandel, N. H., Smith, C. I. E., Lopes, M., Zain, R., & Mirkin, S. M. (2023). Large-scale expansions of Friedreich’s ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Research, 51, 8532–8549. https://doi.org/10.1093/nar/gkad441
  - Andrs, M., Stoy, H., Boleslavska, B., Chappidi, N., Kanagaraj, R., Nascakova, Z., Menon, S., Rao, S., Oravetzova, A., Dobrovolna, J., Surendranath, K., Lopes, M., & Janscak, P. (2023). Excessive reactive oxygen species induce transcription-dependent replication stress Nature Communications, 14, 1791. https://doi.org/10.1038/s41467-023-37341-y
  - Stoy, H., Zwicky, K., Kuster, D., Lang, K. S., Krietsch, J., Crossley, M. P., Schmid, J. A., Cimprich, K. A., Merrikh, H., & Lopes, M. (2023). Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids Nature Structural & Molecular Biology, 30, 348–359. https://doi.org/10.1038/s41594-023-00928-6
  - Clerbaux, L.-A., Cordier, P., Desboeufs, N., Unger, K., Leary, P., Semere, G., Boege, Y., Chan, L. K., Desdouets, C., Lopes, M., & Weber, A. (2023). Mcl-1 deficiency in murine livers leads to nuclear polyploidisation and mitotic errors: Implications for hepatocellular carcinoma JHEP Reports, 5, 100838. https://doi.org/10.1016/j.jhepr.2023.100838
2022
- Journal Article
  - Jacobs, K., Doerdelmann, C., Krietsch, J., González-Acosta, D., Mathis, N., Kushinsky, S., Guarino, E., Gómez-Escolar, C., Martinez, D., Schmid, J. A., Leary, P. J., Freire, R., Ramiro, A. R., Eischen, C. M., Mendez, J., & Lopes, M. (2022). Stress-triggered hematopoietic stem cell proliferation relies on PrimPol-mediated repriming Molecular Cell, 82, 4176-4188.e8. https://doi.org/10.1016/j.molcel.2022.09.009
  - Dibitetto, D., Marshall, S., Sanchi, A., Liptay, M., Badar, J., Lopes, M., Rottenberg, S., & Smolka, M. B. (2022). DNA-PKcs promotes fork reversal and chemoresistance Molecular Cell, 82, 3932-3942.e6. https://doi.org/10.1016/j.molcel.2022.08.028
  - Giansanti, C., Manzini, V., Dickmanns, A., Dickmanns, A., Palumbieri, M. D., Sanchi, A., Kienle, S. M., Rieth, S., Scheffner, M., Lopes, M., & Dobbelstein, M. (2022). MDM2 binds and ubiquitinates PARP1 to enhance DNA replication fork progression Cell Reports, 39, 110879. https://doi.org/10.1016/j.celrep.2022.110879
2021
- Journal Article
  - Tromans-Coia, C., Sanchi, A., Moeller, G. K., Timinszky, G., Lopes, M., & Ahel, I. (2021). TARG1 protects against toxic DNA ADP-ribosylation Nucleic Acids Research, 49, 10477–10492. https://doi.org/10.1093/nar/gkab771
  - González-Acosta, D., Blanco-Romero, E., Ubieto-Capella, P., Mutreja, K., Míguez, S., Llanos, S., García, F., Muñoz, J., Blanco, L., Lopes, M., & Méndez, J. (2021). PrimPol-mediated repriming facilitates replication traverse of DNA interstrand crosslinks The EMBO Journal, 40, e106355. https://doi.org/10.15252/embj.2020106355
2020
- Journal Article
  - Rainey, M. D., Quinlan, A., Cazzaniga, C., Mijic, S., Martella, O., Krietsch, J., Göder, A., Lopes, M., & Santocanale, C. (2020). CDC7 kinase promotes MRE11 fork processing, modulating fork speed and chromosomal breakage EMBO Reports, 21, e48920. https://doi.org/10.15252/embr.201948920
  - Berti, M., Teloni, F., Mijic, S., Ursich, S., Fuchs, J., Palumbieri, M. D., Krietsch, J., Schmid, J. A., Garcin, E. B., Gon, S., Modesti, M., Altmeyer, M., & Lopes, M. (2020). Sequential role of RAD51 paralog complexes in replication fork remodeling and restart Nature Communications, 11, 3531. https://doi.org/10.1038/s41467-020-17324-z
  - Takizawa, H., Fritsch, K., Kovtonyuk, L. V., Saito, Y., Yakkala, C., Jacobs, K., Ahuja, A. K., Lopes, M., Hausmann, A., Hardt, W.-D., Gomariz, Á., Nombela-Arrieta, C., & Manz, M. G. (2020). Pathogen-induced TLR4-TRIF innate immune signaling in hematopoietic stem cells promotes proliferation but reduces competitive fitness Cell Stem Cell, 27, 177. https://doi.org/10.1016/j.stem.2020.06.010
  - Bai, G., Kermi, C., Stoy, H., Schiltz, C. J., Bacal, J., Zaino, A. M., Hadden, M. K., Eichman, B. F., Lopes, M., & Cimprich, K. A. (2020). HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis Molecular Cell, 78, 1237-1251.e7. https://doi.org/10.1016/j.molcel.2020.04.031
  - Chappidi, N., Nascakova, Z., Boleslavska, B., Zellweger, R., Isik, E., Andrs, M., Menon, S., Dobrovolna, J., Balbo Pogliano, C., Matos, J., Porro, A., Lopes, M., & Janscak, P. (2020). Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops Molecular Cell, 77, 528-541.e8. https://doi.org/10.1016/j.molcel.2019.10.026
  - Berti, M., Cortez, D., & Lopes, M. (2020). The plasticity of DNA replication forks in response to clinically relevant genotoxic stress Nature Reviews. Molecular Cell Biology, 21, 633–651. https://doi.org/10.1038/s41580-020-0257-5
2019
- Journal Article
  - Gogola, E., Duarte, A. A., de Ruiter, J. R., Wiegant, W. W., Schmid, J. A., de Bruijn, R., James, D. I., Llobet, S. G., Vis, D. J., Annunziato, S., van den Broek, B., Barazas, M., Kersbergen, A., van de Ven, M., Tarsounas, M., Ogilvie, D. J., van Vugt, M., Wessels, L. F. A., Bartkova, J., … Rottenberg, S. (2019). Correction: Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality Cancer Cell, 35, 950–952. https://doi.org/10.1016/j.ccell.2019.05.012
  - Garzón, J., Ursich, S., Lopes, M., Hiraga, S.-I., & Donaldson, A. D. (2019). Human RIF1-Protein Phosphatase 1 Prevents Degradation and Breakage of Nascent DNA on Replication Stalling Cell Reports, 27, 2558-2566.e4. https://doi.org/10.1016/j.celrep.2019.05.002
2018
- Journal Article
  - Mutreja, K., Krietsch, J., Hess, J., Ursich, S., Berti, M., Roessler, F. K., Zellweger, R., Patra, M., Gasser, G., & Lopes, M. (2018). ATR-Mediated Global Fork Slowing and Reversal Assist Fork Traverse and Prevent Chromosomal Breakage at DNA Interstrand Cross-Links Cell Reports, 24, 2629-2642.e5. https://doi.org/10.1016/j.celrep.2018.08.019
  - Schmid, J. A., Berti, M., Walser, F., Raso, M. C., Schmid, F., Krietsch, J., Stoy, H., Zwicky, K., Ursich, S., Freire, R., Lopes, M., & Penengo, L. (2018). Histone Ubiquitination by the DNA Damage Response Is Required for Efficient DNA Replication in Unperturbed S Phase Molecular Cell, 71, 897-910.e8. https://doi.org/10.1016/j.molcel.2018.07.011
  - Menin, L., Ursich, S., Trovesi, C., Zellweger, R., Lopes, M., Longhese, M. P., & Clerici, M. (2018). Tel1/ATM prevents degradation of replication forks that reverse after topoisomerase poisoning EMBO Reports, e45535. https://doi.org/10.15252/embr.201745535
  - Hafner, L., Lezaja, A., Zhang, X., Lemmens, L., Shyian, M., Albert, B., Follonier, C., Nunes, J. M., Lopes, M., Shore, D., & Mattarocci, S. (2018). Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration Cell Reports, 23, 983–992. https://doi.org/10.1016/j.celrep.2018.03.113
2017
- Journal Article
  - Mijic, S., Zellweger, R., Chappidi, N., Berti, M., Jacobs, K., Mutreja, K., Ursich, S., Ray Chaudhuri, A., Nussenzweig, A., Janscak, P., & Lopes, M. (2017). Replication fork reversal triggers fork degradation in BRCA2-defective cells Nature Communications, 8, 859. https://doi.org/10.1038/s41467-017-01164-5
  - Boege, Y., Malehmir, M., Healy, M. E., Wolf, M. J., Böhm, F., Frick, L., Maire, R., Moch, H., Heikenwalder, M., Weber, A., Lopes, M., & et al. (2017). A Dual Role of Caspase-8 in Triggering and Sensing Proliferation-Associated DNA Damage, a Key Determinant of Liver Cancer Development Cancer Cell, 32, 342-359.e10. https://doi.org/10.1016/j.ccell.2017.08.010
  - Vujanovic, M., Krietsch, J., Raso, M. C., Terraneo, N., Zellweger, R., Schmid, J. A., Taglialatela, A., Huang, J.-W., Holland, C. L., Zwicky, K., Herrador, R., Jacobs, H., Cortez, D., Ciccia, A., Penengo, L., & Lopes, M. (2017). Replication Fork Slowing and Reversal upon DNA Damage Require PCNA Polyubiquitination and ZRANB3 DNA Translocase Activity Molecular Cell, 67, 882-890.e5. https://doi.org/10.1016/j.molcel.2017.08.010
  - Takizawa, H., Fritsch, K., Kovtonyuk, L. V., Saito, Y., Yakkala, C., Jacobs, K., Ahuja, A. K., Lopes, M., Hausmann, A., Hardt, W.-D., Gomariz, Á., Nombela-Arrieta, C., & Manz, M. G. (2017). Pathogen-induced TLR4-TRIF innate immune signaling in hematopoietic stem cells promotes proliferation but reduces competitive fitness Cell Stem Cell, 21, 225-240.e5. https://doi.org/10.1016/j.stem.2017.06.013
  - Vindigni, A., & Lopes, M. (2017). Combining electron microscopy with single molecule DNA fiber approaches to study DNA replication dynamics Biophysical Chemistry, 225, 3–9. https://doi.org/10.1016/j.bpc.2016.11.014
2016
- Journal Article
  - Piwko, W., Mlejnkova, L. J., Mutreja, K., Ranjha, L., Stafa, D., Smirnov, A., Brodersen, M. M. L., Zellweger, R., Sturzenegger, A., Janscak, P., Lopes, M., Peter, M., & Cejka, P. (2016). The MMS22L-TONSL heterodimer directly promotes RAD51-dependent recombination upon replication stress The EMBO Journal, 35, 2584–2601. https://doi.org/10.15252/embj.201593132
  - Ribeyre, C., Zellweger, R., Chauvin, M., Bec, N., Larroque, C., Lopes, M., & Constantinou, A. (2016). Nascent DNA proteomics reveals a chromatin remodeler required for topoisomerase i loading at replication forks Cell Reports, 15, 300–309. https://doi.org/10.1016/j.celrep.2016.03.027
  - Galanos, P., Vougas, K., Walter, D., Polyzos, A., Maya-Mendoza, A., Haagensen, E. J., Kokkalis, A., Roumelioti, F.-M., Gagos, S., Tzetis, M., Canovas, B., Igea, A., Ahuja, A. K., Zellweger, R., Havaki, S., Kanavakis, E., Kletsas, D., Roninson, I. B., Garbis, S. D., … Gorgoulis, V. G. (2016). Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing Nature Cell Biology, 18, 777–789. https://doi.org/10.1038/ncb3378
  - Ahuja, A. K., Jodkowska, K., Teloni, F., Bizard, A. H., Zellweger, R., Herrador, R., Ortega, S., Hickson, I. D., Altmeyer, M., Mendez, J., & Lopes, M. (2016). A short G1 phase imposes constitutive replication stress and fork remodelling in mouse embryonic stem cells Nature Communications, 7, 10660–10671. https://doi.org/10.1038/ncomms10660
2015
- Journal Article
  - Fugger, K., Mistrik, M., Neelsen, K. J., Yao, Q., Zellweger, R., Kousholt, A. N., Haahr, P., Chu, W. K., Bartek, J., Lopes, M., Hickson, I. D., & Sørensen, C. S. (2015). FBH1 Catalyzes Regression of Stalled Replication Forks Cell Reports, 10, 1749–1757. https://doi.org/10.1016/j.celrep.2015.02.028
  - Zellweger, R., Dalcher, D., Mutreja, K., Berti, M., Schmid, J. A., Herrador, R., Vindigni, A., & Lopes, M. (2015). Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells Journal of Cell Biology, 208, 563–579. https://doi.org/10.1083/jcb.201406099
  - Thangavel, S., Berti, M., Levikova, M., Pinto, C., Gomathinayagam, S., Vujanovic, M., Zellweger, R., Moore, H., Lee, E. H., Hendrickson, E. A., Cejka, P., Stewart, S., Lopes, M., & Vindigni, A. (2015). DNA2 drives processing and restart of reversed replication forks in human cells Journal of Cell Biology, 208, 545–562. https://doi.org/10.1083/jcb.201406100
  - Neelsen, K. J., & Lopes, M. (2015). Replication fork reversal in eukaryotes: from dead end to dynamic response Nature Reviews. Molecular Cell Biology, 16, 207–220. https://doi.org/10.1038/nrm3935
  - Fumasoni, M., Zwicky, K., Vanoli, F., Lopes, M., & Branzei, D. (2015). Error-Free DNA Damage Tolerance and Sister Chromatid Proximity during DNA Replication Rely on the Polα/Primase/Ctf4 Complex Molecular Cell, 1–13. https://doi.org/10.1016/j.molcel.2014.12.038
  - Gemble, S., Ahuja, A., Buhagiar-Labarchède, G., Onclercq-Delic, R., Dairou, J., Biard, D. S. F., Lambert, S., Lopes, M., & Amor-Guéret, M. (2015). Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA PLoS Genetics, 11, e1005384. https://doi.org/10.1371/journal.pgen.1005384
2014
- Journal Article
  - Ray Chaudhuri, A., Ahuja, A. K., Herrador, R., & Lopes, M. (2014). Poly(ADP-ribosyl)gycohydrolase (PARG) prevents the accumulation of unusual replication structures during unperturbed S phase Molecular and Cellular Biology, 1–33. https://doi.org/10.1128/MCB.01077-14
  - Giannattasio, M., Zwicky, K., Follonier, C., Foiani, M., Lopes, M., & Branzei, D. (2014). Visualization of recombination-mediated damage bypass by template switching Nature Structural & Molecular Biology, 21, 884–892. https://doi.org/10.1038/nsmb.2888
  - Mejlvang, J., Feng, Y., Alabert, C., Neelsen, K. J., Jasencakova, Z., Zhao, X., Lees, M., Sandelin, A., Pasero, P., Lopes, M., & Groth, A. (2014). New histone supply regulates replication fork speed and PCNA unloading Journal of Cell Biology, 204, 29–43. https://doi.org/10.1083/jcb.201305017
2013
- Journal Article
  - Follonier, C., Oehler, J., Herrador, R., & Lopes, M. (2013). Friedreich’s ataxia-associated GAA repeats induce replication-fork reversal and unusual molecular junctions. Nature Structural & Molecular Biology, 20, 486–494. https://doi.org/10.1038/nsmb.2520
  - Neelsen, K. J., Zanini, I. M. Y., Herrador, R., & Lopes, M. (2013). Oncogenes induce genotoxic stress by mitotic processing of unusual replication intermediates Journal of Cell Biology, 200, 699–708. https://doi.org/10.1083/jcb.201212058
  - Neelsen, K. J., Zanini, I. M. Y., Mijic, S., Herrador, R., Zellweger, R., Ray Chaudhuri, A., Creavin, K. D., Blow, J. J., & Lopes, M. (2013). Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template Genes and Development, 27, 2537–2542. https://doi.org/10.1101/gad.226373.113
  - Berti, M., Chaudhuri, A. R., Thangavel, S., Gomathinayagam, S., Kenig, S., Vujanovic, M., Odreman, F., Glatter, T., Graziano, S., Mendoza-Maldonado, R., Marino, F., Lucic, B., Biasin, V., Gstaiger, M., Aebersold, R., Sidorova, J. M., Monnat, R. J., Lopes, M., & Vindigni, A. (2013). Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition Nature Structural & Molecular Biology, 20, 347–354. https://doi.org/10.1038/nsmb.2501
2012
- Journal Article
  - Ray Chaudhuri, A., Hashimoto, Y., Herrador, R., Neelsen, K. J., Fachinetti, D., Bermejo, R., Cocito, A., Costanzo, V., & Lopes, M. (2012). Topoisomerase I poisoning results in PARP-mediated replication fork reversal Nature Structural & Molecular Biology, 19, 417–423. https://doi.org/10.1038/nsmb.2258
  - Peña-Diaz, J., Bregenhorn, S., Ghodgaonkar, M., Follonier, C., Artola-Borán, M., Castor, D., Lopes, M., Sartori, A. A., & Jiricny, J. (2012). Noncanonical Mismatch Repair as a Source of Genomic Instability in Human Cells Molecular Cell, 47, 669–680. https://doi.org/10.1016/j.molcel.2012.07.006
2011
- Journal Article
  - Engels, K., Giannattasio, M., Muzi-Falconi, M., Lopes, M., & Ferrari, S. (2011). 14-3-3 proteins regulate exonuclease 1-dependent processing of stalled replication forks PLoS Genetics, 7, e1001367. https://doi.org/10.1371/journal.pgen.1001367
  - Toller, I. M., Neelsen, K. J., Steger, M., Hartung, M. L., Hottiger, M. O., Stucki, M., Kalali, B., Gerhard, M., Sartori, A. A., Lopes, M., & Müller, A. (2011). Carcinogenic bacterial pathogen Helicobacter pylori triggers DNA double-strand breaks and a DNA damage response in its host cells Proceedings of the National Academy of Sciences of the United States of America, 108, 14944–14949. https://doi.org/10.1073/pnas.1100959108
2010
- Journal Article
  - Hashimoto, Y., Chaudhuri, A. R., Lopes, M., & Costanzo, V. (2010). Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis Nature Structural & Molecular Biology, 17, 1305–1311. https://doi.org/10.1038/nsmb.1927
  - Giannattasio, M., Follonier, C., Tourrière, H., Puddu, F., Lazzaro, F., Pasero, P., Lopes, M., Plevani, P., & Muzi-Falconi, M. (2010). Exo1 competes with repair synthesis, converts NER intermediates to long ssDNA gaps, and promotes checkpoint activation Molecular Cell, 40, 50–62. https://doi.org/10.1016/j.molcel.2010.09.004
2009
- Journal Article
  - Lopes, M. (2009). Electron microscopy methods for studying in vivo DNA replication intermediates Methods in Molecular Biology, 521, 605–631. https://doi.org/10.1007/978-1-60327-815-7_34
2007
- Journal Article
  - Mojas, N., Lopes, M., & Jiricny, J. (2007). Mismatch repair-dependent processing of methylation damage gives rise to persistent single-stranded gaps in newly replicated DNA Genes and Development, 21, 3342–3355. https://doi.org/10.1101/gad.455407
2006
- Journal Article
  - Lopes, M., Foiani, M., & Sogo, J. M. (2006). Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions Molecular Cell, 21, 15–27. https://doi.org/10.1016/j.molcel.2005.11.015
  - Liberi, G., Cotta-Ramusino, C., Lopes, M., Sogo, J., Conti, C., Bensimon, A., & Foiani, M. (2006). Methods to study replication fork collapse in budding yeast Methods in Enzymology, 409, 442–462. https://doi.org/10.1016/S0076-6879(05)09026-9
2005
- Journal Article
  - Cotta-Ramusino, C., Fachinetti, D., Lucca, C., Doksani, Y., Lopes, M., Sogo, J., & Foiani, M. (2005). Exo1 processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells Molecular Cell, 17, 153–159. https://doi.org/10.1016/j.molcel.2004.11.032
  - Liberi, G., Maffioletti, G., Lucca, C., Chiolo, I., Baryshnikova, A., Cotta-Ramusino, C., Lopes, M., Pellicioli, A., Harber, J. E., & Foiani, M. (2005). Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase Genes and Development, 19, 339–350. https://doi.org/10.1101/gad.322605
2004
- Journal Article
  - Grossi, S., Puglisi, A., Dmitriev, P. V., Lopes, M., & Shore, D. (2004). Pol12, the B subunit of DNA polymerase alpha, functions in both telomere capping and length regulation Genes and Development, 18, 992–1006. https://doi.org/10.1101/gad.300004
2003
- Journal Article
  - Lopes, M., Cotta-Ramusino, C., Liberi, G., & Foiani, M. (2003). Branch migrating sister chromatid junctions form at replication origins through Rad51/Rad52-independent mechanisms Molecular Cell, 12, 1499–1510. https://doi.org/10.1016/S1097-2765(03)00473-8
2002
- Journal Article
  - Sogo, J. M., Lopes, M., & Foiani, M. (2002). Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects Science, 297, 599–602. https://doi.org/10.1126/science.1074023

M. Lopes, C. Cotta-Ramusino, A. Pellicioli, G. Liberi, P. Plevani, M. Muzi-Falconi, C. S. Newlon and M. Foiani The DNA replication checkpoint response stabilizes stalled replication forks Nature 412, 557-561 (2001)

M.Foiani, A.Pellicioli, M.Lopes, C.Lucca, M.Ferrari, G.Liberi, M.Muzi Falconi, and P.PLevani. DNA damage checkpoints and DNA replication controls in Saccharomyces cerevisiae. Mutat Res.451(1-2):187-96.(2000)

G. Liberi, Chiolo I., Pellicioli A., Lopes M., Muzi-Falconi M., Plevani P. and Foiani M. Srs2 DNA helicase is involved in checkpoint response and its regulation requires a functional Mec1- dependent pathway and CDK1 activity. EMBO J. 19, 1, (2000).

A.Pellicioli, C.Lucca, G.Liberi, F.Marini, M.Lopes, P.Plevani, A.Romano, P.Di Fiore, and M.Foiani. (1999) Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J., 18, 6561-6572. (1999)

M.Foiani, M.Ferrari, G.Liberi, M.Lopes, C.Lucca, F.Marini, A.Pellicioli, M.Muzi-Falconi, P.Plevani (1998). S-phase DNA damage checkpoint in budding yeast. Biol.Chem. 379, 1019-1023.

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