• Christina Ambrosi, Ramon Pfaendler, Kristeli Eleftheriou, Stefan Butz, Davide C. Recchia, Xue Bao, Richard Cardoso da Silva, Niklas Kupfer, Ilse Lagerwaard, Hanneke Vlaming, Nina Schnolka, Vivek Bhardwaj, Tuncay Baubec (2026). The H3K36me3 methyltransferase SETD2 contributes to PAF1C interactions with RNA Pol II and is required for neuronal differentiation. EMBO Journal Apr 10;45(7)
doi: https://doi.org/10.1038/s44318-026-00768-2
• Richard Cardoso da Silva*, Kristeli Eleftheriou, Davide C. Recchia, Vincent Portegijs, Douwe ten Bulte, Niklas Kupfer, Nathalie Vroegindeweij-de Wagenaar, Xabier Vergara, Ayoub Ouchene, Sander van den Heuvel, Tuncay Baubec* (2025). Engineered chromatin readers track damaged chromatin dynamics in live cells and animals. Nature Communications. Oct 29;14(1):384
doi: https://doi.org/10.1038/s41467-025-65706-y
• Davide C. Recchia, Richard Cardoso da Silva, Niklas Kupfer, Angela Topic, Sara Giuliani, Rodrigo Villaseñor, Tuncay Baubec (2025). A modular toolbox for in cellulo screening of small molecule inhibitors targeting chromatin reader domains. BioRxiv. September/2025.
doi: https://doi.org/10.1101/2025.09.06.674632
• Xabier Vergara, Anna G. Manjón, Marco Novais-Cruz, Marcel de Haas, Ayoub Ouchene, Tom van Schaik, Stefano G. Manzo, Richard Cardoso da Silva, Tuncay Baubec, Bas van Steensel, René H. Medema (2025). Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks. BioRxiv. July/2025.
doi: https://doi.org/10.1101/2025.07.03.662902
• Gibbs VJ, Lin YH, Ghuge AA, Anderson RA, Schiemann AH, Conaglen L, Sansom BJM, Richard Cardoso da Silva, Evelyn Sattlegger (2024). GCN2 in viral Defence and the Subsersive Tactics Employed by Viruses. Journal of Molecular Biology.May 7;168594
doi: https://doi.org/10.1016/j.jmb.2024.168594
• Richard Cardoso da Silva*, Davide C. Recchia, Cristina M. Trueba-Sanchez, Kelly E. Stecker, Tuncay Baubec* (2024). Probing DNA damage sites reveals context-dependent and novel DNA damage response factors. BioRxiv. October/2024
doi: https://doi.org/10.1101/2024.10.23.619792
• Schmolka N, Karemaker ID, Richard Cardoso da Silva, Recchia DC, Spegg V, Bhaskaran J, Teske M, DeWagenaar NP, Altmeyer M, Tuncay Baubec (2023). Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation. Nature Communications. Jun 29;14(1):384
doi: https://doi.org/10.1038/s41467-023-39551-w
• Richard Cardoso da Silva and Gerben Vader (2021). Getting there: understanding the chromosomal recruitment of the AAA+ATPase Pch2/TRIP13 during meiosis. Current Genetics. Aug;67(4):553-565
doi: https://doi.org/10.1007/s00294-021-01166-3
• Mueller F, Friese A, Pathe C, Richard Cardoso da Silva, Rodriguez KB, Musacchio A, Tanja Bange (2021). Overlap of NatA and IAP substrates implicates N-terminal acetylation in protein stabilization. Science Advances. 15;7(3):eabc8590
doi: https://doi.org/10.1126/sciadv.abc8590
• Rondelet A, Pozniakovsky A, Leuschner M, Namboodiri D, Richard Cardoso da Silva, Singh D, Leuschnert M, Poser I, Ssykor A, Berlitz J, Schmidt N, Rohder L, Hyman A, Vader G, Alex Bird (2020). ESI mutagenesis: A one-step method for introducing point mutations into bacterial artificial chromosome transgenes. Life Science Alliance. 8;4(2):e202000836
doi: https://doi.org/10.26508/lsa.202000836
• Villar-Fernández MA, Richard Cardoso da Silva, Pan D, Weir E, Sarembe A, Raina VB, Weir J, Gerben Vader (2020). Biochemical and functional characterization of a meiosis-specific Pch2/ORC AAA+ assembly. Life Science Alliance. 3(11):e20190063
doi: https://doi.org/10.26508/lsa.201900630
BioRxiv: https://doi.org/10.1101/598128
• Richard Cardoso da Silva, Maria A. Villar-Fernández, Gerben Vader (2020). Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase. PLoS Genetics 16(6):e1008905
doi: https://doi.org/10.1371/journal.pgen.1008905
BioRxiv: https://doi.org/10.1101/777003
• Z Akram, Z, Ahmed I, Mack H, Kaur R, Richard Cardoso da Silva, Castilho BA, Friant S, Evelyn Sattlegger, Alan Munn (2020). Yeast as a model to understand actin-mediated cellular functions in mammals - Illustrated with Four Actin Cytoskeleton Proteins. Cells 9 (3), 672
doi: https://doi.org/10.3390/cells9030672
• Richard Cardoso da Silva, Beatriz A. Castilho, Evelyn Sattlegger (2018). A Rapid Extraction Method for mammalian cell cultures, suitable for quantitative immunoblotting analysis of proteins, including phosphorylated GCN2 and eIF2a. MethodsX. Vol5, jan;75-82
doi: https://doi.org/10.1016/j.mex.2017.10.008
• Lee SJ, Ramesh R, de Boor V, Gebler JM, Richard Cardoso da Silva, Evelyn Sattlegger (2017). Cost-effective and rapid lysis of Saccharomyces cerevisiae cells for quantitative western blot analysis of proteins, including phosphorylated eIF2a. Yeast. Sep; 34(9):371-382
doi: https://doi.org/10.1002/yea.3239
• Di Genova BM, Richard Cardoso da Silva, da Cunha JPC, Gargantini PR, Mortara RA, Renata R. Tonelli (2016). Protein SUMOylation is involved in cell cycle Progression in Giardia lamblia. Journal of Eukaryotic Microbiology. Jul;64(4):491-503
doi: https://doi.org/10.1111/jeu.12386
• Richard Cardoso da Silva, Evelyn Sattlegger, Beatriz A. Castilho (2016). Perturbations in actin dynamics reconfigure protein complexes that modulate GCN2 activity and promote an eIF2 response. Journal of Cell Science. Dec 15;129 (24):4521-4533
doi: https://doi.org/10.1242/jcs.194738
• RC, Camara H, De-Souza EA, Pinto S, Pinca AP, Richard Cardoso da Silva, Sato VN, Castilho BA, Marcelo A. Mori (2016). IMPACT is a GCN2 inhibitor that limits lifespan in Caenorhabditis elegans. BMC Biology. Oct7;14(1):87
doi: https://doi.org/10.1186/s12915-016-0301-2
• Richard Cardoso da Silva, Martina Dautel, Bruno M. Di Genova, Davide Amberg, Beatriz A. Castilho, Evelyn Sattlegger (2015). The Gcn2 regulator Yih1 interacts with the cyclin-dependent kinase Cdc28 and promotes cell cycle progression through G2/M in budding yeast. PLoS ONE 10(7): e0131070
doi: https://doi.org/10.1371/journal.pone.0131070
• Castilho BA, Shanmugan R, Richard Cardoso da Silva, Ramesh R, Himme BM, Evelyn Sattlegger (2014). Keeping the eIF2 alpha kinase Gcn2 in check. Biochimica et Biophysica Acta. v. 1843, p. 1948-1968
doi: https://doi.org/10.1016/j.bbamcr.2014.04.006
• Richard Cardoso da Silva#., Ana Carolina B#. Padovan, Daniel C. Pimenta, Renata C. Ferreira, Claudio V. Da Silva, Marcelo RS Briones (2014). Extracellular enolase of Candida albicans is involved in the colonization of mammalian intestinal epithelium. Frontiers in Cellular and Infection Microbiology. v. 4, p. 66-66
doi: https://doi.org/10.3389/fcimb.2014.00066
#shared first authorship
• Wiedemann M, Lee SJ, Richard Cardoso da Silva, Viesweswaraiah J, Soppert J, Evelyn Sattlegger (2013). Simultaneous semi-dry electrophoretic transfer of a wide range of differently sized proteins for immunoblotting. Protocol Exchange, v. 2925, p.e2013.095
doi: dx.doi.org/10.1038/protex.2013.095
• Silva DCF, Richard Cardoso da Silva, Ferreira RC, Marcelo RS Briones (2013). Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins. Frontiers in Genetics, Aug 16;4:143
doi: https://doi.org/10.3389/fgene.2013.00143
arXiv: https://doi.org/10.48550/arXiv.1211.6611
• Cortez C, Martins RM, Alves RM, Richard Cardoso da Silva, Bilches LC, Macedo S, Atayde VD, Kawashita SY, Briones MRS, Nobuko Yoshida (2012). Differential infectivity by the oral route of Trypanosoma cruzi lineages derived from Y strain. PLoS Neglected Tropical Diseases. v.6, p. e1804
doi: https://doi.org/10.1371/journal.pntd.0001804