• 2025
  Hipp C, Mussgnug S, Choudhary P, Kang HS, Asami S, Sastre J, Donau C, Böttcher R, Gemmecker G, Boekhoven J, Förstemann K, Sattler M, Molecular mechanisms of biomolecular condensate formation in Drosophila melanogaster siRNA biogenesis., Nucleic Acids Res 2025 Jul; 53(14): .
• 2025
  Parul Singh, Justine Couble, Jacques Serizay, Maureen D Cabahug, Catarina Rosa, Patty Chen, Artur Scherf, Romain Koszul, Sebastian Baumgarten, Jessica M Bryant, High-resolution map of the Plasmodium falciparum genome reveals MORC/ ApiAP2-mediated links between distant, functionally related genes, Nature Microbiology, 2025, 10 (7), pp.1665-1683. ⟨10.1038/s41564-025-02038-z⟩.
• 2024
  Vignolini T, Capitanio M, Caldini C, Gardini L, Pavone FS, Highly inclined light sheet allows volumetric super-resolution imaging of efflux pumps distribution in bacterial biofilms., Sci Rep 2024 Jun; 14(1): 12902.
• 2024
  Vignolini T, Couble JEC, Doré GRG, Baumgarten S, Transcript tinkering: RNA modifications in protozoan parasites., Curr Opin Microbiol 2024 Jun; 79(): 102477.
• 2023
  Rosa C, Singh P, Chen P, Sinha A, Claës A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM, Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite., EMBO Rep 2023 Aug; (): e57090.
• 2023
  Gardini L, Vignolini T, Curcio V, Pavone FS, Capitanio M, Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy., Opt Express 2023 Jul; 31(16): 26208-26225.
• 2023
  Yılmaz VM, Ramnarine TJS, Königer A, Mussgnug S, Grath S, Tropical super flies: Integrating Cas9 into Drosophila ananassae and its phenotypic effects., J Insect Physiol 2023 Jun; 147(): 104516.
• 2023
  Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A, , Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion., Life Sci Alliance 2023 Jan; 6(1): .
• 2022
  Casalone E, Vignolini T, Braconi L, Gardini L, Capitanio M, Pavone FS, Giovannelli L, Dei S, Teodori E, Characterization of substituted piperazines able to reverse MDR in Escherichia coli strains overexpressing resistance-nodulation-cell division (RND) efflux pumps., J Antimicrob Chemother 2022 Feb; 77(2): 413-424.
• 2021
  Elie Hammam, Ameya Sinha, Sebastian Baumgarten, Flore Nardella, Jiaqi Liang, Samia Miled, Frédéric Bonhomme, Diane Erdmann, Benoit Arcangioli, Paola B. Arimondo, Peter Dedon, Peter Preiser, Artur Scherf, Malaria Parasite Stress Tolerance Is Regulated by DNMT2-Mediated tRNA Cytosine Methylation, mBio. 2021 Nov-Dec; 12(6): e02558-21.
• 2021
  Sinha A, Baumgarten S, Distiller A, McHugh E, Chen P, Singh M, Bryant JM, Liang J, Cecere G, Dedon PC, Preiser PR, Ralph SA, Scherf A, , Functional Characterization of the m6A-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite., mBio 2021 04; 12(2): .
• 2021
  Dard C, Swale C, Brenier-Pinchart MP, Farhat DC, Bellini V, Robert MG, Cannella D, Pelloux H, Tardieux I, Hakimi MA, , A brain cyst load-associated antigen is a Toxoplasma gondii biomarker for serodetection of persistent parasites and chronic infection., BMC Biol 2021 02; 19(1): 25.
• 2020
  Bryant JM, Baumgarten S, Dingli F, Loew D, Sinha A, Claës A, Preiser PR, Dedon PC, Scherf A, , Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite., Mol Syst Biol 2020 08; 16(8): e9569.
• 2020
  Omelianczyk RI, Loh HP, Chew M, Hoo R, Baumgarten S, Renia L, Chen J, Preiser PR, , Rapid activation of distinct members of multigene families in Plasmodium spp., Commun Biol 2020 07; 3(1): 351.
• 2020
  Casalone E, Vignolini T, Braconi L, Gardini L, Capitanio M, Pavone FS, Dei S, Teodori E, 1-benzyl-1,4-diazepane reduces the efflux of resistance-nodulation-cell division pumps in Escherichia coli., Future Microbiol 2020 Jul; 15(): 987-999.
• 2020
  Farhat DC, Swale C, Dard C, Cannella D, Ortet P, Barakat M, Sindikubwabo F, Belmudes L, De Bock PJ, Couté Y, Bougdour A, Hakimi MA, , A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment., Nat Microbiol 2020 04; 5(4): 570-583.
• 2019
  Baumgarten S, Bryant JM, Sinha A, Reyser T, Preiser PR, Dedon PC, Scherf A, , Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development., Nat Microbiol 2019 12; 4(12): 2246-2259.
• 2018
  Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A, Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti., ACS Synth Biol 2018 Oct; 7(10): 2365-2378.
• 2018
  Droll D, Wei G, Guo G, Fan Y, Baumgarten S, Zhou Y, Xiao Y, Scherf A, Zhang Q, , Disruption of the RNA exosome reveals the hidden face of the malaria parasite transcriptome., RNA Biol 2018 ; 15(9): 1206-1214.
• 2018
  Zanghì G, Vembar SS, Baumgarten S, Ding S, Guizetti J, Bryant JM, Mattei D, Jensen ATR, Rénia L, Goh YS, Sauerwein R, Hermsen CC, Franetich JF, Bordessoulles M, Silvie O, Soulard V, Scatton O, Chen P, Mecheri S, Mazier D, Scherf A, , A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection., Cell Rep 2018 03; 22(11): 2951-2963.
• 2018
  Vignolini T, Mengoni A, Fondi M, Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models., Methods Mol Biol 2018 ; 1716(): 177-196.
• 2017
  Baumgarten S, Cziesielski MJ, Thomas L, Michell CT, Esherick LY, Pringle JR, Aranda M, Voolstra CR, , Evidence for miRNA-mediated modulation of the host transcriptome in cnidarian-dinoflagellate symbiosis., Mol Ecol 2018 01; 27(2): 403-418.
• 2017
  Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M, , Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals., Sci Rep 2017 12; 7(1): 17583.
• 2017
  Yum LK, Baumgarten S, Röthig T, Roder C, Roik A, Michell C, Voolstra CR, , Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals., Sci Rep 2017 07; 7(1): 6442.
• 2017
  Liew YJ, Li Y, Baumgarten S, Voolstra CR, Aranda M, , Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum., PLoS Genet 2017 02; 13(2): e1006619.
• 2016
  Wolfowicz I, Baumgarten S, Voss PA, Hambleton EA, Voolstra CR, Hatta M, Guse A, , Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians., Sci Rep 2016 09; 6(): 32366.
• 2016
  Vignolini T, Macera L, Antonelli G, Pistello M, Maggi F, Giannecchini S, Investigation on torquetenovirus (TTV) microRNA transcriptome in vivo., Virus Res 2016 Jun; 217(): 18-22.
• 2016
  Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG, , Comparative genomics explains the evolutionary success of reef-forming corals., Elife 2016 05; 5(): .
• 2016
  Ryu T, Seridi L, Moitinho-Silva L, Oates M, Liew YJ, Mavromatis C, Wang X, Haywood A, Lafi FF, Kupresanin M, Sougrat R, Alzahrani MA, Giles E, Ghosheh Y, Schunter C, Baumgarten S, Berumen ML, Gao X, Aranda M, Foret S, Gough J, Voolstra CR, Hentschel U, Ravasi T, , Hologenome analysis of two marine sponges with different microbiomes., BMC Genomics 2016 Feb; 17(): 158.
• 2016
  Parkinson JE, Baumgarten S, Michell CT, Baums IB, LaJeunesse TC, Voolstra CR, , Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium., Genome Biol Evol 2016 Feb; 8(3): 665-80.
• 2015
  Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra CR, , The genome of Aiptasia, a sea anemone model for coral symbiosis., Proc Natl Acad Sci U S A 2015 Sep; 112(38): 11893-8.
• 2014
  Liew YJ, Aranda M, Carr A, Baumgarten S, Zoccola D, Tambutté S, Allemand D, Micklem G, Voolstra CR, , Identification of microRNAs in the coral Stylophora pistillata., PLoS One 2014 ; 9(3): e91101.
• 2013
  Baumgarten S, Bayer T, Aranda M, Liew YJ, Carr A, Micklem G, Voolstra CR, , Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals., BMC Genomics 2013 Oct; 14(): 704.