Peer-reviewd papers | Preprints

  1. Luo, J., Vale-Silva, L.A., Raghavan, A.R., Mercy, G., Heldrich, J., Sun, X., Li, M.K., Zhang, W., Agmon, N., Yang, K., Cai, J., Stracquadanio, G., Thierry, A., Zhao, Y., Coelho, C., McCulloch, L.H., Lauer, S., Build-A-Genome Class, Kaback, D.B., Bader, J.S., Mitchell, L.A., Mozziconacci, J., Koszul, R., Hochwagen, A., Boeke, J.D. (2023) Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. Cell Genom. Pubmed

  2. Rahimi, A., Vale-Silva, L.A., Savitski, M.F., Tanevski, J., Saez-Rodriguez, J. (2023) DOT: A flexible multi-objective optimization framework for transferring features across single-cell and spatial omics. Preprint arXiv doi: 10.48550/arXiv.2301.01682 arXiv

  3. Heldrich, J., Milano, C.R., Markowitz, T.E., Ur, S.N., Vale-Silva, L.A., Corbett, K.D., Hochwagen, A. (2022) Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae. Preprint bioRxiv doi: 10.1101/2020.08.11.247122 and Nucleic Acids Res. bioRxiv | Pubmed

  4. Vale-Silva, L.A. & Rohr, K. (2020) Long-term cancer survival prediction using multimodal deep learning. Preprint medRxiv doi: 10.1101/2020.08.06.20169698 and Sci Rep. 11:13505.medRxiv | Pubmed | Full text

  5. Dao Thi, V.L., Wu, X., Belote, R., Andreo, U., Takacs, C., Fernandez, J., Vale Silva, L.A., Prallet, S., Decker, C., Fu, R., Qu, B., Uryu, K., Molina, H., Saeed, M., Steinmann, E., Urban, S., Singaraja, R., Schneider, W., Simon, S. and Rice, C.M. (2020) Stem cell-derived polarized hepatocytes. Nat Commun. 11, 1677. Pubmed

  6. Heldrich. J., Sun, X., Vale-Silva, L.A., Markowitz, T.E., Hochwagen, A. (2019) Topoisomerases modulate the timing of meiotic DNA breakage and repair. Preprint bioRxiv doi: 10.1101/672337 and Genetics 215, 59-73. bioRxiv | Pubmed

  7. Vale-Silva, L.A., Markowitz, T.E., Hochwagen, A. (2019) SNP-ChIP: A versatile and tag-free method to quantify changes in protein binding across the genome. Preprint bioRxiv doi: 10.1101/390005 and BMC Genomics 20, 54.bioRxiv | Pubmed

  8. Subramanian, V.V., Markowitz, T.M., Vale-Silva, L.A., San-Segundo, P., Hollingsworth, N., and Hochwagen, A. (2019) Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on small chromosomes. Preprint bioRxiv doi: 10.1101/201889 and Nat Commun. 10, 970.bioRxiv | Pubmed

  9. Luo, J., Mercy, G., Vale-Silva, L.A. et al. (2018) Synthetic chromosome fusion: effects on genome structure and function. Preprint bioRxiv doi: 10.1101/381137.bioRxiv

  10. Wu, X., Dao Thi, V.L., Huang, Y., Billerbeck, E., Saha, D., Hoffmann, H., Wang, Y., Vale Silva, L.A., Sarbanes, S., Sun, T., Andrus, L., Yu, Y., Quirk, C., Li, M., MacDonald, M.R., Schneider, W.M., An, X., Rosenberg, B.R. and Rice, C.M. (2018) Intrinsic Immunity Shapes Viral Resistance of Stem Cells. Cell 172, 423-438.Pubmed

  11. Vale-Silva, L.A., Beaudoing, E., Tran, V.D.T., and Sanglard, D. (2017) Comparative genomics of two sequential Candida glabrata isolates. Preprint bioRxiv doi: 10.1101/132464 and G3 (Bethesda) 7, 2413-2426.bioRxiv | Pubmed

  12. Vale-Silva, L.A., Moeckli, B., Torelli, R., Posteraro, B., Sanguinetti, M., and Sanglard, D. (2016) Upregulation of the adhesin EPA1 mediated by PDR1 in Candida glabrata leads to enhanced host colonization. mSphere 1, 00065-15.Pubmed

  13. Nishikawa, J.L., Boeszoermenyi, A., Vale-Silva, L.A., Torelli, R., Posteraro, B., Sohn, Y.J., Ji, F., Gelev, V., Sanglard, D., Sanguinetti, M., Sadreyev, R.I., Buhrlage, S.J., Gray, N.S., Wagner, G., Naar, A.M., and Arthanari, H. (2016) Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction. Nature 530, 485-489.Pubmed

  14. Vale-Silva, L.A. and Sanglard, D. (2015) Tipping the balance both ways: drug resistance and virulence in Candida glabrata. FEMS Yeast Res. 15, fov025.Pubmed

  15. Jensen, R.H., Astvad, K.M., Silva, L.V., Sanglard, D., Jørgensen, R., Nielsen, K.F., Mathiasen, E.G., Doroudian, G., Perlin, D.S., and Arendrup, M.C. (2015) Stepwise emergence of azole, echinocandin and amphotericin B multidrug resistance in vivo in Candida albicans orchestrated by multiple genetic alterations. J Antimicrob Chemother. 70, 2551-2555.Pubmed

  16. Pinto, E., Lago, M., Branco, L., Vale-Silva, L.A., and Pinheiro, M.D. (2014) Evaluation of Etest performed in Mueller-Hinton agar supplemented with glucose for antifungal susceptibility testing of clinical isolates of filamentous fungi. Mycopathologia 177, 157-166.Pubmed

  17. Vale-Silva, L., Ischer, F., Leibundgut-Landmann, S., and Sanglard, D. (2013) Gain-of-function mutations in PDR1, a regulator of antifungal drug resistance in Candida glabrata, control adherence to host cells. Infect Immun. 81, 1709-1720.Pubmed

  18. Silva, L.V., Sanguinetti, M., Vandeputte, P., Torelli, R., Rochat, B., and Sanglard, D. (2013) Milbemycins: more than efflux inhibitors for fungal pathogens. Antimicrob Agents Chemother. 57, 873-886.Pubmed

  19. Eddouzi, J., Parker, J.E., Vale-Silva, L.A., Coste, A., Ischer, F., Kelly, S., Manai, M., and Sanglard, D. (2013) Molecular mechanisms of drug resistance in clinical Candida species isolated from Tunisian hospitals. Antimicrob Agents Chemother. 57, 3182-3193.Pubmed

  20. Pinto, E., Goncalves, M.J., Hrimpeng, K., Pinto, J., Vaz, S., Vale-Silva, L.,Cavaleiro, C., and Salgueiro, L. (2013) Antifungal activity of the essential oil of Thymus villosus subsp. lusitanicus against Candida, Cryptococcus, Aspergillus and dermatophyte species. Ind Crops Prod. 51, 93-99. SienceDirect

  21. Vale-Silva, L.A., Coste, A., Ischer, F., Parker, J.E., Kelly, S.L., Pinto, E., and Sanglard, D. (2012) Azole resistance by loss of function of the sterol Δ5,6-desaturase gene (ERG3) in Candida albicans does not necessarily decrease virulence. Antimicrob Agents Chemother. 56, 1960-1968.Pubmed

  22. Vale-Silva, L.A., Pinto, P., Lopes, V., Ramos, H., and Pinto, E. (2012) Comparison of the Etest and a rapid flow cytometry-based method with the reference CLSI broth microdilution protocol M27-A3 for the echinocandin susceptibility testing of Candida spp. Eur J Clin Microbiol Infect Dis. 31, 941-946. Pubmed

  23. Vale-Silva, L.A., Silva, M.J., Oliveira, D., Goncalves, M.J., Cavaleiro, C., Salgueiro, L., and Pinto, E. (2012) Correlation of the chemical composition of essential oils from Origanum vulgare subsp. virens with their in vitro activity against pathogenic yeasts and filamentous fungi. J Med Microbiol 61, 252-260. Pubmed

  24. Calhelha, R.C., Ferreira, I.C., Peixoto, D., Abreu, R.M., Vale-Silva, L.A., Pinto, E., Lima, R.T., Alvelos, M.I., Vasconcelos, M.H., and Queiroz, M.J. (2012) Aminodi(hetero)arylamines in the thieno[3,2-b]pyridine series: synthesis, effects in human tumor cells growth, cell cycle analysis, apoptosis and evaluation of toxicity using non-tumor cells. Molecules 17, 3834-3843. Pubmed

  25. Zuzarte, M., Vale-Silva, L., Goncalves, M.J., Cavaleiro, C., Vaz, S., Canhoto, J., Pinto, E., and Salgueiro, L. (2012) Antifungal activity of phenolic-rich Lavandula multifida L. essential oil. Eur J Clin Microbiol Infect Dis. 31, 1359-1366. Pubmed

  26. Queiroz, M.-J.R.P., Dias, S., Peixoto, D., Rodrigues, A.R.O., Oliveira, A.D.S., Coutinho, P.J.G., Vale-Silva, L., Pinto, E., and Castanheira, E.M.S. (2012) New potential antitumoral di(hetero)arylether derivatives in the thieno[3,2-b]pyridine series: Synthesis and fluorescence studies in solution and in nanoliposomes. J Photochem Photobiol A Chem. 238, 71-80. SienceDirect

  27. Abreu, A.S., Castanheira, E.M.S., Coutinho, P.J.G., Queiroz, M.-J.R.P., Ferreira, P.M.T., Vale-Silva, L., and Pinto, E. (2012) Interaction of antitumoral fluorescent heteroaromatic compounds, a benzothienopyrrole and two thienoindoles, with DNA and lipid membranes. J Photochem Photobiol A Chem. 240, 14-25. SienceDirect

  28. Coelho, D., Silva, S., Vale-Silva, L., Gomes, H., Pinto, E., Sarmento, A., and Pinheiro, M.D. (2011) Aspergillus viridinutans: an agent of adult chronic invasive aspergillosis. Med Mycol. 49, 755-759. Pubmed

  29. Pinto, E., Afonso, C., Duarte, S., Vale-Silva, L., Costa, E., Sousa, E., and Pinto, M. (2011) Antifungal activity of xanthones: evaluation of their effect on ergosterol biosynthesis by high-performance liquid chromatography. Chem Biol Drug Des. 77, 212-222. Pubmed

  30. Abreu, A.S., Castanheira, E.M., Queiroz, M.J., Ferreira, P.M., Vale-Silva, L.A., and Pinto, E. (2011) Nanoliposomes for encapsulation and delivery of the potential antitumoral methyl 6-methoxy-3-(4-methoxyphenyl)-1H-indole-2-carboxylate. Nanoscale Res Lett. 6, 482. Pubmed

  31. Queiroz, M.J., Calhelha, R.C., Vale-Silva, L.A., Pinto, E., Almeida, G.M., and Vasconcelos, M.H. (2011) Synthesis and evaluation of tumor cell growth inhibition of methyl 3-amino-6-[(hetero)arylethynyl]thieno[3,2-b]pyridine-2-carboxylates. Structure-activity relationships, effects on the cell cycle and apoptosis. Eur J Med Chem. 46, 236-240. Pubmed

  32. Zuzarte, M., Goncalves, M.J., Cavaleiro, C., Canhoto, J., Vale-Silva, L., Silva, M.J., Pinto, E., and Salgueiro, L. (2011) Chemical composition and antifungal activity of the essential oils of Lavandula viridis L'Her. J Med Microbiol. 60, 612-618. Pubmed

  33. Vale-Silva, L.A., Goncalves, M.J., Cavaleiro, C., Salgueiro, L., and Pinto, E. (2010) Antifungal activity of the essential oil of Thymus x viciosoi against Candida, Cryptococcus, Aspergillus and dermatophyte species. Planta Med. 76, 882-888. Pubmed

  34. Queiroz, M.J., Calhelha, R.C., Vale-Silva, L.A., Pinto, E., and Sao-Jose Nascimento, M. (2010) Novel 6-[(hetero)arylamino]thieno[3,2-b]pyridines: synthesis and antitumoral activities. Eur J Med Chem. 45, 5732-5738.Pubmed

  35. Taveira, M., Silva, L.R., Vale-Silva, L.A., Pinto, E., Valentao, P., Ferreres, F., Guedes de Pinho, P., and Andrade, P.B. (2010) Lycopersicon esculentum seeds: an industrial byproduct as an antimicrobial agent. J Agric Food Chem. 58, 9529-9536.Pubmed

  36. Queiroz, M.J., Calhelha, R.C., Vale-Silva, L.A., Pinto, E., Lima, R.T., and Vasconcelos, M.H. (2010) Efficient synthesis of 6-(hetero)arylthieno[3,2-b]pyridines by Suzuki-Miyaura coupling. Evaluation of growth inhibition on human tumor cell lines, SARs and effects on the cell cycle. Eur J Med Chem. 45, 5628-5634. Pubmed

  37. Queiroz, M.J., Calhelha, R.C., Vale-Silva, L.A., Pinto, E., and Sao-Jose Nascimento, M. (2009) Synthesis of novel 3-(aryl)benzothieno[2,3-c]pyran-1-ones from Sonogashira products and intramolecular cyclization: Antitumoral activity evaluation. Eur J Med Chem. 44, 1893-1899.Pubmed

  38. Pinto, E., Vale-Silva, L., Cavaleiro, C., and Salgueiro, L. (2009) Antifungal activity of the clove essential oil from Syzygium aromaticum on Candida, Aspergillus and dermatophyte species. J Med Microbiol. 58, 1454-1462.Pubmed

  39. Pereira, D.M., Noites, A., Valentao, P., Ferreres, F., Pereira, J.A., Vale-Silva, L., Pinto, E., and Andrade, P.B. (2009) Targeted metabolite analysis and biological activity of Pieris brassicae fed with Brassica rapa var. rapa. J Agric Food Chem. 57, 483-489.Pubmed

  40. Pinto, E., Queiroz, M.J., Vale-Silva, L.A., Oliveira, J.F., Begouin, A., Begouin, J.M., and Kirsch, G. (2008) Antifungal activity of synthetic di(hetero)arylamines based on the benzo[b]thiophene moiety. Bioorg Med Chem. 16, 8172-8177.Pubmed

  41. Buchta, V., Vejsova, M., and Vale-Silva, L.A. (2008) Comparison of disk diffusion test and Etest for voriconazole and fluconazole susceptibility testing. Folia Microbiol. (Praha) 53, 153-160. Pubmed

  42. Vale-Silva, L.A., Buchta, V., and Valentova, E. (2007) Effect of subinhibitory concentration of some established and experimental antifungal compounds on the germ tube formation in Candida albicans. Folia Microbiol. (Praha) 52, 39-43.Pubmed

  43. Vale-Silva, L.A. and Buchta, V. (2006) Antifungal susceptibility testing by flow cytometry: is it the future? Mycoses 49, 261-273.Pubmed

  44. Vale-Silva, L.A., Buchta, V., Vokurkova, D., and Pour, M. (2006) Investigation of the mechanism of action of 3-(4-bromophenyl)-5-acyloxymethyl-2,5-dihydrofuran-2-one against Candida albicans by flow cytometry. Bioorg Med Chem Lett. 16, 2492-2495.Pubmed

  45. Musiol, R., Jampilek, J., Buchta, V., Silva, L., Niedbala, H., Podeszwa, B., Palka, A., Majerz-Maniecka, K., Oleksyn, B., and Polanski, J. (2006) Antifungal properties of new series of quinoline derivatives. Bioorg Med Chem. 14, 3592-3598.Pubmed

  46. Opletalova, V., Pour, M., Kunes, J., Buchta, V., Silva, L., Kralova, K., Chlupacova, M., Meltrova, D., Peterka, M., Poslednikova, M. (2006) Synthesis and biological evaluation of (E)-3-(nitrophenyl)-1-(pyrazin-2-yl)prop-2-en-1-ones. Collect Czech Chem Commun. 71, 44-58.Journal's website

  47. Jampilek, J., Dolezal, M., Kunes, J., Buchta, V., Silva, L., and Kralova, K. (2005) Quinaldine derivatives: preparation and biological activity. Med Chem. 1, 591-599.Pubmed

  48. Novak, P., Lycka, A., Cisarova, I., Buchta, V., Silva, L., Kolarova, L., Ruzicka, A. and Holecek, J. (2005) Structure of azo dye organotin(IV) compounds containing a C,N‐chelating ligand, part II, and their in vitro antifungal activity. Appl Organometal Chem. 19, 500-509.Journal's website

  49. Braunerova, G., Buchta, V., Silva, L., Kunes, J., and Palat, K., Jr. (2004) Synthesis and in vitro antifungal activity of 4-substituted phenylguanidinium salts. Farmaco 59, 443-450.Pubmed

  50. Buchta, V., Pour, M., Kubanova, P., Silva, L., Votruba, I., Voprsalova, M., Schiller, R., Fakova, H., and Spulak, M. (2004) In vitro activities of 3-(halogenated phenyl)-5-acyloxymethyl-2,5-dihydrofuran-2-ones against common and emerging yeasts and molds. Antimicrob Agents Chemother. 48, 873-878.Pubmed

Book chapter

  • Vale-Silva, L.A. (2015) Molecular mechanisms of resistance of Candida spp. to membrane-targeting antifungals. In Antifungals: from genomics to resistance and the development of novel agents. Coste A.C. and Vandeputte P., eds. Caister Academic Press, UK. [ISBN: 978-1-910190-01-2]Publisher's website