Publicaciones Departamento de Genómica
Período 2016 - 2024
2024
Sabalette KB, Campo VA, Sotelo-Silveira JR, Smircich P*, De Gaudenzi JG*. 2024. Transcriptomic analysis of N-terminal mutated Trypanosoma cruzi UBP1 knockdown underlines the importance of this RNA-binding protein in parasite development. PLoS Neglected Tropical Diseases.
Rodríguez-Decuadro S, Ramos S, Rodríguez-Ustra MJ, Marques A, Smircich P, Vaio M. 2024. Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes. Functional & Integrative Genomics.
Romeo-Cardeillac C, Trovero MF, Radío S, Smircich P, Rodríguez-Casuriaga R, Geisinger A*, Sotelo-Silveira J*.. 2024. Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis. BMC Genomics.
Sabalette K, Campo V, Sotelo-Silveira JR, Smircich P, De Gaudenzi J. 2024. RNA-seq data exploration after trypanosome RNA-binding protein UBP1 expression is altered by CRISPR-Cas9 gene editing and overexpression. Data in Brief.
Bilbao L, Acquistapace S, Umpiérrez A, Smircich P, Alonzo P, Sotelo-Silveira JR, Zunino P. 2024. Genomic characterization of Moraxella bovis and Moraxella bovoculi Uruguayan strains isolated from calves with infectious bovine keratoconjunctivitis. Revista Argentina de Microbiología.
Cosse* M, Bruno A, Mannise N, Bou N, Zabaleta M, Bonifacino M, Camargo A, Smircich P, Iriarte A, Brazeiro A. 2024. Applicability of DNA barcoding-based analyses on the diet of the gray brocket deer (Subulo gouazoubira) in xeric hillside forests. Therya
Papa, N. G., Sotelo-Silveira, J., Inchausti, L., Valdivieso, C., Pereiro, L., Gajardo, F., Di Genova, A., Glavic, A., Chalar, C., Berois, N., Allende, M. L., & Arezo, M. J. 2024. Exploring the molecular basis of diapause I induction in the annual killifish Garcialebias charrua: a transcriptomic approach. Environmental Biology of Fishes.
Lamela, F., Bologna-Molina, R., Parietti, F., Pereira-Prado, V., Millán, M., Silva, A., Llaguno, J., Alonso, J., Fernández, A., Sotelo-Silveira, J., Domingues, M., Arocena*, M., & Hochmann, J*. 2024. Differential effects of coverslip-induced hypoxia and cobalt chloride mimetic hypoxia on cellular stress, metabolism, and nuclear structure. Tissue & cell.
Pablo Peraza, Tamara Fernández-Calero, Hugo Naya, José Sotelo-Silveira, Elly A. Navajas. 2024. Exploring the linkage between ruminal microbial communities on postweaning and finishing diets and their relation to residual feed intake in beef cattle. Microorganisms.
2023
Hochmann, J., Millán, M., Hernández, P., Lafon-Hughes, L., Aiuto, N., Silva, A., Llaguno, J., Alonso, J., Fernández, A., Pereira-Prado, V., Sotelo-Silveira, J., Bologna-Molina, R., & Arocena, M. (2023). Contributions of viral oncogenes of HPV-18 and hypoxia to oxidative stress and genetic damage in human keratinocytes. Scientific Reports.
Ciganda, M., Sotelo-Silveira, J., Dubey, A. P., Pandey, P., Smith, J. T., Shen, S., Qu, J., Smircich, P., & Read, L. K. (2023). Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. RNA.
Sainz, M. M., Filippi, C. V., Eastman, G., Sotelo-Silveira, J., Borsani, O., & Sotelo-Silveira, M. (2023). Analysis of Thioredoxins and Glutaredoxins in Soybean: Evidence of Translational Regulation under Water Restriction. Antioxidants.
D'Aiuto, N., Hochmann, J., Millán, M., Di Paolo, A., Bologna-Molina, R., Sotelo Silveira, J., & Arocena, M. (2023). Hypoxia, acidification and oxidative stress in cells cultured at large distances from an oxygen source. Scientific Reports.
Rivara-Espasandín, M., Palumbo, M. C., Sosa, E. J., Radío, S., Turjanski, A. G., Sotelo-Silveira, J., Fernandez Do Porto, D., & Smircich, P. (2023). Omics data integration facilitates target selection for new antiparasitic drugs against TriTryp infections. Frontiers in Pharmacology.
Millán, M., Villarreal, L., D'Aiuto, N., Bologna-Molina, R., Sotelo-Silveira, J., Benech, J. C., Hochmann, J., & Arocena, M. (2023). Mechanical profile of human keratinocytes expressing HPV-18 oncogenes. Biochemical and Biophysical Research Communications.
Sabalette, K. B., Sotelo-Silveira, J. R., Smircich, P., & De Gaudenzi, J. G. (2023). RNA-Seq reveals that overexpression of TcUBP1 switches the gene expression pattern toward that of the infective form of Trypanosoma cruzi. The Journal of Biological Chemistry.
Smircich, P., Pérez-Díaz, L., Hernández, F., Duhagon, M. A., & Garat, B. (2023). Transcriptomic analysis of the adaptation to prolonged starvation of the insect-dwelling Trypanosoma cruzi epimastigotes. Frontiers in Cellular and Infection Microbiology.
Trinidad-Barnech, J. M., Fort, R. S., Trinidad Barnech, G., Garat, B., & Duhagon, M. A. (2023). Transcriptome-Wide Analysis of microRNA-mRNA Correlations in Tissue Identifies microRNA Targeting Determinants. Noncoding RNA.
Sun, X., Eastman, G., Shi, Y., Saibaba, S., Oliveira, A. K., Lukens, J. R., Norambuena, A., Thompson, J. A., Purdy, M. D., Dryden, K., Pardo Huguet, E., Mandell, J. W., & Bloom, G. S. (2023). Structural and functional damage to neuronal nuclei caused by extracellular tau oligomers. Alzheimer's & Dementia.
2022
Freeman, S.L., Skafar, F., Kwon, H., Fielding, A.J., Moody, P.C.E., Martínez, A., Issoglio, F., Inchausti, L., Smircich, P., Zeida, A., Piacenza, L., Radi, R., Raven, E.L. 2022. Crystal Structure of Trypanosoma cruzi Heme Peroxidase and Characterisation of its Substrate Specificity and Compound I Intermediate. Journal of Biological Chemistry.
Rivara-Espasandín M., Balestrazzi L., Dufort y Álvarez G., Ochoa I., Seroussi G., Smircich P., Sotelo-Silveira J., Martín A. 2022. Nanopore quality score resolution can be reduced with little effect on downstream analysis. Bioinformatics Advances.
Sainz MM, Filippi CV, Eastman G, Sotelo-Silveira J, Borsani O, Sotelo-Silveira M. 2022. Analysis of Thioredoxins and Glutaredoxins in Soybean: Evidence of Translational Regulation under Water Restriction. Antioxidants (Basel)
Sainz MM, Filippi CV, Eastman G, Sotelo-Silveira M, Martinez CM, Borsani O, Sotelo-Silveira J. 2022. Polysome Purification from Soybean Symbiotic Nodules. J Vis Exp.
Eastman G, Sharlow ER, Lazo JS, Bloom GS, Sotelo-Silveira JR. 2022. Transcriptome and Translatome Regulation of Pathogenesis in Alzheimer 's Disease Model Mice. J Alzheimers Dis.
Fort RS, Chavez S, Trinidad Barnech JM, Oliveira-Rizzo C, Smircich P, Sotelo-Silveira JR, Duhagon MA. 2022. Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA.
Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. 2022. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol.
Oliveira-Rizzo C, Ottati MC, Fort RS, Chavez S, Trinidad JM, DiPaolo A, Garat B, Sotelo-Silveira JR, Duhagon MA. 2022. Hsa-miR-183-5p Modulates Cell Adhesion by Repression of ITGB1 Expression in Prostate Cancer. Noncoding RNA.
2021
M. C. Rodríguez-Esperón, G. Eastman, L. Sandes, F. Garabato, I. Eastman, A. Iriarte, E. Fabiano, J. R. Sotelo-Silveira, R. Platero. 2021. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environmental Microbiology 2021, 10.1111/1462-2920.15845
Sofia Acquistapace, Ana Umpiérrez, Sofía Fernández, José Sotelo, Pablo Zunino. 2021 Outer membrane protein CD of Moraxella bovis as a potential antigen against infectious bovine keratoconjunctivitis. Veterinaria (Montevideo) 10.29155/VET.57.216.4
Andres Di Paolo, Joaquina Farias, Joaquin Garat, Andrew Macklin, Vladimir Ignatchenko, Thomas Kislinger, José Sotelo Silveira. 2021. Rat Sciatic Nerve Axoplasm Proteome Is Enriched with Ribosomal Proteins during Regeneration Processes.
Rego N, Salazar C, Paz M, Costábile A, Fajardo A, Ferrés I, Perbolianachis P, Fernández-Calero T, Noya V, Machado MR, Brandes M, Arce R, Arleo M, Possi T, Reyes N, Bentancor MN, Lizasoain A, Bortagaray V, Moller A, Chappos O, Nin N, Hurtado J, Duquía M, González MB, Griffero L, Méndez M, Techera MP, Zanetti J, Pereira E, Rivera B, Maidana M, Alonso M, Smircich P, Arantes I, Mir D, Alonso C, Medina J, Albornoz H, Colina R, Bello G, Moreno P, Moratorio G, Iraola G, Spangenberg L. 2021. Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Viruses. Sep 10;13(9):1801. doi: 10.3390/v13091801.
Chávez S, Urbaniak MD, Benz C, Smircich P, Garat B, Sotelo-Silveira JR, Duhagon MA. 2021. Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics. mSphere. Oct 27;6(5):e0036621. doi: 10.1128/mSphere.00366-21. Epub 2021 Sep 1.
Rego N, Costábile A, Paz M, Salazar C, Perbolianachis P, Spangenberg L, Ferrés I, Arce R, Fajardo A, Arleo M, Possi T, Reyes N, Bentancor MN, Lizasoain A, Benítez MJ, Bortagaray V, Moller A, Bello G, Arantes I, Brandes M, Smircich P, Chappos O, Duquía M, González B, Griffero L, Méndez M, Techera MP, Zanetti J, Rivera B, Maidana M, Alonso M, Alonso C, Medina J, Albornoz H, Colina R, Noya V, Iraola G, Fernández-Calero T, Moratorio G, Moreno P. 2021. Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay. Emerg Infect Dis. Nov;27(11):2957-2960. doi: 10.3201/eid2711.211198. Epub 2021 Aug 26.
Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. 2021. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci.; 15:686722. doi: 10.3389/fncel.2021.686722. eCollection 2021.
Dufort Y Álvarez G, Seroussi G, Smircich P, Sotelo-Silveira J, Ochoa I, Martín Á RENANO. 2021. a REference-based compressor for NANOpore FASTQ files. (2021). Bioinformatics. Jun 15:btab437. doi: 10.1093/bioinformatics/btab437. Online ahead of print.
Mir D, Rego N, Resende PC, Tort F, Fernández-Calero T, Noya V, Brandes M, Possi T, Arleo M, Reyes N, Victoria M, Lizasoain A, Castells M, Maya L, Salvo M, Schäffer Gregianini T, Mar da Rosa MT, Garay Martins L, Alonso C, Vega Y, Salazar C, Ferrés I, Smircich P, Sotelo Silveira J, Fort RS, Mathó C, Arantes I, Appolinario L, Mendonça AC, Benítez-Galeano MJ, Simoes C, Graña M, Motta F, Siqueira MM, Bello G, Colina R, Spangenberg L. 2021. Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan-Brazilian Border. Front Microbiol. May 28;12:653986. doi: 10.3389/fmicb.2021.653986. eCollection 2021.
Rodríguez-Decuadro S, da Rosa G, Radío S, Barraco-Vega M, Benko-Iseppon AM, Dans PD, Smircich P, Cecchetto G. 2021. Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium. Biochimie. Jan;180:229-242. doi: 10.1016/j.biochi.2020.11.005. Epub 2020 Nov 13.
Fort, R. S., Duhagon, M. A. 2021. Pan-Cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Research. DOI: 10.12688/f1000research.28510.2.
Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. 2021. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol. doi: 10.1111/1462-2920.15845. Online ahead of print.
Mesquita-Ribeiro, R., Fort R. S., Rathbone, A., Farias, J., Lucci, C., James, V., Sotelo-Silveira, J., Duhagon, M. A., Dajas-Bailador, F. 2021. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biology. In Press.
Sofia Acquistapace, Ana Umpiérrez, Sofía Fernández, José Sotelo, Pablo Zunino. 2021. Outer membrane protein CD of Moraxella bovis as a potential antigen against infectious bovine keratoconjunctivitis. Veterinaria (Montevideo) 10.29155/VET.57.216.4
Eastman G, Sharlow ER, Lazo JS, Bloom GS, Sotelo-Silveira JR. 2021. Transcriptional and translational regulation of pathogenesis in Alzheimer’s disease model mice. bioRXiv. doi: https://doi.org/10.1101/2021.09.17.460831
2019
Langleib M, Beracochea M, Zabaleta M, Battistoni F, Sotelo-Silveira J, Fabiano E, Iriarte A, Platero R. 2019. Draft Genome Sequence of Paraburkholderia sp. UYCP14C, a Rhizobium Strain Isolated from Root Nodules of Calliandra parvifolia. Microbiol Resour Announc. 8(16). pii: e00173-19. doi: 10.1128/MRA.00173-19.
Dufort y Álvarez G, Seroussi G, Smircich P, Sotelo J, Ochoa I, Martín Á. Compression of Nanopore FASTQ Files. 2019. In: Rojas I., Valenzuela O., Rojas F., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science, vol 11465. Springer, Cham
Farias J, Sotelo Roberto J, Sotelo-Silveira J. 2019. Towards Axonal System Biology: Genome Wide Views of Local mRNA Translation. Proteomics.26:e1900054. doi: 10.1002/pmic.201900054.
Becco L, Smircich P, Garat B. 2019. Conserved motifs in nuclear genes encoding predicted mitochondrial proteins in Trypanosoma cruzi. PLoS One. 14(4):e0215160. doi: 10.1371/journal.pone.0215160.
Marizcurrena JJ, Morales D, Smircich P, Castro-Sowinski S. 2019. Draft Genome Sequence of the UV-Resistant Antarctic Bacterium Sphingomonas sp. Strain UV9. Microbiol Resour Announc. 14;8(7). pii: e01651-18. doi: 10.1128/MRA.01651-18.
Arocena M, Landeira M, Di Paolo A, Silva A, Sotelo-Silveira J, Fernández A, Alonso J. 2019. Using a variant of coverslip hypoxia to visualize tumor cell alterations at increasing distances from an oxygen source. J Cell Physiol. doi: 10.1002/jcp.28507.
2018
Radío S, Fort RS, Garat B, Sotelo-Silveira, JR, Smircich P. 2018. UTRme: a scoring-based tool to annotate untranslated regions in trypanosomatid genomes. Frontiers in genetics, 9, 671.
Eastman G, Smircich P, Sotelo-Silveira JR. 2018. Following Ribosome Footprints to Understand Translation at a Genome Wide Level. Comput Struct Biotechnol J. 16:167-176. doi: 10.1016/j.csbj.2018.04.001. eCollection 2018. Review.
Arocena M, Pérez Zerpa JM, Di Paolo A, Aguilera PA, Sotelo-Silveira J. 2018. Lamellipodial wrinkles in fish keratocytes as markers of imperfect coordination between extension and retraction during cell migration. Biochemical and Biophysical Research Communications 498: 680–685.
Solana, M.V.; Domínguez, M.F.; Scarcella, S.; Radio, S.; Smircich, P.; Fernández, S.; Solana, H.; Tort, J.F. 2018. Different SNPs in Fasciola hepatica P-glycoprotein from diverse Latin American populations are not associated with Triclabendazole resistance. Mol Biochem Parasitol. 224:57-60. 2018. doi: 10.1016/j.molbiopara.2018.07.005
Fort RS, Mathó C, Oliveira-Rizzo C, Garat B, Sotelo-Silveira JR, Duhagon MA. 2018. An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. Exp Hematol Oncol. 7:10. doi: 10.1186/s40164-018-0102-0. eCollection2018.
Sotelo-Silveira M, Chávez Montes RA, Sotelo-Silveira JR, Marsch-Martínez N, deFolter S. 2018. Entering the Next Dimension: Plant Genomes in 3D. Trends Plant Sci. 23(7):598-612. doi: 10.1016/j.tplants.2018.03.014. Epub 2018 Apr 24.Review. PubMed PMID: 29703667.
Fort RS, Mathó C, Geraldo MV, Ottati MC, Yamashita AS, Saito KC, Leite KRM,Méndez M, Maedo N, Méndez L, Garat B, Kimura ET, Sotelo-Silveira JR, Duhagon MA. 2018. Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth. BMC Cancer. 2;18(1):127. doi: 10.1186/s12885-018-4049-7.
Radio S, Fontenla S, Solana V, Matos Salim AC, Araújo FMG, Ortiz P, Hoban C, Miranda E, Gayo V, Pais FS, Solana H, Oliveira G, Smircich P, Tort JF. 2018. Pleiotropic alterations in gene expression in Latin American Fasciola hepatica isolates with different susceptibility to drugs. Parasit Vectors. 11(1):56. doi: 10.1186/s13071-017-2553-2.
2017
Chávez S, Eastman G, Smircich P, Becco LL, Oliveira-Rizzo C, Fort R, Potenza M, Garat B, Sotelo-Silveira JR, Duhagon MA. 2017. Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control. PLoS One. 12(11):e0188441. doi: 10.1371/journal.pone.0188441. eCollection 2017.
Marcon BH, Holetz FB, Eastman G, Origa-Alves AC, Amorós MA, de Aguiar AM, Rebelatto CK, Brofman PRS, Sotelo-Silveira J, Dallagiovanna B. 2017. Downregulation of the protein synthesis machinery is a major regulatory event during early adipogenic differentiation of human adipose-derived stromal cells. Stem Cell Res. 25:191-201. doi: 10.1016/j.scr.2017.10.027. Epub 2017 Nov 1.
Pastro L, Smircich P, Di Paolo A, Becco L, Duhagon MA, Sotelo-Silveira JR, Garat B. 2017. Nuclear Compartmentalization Contributes to Stage-Specific Gene Expression Control in Trypanosoma cruzi. Front Cell Dev Biol. 5: 8. Published online 2017 Feb 13. doi: 10.3389/fcell.2017.00008
Smircich P, El-Sayed NM, Garat B. 2017. Intrinsic DNA curvature in trypanosomes. BMC Res Notes. 10(1):585. doi: 10.1186/s13104-017-2908-y.
Fontenla S, Rinaldi G, Smircich P, Tort JF. 2017. Conservation and diversification of small RNA pathways within flatworms. BMC Evol Biol.17(1):215. doi: 10.1186/s12862-017-1061-5.
Rozenblum E, Sotelo-Silveira JR, Kim GY, Zhu JY, Lau CC, McNeil N, Korolevich S, Liao H, Cherry JM, Munroe DJ, Ried T, Meltzer PS, Kuehl WM, Roschke AV. 2017. Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor. PLoS One. 12(8):e0182610. doi: 10.1371/journal.pone.0182610. eCollection 2017.
Prieto D, Aparicio G, Sotelo-Silveira JR. 2017. Cell migration analysis: A low-cost laboratory experiment for cell and developmental biology courses using keratocytes from fish scales. Biochem Mol Biol Educ. 2017 Nov;45(6):475-482. doi: 10.1002/bmb.21071. Epub 2017 Jun 19. PubMed PMID: 2862773
McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, Fontenla S, Choi YJ, Tyagi R, Hallsworth-Pepin K, Mann VH, Kammili L, Latham PS, Dell'Oca N, Dominguez F, Carmona C, Fischer PU, Brindley PJ, Mitreva M. 2017. Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers. PLoS Genet. 2017 Jan 6;13(1):e1006537. doi: 10.1371/journal.pgen.1006537. eCollection 2017 Jan
2016
Iriarte A, Platero R, Romero V, Fabiano E, Sotelo-Silveira JR. 2016. Draft Genome Sequence of Cupriavidus UYMMa02A, a Novel Beta-Rhizobium Species. Genome Announc. 4(6): e01258-16. Published online 2016 Nov 10. doi: 10.1128/genomeA.01258-16
Giorello FM, Romero V, Farias J, Scavone P, Umpiérrez A, Zunino P, Sotelo Silveira JR. 2016. Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus mirabilis Pr2921. Genome Announc. 4(3): e00564-16. Published online 2016 Jun 23. doi: 10.1128/genomeA.00564-16
Da Cruz I, Rodríguez-Casuriaga R, Santiñaque FF, Farías J, Curti G, Capoano CA, Folle GA, Benavente R, Sotelo-Silveira JR, Geisinger A. 2016. Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage. BMC Genomics. 2016; 17: 294. Published online 2016 Apr 19. doi: 10.1186/s12864-016-2618-1