Publications

• Rodríguez, M. I. A., Rueda, A. J. V., Hernández-Pérez, J., Benavides, J., & Sanchez, M. L. (2024). Homology-based identification and structural analysis of Pangasius hypophthalmus Annexins and Serine proteases to search molecules for wound healing applications. Computational and Structural Biotechnology Journal, 23, 3680-3691. https://doi.org/10.1016/j.csbj.2024.10.015

• Mac Donagh, J., Marchesini, A., Spiga, A., Fallico, M. J., Arrías, P. N., Monzon, A. M., ... & Andrade-Navarro, M. A. (2024). Structured Tandem Repeats in Protein Interactions. International Journal of Molecular Sciences, 25(5), 2994. https://doi.org/10.3390/ijms25052994

• Escobedo, N., Saldaño, T., Mac Donagh, J., Sawicki, L. R., Palopoli, N., Alberti, S. F., ... & Parisi, G. (2024). Revealing missing protein-ligand interactions using AlphaFold predictions. Journal of Molecular Biology, 168852. https://doi.org/10.1016/j.jmb.2024.168852

• Doni, D., Cavallari, E., Noguera, M. E., Gentili, H. G., Cavion, F., Parisi, G., ... & Bortolus, M. (2024). Searching for Frataxin Function: Exploring the Analogy with Nqo15, the Frataxin-like Protein of Respiratory Complex I from Thermus thermophilus. International Journal of Molecular Sciences, 25(3), 1912. https://doi.org/10.3390/ijms25031912

• Aspromonte, M. C., Nugnes, M. V., Quaglia, F., Bouharoua, A., Tosatto, S. C., & Piovesan, D. (2024). DisProt in 2024: improving function annotation of intrinsically disordered proteins. Nucleic Acids Research, 52(D1), D434-D441. https://10.1093/nar/gkad928

• Lagares, F., Edelsztein, V., Parisi, G., & Rieznik, A. A. (2023). The effect of handedness on mental arithmetic: A longitudinal large-scale investigation through smart mobile devices. Journal of Applied Research in Memory and Cognition, 12(2), 280. https://doi.org/10.1037/mac0000047

• Ormazábal, A., Carletti, M. S., Saldaño, T. E., Gonzalez Buitron, M., Marchetti, J., Palopoli, N., & Bateman, A. (2023). Expanding the repertoire of human tandem repeat RNA-binding proteins. Plos one,, 18(9), e0290890. https://doi.org/10.1371/journal.pone.0290890

• Kumar, M., Michael, S., Alvarado-Valverde, J., Zeke, A., Lazar, T., Glavina, J., ... & Gibson, T. J. (2024). ELM—the Eukaryotic Linear Motif resource—2024 update. Nucleic acids research, 52(D1), D442-D455. https://doi.org/10.1093/nar/gkad1058

• Monzon, A. M., Arrías, P. N., Elofsson, A., Mier, P., Andrade-Navarro, M. A., Bevilacqua, M., ... & Tosatto, S. C. (2023). A STRP-ed definition of Structured Tandem Repeats in Proteins. Journal of Structural Biology, 215(4), 108023. https://doi.org/10.1016/j.jsb.2023.108023

• Escobedo, N., Monzon, A. M., Fornasari, M. S., Palopoli, N., & Parisi, G. (2023). Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS‐Q. Current Protocols, 3(5), e764. https://doi.org/10.1002/cpz1.764

• Velez Rueda, A. J., Gonano, L. A., Smith, A. G., Parisi, G., Fornasari, M. S., & Sommese, L. M. (2023). CardIAP: calcium transients confocal image analysis tool. Frontiers in Bioinformatics, 3, 1137815. https://doi.org/10.3389/fbinf.2023.1137815

• Velez Rueda, A. J., Bulgarelli, F. L., Palopoli, N., & Parisi, G. (2023). CaviDB: a database of cavities and their features in the structural and conformational space of proteins. Database, 2023, baad010. https://doi.org/10.1093/database/baad010

• Mészáros, B., Hatos, A., Palopoli, N., Quaglia, F., Salladini, E., Van Roey, K., ... & Davey, N. E. (2023). Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions. Nature Methods, 20(9), 1291-1303. https://doi.org/10.1038/s41592-023-01915-x

• Brizuela, M. E., Goñi, S. E., Cardama, G. A., Zinni, M. A., Castello, A. A., Sommese, L. M., & Farina, H. G. (2022). Correlation of SARS-CoV-2 viral load and clinical evolution of pediatric patients in a general hospital from Buenos Aires, Argentina. Frontiers in pediatrics,, 10, 883395. https://doi.org/10.3389/fped.2022.883395

• Sommese, L. M., Racioppi, M. F., Shen, X., Orlowski, A., Valverde, C. A., Louch, W. E., ... & Gonano, L. A. (2022). Discordant Ca2+ release in cardiac myocytes: characterization and susceptibility to pharmacological RyR2 modulation. Pflügers Archiv-European Journal of Physiology, 474(6), 625-636. https://doi.org/10.1007/s00424-022-02678-8

• OBI: A computational tool for the analysis and systematization of the positive selection in proteins MethodsX, 9, 101786. https://doi.org/10.1016/j.mex.2022.101786

• Rueda, A. J. V., Conteville, L., Pantano, S., & González, W. (2022). Women in bioinformatics & data science-Latin America. MethodsX, 9. https://doi.org/10.1016/j.mex.2022.101907

• Glavina, J., Palopoli, N., & Chemes, L. B. (2022). Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins. Essays in Biochemistry, 66(7), 945-958. https://doi.org/10.1042/EBC20220059

• Escobedo, N., Tunque Cahui, R. R., Caruso, G., García Ríos, E., Hirsh, L., Monzon, A. M., ... & Palopoli, N. (2022). CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure. Biochimie, 38(21), 4959-4961. https://doi.org/10.1093/bioinformatics/btac627

• Saldaño T, Escobedo N, Marchetti J, et al. (2022). Impact of protein conformational diversity on AlphaFold predictions. Bioinformatics, btac202. https://doi.org/10.1093/bioinformatics/btac202

• Velez Rueda, A. J., Benítez, G. I., Sommese, L. M., Ardanaz, S. M., Borucki, E. L., Palopoli, N., Iglesias, L. E., & Parisi, G. (2022). Structural and evolutionary analysis unveil functional adaptations in the promiscuous behavior of serum albumins. Biochimie, 197, 113–120. Advance online publication. https://doi.org/10.1016/j.biochi.2022.02.004

• Quaglia, F., Mészáros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L. B., ... & Piovesan, D. (2022). DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic acids research, 50(D1), D480-D487. https://doi.org/10.1093/nar/gkab1082

• Jiménez, L., Conteville, L. C., Feldfeber, I., Didier, M. G., Stegmayer, G., Marino-Buslje, C., & Rueda, A. J. V. (2021). Highlights of the 1st Latin American Conference of Women in Bioinformatics and Data Science. The Biophysicist, 2(3), 99-102. https://doi.org/10.35459/tbp.2020.000174

• Parisi, G., Palopoli, N., Tosatto, S., Fornasari, M. S., & Tompa, P. (2021). "Protein" no longer means what it used to. Current research in structural biology, 3, 146–152. https://doi.org/10.1016/j.crstbi.2021.06.002

• Buitrón, M. G., Cahui, R., Ríos, E. G., Hirsh, L., Parisi, G., Fornasari, M. S., & Palopoli, N. (2021). CoDNaS-RNA: a database of Conformational Diversity in the Native State of RNA. Bioinformatics (Oxford, England), btab858. Advance online publication. https://doi.org/10.1093/bioinformatics/btab858

• Palopoli, N., Marchetti, J., Monzon, A. M., Zea, D. J., Tosatto, S., Fornasari, M. S., & Parisi, G. (2021). Intrinsically Disordered Protein Ensembles Shape Evolutionary Rates Revealing Conformational Patterns. Journal of molecular biology, 433(3), 166751. https://doi.org/10.1016/j.jmb.2020.166751

• Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Méndez, N. A., Garrone, N. A., Saldaño, T. E., Marchetti, J., Rueda, A., Bernadó, P., Blackledge, M., Cordeiro, T. N., Fagerberg, E., Forman-Kay, J. D., Fornasari, M. S., Gibson, T. J., Gomes, G. W., Gradinaru, C. C., … Piovesan, D. (2021). PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic acids research, 49(D1), D404–D411. https://doi.org/10.1093/nar/gkaa1021

• Paladin, L., Bevilacqua, M., Errigo, S., Piovesan, D., Mičetić, I., Necci, M., ... & Tosatto, S. C. (2021). RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. Nucleic Acids Research, 49(D1), D452-D457. https://doi.org/10.1093/nar/gkaa1097

• Piovesan, D., Necci, M., Escobedo, N., Monzon, A. M., Hatos, A., Mičetić, I., Quaglia, F., Paladin, L., Ramasamy, P., Dosztányi, Z., Vranken, W. F., Davey, N. E., Parisi, G., Fuxreiter, M., & Tosatto, S. (2021). MobiDB: intrinsically disordered proteins in 2021. Nucleic acids research, 49(D1), D361–D367. https://doi.org/10.1093/nar/gkaa1058

• Balatti, G. E., Barletta, G. P., Parisi, G., Tosatto, S. C., Bellanda, M., & Fernandez-Alberti, S. (2021). Intrinsically Disordered Region Modulates Ligand Binding in Glutaredoxin 1 from Trypanosoma Brucei. The Journal of Physical Chemistry B, 125(49), 13366-13375. https://doi.org/10.1021/acs.jpcb.1c07035

• Carletti, M. S., Monzon, A. M., Garcia-Rios, E., Benitez, G., Hirsh, L., Fornasari, M. S., & Parisi, G. (2020). Revenant: a database of resurrected proteins. Database : the journal of biological databases and curation, 2020, baaa031. https://doi.org/10.1093/database/baaa031

• Saldaño, T. E., Freixas, V. M., Tosatto, S., Parisi, G., & Fernandez-Alberti, S. (2020). Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis. Journal of chemical information and modeling, 60(6), 3068–3080. https://doi.org/10.1021/acs.jcim.9b01136

• Palopoli, N., Iserte, J. A., Chemes, L. B., Marino-Buslje, C., Parisi, G., Gibson, T. J., & Davey, N. E. (2020). The articles. ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database : the journal of biological databases and curation, 2020, baaa040. https://doi.org/10.1093/database/baaa040

• Kumar, M., Gouw, M., Michael, S., Sámano-Sánchez, H., Pancsa, R., Glavina, J., Diakogianni, A., Valverde, J. A., Bukirova, D., Čalyševa, J., Palopoli, N., Davey, N. E., Chemes, L. B., & Gibson, T. J. (2020). ELM-the eukaryotic linear motif resource in 2020. Nucleic acids research, 48(D1), D296–D306. https://doi.org/10.1093/nar/gkz1030

• Nardo, A. E., Suárez, S., Quiroga, A. V., & Añón, M. C. (2020). Amaranth as a Source of Antihypertensive Peptides. Frontiers in plant science, 11, 578631. https://doi.org/10.3389/fpls.2020.578631

• Nardo, A. E., Añón, M. C., & Quiroga, A. V. (2020). Identification of renin inhibitors peptides from amaranth proteins by docking protocols. Journal of Functional Foods, 64, 103683. https://doi.org/10.1016/j.jff.2019.103683

• Hatos, A., Hajdu-Soltész, B., Monzon, A. M., Palopoli, N., Álvarez, L., Aykac-Fas, B., Bassot, C., Benítez, G. I., Bevilacqua, M., Chasapi, A., Chemes, L., Davey, N. E., Davidović, R., Dunker, A. K., Elofsson, A., Gobeill, J., Foutel, N., Sudha, G., Guharoy, M., Horvath, T., … Piovesan, D. (2020). DisProt: intrinsic protein disorder annotation in 2020. Nucleic acids research, 48(D1), D269–D276. https://doi.org/10.1093/nar/gkz975

• Scheps, K. G., Hasenahuer, M. A., Parisi, G., Targovnik, H. M., & Fornasari, M. S. (2020). Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis. Human mutation, 41(1), 81–102. https://doi.org/10.1002/humu.23925

• Rodriguez Sawicki, L., Garcia, K. A., Corsico, B., & Scaglia, N. (2019). De novo lipogenesis at the mitotic exit is used for nuclear envelope reassembly/expansion. Implications for combined chemotherapy. Cell cycle (Georgetown, Tex.), 18(14), 1646–1659. https://doi.org/10.1080/15384101.2019.1629792

• Biedma, M. E., Cayet, D., Tabareau, J., Rossi, A. H., Ivičak-Kocjan, K., Moreno, G., Errea, A., Soulard, D., Parisi, G., Jerala, R., Berguer, P., Rumbo, M., & Sirard, J. C. (2019). Recombinant flagellins with deletions in domains D1, D2, and D3: Characterization as novel immunoadjuvants. Vaccine, 37(4), 652–663. https://doi.org/10.1016/j.vaccine.2018.12.009

• Monzon, A. M., Fornasari, M. S., Zea, D. J., & Parisi, G. (2019). Exploring Protein Conformational Diversity. Methods in molecular biology (Clifton, N.J.), 1851, 353–365. https://doi.org/10.1007/978-1-4939-8736-8_20

• Velez Rueda, A. J., Palopoli, N., Zacarías, M., Sommese, L. M., & Parisi, G. (2019). ProtMiscuity: a database of promiscuous proteins. Database : the journal of biological databases and curation, 2019, baz103. https://doi.org/10.1093/database/baz103

• Marino-Buslje, C., Monzon, A. M., Zea, D. J., Fornasari, M. S., & Parisi, G. (2019). On the dynamical incompleteness of the Protein Data Bank. Briefings in bioinformatics, 20(1), 356–359. https://doi.org/10.1093/bib/bbx084

• Marchetti, J., Monzon, A. M., Tosatto, S., Parisi, G., & Fornasari, M. S. (2019). Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution. Journal of molecular biology, 431(6), 1298–1307. https://doi.org/10.1016/j.jmb.2019.01.031

• Saldaño, T. E., Tosatto, S., Parisi, G., & Fernandez-Alberti, S. (2019). Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes. European biophysics journal : EBJ, 48(6), 559–568. https://doi.org/10.1007/s00249-019-01384-1

• Velez Rueda, A. J., Benítez, G. I., Marchetti, J., Hasenahuer, M. A., Fornasari, M. S., Palopoli, N., & Parisi, G. (2019). Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools. PLoS computational biology, 15(2), e1006473. https://doi.org/10.1371/journal.pcbi.1006473

• Ardanaz, S. M., Borucki, E. L., Rueda, A. J. V., Parisi, G., Iribarren, A. M., & Iglesias, L. E. (2019). Bovine serum albumin-catalysed cross aldol condensation: Influence of ketone structure. Process Biochemistry, 86, 50-57. https://doi.org/10.1016/j.procbio.2019.08.003

• Palopoli, N. (2019). Assessment of Structure Quality (RNA and Protein). https://doi.org/10.1016/B978-0-12-809633-8.20147-7

• Echeverría, E., Velez Rueda, A. J., Cabrera, M., Juritz, E., Burghi, V., Fabián, L., Davio, C., Lorenzano Menna, P., & Fernández, N. C. (2019). Identification of inhibitors of the RGS homology domain of GRK2 by docking-based virtual screening. Life sciences, 239, 116872. https://doi.org/10.1016/j.lfs.2019.116872

• Pinciroli, M., Aphalo, P., Nardo, A. E., Añón, M. C., & Quiroga, A. V. (2019). Broken Rice as a Potential Functional Ingredient with Inhibitory Activity of Renin and Angiotensin-Converting Enzyme(ACE). Plant foods for human nutrition (Dordrecht, Netherlands), 74(3), 405–413. https://doi.org/10.1007/s11130-019-00754-6

• Palopoli, N., González Foutel, N. S., Gibson, T. J., & Chemes, L. B. (2018). Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity. Protein engineering, design & selection : PEDS, 31(3), 69–77. https://doi.org/10.1093/protein/gzx068

• Barchiesi, J., Velazquez, M. B., Palopoli, N., Iglesias, A. A., Gomez-Casati, D. F., Ballicora, M. A., & Busi, M. V. (2018). Starch Synthesis in Ostreococcus tauri: The Starch-Binding Domains of Starch Synthase III-B Are Essential for Catalytic Activity. Frontiers in plant science, 9, 1541. https://doi.org/10.3389/fpls.2018.01541

• Rueda, A., Monzon, A. M., Ardanaz, S. M., Iglesias, L. E., & Parisi, G. (2018). Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. BMC bioinformatics, 19(1), 27. https://doi.org/10.1186/s12859-018-2044-2

• Nardo, A. E., Añón, M. C., & Parisi, G. (2018). Large-scale mapping of bioactive peptides in structural and sequence space. PloS one, 13(1), e0191063. https://doi.org/10.1371/journal.pone.0191063

• Zea, D. J., Monzon, A. M., Parisi, G., & Marino-Buslje, C. (2018). How is structural divergence related to evolutionary information?. Molecular phylogenetics and evolution, 127, 859–866. https://doi.org/10.1016/j.ympev.2018.06.033

• Piovesan, D., Tabaro, F., Paladin, L., Necci, M., Micetic, I., Camilloni, C., Davey, N., Dosztányi, Z., Mészáros, B., Monzon, A. M., Parisi, G., Schad, E., Sormanni, P., Tompa, P., Vendruscolo, M., Vranken, W. F., & Tosatto, S. (2018). MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic acids research, 46(D1), D471–D476. https://doi.org/10.1093/nar/gkx1071

• Scheps, K. G., Hasenahuer, M. A., Parisi, G., Targovnik, H. M., García, E., Veber, E. S., Crisp, R., Elena, G., Varela, V., & Fornasari, M. S. (2018). Two novel unstable hemoglobin variants due to in-frame deletions of key amino acids in the β-globin chain. European journal of haematology, 100(6), 529–535. https://doi.org/10.1111/ejh.13029

• Barletta, G. P., Hasenahuer, M. A., Fornasari, M. S., Parisi, G., & Fernandez-Alberti, S. (2018). Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase. Journal of computational chemistry, 39(29), 2472–2480. https://doi.org/10.1002/jcc.25590

• Hasenahuer, M. A., Barletta, G. P., Fernandez-Alberti, S., Parisi, G., & Fornasari, M. S. (2018). Correction: Pockets as structural descriptors of EGFR kinase conformations. PloS one, 13(2), e0192815. https://doi.org/10.1371/journal.pone.0192815

• Rueda, A., Monzon, A. M., Ardanaz, S. M., Iglesias, L. E., & Parisi, G. (2018). Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. BMC bioinformatics, 19(1), 27. https://doi.org/10.1186/s12859-018-2044-2

• Ardanaz, S. M., Velez Rueda, A. J., Parisi, G., Iribarren, A. M., & Iglesias, L. E. (2018). A mild procedure for enone preparation catalysed by bovine serum albumin in a green and easily available medium. Catalysis Letters, 148(6), 1750-1757. https://doi.org/10.1007/s10562-018-2386-4

• Gouw, M., Michael, S., Sámano-Sánchez, H., Kumar, M., Zeke, A., Lang, B., Bely, B., Chemes, L. B., Davey, N. E., Deng, Z., Diella, F., Gürth, C. M., Huber, A. K., Kleinsorg, S., Schlegel, L. S., Palopoli, N., Roey, K. V., Altenberg, B., Reményi, A., Dinkel, H., … Gibson, T. J. (2018). The eukaryotic linear motif resource - 2018 update. Nucleic acids research, 46(D1), D428–D434. https://doi.org/10.1093/nar/gkx1077

• Rodriguez Sawicki, L., Bottasso Arias, N. M., Scaglia, N., Falomir Lockhart, L. J., Franchini, G. R., Storch, J., & Córsico, B. (2017). FABP1 knockdown in human enterocytes impairs proliferation and alters lipid metabolism. Biochimica et biophysica acta. Molecular and cell biology of lipids, 1862(12), 1587–1594. https://doi.org/10.1016/j.bbalip.2017.09.006

• Monzon, A. M., Hasenahuer, M. A., Mancini, E., Coimbra, N., Cravero, F., Cáceres-Molina, J., Ramírez-Sarmiento, C. A., Palopoli, N., Meysman, P., & Parra, R. G. (2017). Second ISCB Latin American Student Council Symposium (LA-SCS) 2016. F1000Research, 6, ISCB Comm J-1491. https://doi.org/10.12688/f1000research.12321.1

• Monzon, A. M., Zea, D. J., Marino-Buslje, C., & Parisi, G. (2017). Homology modeling in a dynamical world. Protein science : a publication of the Protein Society, 26(11), 2195–2206. https://doi.org/10.1002/pro.3274

• Hasenahuer, M. A., Barletta, G. P., Fernandez-Alberti, S., Parisi, G., & Fornasari, M. S. (2017). Pockets as structural descriptors of EGFR kinase conformations. PloS one, 12(12), e0189147. https://doi.org/10.1371/journal.pone.0189147

• Salas, M. E., Lozano, M. J., López, J. L., Draghi, W. O., Serrania, J., Torres Tejerizo, G. A., Albicoro, F. J., Nilsson, J. F., Pistorio, M., Del Papa, M. F., Parisi, G., Becker, A., & Lagares, A. (2017). Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization. Environmental microbiology, 19(9), 3423–3438. https://doi.org/10.1111/1462-2920.13820

• Monzon, A. M., Zea, D. J., Fornasari, M. S., Saldaño, T. E., Fernandez-Alberti, S., Tosatto, S. C., & Parisi, G. (2017). Conformational diversity analysis reveals three functional mechanisms in proteins. PLoS computational biology, 13(2), e1005398. https://doi.org/10.1371/journal.pcbi.1005398

• Saldaño, T. E., Zanotti, G., Parisi, G., & Fernandez-Alberti, S. (2017). Evaluating the effect of mutations and ligand binding on transthyretin homotetramer dynamics. PloS one, 12(7), e0181019. https://doi.org/10.1371/journal.pone.0181019

• Federico, M., Portiansky, E. L., Sommese, L., Alvarado, F. J., Blanco, P. G., Zanuzzi, C. N., Dedman, J., Kaetzel, M., Wehrens, X., Mattiazzi, A., & Palomeque, J. (2017). Calcium-calmodulin-dependent protein kinase mediates the intracellular signalling pathways of cardiac apoptosis in mice with impaired glucose tolerance. The Journal of physiology, 595(12), 4089–4108. https://doi.org/10.1113/JP273714

• Quiroga, A. V., Aphalo, P., Nardo, A. E., & Añón, M. C. (2017). In Vitro Modulation of Renin-Angiotensin System Enzymes by Amaranth (Amaranthus hypochondriacus) Protein-Derived Peptides: Alternative Mechanisms Different from ACE Inhibition. Journal of agricultural and food chemistry, 65(34), 7415–7423. https://doi.org/10.1021/acs.jafc.7b02240

• Shome, S., Meysman, P., Parra, R. G., Monzon, A. M., Palopoli, N., White, B., Rahman, F., Hassan, M., Özkeserli, Z., Ashano, E., Hughitt, V. K., Uzair Khan, M., & Murphy, D. J. (2016). ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016. F1000Research, 5, ISCB Comm J-2882. https://doi.org/10.12688/f1000research.10420.1

• Saldaño, T. E., Monzon, A. M., Parisi, G., & Fernandez-Alberti, S. (2016). Evolutionary Conserved Positions Define Protein Conformational Diversity. PLoS computational biology, 12(3), e1004775. https://doi.org/10.1371/journal.pcbi.1004775

• Zea, D. J., Monzon, A. M., Gonzalez, C., Fornasari, M. S., Tosatto, S. C., & Parisi, G. (2016). Disorder transitions and conformational diversity cooperatively modulate biological function in proteins. Protein science : a publication of the Protein Society, 25(6), 1138–1146. https://doi.org/10.1002/pro.2931

• Sabbione, A. C., Nardo, A. E., Añón, M. C., & Scilingo, A. (2016). Amaranth peptides with antithrombotic activity released by simulated gastrointestinal digestion. Journal of Functional Foods, 20, 204-214. https://doi.org/10.1016/j.jff.2015.10.015

• Palopoli, N., Monzon, A. M., Parisi, G., & Fornasari, M. S. (2016). Addressing the Role of Conformational Diversity in Protein Structure Prediction. PloS one, 11(5), e0154923. https://doi.org/10.1371/journal.pone.0154923

• Monzon, A. M., Rohr, C. O., Fornasari, M. S., & Parisi, G. (2016). CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. Database : the journal of biological databases and curation, 2016, baw038. https://doi.org/10.1093/database/baw038

• Cattelan, N., Villalba, M. I., Parisi, G., Arnal, L., Serra, D. O., Aguilar, M., & Yantorno, O. (2016). Outer membrane protein OmpQ of Bordetella bronchiseptica is required for mature biofilm formation. Microbiology (Reading, England), 162(2), 351–363. https://doi.org/10.1099/mic.0.000224

• Mongiardini, E. J., Parisi, G. D., Quelas, J. I., & Lodeiro, A. R. (2016). The tight-adhesion proteins TadGEF of Bradyrhizobium diazoefficiens USDA 110 are involved in cell adhesion and infectivity on soybean roots. Microbiological research, 182, 80–88. https://doi.org/10.1016/j.micres.2015.10.001

• Sommese, L., Valverde, C. A., Blanco, P., Castro, M. C., Rueda, O. V., Kaetzel, M., Dedman, J., Anderson, M. E., Mattiazzi, A., & Palomeque, J. (2016). Ryanodine receptor phosphorylation by CaMKII promotes spontaneous Ca(2+) release events in a rodent model of early stage diabetes: The arrhythmogenic substrate. International journal of cardiology, 202, 394–406. https://doi.org/10.1016/j.ijcard.2015.09.022

• Mazzocchi, G., Sommese, L., Palomeque, J., Felice, J. I., Di Carlo, M. N., Fainstein, D., Gonzalez, P., Contreras, P., Skapura, D., McCauley, M. D., Lascano, E. C., Negroni, J. A., Kranias, E. G., Wehrens, X. H., Valverde, C. A., & Mattiazzi, A. (2016). Phospholamban ablation rescues the enhanced propensity to arrhythmias of mice with CaMKII-constitutive phosphorylation of RyR2 at site S2814. The Journal of physiology, 594(11), 3005–3030. https://doi.org/10.1113/JP271622

• Orsini Delgado, M. C., Nardo, A., Pavlovic, M., Rogniaux, H., Añón, M. C., & Tironi, V. A. (2016). Identification and characterization of antioxidant peptides obtained by gastrointestinal digestion of amaranth proteins. Food chemistry, 197 Pt B, 1160–1167. https://doi.org/10.1016/j.foodchem.2015.11.092

• Olorin, E., O'Brien, K. T., Palopoli, N., Pérez-Bercoff, Å., Shields, D. C., & Edwards, R. J. (2015). SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. F1000Research, 4, 477. https://doi.org/10.12688/f1000research.6773.1

• Palopoli, N., Lythgow, K. T., & Edwards, R. J. (2015). QSLiMFinder: improved short linear motif prediction using specific query protein data. Bioinformatics (Oxford, England), 31(14), 2284–2293. https://doi.org/10.1093/bioinformatics/btv155

• Edwards, R. J., & Palopoli, N. (2015). Computational prediction of short linear motifs from protein sequences. Methods in molecular biology (Clifton, N.J.), 1268, 89–141. https://doi.org/10.1007/978-1-4939-2285-7_6

• Parisi, G., Zea, D. J., Monzon, A. M., & Marino-Buslje, C. (2015). Conformational diversity and the emergence of sequence signatures during evolution. Current opinion in structural biology, 32, 58–65. https://doi.org/10.1016/j.sbi.2015.02.005

• Hasenahuer, M. A., Parisi, G., Gautier, M., Lazarowski, A., Bramuglia, G. F., & Fornasari, M. S. (2015). Twenty-One Novel EGFR Kinase Domain variants in Patients with Nonsmall Cell Lung Cancer. Annals of human genetics, 79(6), 385–393. https://doi.org/10.1111/ahg.12127

• Grosso, M., Kalstein, A., Parisi, G., Roitberg, A. E., & Fernandez-Alberti, S. (2015). On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein. The Journal of chemical physics, 142(24), 245101. https://doi.org/10.1063/1.4922925

• Scheps, K. G., Hasenahuer, M. A., Parisi, G., Fornasari, M. S., Pennesi, S. P., Erramouspe, B., Basack, F. N., Veber, E. S., Aversa, L., Elena, G., & Varela, V. (2015). Hb Wilde and Hb Patagonia: two novel elongated beta-globin variants causing dominant beta-thalassemia. European journal of haematology, 94(6), 498–503. https://doi.org/10.1111/ejh.12456

• Sawicki, L. R., Guerbi, M. X., Falomir Lockhart, L. J., Curto, L. M., Delfino, J. M., Córsico, B., & Franchini, G. R. (2014). Characterization of fatty acid binding and transfer from Δ98Δ, a functional all-β abridged form of IFABP. Biochimica et biophysica acta, 1841(12), 1733–1740. https://doi.org/10.1016/j.bbalip.2014.09.022

• de Gerónimo, E., Rodriguez Sawicki, L., Bottasso Arias, N., Franchini, G. R., Zamarreño, F., Costabel, M. D., Córsico, B., & Falomir Lockhart, L. J. (2014). IFABP portal region insertion during membrane interaction depends on phospholipid composition. Biochimica et biophysica acta, 1841(1), 141–150. https://doi.org/10.1016/j.bbalip.2013.10.011

• Curciarello, R., Smaldini, P. L., Candreva, A. M., González, V., Parisi, G., Cauerhff, A., Barrios, I., Blanch, L. B., Fossati, C. A., Petruccelli, S., & Docena, G. H. (2014). Targeting a cross-reactive Gly m 5 soy peptide as responsible for hypersensitivity reactions in a milk allergy mouse model. PloS one, 9(1), e82341. https://doi.org/10.1371/journal.pone.0082341

• Di Carlo, M. N., Said, M., Ling, H., Valverde, C. A., De Giusti, V. C., Sommese, L., Palomeque, J., Aiello, E. A., Skapura, D. G., Rinaldi, G., Respress, J. L., Brown, J. H., Wehrens, X. H., Salas, M. A., & Mattiazzi, A. (2014). CaMKII-dependent phosphorylation of cardiac ryanodine receptors regulates cell death in cardiac ischemia/reperfusion injury. Journal of molecular and cellular cardiology, 74, 274–283. https://doi.org/10.1016/j.yjmcc.2014.06.004

• Lagakos, W. S., Guan, X., Ho, S. Y., Sawicki, L. R., Corsico, B., Kodukula, S., Murota, K., Stark, R. E., & Storch, J. (2013). Liver fatty acid-binding protein binds monoacylglycerol in vitro and in mouse liver cytosol. The Journal of biological chemistry, 288(27), 19805–19815. https://doi.org/10.1074/jbc.M113.473579

• Juritz, E., Palopoli, N., Fornasari, M. S., Fernandez-Alberti, S., & Parisi, G. (2013). Protein conformational diversity modulates sequence divergence. Molecular biology and evolution, 30(1), 79–87. https://doi.org/10.1093/molbev/mss080

• Javier Zea, D., Miguel Monzon, A., Fornasari, M. S., Marino-Buslje, C., & Parisi, G. (2013). Protein conformational diversity correlates with evolutionary rate. Molecular biology and evolution, 30(7), 1500–1503. https://doi.org/10.1093/molbev/mst065

• Quelas, J. I., Mongiardini, E. J., Pérez-Giménez, J., Parisi, G., & Lodeiro, A. R. (2013). Analysis of two polyhydroxyalkanoate synthases in Bradyrhizobium japonicum USDA 110. Journal of bacteriology, 195(14), 3145–3155. https://doi.org/10.1128/JB.02203-12

• Monzon, A. M., Juritz, E., Fornasari, M. S., & Parisi, G. (2013). CoDNaS: a database of conformational diversity in the native state of proteins. Bioinformatics (Oxford, England), 29(19), 2512–2514. https://doi.org/10.1093/bioinformatics/btt405

• Palopoli, N., Lanzarotti, E., & Parisi, G. (2013). BeEP Server: Using evolutionary information for quality assessment of protein structure models. Nucleic acids research, 41(Web Server issue), W398–W405. https://doi.org/10.1093/nar/gkt453

• Díaz-Nieto, L. M., Maciá, A., Parisi, G., Farina, J. L., Vidal-Domínguez, M. E., Perotti, M. A., & Berón, C. M. (2013). Distribution of mosquitoes in the south east of Argentina and first report on the analysis based on 18S rDNA and COI sequences. PloS one, 8(9), e75516. https://doi.org/10.1371/journal.pone.0075516

• Velez Rueda, A. J., Mistchenko, A. S., & Viegas, M. (2013). Phylogenetic and phylodynamic analyses of human metapneumovirus in Buenos Aires (Argentina) for a three-year period (2009-2011). PloS one, 8(4), e63070. https://doi.org/10.1371/journal.pone.0063070

• Lufrano, D., Faro, R., Castanheira, P., Parisi, G., Veríssimo, P., Vairo-Cavalli, S., Simões, I., & Faro, C. (2012). Molecular cloning and characterization of procirsin, an active aspartic protease precursor from Cirsium vulgare (Asteraceae). Phytochemistry, 81, 7–18. https://doi.org/10.1016/j.phytochem.2012.05.028

• Juritz, E., Fornasari, M. S., Martelli, P. L., Fariselli, P., Casadio, R., & Parisi, G. (2012). On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC genomics, 13 Suppl 4(Suppl 4), S5. https://doi.org/10.1186/1471-2164-13-S4-S5

• Bolser, D. M., Chibon, P. Y., Palopoli, N., Gong, S., Jacob, D., Del Angel, V. D., Swan, D., Bassi, S., González, V., Suravajhala, P., Hwang, S., Romano, P., Edwards, R., Bishop, B., Eargle, J., Shtatland, T., Provart, N. J., Clements, D., Renfro, D. P., Bhak, D., … Bhak, J. (2012). MetaBase--the wiki-database of biological databases. Nucleic acids research, 40(Database issue), D1250–D1254. https://doi.org/10.1093/nar/gkr1099

• Juritz, E. I., Alberti, S. F., & Parisi, G. D. (2011). PCDB: a database of protein conformational diversity. Nucleic acids research, 39(Database issue), D475–D479. https://doi.org/10.1093/nar/gkq1181

• Alvarez Hayes, J., Erben, E., Lamberti, Y., Ayala, M., Maschi, F., Carbone, C., Gatti, B., Parisi, G., & Rodriguez, M. E. (2011). Identification of a new protective antigen of Bordetella pertussis. Vaccine, 29(47), 8731–8739. https://doi.org/10.1016/j.vaccine.2011.07.143

• Salem, T., Mazzella, A., Barberini, M. L., Wengier, D., Motillo, V., Parisi, G., & Muschietti, J. (2011). Mutations in two putative phosphorylation motifs in the tomato pollen receptor kinase LePRK2 show antagonistic effects on pollen tube length. The Journal of biological chemistry, 286(6), 4882–4891. https://doi.org/10.1074/jbc.M110.147512

• Foresi, N., Correa-Aragunde, N., Parisi, G., Caló, G., Salerno, G., & Lamattina, L. (2010). Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. The Plant cell, 22(11), 3816–3830. https://doi.org/10.1105/tpc.109.073510

• Busi, M. V., Palopoli, N., Valdez, H. A., Fornasari, M. S., Wayllace, N. Z., Gomez-Casati, D. F., Parisi, G., & Ugalde, R. A. (2008). Functional and structural characterization of the catalytic domain of the starch synthase III from Arabidopsis thaliana. Proteins, 70(1), 31–40. https://doi.org/10.1002/prot.21469

• Valdez, H. A., Busi, M. V., Wayllace, N. Z., Parisi, G., Ugalde, R. A., & Gomez-Casati, D. F. (2008). Role of the N-terminal starch-binding domains in the kinetic properties of starch synthase III from Arabidopsis thaliana. Biochemistry, 47(9), 3026–3032. https://doi.org/10.1021/bi702418h

• Valverde, C., Livny, J., Schlüter, J. P., Reinkensmeier, J., Becker, A., & Parisi, G. (2008). Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC genomics, 9, 416. https://doi.org/10.1186/1471-2164-9-416

• Fornasari, M. S., Parisi, G., & Echave, J. (2008). Teaching noncovalent interactions using protein molecular evolution. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 36(4), 284–286. https://doi.org/10.1002/bmb.20195

• Bassi, S., González, V., & Parisi, G. (2007). Computational biology in Argentina. PLoS computational biology, 3(12), e257. https://doi.org/10.1371/journal.pcbi.0030257

• Fornasari, M. S., Parisi, G., & Echave, J. (2007). Quaternary structure constraints on evolutionary sequence divergence. Molecular biology and evolution, 24(2), 349–351. https://doi.org/10.1093/molbev/msl181

• Maguid, S., Fernández-Alberti, S., Parisi, G., & Echave, J. (2006). Evolutionary conservation of protein backbone flexibility. Journal of molecular evolution, 63(4), 448–457. https://doi.org/10.1007/s00239-005-0209-x

• Palopoli, N., Busi, M. V., Fornasari, M. S., Gomez-Casati, D., Ugalde, R., & Parisi, G. (2006). Starch-synthase III family encodes a tandem of three starch-binding domains. Proteins, 65(1), 27–31. https://doi.org/10.1002/prot.21007

• Di Rocco, F., Parisi, G., Zambelli, A., & Vida-Rioja, L. (2006). Rapid evolution of cytochrome c oxidase subunit II in camelids (Tylopoda, Camelidae). Journal of bioenergetics and biomembranes, 38(5-6), 293–297. https://doi.org/10.1007/s10863-006-9048-8

• Parisi, G., & Echave, J. (2005). Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene, 345(1), 45–53. https://doi.org/10.1016/j.gene.2004.11.025

• Parisi, G., Perales, M., Fornasari, M. S., Colaneri, A., González-Schain, N., Gómez-Casati, D., Zimmermann, S., Brennicke, A., Araya, A., Ferry, J. G., Echave, J., & Zabaleta, E. (2004). Gamma carbonic anhydrases in plant mitochondria. Plant molecular biology, 55(2), 193–207. https://doi.org/10.1007/s11103-004-0149-7

• Parisi, G., Fornasari, M. S., & Echave, J. (2004). Dynactins p25 and p27 are predicted to adopt the LbetaH fold. FEBS letters, 562(1-3), 1–4. https://doi.org/10.1016/S0014-5793(04)00165-6

• Perales, M., Parisi, G., Fornasari, M. S., Colaneri, A., Villarreal, F., González-Schain, N., Echave, J., Gómez-Casati, D., Braun, H. P., Araya, A., & Zabaleta, E. (2004). Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I. Plant molecular biology, 56(6), 947–957. https://doi.org/10.1007/s11103-004-6324-z

• Parisi, G., & Echave, J. (2004). The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. BMC evolutionary biology, 4, 41. https://doi.org/10.1186/1471-2148-4-41

• Fornasari, M. S., Parisi, G., & Echave, J. (2002). Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Molecular biology and evolution, 19(3), 352–356. https://doi.org/10.1093/oxfordjournals.molbev.a004089

• Parisi, G., & Echave, J. (2001). Structural constraints and emergence of sequence patterns in protein evolution. Molecular biology and evolution, 18(5), 750–756. https://doi.org/10.1093/oxfordjournals.molbev.a003857

• Parisi, G., Fornasari, M., & Echave, J. (2000). Evolutionary analysis of gamma-carbonic anhydrase and structurally related proteins. Molecular phylogenetics and evolution, 14(3), 323–334. https://doi.org/10.1006/mpev.1999.0734

• Parisi, G., Echave, J., Ghiringhelli, D., & Romanowski, V. (1996). Computational characterisation of potential RNA-binding sites in arenavirus nucleocapsid proteins. Virus genes, 13(3), 247–254. https://doi.org/10.1007/BF00366985