Juliana Silva Bernardes

Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KRei, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MOzorio, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, et al.. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell . (2021).

Bernardes JS, Eberle RJ, Vieira FRJ, Coronado MA. A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains. Journal of Biomolecular Structure and Dynamics. pp.1-13 (2020).

Nivina A, Grieb MSvea, Loot C, Bikard D, Cury J, Shehata L, Bernardes JS, Mazel D. Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement. Science Advances. 6, (2020).

Campos DA, Pereira EC, Jardim R, Cuadrat RRC, Bernardes JS, Dávila AMR. Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. Evolutionary Bioinformatics. 14, pp.1176934318785138 (2018).

Briquet S, Ourimi A, Pionneau C, Bernardes JS, Carbone A*, Chardonnet S, Vaquero C. Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation. PLoS One. (2018).

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A*, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes JS, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes* A. Meet-U: Educating through research immersion. PLOS Computational Biology. 14, pp.1-10 (2018).

Ugarte A, Vicedomini R, Bernardes JS, Carbone A*. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. Microbiome. (2018).

Bernardes JS, Vaquero C, Carbone A*. Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. Malar J. 16(1), (2017).

Fortunato AE, Jaubert M, Enomoto G, Bouly J-P, Raniello R, Thaler M, Malviya S, Bernardes JS, Rappaport F, Gentili B, Huysman MJJ, Carbone A*, Bowler C, Riberà d'Alcalà M, Ikeuchi M, Falciatore A. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean. The Plant Cell. 28(3), pp.616 - 628 (2016).

Bernardes JS, Zaverucha G, Vaquero C, Carbone A*. Improvement in protein domain identification is reached by breaking consensus, with the agreement of many profiles and domain co-occurrence. PLoS Computational Biology. 12(7), (2016).

Bernardes JS, Vieira F, Costa L, Zaverucha G. Evaluation and improvements of clustering algorithms for detecting remote homologous protein families. BMC Bioinformatics. 16(1), pp.34 (2015).

Bernardes JS, Vieira FRJ, Zaverucha G, Carbone A*. A multi-objective optimization approach accurately resolves protein domain architectures. Bioinformatics. (2015).

Bernardes JS, Pedreira CE. A Review of Protein Function Prediction Under Machine Learning Perspective. (2013).

Bernardes JS, Carbone A*, Zaverucha G. A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. BMC Bioinformatics. 12, pp.83 (2011).

Costa J, Bernardes JS, Santos V, Zaverucha G Remote Homology Detection Through Discriminative Statistical Relational Learning. in The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases. (2008)

Bernardes JS, Fernandez JH, Vasconcelos ATereza R. Structural descriptor database: a new tool for sequence-based functional site prediction. BMC Bioinformatics. 9, pp.492 (2008).

Bernardes JS, Dávila AMR, Costa VS, Zaverucha G. Improving model construction of profile HMMs for remote homology detection through structural alignment. BMC Bioinformatics. 8, pp.435 (2007).