Publications

Papers in journals

  • SAIGHI P.; CHADI J.; VIEIRA, F. R. J; BERNARDES, J. S.; DAVI: a tool for clustering and visualising protein domain architectures 2020. To be submitted

  • ABDOLLAHI N.; SEPTENVILLE AL.; DAVI F.; BERNARDES, J. S.; Automatic generation of ground truth data for the evaluation of clonal grouping methods in B-cell populations. Biorxiv 2020 (pdf)

  • NIVINA A.; GRIEB M.S; LOOT C.; BIKARD D.; CURY J.; SHEHATA L.; BERNARDES, J. S.; MAZEL D. Structure-specific DNA recombination sites: Design validation and machine learning–based refinement. Science Advances 2020 6(30) (pdf)

  • BERNARDES, J. S.; EBERLE, R. J; VIEIRA, F. R. J; coronado, M. A. A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains. Journal of Biomolecular Structure and Dynamics 2020 1-13 (pdf)

  • LOTUN, D. P.; COCHARD, C; VIEIRA, F. R. J; BERNARDES, J. S.. 2dSS: a web server for protein secondary structure visualization. Biorxiv 2019 (pdf)

  • BRIQUET S.; OURIMI A.; CHARDONNET S.; PIONNEAU C.; BERNARDES, J. S.; CARBONE A.; VAQUERO C. Identification of nuclear Plasmodium falciparum proteins via Mass Spectrometry and proposed protein annotation. PLoSOne 2018 13(10):e0205596 (pdf).

  • URGATI A.; VICEDOMINI R.; BERNARDES, J. S.; CARBONE A. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. Microbiome 2018 6:149 (pdf)

  • CAMPOS D.A; CUADRAT R.R.C; JARDIN R; PEREIRA E.C.; BERNARDES, J. S.; JARDIM R; DAVILA A. Homology-based SUpergroups using a reconciliation approach for the comparative genomics of Protozoa. Evolutionary Bioinformatics Online. 2018 14:1176934318785138. (pdf)

  • ABDOLLAHI N.; ..., BERNARDES, J. S.; ..., LAINE E.; LOPES A. Meet-U: Educating through research immersion. PLOS Computational Biology. 2018 14(3): e1005992. (pdf)

  • BERNARDES, J. S.; VAQUERO C.;CARBONE A.; Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. Malaria Journal, 2017 16:241 (pdf)

  • BERNARDES, J. S.; 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 Comput Biol. 2016 12(7):e1005038. (pdf)

  • BERNARDES, J. S.; VIEIRA, F. R. J; ZAVERUCHA, G.; CARBONE, A.; A multi-objective optimisation approach accurately resolves pro tein domain architectures. Bioinformatics. 2016 32(3):345–353.(pdf)

  • FORTUNATO, A; ... BERNARDES, J. S.; et al;Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean . The Plant Cell. 2016 28(3):616-628.(pdf)

  • BERNARDES, J. S.; VIEIRA, F. R. J; COSTA L. M. M; ZAVERUCHA, G.; Evaluation and improvements of clustering algorithms for dete cting remote homologous protein families, BMC Bioinformatics, v. 16, p. 34, 2015 (pdf)

  • BERNARDES, J. S.; PEDREIRA, C. E.; A Review of Protein Function Prediction Under Machine Learning Perspective. Recent Patents on Biotechnology. Recent Patents on Biotechnology, v.9 99, p.25 - 30, 2013 (p df)

  • BERNARDES, J. S.; CARBONE, A.; ZAVERUCHA, G. A discriminative method for family-based protein remote homology detection that c ombines inductive logic programming and propositional models. BMC Bioinformatics, v. 12, p. 83, 2011. (pdf)

  • BERNARDES, J. S.; Fernandez, J. H ; Vasconcelos, A.T.R. Structural descriptor database: a new tool for sequence based functiona l site prediction. BMC Bioinformatics, v. 9, p. 492, 2008 (pdf)

  • BERNARDES, J. S.; DAVILA, A. ; SANTOS, V. ; ZAVERUCHA, G. Improving model construction of profile HMMs for remote homology dete ction through structural alignment. BMC Bioinformatics, v. 8, p. 435, 2007. (pdf)

Papers in conference

  • COSTA, J. B. ; BERNARDES, J. S.; 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, Belgica. In: Workshop on Statistical and Relational Learning in Bioinformatics (StReBio), 2008. (pdf)

Abstract published in conferences

  • VIEIRA, F. R. J; BERNARDES, J. S.. Greedy cluster, a fast and sensitive method for grouping protein sequences. In: Machine Learning in Systems Biology, 2014, Strasbourg, 2014

  • BERNARDES, J. S.; PEDREIRA, C. E. Gene selection and classification for cancer microarray data with multiple ordering criteria. In: X-Meeting & Brazilian Symposium on Bioinformatics. Recife, Brazil, 2013.

  • BERNARDES, J. S.; ZAVERUCHA, G.; C. VAQUERO,; CARBONE, A. Large scale analysis of the Plasmodium falciparum proteome through a multitude of diversified probablistic models.In: 24th Annual Molecular Parasitology Meeting. Woods Hole, USA, 2013.

  • FORTUNATO, A. E.; BERNARDES, J. S.; CARBONE, A.; FALCIATORE, A. Looking for the circadian clock components in marine diatoms. In: EMBO workshop "The Molecular life of Diatoms". Paris, France, 2013.

  • BERNARDES, J. S.; FORTUNATO, A. E.; FALCIATORE, A; CARBONE, A. Phaeodactylum tricornutum genome re-annotation through multiple evolutionary models. In: EMBO workshop "The Molecular life of Diatoms". Paris, France, 2013.

  • BERNARDES, J. S.; DAVILA, A. ; SANTOS, V. ; ZAVERUCHA, G. Remote Homology detection with HMMs and Structural IsSUes. In: International Workshop on Genomic Databases. Rio de Janeiro, Brazil, 2005.

  • BERNARDES, J. S.; DAVILA, A. ; SANTOS, V. ; ZAVERUCHA, G. GIBTs - Graphical Interface to Bioinformatics Tools. In: International Conference on Bioinformatics and Computation Biology, Angra dos Reis, Rio de Janeiro, Brazil, 2004.

  • BERNARDES, J. S.; DOLESI, A. SUper scalar Processor. In: Scientific Initiation Seminary, 10 º Seminary of Scientific Initiation, Federal Fluminense University, Niteroi, Brazil, 2000.

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