| Diatom phytochromes reveal the existence of far-red-light-based sensing in the ocean AE Fortunato, M Jaubert, G Enomoto, JP Bouly, R Raniello, M Thaler, ... The Plant Cell 28 (3), 616-628, 2016 | 124 | 2016 |
| A review of protein function prediction under machine learning perspective J S Bernardes Recent patents on biotechnology 7 (2), 122-141, 2013 | 59 | 2013 |
| A multi-objective optimization approach accurately resolves protein domain architectures JS Bernardes, FRJ Vieira, G Zaverucha, A Carbone Bioinformatics 32 (3), 345-353, 2016 | 48 | 2016 |
| A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling A Ugarte, R Vicedomini, J Bernardes, A Carbone Microbiome 6, 1-27, 2018 | 41 | 2018 |
| Improvement in protein domain identification is reached by breaking consensus, with the agreement of many profiles and domain co-occurrence J Bernardes, G Zaverucha, C Vaquero, A Carbone PLoS computational biology 12 (7), e1005038, 2016 | 39 | 2016 |
| Evaluation and improvements of clustering algorithms for detecting remote homologous protein families JS Bernardes, FRJ Vieira, LMM Costa, G Zaverucha BMC bioinformatics 16 (1), 1-14, 2015 | 38 | 2015 |
| Improving model construction of profile HMMs for remote homology detection through structural alignment JS Bernardes, AMR Dávila, VS Costa, G Zaverucha BMC bioinformatics 8, 1-12, 2007 | 32 | 2007 |
| Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement A Nivina, MS Grieb, C Loot, D Bikard, J Cury, L Shehata, J Bernardes, ... Science Advances 6 (30), eaay2922, 2020 | 19 | 2020 |
| Structural descriptor database: a new tool for sequence-based functional site prediction JS Bernardes, JH Fernandez, ATR Vasconcelos BMC bioinformatics 9, 1-12, 2008 | 19 | 2008 |
| Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation S Briquet, A Ourimi, C Pionneau, J Bernardes, A Carbone, S Chardonnet, ... PLoS One 13 (10), e0205596, 2018 | 17 | 2018 |
| A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models JS Bernardes, A Carbone, G Zaverucha BMC bioinformatics 12 (1), 1-13, 2011 | 13 | 2011 |
| 2dSS: a web server for protein secondary structure visualization DP Lotun, C Cochard, FRJ Vieira, JS Bernardes BioRxiv, 649426, 2019 | 9 | 2019 |
| Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances N Abdollahi, L Jeusset, A de Septenville, F Davi, JS Bernardes BMC bioinformatics 24 (1), 70, 2023 | 8 | 2023 |
| A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains JS Bernardes, RJ Eberle, FRJ Vieira, MA Coronado Journal of Biomolecular Structure and Dynamics 39 (18), 6974-6986, 2021 | 8 | 2021 |
| Meet-U: educating through research immersion N Abdollahi, A Albani, E Anthony, A Baud, M Cardon, R Clerc, ... PLoS computational biology 14 (3), e1005992, 2018 | 6 | 2018 |
| Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes J Bernardes, C Vaquero, A Carbone Malaria Journal 16 (1), 1-10, 2017 | 6 | 2017 |
| A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data N Abdollahi, L Jeusset, AL De Septenville, H Ripoche, F Davi, ... PLoS computational biology 18 (8), e1010411, 2022 | 5 | 2022 |
| ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors JSB Lucile Jeusset, Nika Abdollahi, Thibaud Verny, Marine Armand, Anne ... NAR Genomics and Bioinformatics 5 (2), 1-13, 2023 | 3* | 2023 |
| Reconstructing the evolutionary history of a B cell lineage with minimum spanning tree and genotype abundances N Abdollahi, L Jeusset, A de Septenville, F Davi, JS Bernardes bioRxiv, 2022.02. 27.481992, 2022 | 1 | 2022 |
| A multi-objective based clustering for inferring BCR clones from high-throughput B cell repertoire data N Abdollahi, A de Septenville, H Ripoche, F Davi, JS Bernardes bioRxiv, 2021.10. 01.462736, 2021 | 1 | 2021 |
gerson zaveruchaProfessor, Universidade Federal do Rio de JaneiroVerified email at cos.ufrj.br
