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Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean.
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- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-99708-9
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A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.
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- Plant Biotechnology Journal, 2015, v. 13, n. 5, p. 648, doi. 10.1111/pbi.12288
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- Article
Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa.
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- Journal of Microbiology, 2024, v. 62, n. 9, p. 759, doi. 10.1007/s12275-024-00155-8
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- Article
A Glance into MTHFR Deficiency at a Molecular Level.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 1, p. 167, doi. 10.3390/ijms23010167
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Huntingtin: A Protein with a Peculiar Solvent Accessible Surface.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 6, p. 2878, doi. 10.3390/ijms22062878
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Functional and Structural Features of Disease-Related Protein Variants.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 7, p. 1530, doi. 10.3390/ijms20071530
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- Article
BUSCA: an integrative web server to predict subcellular localization of proteins.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W459, doi. 10.1093/nar/gky320
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- Article
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W375, doi. 10.1093/nar/gkr282
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eSLDB: eukaryotic subcellular localization database.
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- Nucleic Acids Research, 2007, v. 35, p. d208, doi. 10.1093/nar/gkl775
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- Article
CoCoNat: a novel method based on deep learning for coiled-coil prediction.
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- Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad495
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- Article
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.
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- Bioinformatics, 2022, v. 38, n. 23, p. 5168, doi. 10.1093/bioinformatics/btac678
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- Article
In silico prediction of the structure of membrane proteins: Is it feasible?
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- Briefings in Bioinformatics, 2003, v. 4, n. 4, p. 341, doi. 10.1093/bib/4.4.341
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- Article
Machine learning solutions for predicting protein–protein interactions.
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- WIREs: Computational Molecular Science, 2022, v. 12, n. 6, p. 1, doi. 10.1002/wcms.1618
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- Article
A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase.
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- Proteins, 2008, v. 71, n. 4, p. 1843, doi. 10.1002/prot.21868
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- Article
Predictions of protein segments with the same aminoacid sequence and different secondary structure: A benchmark for predictive methods.
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- Proteins, 2000, v. 41, n. 4, p. 535, doi. 10.1002/1097-0134(20001201)41:4<535::AID-PROT100>3.0.CO;2-C
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- Article
Large scale analysis of protein stability in OMIM disease related human protein variants.
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- BMC Genomics, 2016, v. 17, p. 239, doi. 10.1186/s12864-016-2726-y
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- Article
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.
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- Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bat065
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- Article
MIMO: an efficient tool for molecular interaction maps overlap.
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- BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-159
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- Article
How to inherit statistically validated annotation within BAR+ protein clusters.
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- BMC Bioinformatics, 2013, v. 14, n. S3, p. 1, doi. 10.1186/1471-2105-14-S3-S4
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- Article
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.
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- BMC Bioinformatics, 2013, v. 14, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-14-S1-S10
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- Article
The human "magnesome": detecting magnesium binding sites on human proteins.
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- BMC Bioinformatics, 2012, v. 13, n. Suppl 14, p. 1, doi. 10.1186/1471-2105-13-S14-S10
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- Article
PredGPI: a GPI-anchor predictor.
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- BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-392
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- Article
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
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- BMC Bioinformatics, 2005, v. 6, p. S12, doi. 10.1186/1471-2105-6-S4-S12
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- Article
Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length.
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- Molecules, 2024, v. 29, n. 19, p. 4616, doi. 10.3390/molecules29194616
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Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa.
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- Microorganisms, 2021, v. 9, n. 3, p. 570, doi. 10.3390/microorganisms9030570
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- Article
TRAMPLE: the transmembrane protein labelling environment.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w198, doi. 10.1093/nar/gki440
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- Article
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks.
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- Protein Engineering, 2002, v. 15, n. 12, p. 951, doi. 10.1093/protein/15.12.951
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- Article
A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus.
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- Protein Engineering, 2002, v. 15, n. 3, p. 215, doi. 10.1093/protein/15.3.215
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- Article
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito.
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- BMC Bioinformatics, 2020, v. 21, p. N.PAG, doi. 10.1186/s12859-020-03617-z
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- Article
The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation.
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- Briefings in Functional Genomics & Proteomics, 2008, v. 7, n. 1, p. 63, doi. 10.1093/bfgp/eln003
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- Article
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study.
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- Proteomics, 2023, v. 23, n. 17, p. 1, doi. 10.1002/pmic.202200323
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- Article
Quantum computing algorithms: getting closer to critical problems in computational biology.
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- Briefings in Bioinformatics, 2022, v. 23, n. 6, p. 1, doi. 10.1093/bib/bbac437
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On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.
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- Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 601, doi. 10.1093/bib/bbz168
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- Article
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes.
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- BMC Genomics, 2017, v. 18, p. 25, doi. 10.1186/s12864-017-3911-3
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Effect of molecular confinement on internal enzyme dynamics: Frequency domain fluorometry and molecular dynamics simulation studies.
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- Biopolymers, 2002, v. 67, n. 2, p. 85, doi. 10.1002/bip.10058
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MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
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- Bioinformatics, 2003, v. 19, n. 4, p. 500, doi. 10.1093/bioinformatics/btg023
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A sequence-profile-based HMM for predicting and discriminating β barrel membrane proteins.
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- Bioinformatics, 2002, v. 18, p. S46, doi. 10.1093/bioinformatics/18.suppl_1.S46
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MultifacetedProtDB: a database of human proteins with multiple functions.
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- Nucleic Acids Research, 2024, v. 52, n. D1, p. D494, doi. 10.1093/nar/gkad783
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- Article
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.
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- Nucleic Acids Research, 2021, v. 49, n. W1, p. W60, doi. 10.1093/nar/gkab328
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
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- Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1037-6
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PhenPath: a tool for characterizing biological functions underlying different phenotypes.
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- BMC Genomics, 2019, v. 20, n. 8, p. N.PAG, doi. 10.1186/s12864-019-5868-x
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- Article
Assessing predictions of the impact of variants on splicing in CAGI5.
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- Human Mutation, 2019, v. 40, n. 9, p. 1215, doi. 10.1002/humu.23869
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CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases.
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- Human Mutation, 2019, v. 40, n. 9, p. 1373, doi. 10.1002/humu.23874
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Assessing computational predictions of the phenotypic effect of cystathionine‐beta‐synthase variants.
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- Human Mutation, 2019, v. 40, n. 9, p. 1530, doi. 10.1002/humu.23868
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Assessing predictions on fitness effects of missense variants in calmodulin.
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- Human Mutation, 2019, v. 40, n. 9, p. 1463, doi. 10.1002/humu.23857
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Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.
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- Human Mutation, 2019, v. 40, n. 9, p. 1612, doi. 10.1002/humu.23849
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Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge.
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- Human Mutation, 2019, v. 40, n. 9, p. 1392, doi. 10.1002/humu.23843
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Assessment of methods for predicting the effects of PTEN and TPMT protein variants.
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- Human Mutation, 2019, v. 40, n. 9, p. 1495, doi. 10.1002/humu.23838
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- Article
Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
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- Human Mutation, 2019, v. 40, n. 9, p. 1314, doi. 10.1002/humu.23825
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Are machine learning based methods suited to address complex biological problems? Lessons from CAGI‐5 challenges.
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- Human Mutation, 2019, v. 40, n. 9, p. 1455, doi. 10.1002/humu.23784
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