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Biologically meaningful genome interpretation models to address data underdetermination for the leaf and seed ionome prediction in Arabidopsis thaliana.
- Published in:
- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-63855-6
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- Article
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.
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- BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S8-S6
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- Article
WS-SNPs&GO: a web server for predicting the eleterious effect of human protein variants sing functional annotation.
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- BMC Genomics, 2013, v. 14, n. Suppl 3, p. 1, doi. 10.1186/1471-2164-14-S3-S6
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- Article
Predicting cancer-associated germline variations in proteins.
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- BMC Genomics, 2012, v. 13, n. Suppl 4, p. 1, doi. 10.1186/1471-2164-13-S4-S8
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- Publication type:
- Article
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions.
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- BMC Genomics, 2012, v. 13, n. Suppl 4, p. 1, doi. 10.1186/1471-2164-13-S4-S5
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- Publication type:
- Article
Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics.
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- PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011474
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- Publication type:
- Article
Analysis of hard protein corona composition on selective iron oxide nanoparticles by MALDI-TOF mass spectrometry: identification and amplification of a hidden mastitis biomarker in milk proteome.
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- Analytical & Bioanalytical Chemistry, 2018, v. 410, n. 12, p. 2949, doi. 10.1007/s00216-018-0976-z
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- Publication type:
- Article
Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network.
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- Proteomics, 2004, v. 4, n. 6, p. 1665, doi. 10.1002/pmic.200300745
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- Publication type:
- Article
Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants.
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- Human Genetics, 2022, v. 141, n. 10, p. 1649, doi. 10.1007/s00439-021-02419-4
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- Article
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants.
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- Nucleic Acids Research, 2023, v. 51, n. W1, p. W451, doi. 10.1093/nar/gkad455
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- Publication type:
- Article
DDGun: an untrained predictor of protein stability changes upon amino acid variants.
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- Nucleic Acids Research, 2022, v. 50, n. W1, p. W222, doi. 10.1093/nar/gkac325
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- Publication type:
- Article
From genotype to phenotype in Arabidopsis thaliana: in-silico genome interpretation predicts 288 phenotypes from sequencing data.
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- Nucleic Acids Research, 2022, v. 50, n. 3, p. e16, doi. 10.1093/nar/gkab1099
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- Publication type:
- Article
Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome.
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- Nucleic Acids Research, 2019, v. 47, n. W1, p. W136, doi. 10.1093/nar/gkz420
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- Publication type:
- 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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- Publication type:
- Article
PhD-SNP<sup>g</sup>: a webserver and lightweight tool for scoring single nucleotide variants.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W247, doi. 10.1093/nar/gkx369
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- Publication type:
- Article
Longitudinal transcriptomic and genetic landscape of radiotherapy response in canine melanoma.
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- Veterinary & Comparative Oncology, 2019, v. 17, n. 3, p. 308, doi. 10.1111/vco.12473
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- Publication type:
- Article
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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- Article
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification.
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- Bioinformatics, 2024, v. 40, n. 5, p. 1, doi. 10.1093/bioinformatics/btae320
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- Publication type:
- Article
Nonlinear data fusion over Entity–Relation graphs for Drug–Target Interaction prediction.
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- Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad348
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- Publication type:
- Article
Calibrating variant-scoring methods for clinical decision making.
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- Bioinformatics, 2020, v. 36, n. 24, p. 5709, doi. 10.1093/bioinformatics/btaa943
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- Article
On the biases in predictions of protein stability changes upon variations: the INPS test case.
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- Bioinformatics, 2019, v. 35, n. 14, p. 2525, doi. 10.1093/bioinformatics/bty979
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- Article
A natural upper bound to the accuracy of predicting protein stability changes upon mutations.
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- Bioinformatics, 2019, v. 35, n. 9, p. 1513, doi. 10.1093/bioinformatics/bty880
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- Publication type:
- Article
DeepSig: deep learning improves signal peptide detection in proteins.
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- Bioinformatics, 2018, v. 34, n. 10, p. 1690, doi. 10.1093/bioinformatics/btx818
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- Article
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.
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- 2017
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- Publication type:
- Product Review
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.
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- Bioinformatics, 2017, v. 33, n. 3, p. 347, doi. 10.1093/bioinformatics/btw656
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- Publication type:
- Article
NET-GE: a web-server for NETwork-based human gene enrichment.
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- Bioinformatics, 2016, v. 32, n. 22, p. 3489, doi. 10.1093/bioinformatics/btw508
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- Publication type:
- Article
INPS-MD: a web server to predict stability of protein variants from sequence and structure.
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- Bioinformatics, 2016, v. 32, n. 16, p. 2542, doi. 10.1093/bioinformatics/btw192
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- Publication type:
- Article
AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints.
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- Bioinformatics, 2015, v. 31, n. 23, p. 3841, doi. 10.1093/bioinformatics/btv451
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- Publication type:
- Article
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
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- Bioinformatics, 2015, v. 31, n. 20, p. 3269, doi. 10.1093/bioinformatics/btv367
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- Publication type:
- Article
INPS: predicting the impact of non-synonymous variations on protein stability from sequence.
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- Bioinformatics, 2015, v. 31, n. 17, p. 2816, doi. 10.1093/bioinformatics/btv291
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- Publication type:
- Article
Unravelling the instability of mutational signatures extraction via archetypal analysis.
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- Frontiers in Genetics, 2023, v. 13, p. 1, doi. 10.3389/fgene.2022.1049501
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- Publication type:
- Article
Influence of Model Structures on Predictors of Protein Stability Changes from Single-Point Mutations.
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- Genes, 2023, v. 14, n. 12, p. 2228, doi. 10.3390/genes14122228
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- Publication type:
- Article
A Deep-Learning Sequence-Based Method to Predict Protein Stability Changes Upon Genetic Variations.
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- Genes, 2021, v. 13, n. 6, p. 911, doi. 10.3390/genes12060911
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- Publication type:
- Article
Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks.
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- Genes, 2021, v. 12, n. 2, p. 319, doi. 10.3390/genes12020319
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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
Context dependency of nucleotide probabilities and variants in human DNA.
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- BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-021-08246-1
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- Publication type:
- Article
Context dependency of nucleotide probabilities and variants in human DNA.
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- BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-021-08246-1
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- Publication type:
- Article
Correction to: Context dependency of nucleotide probabilities and variants in human DNA.
- Published in:
- 2022
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- Publication type:
- Correction Notice
Preventing illegal seafood trade using machine-learning assisted microbiome analysis.
- Published in:
- BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-02005-w
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- Article
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
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- Bioinformatics, 2014, v. 30, n. 20, p. 2973, doi. 10.1093/bioinformatics/btu411
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- Publication type:
- Article
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
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- Bioinformatics, 2013, v. 29, n. 24, p. 3151, doi. 10.1093/bioinformatics/btt555
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- Publication type:
- Article
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.
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- Bioinformatics, 2013, v. 29, n. 8, p. 981, doi. 10.1093/bioinformatics/btt089
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- Publication type:
- Article
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
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- Bioinformatics, 2013, v. 29, n. 4, p. 504, doi. 10.1093/bioinformatics/bts728
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- Publication type:
- Article
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.
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- Bioinformatics, 2011, v. 27, n. 22, p. 3123, doi. 10.1093/bioinformatics/btr549
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- Publication type:
- Article
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
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- Bioinformatics, 2011, v. 27, n. 16, p. 2224, doi. 10.1093/bioinformatics/btr387
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- Publication type:
- Article
Fast overlapping of protein contact maps by alignment of eigenvectors.
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- Bioinformatics, 2010, v. 26, n. 18, p. 2250, doi. 10.1093/bioinformatics/btq402
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- Publication type:
- Article
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.
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- Bioinformatics, 2009, v. 25, n. 21, p. 2757, doi. 10.1093/bioinformatics/btp539
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- Publication type:
- Article
Predicting protein thermostability changes from sequence upon multiple mutations.
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- Bioinformatics, 2008, v. 24, n. 13, p. i190, doi. 10.1093/bioinformatics/btn166
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- Publication type:
- Article
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
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- Bioinformatics, 2008, v. 24, n. 10, p. 1313, doi. 10.1093/bioinformatics/btn115
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- Article
Predicting protein stability changes from sequences using support vector machines.
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- Bioinformatics, 2005, v. 21, p. ii54, doi. 10.1093/bioinformatics/bti1109
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- Publication type:
- Article