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Prediction of Function Divergence in Protein Families Using the Substitution Rate Variation Parameter Alpha.
- Published in:
- Molecular Biology & Evolution, 2006, v. 23, n. 7, p. 1406, doi. 10.1093/molbev/msl002
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- Article
Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction.
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- Molecular Biology & Evolution, 2005, v. 22, n. 11, p. 2257, doi. 10.1093/molbev/msi224
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- Article
An HMM posterior decoder for sequence feature prediction that includes homology information.
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- Bioinformatics, 2005, v. 21, p. i251, doi. 10.1093/bioinformatics/bti1014
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- Article
An HMM posterior decoder for sequence feature prediction that includes homology information.
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- Bioinformatics, 2005, v. 21, n. 1, p. i251, doi. 10.1093/bioinformatics/bti1014
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- Article
Sfixem—graphical sequence feature display in Java.
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- Bioinformatics, 2004, v. 20, n. 15, p. 2488, doi. 10.1093/bioinformatics/bth265
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- Article
ChromoWheel: a new spin on eukaryotic chromosome visualization.
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- Bioinformatics, 2004, v. 20, n. 4, p. 576, doi. 10.1093/bioinformatics/btg448
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- Article
Computational antisense oligo prediction with a neural network model.
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- Bioinformatics, 2002, v. 18, n. 12, p. 1567, doi. 10.1093/bioinformatics/18.12.1567
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- Article
OrthoGUI: graphical presentation of Orthostrapper results.
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- Bioinformatics, 2002, v. 18, n. 9, p. 1272, doi. 10.1093/bioinformatics/18.9.1272
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- Article
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
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- Bioinformatics, 2002, v. 18, n. 1, p. 92, doi. 10.1093/bioinformatics/18.1.92
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- Article
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
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- Bioinformatics, 2001, v. 17, n. 7, p. 656, doi. 10.1093/bioinformatics/17.7.656
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- Article
NIFAS: visual analysis of domain evolution in proteins.
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- Bioinformatics, 2001, v. 17, n. 4, p. 343, doi. 10.1093/bioinformatics/17.4.343
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- Article
A comparison of sequence and structure protein domain families as a basis for structural genomics.
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- Bioinformatics, 1999, v. 15, n. 6, p. 480, doi. 10.1093/bioinformatics/15.6.480
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- Article
Employing conservation of co-expression to improve functional inference.
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- BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-81
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- Article
Domain Tree-Based Analysis of Protein Architecture Evolution.
- Published in:
- Molecular Biology & Evolution, 2008, v. 25, n. 2, p. 254, doi. 10.1093/molbev/msm254
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- Article
Orthology confers intron position conservation.
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- BMC Genomics, 2010, v. 11, p. 412, doi. 10.1186/1471-2164-11-412
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- Article
Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family.
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- BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-19
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- Article
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs.
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- BMC Genomics, 2004, v. 5, p. 1, doi. 10.1186/1471-2164-5-85
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- Article
Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression.
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- Scientific World Journal, 2012, p. 1, doi. 10.1100/2012/130491
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- Article
Benchmarking enrichment analysis methods with the disease pathway network.
- Published in:
- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae069
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- Article
Genome-wide functional association networks: background, data & state-of-the-art resources.
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- Briefings in Bioinformatics, 2020, v. 21, n. 4, p. 1224, doi. 10.1093/bib/bbz064
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- Article
Automatic extraction of reliable regions from multiple sequence alignments.
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- BMC Bioinformatics, 2007, v. 8, p. S9, doi. 10.1186/1471-2105-8-S5-S9
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- Article
Kalign -- an accurate and fast multiple sequence alignment algorithm.
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- BMC Bioinformatics, 2005, v. 6, p. 1, doi. 10.1186/1471-2105-6-298
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- Article
Scoredist: A simple and robust protein sequence distance estimator.
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- BMC Bioinformatics, 2005, v. 6, p. 1, doi. 10.1186/1471-2105-6-108
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- Article
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
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- BMC Bioinformatics, 2005, v. 6, p. 99, doi. 10.1186/1471-2105-6-99
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- Article
Profiled support vector machines for antisense oligonucleotide efficacy prediction.
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- BMC Bioinformatics, 2004, v. 5, p. 135, doi. 10.1186/1471-2105-5-135
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- Article
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.
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- Bioinformatics, 2022, v. 38, n. 10, p. 2918, doi. 10.1093/bioinformatics/btac194
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- Article
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.
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- Bioinformatics, 2022, v. 38, n. 9, p. 2659, doi. 10.1093/bioinformatics/btac153
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- Article
Fast and accurate gene regulatory network inference by normalized least squares regression.
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- Bioinformatics, 2022, v. 38, n. 8, p. 2263, doi. 10.1093/bioinformatics/btac103
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- Article
Inferring the experimental design for accurate gene regulatory network inference.
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- Bioinformatics, 2021, v. 37, n. 20, p. 3553, doi. 10.1093/bioinformatics/btab367
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- Article
A generalized framework for controlling FDR in gene regulatory network inference.
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- Bioinformatics, 2019, v. 35, n. 6, p. 1026, doi. 10.1093/bioinformatics/bty764
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- Article
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms.
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- Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-70941-y
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- Article
Pathway-specific model estimation for improved pathway annotation by network crosstalk.
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- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-70239-z
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- Article
Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks.
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- PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0054945
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- Article
Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity.
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- PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010465
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- Article
PathBIX—a web server for network-based pathway annotation with adaptive null models.
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- Bioinformatics Advances, 2021, v. 1, n. 1, p. 1, doi. 10.1093/bioadv/vbab010
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- Article
Discovering viral genomes in human metagenomic data by predicting unknown protein families.
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- Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-017-18341-7
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- Article
A large-scale benchmark of gene prioritization methods.
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- Scientific Reports, 2017, p. 46598, doi. 10.1038/srep46598
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- Article
Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference.
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- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.855770
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- Article
Corrigendum: Network Crosstalk as a Basis for Drug Repurposing.
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- 2022
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- Correction Notice
Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.
- Published in:
- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.855766
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- Article
Network Crosstalk as a Basis for Drug Repurposing.
- Published in:
- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.792090
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- Publication type:
- Article
Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.
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- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.815692
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- Article
Fusion transcript detection using spatial transcriptomics.
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- BMC Medical Genomics, 2020, v. 13, p. 1, doi. 10.1186/s12920-020-00738-5
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- Article
MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.
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- BMC Medical Genomics, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s12920-020-00731-y
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- Publication type:
- Article
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence.
- Published in:
- FEBS Journal, 2005, v. 272, n. 11, p. 2727, doi. 10.1111/j.1742-4658.2005.04691.x
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- Article
TOPAS, a network-based approach to detect disease modules in a top-down fashion.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 4, p. 1, doi. 10.1093/nargab/lqac093
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- Publication type:
- Article
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19.
- Published in:
- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-99721-y
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- Article
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. W1, p. W398, doi. 10.1093/nar/gkac377
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- Article
Pfam: The protein families database in 2021.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. D1, p. D412, doi. 10.1093/nar/gkaa913
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- Article
The Pfam protein families database in 2019.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. D1, p. D427, doi. 10.1093/nar/gky995
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- Article