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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
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
GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae121
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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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- Article
Knowledge of the perturbation design is essential for accurate gene regulatory network inference.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-19005-x
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- Article
The Pfam protein families database in 2019.
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- Nucleic Acids Research, 2019, v. 47, n. D1, p. D427, doi. 10.1093/nar/gky995
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- Article
FunCoup 4: new species, data, and visualization.
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- Nucleic Acids Research, 2018, v. 46, n. D1, p. D601, doi. 10.1093/nar/gkx1138
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A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.
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- Nucleic Acids Research, 2017, v. 45, n. 2, p. 1, doi. 10.1093/nar/gkw849
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- Article
HieranoiDB: a database of orthologs inferred by Hieranoid.
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- Nucleic Acids Research, 2017, v. 45, n. D1, p. D687, doi. 10.1093/nar/gkw923
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- Article
PathwAX: a web server for network crosstalk based pathway annotation.
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- Nucleic Acids Research, 2016, v. 44, n. W1, p. W105, doi. 10.1093/nar/gkw356
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- Article
Pfam: the protein families database.
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- Nucleic Acids Research, 2014, v. 42, n. D1, p. D222, doi. 10.1093/nar/gkt1223
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- Article
FunCoup 3.0: database of genome-wide functional coupling networks.
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- Nucleic Acids Research, 2014, v. 42, n. D1, p. D380, doi. 10.1093/nar/gkt984
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- Article
The Pfam protein families database.
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- Nucleic Acids Research, 2012, p. D290, doi. 10.1093/nar/gkr1065
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- Article
Comparative interactomics with Funcoup 2.0.
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- Nucleic Acids Research, 2012, p. D821, doi. 10.1093/nar/gkr1062
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- Article
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
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- Nucleic Acids Research, 2010, v. 38, p. D196, doi. 10.1093/nar/gkp931
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- Article
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
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- Nucleic Acids Research, 2009, v. 37, n. 3, p. 858, doi. 10.1093/nar/gkn1006
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- Article
The Pfam protein families database.
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- Nucleic Acids Research, 2008, v. 36, p. D281
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- Article
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
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- Nucleic Acids Research, 2008, v. 36, p. D263
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- Article
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence.
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- FEBS Journal, 2005, v. 272, n. 11, p. 2727, doi. 10.1111/j.1742-4658.2005.04691.x
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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
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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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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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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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
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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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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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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Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
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- Nucleic Acids Research, 2006, v. 34, n. 11, p. w596, doi. 10.1093/nar/gkl191
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- Article
Pfam: clans, web tools and services.
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- Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d247, doi. 10.1093/nar/gkj149
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- Article
Automatic assessment of alignment quality.
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- Nucleic Acids Research, 2005, v. 33, n. 22, p. 7120, doi. 10.1093/nar/gki1020
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- Article
siRNAdb: a database of siRNA sequences.
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- Nucleic Acids Research, 2005, v. 33, n. 5, p. 1737, doi. 10.1093/nar/gki294
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- Article
Inparanoid: a comprehensive database of eukaryotic orthologs.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d476
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- Article
siRNAdb: a database of siRNA sequences.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d131
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- Article
FunShift: a database of function shift analysis on protein subfamilies.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d197
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The Pfam protein families database.
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- Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d138
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- Article
The Pfam Protein Families Database.
- Published in:
- Nucleic Acids Research, 2002, v. 30, n. 1, p. 276, doi. 10.1093/nar/30.1.276
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- Article
The Pfam Protein Families Database.
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- Nucleic Acids Research, 2000, v. 28, n. 1, p. 263, doi. 10.1093/nar/28.1.263
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- Article
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
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- Nucleic Acids Research, 1999, v. 27, n. 1, p. 260, doi. 10.1093/nar/27.1.260
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- Article
Pfam: multiple sequence alignments and HMM‐profiles of protein domains.
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- Nucleic Acids Research, 1998, v. 26, n. 1, p. 322
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- Article
Domainoid: domain-oriented orthology inference.
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- BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3137-2
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- Article
Benchmarking enrichment analysis methods with the disease pathway network.
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- 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
Domain Tree-Based Analysis of Protein Architecture Evolution.
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- Molecular Biology & Evolution, 2008, v. 25, n. 2, p. 254, doi. 10.1093/molbev/msm254
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- Article