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Quest for Orthologs in the Era of Biodiversity Genomics.
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- Genome Biology & Evolution, 2024, v. 16, n. 10, p. 1, doi. 10.1093/gbe/evae224
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Genomic Encryption of Digital Data Stored in Synthetic DNA.
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- Angewandte Chemie, 2020, v. 132, n. 22, p. 8554, doi. 10.1002/ange.202001162
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- Article
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31564-1
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Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31564-1
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A generalized Robinson-Foulds distance for labeled trees.
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- BMC Genomics, 2020, v. 21, p. N.PAG, doi. 10.1186/s12864-020-07011-0
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A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor.
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- eLife, 2020, p. 1, doi. 10.7554/eLife.62507
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The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
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- Nucleic Acids Research, 2015, v. 43, n. D1, p. D240, doi. 10.1093/nar/gku1158
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- Article
OMA 2011: orthology inference among 1000 complete genomes.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D289, doi. 10.1093/nar/gkq1238
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- Article
The Microbe browser for comparative genomics.
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- Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W296, doi. 10.1093/nar/gkp268
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- Article
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
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- Nature Biotechnology, 2024, v. 42, n. 1, p. 139, doi. 10.1038/s41587-023-01753-4
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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
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- Nature Biotechnology, 2014, v. 32, n. 12, p. 1250, doi. 10.1038/nbt.3079
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ISMB 2022 proceedings.
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- Bioinformatics, 2022, v. 38, p. i8, doi. 10.1093/bioinformatics/btac305
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- Article
OMAMO: orthology-based alternative model organism selection.
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- Bioinformatics, 2022, v. 38, n. 10, p. 2965, doi. 10.1093/bioinformatics/btac163
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- Article
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.
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- Bioinformatics, 2021, v. 37, n. 18, p. 2866, doi. 10.1093/bioinformatics/btab219
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- Article
ISMB/ECCB 2021 proceedings.
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- Bioinformatics, 2021, v. 37, p. i7, doi. 10.1093/bioinformatics/btab382
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- Article
The what, where, how and why of gene ontology—a primer for bioinformaticians.
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- Briefings in Bioinformatics, 2011, v. 12, n. 6, p. 723, doi. 10.1093/bib/bbr002
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- Article
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes).
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- Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 474, doi. 10.1093/bib/bbr038
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- Article
Editorial: Orthology and applications.
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- Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 375, doi. 10.1093/bib/bbr057
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Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
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- Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 423, doi. 10.1093/bib/bbr034
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- Article
Base-calling for next-generation sequencing platforms.
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- Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 489, doi. 10.1093/bib/bbq077
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- Article
iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration.
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- Plant Journal, 2011, v. 67, n. 1, p. 145, doi. 10.1111/j.1365-313X.2011.04582.x
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- Article
The phylogenetic range of bacterial and viral pathogens of vertebrates.
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- Molecular Ecology, 2020, v. 29, n. 17, p. 3361, doi. 10.1111/mec.15463
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Phylogenetic Profiling: How Much Input Data Is Enough?
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- PLoS ONE, 2015, v. 10, n. 2, p. 1, doi. 10.1371/journal.pone.0114701
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The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study.
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- PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0056925
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- Article
Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs.
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- PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0053786
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AI and the democratization of knowledge.
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- Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03099-1
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Enabling semantic queries across federated bioinformatics databases.
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- Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz106
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- Article
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria.
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- Molecular Biology & Evolution, 2022, v. 39, n. 2, p. 1, doi. 10.1093/molbev/msab317
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Ten Years of Collaborative Progress in the Quest for Orthologs.
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- Molecular Biology & Evolution, 2021, v. 38, n. 8, p. 3033, doi. 10.1093/molbev/msab098
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Advances and Applications in the Quest for Orthologs.
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- Molecular Biology & Evolution, 2019, v. 36, n. 10, p. 2157, doi. 10.1093/molbev/msz150
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- Article
Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.
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- Molecular Biology & Evolution, 2016, v. 33, n. 11, p. 2874, doi. 10.1093/molbev/msw164
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Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.
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- Molecular Biology & Evolution, 2016, v. 33, n. 8, p. 2163, doi. 10.1093/molbev/msw080
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- Article
Clustering Genes of Common Evolutionary History.
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- Molecular Biology & Evolution, 2016, v. 33, n. 6, p. 1590, doi. 10.1093/molbev/msw038
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- Article
ALF—A Simulation Framework for Genome Evolution.
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- Molecular Biology & Evolution, 2012, v. 29, n. 4, p. 1115, doi. 10.1093/molbev/msr268
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- Article
Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE.
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- Plant Cell, 2023, v. 35, n. 7, p. 2635, doi. 10.1093/plcell/koad096
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Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.
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- Nucleic Acids Research, 2006, v. 34, n. 11, p. 3309, doi. 10.1093/nar/gkl433
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Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.
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- Genome Biology & Evolution, 2024, v. 16, n. 6, p. 1, doi. 10.1093/gbe/evae100
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- Article
Inferring Horizontal Gene Transfer.
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- PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004095
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Approximate Bayesian Computation.
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- PLoS Computational Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002803
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- Article
Quality of Computationally Inferred Gene Ontology Annotations.
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- PLoS Computational Biology, 2012, v. 8, n. 5, p. 1, doi. 10.1371/journal.pcbi.1002533
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Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs.
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- PLoS Computational Biology, 2012, v. 8, n. 5, p. 1, doi. 10.1371/journal.pcbi.1002514
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Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods.
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- PLoS Computational Biology, 2009, v. 5, n. 1, p. 1, doi. 10.1371/journal.pcbi.1000262
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Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
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- Nature Communications, 2017, v. 8, n. 1, p. 14061, doi. 10.1038/ncomms14061
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Protein length distribution is remarkably uniform across the tree of life.
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- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02973-2
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- Article
Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs.
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- Genome Biology & Evolution, 2021, v. 13, n. 6, p. 1, doi. 10.1093/gbe/evab077
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Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.
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- Genome Biology & Evolution, 2021, v. 13, n. 3, p. 1, doi. 10.1093/gbe/evab010
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Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.
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- Genome Biology & Evolution, 2020, v. 12, n. 8, p. 1355, doi. 10.1093/gbe/evaa127
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- Article
Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.
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- Genome Biology & Evolution, 2016, v. 8, n. 4, p. 1233, doi. 10.1093/gbe/evw075
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Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals.
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- Genome Biology & Evolution, 2013, v. 5, n. 10, p. 1800, doi. 10.1093/gbe/evt132
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- Article
Genomic Encryption of Digital Data Stored in Synthetic DNA.
- Published in:
- Angewandte Chemie International Edition, 2020, v. 59, n. 22, p. 8476, doi. 10.1002/anie.202001162
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- Publication type:
- Article