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Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites.
- Published in:
- Molecular Biology & Evolution, 2007, v. 24, n. 5, p. 1219, doi. 10.1093/molbev/msm042
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- Article
Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection.
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- Molecular Biology & Evolution, 2002, v. 19, n. 6, p. 950, doi. 10.1093/oxfordjournals.molbev.a004152
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- Article
Accuracy and Power of the Likelihood Ratio Test in Detecting Adaptive Molecular Evolution.
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- Molecular Biology & Evolution, 2001, v. 18, n. 8, p. 1585, doi. 10.1093/oxfordjournals.molbev.a003945
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- Article
A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3).
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- Life Science Alliance, 2023, v. 6, n. 4, p. 1, doi. 10.26508/lsa.202201677
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- Article
Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.
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- Journal of Evolutionary Biology, 2023, v. 36, n. 2, p. 321, doi. 10.1111/jeb.14106
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- Article
Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex.
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- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-859
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- Article
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.
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- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04442-8
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- Article
Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.
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- Molecular Biology & Evolution, 2024, v. 41, n. 7, p. 1, doi. 10.1093/molbev/msae109
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- Article
Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions.
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- Molecular Biology & Evolution, 2015, v. 32, n. 8, p. 2208, doi. 10.1093/molbev/msv097
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- Article
Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences.
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- Molecular Biology & Evolution, 2015, v. 32, n. 3, p. 806, doi. 10.1093/molbev/msu340
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- Article
Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes.
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- Molecular Biology & Evolution, 2014, v. 31, n. 5, p. 1132, doi. 10.1093/molbev/msu062
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- Article
CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models.
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- Molecular Biology & Evolution, 2013, v. 30, n. 6, p. 1270, doi. 10.1093/molbev/mst034
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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
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models.
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- Molecular Biology & Evolution, 2009, v. 26, n. 2, p. 255, doi. 10.1093/molbev/msn232
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- Article
The evolution and function of protein tandem repeats in plants.
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- New Phytologist, 2015, v. 206, n. 1, p. 397, doi. 10.1111/nph.13184
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- Article
Functional diversification of the GALA type III effector family contributes to Ralstonia solanacearum adaptation on different plant hosts.
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- New Phytologist, 2011, v. 192, n. 4, p. 976, doi. 10.1111/j.1469-8137.2011.03854.x
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- Article
PANDIT plus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatits resources.
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- Trends in Evolutionary Biology, 2010, v. 2, p. 1, doi. 10.4081/eb.2010.e1
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- Article
Natural Selection on Coding and Noncoding DNA Sequences Is Associated with Virulence Genes in a Plant Pathogenic Fungus.
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- Genome Biology & Evolution, 2014, v. 6, n. 9, p. 2368, doi. 10.1093/gbe/evu192
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- Article
Functional assignment to positively selected sites in the core type III effector RipG7 from R alstonia solanacearum.
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- Molecular Plant Pathology, 2016, v. 17, n. 4, p. 553, doi. 10.1111/mpp.12302
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- Article
Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices.
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- G3: Genes | Genomes | Genetics, 2018, v. 8, n. 10, p. 3173, doi. 10.1534/g3.118.200185
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- Article
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder.
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- Genes, 2020, v. 11, n. 4, p. 1, doi. 10.3390/genes11040407
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- Article
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
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.
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- Systematic Biology, 2023, v. 72, n. 2, p. 307, doi. 10.1093/sysbio/syac050
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- Article
Gene copy number variation and its significance in cyanobacterial phylogeny.
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- BMC Microbiology, 2012, v. 12, n. 1, p. 177, doi. 10.1186/1471-2180-12-177
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- Article
Exome sequencing study of Russian breast cancer patients suggests a predisposing role for USP39.
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- Breast Cancer Research & Treatment, 2020, v. 179, n. 3, p. 731, doi. 10.1007/s10549-019-05492-6
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- Article
Genomes reveal marked differences in the adaptive evolution between orangutan species.
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- Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1562-6
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- Article
Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families.
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- PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0095034
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- Article
Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster.
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- PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022613
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- Article
Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions.
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- PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0020488
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- Article
Origin and Evolution of GALA-LRR, a New Member of the CC-LRR Subfamily: From Plants to Bacteria?
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- PLoS ONE, 2008, v. 3, n. 2, p. 1, doi. 10.1371/journal.pone.0001694
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- Article
Querying knowledge graphs in natural language.
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- Journal of Big Data, 2021, v. 8, n. 1, p. 1, doi. 10.1186/s40537-020-00383-w
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- Article
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes.
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- Systematic Biology, 2011, v. 60, n. 5, p. 685, doi. 10.1093/sysbio/syr041
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- Article
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0.
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- Systematic Biology, 2010, v. 59, n. 3, p. 307, doi. 10.1093/sysbio/syq010
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- Article
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative.
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- Systematic Biology, 2006, v. 55, n. 4, p. 539, doi. 10.1080/10635150600755453
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- Article
Progressive multiple sequence alignment with indel evolution.
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- BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2357-1
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- Publication type:
- Article
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
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- Nucleic Acids Research, 2019, v. 47, n. 21, p. 10994, doi. 10.1093/nar/gkz841
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- Article
Graph-based modeling of tandem repeats improves global multiple sequence alignment.
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- Nucleic Acids Research, 2013, v. 41, n. 17, p. e162, doi. 10.1093/nar/gkt628
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- Article
Repeat or not repeat?—Statistical validation of tandem repeat prediction in genomic sequences.
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- Nucleic Acids Research, 2012, v. 40, n. 20, p. 10005, doi. 10.1093/nar/gks726
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- Article
TRAL: tandem repeat annotation library.
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- Bioinformatics, 2015, v. 31, n. 18, p. 3051, doi. 10.1093/bioinformatics/btv306
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- Article
State-of the art methodologies dictate new standards for phylogenetic analysis.
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- BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-161
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- Article
Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-08233-w
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- Article
Genomic Insights into Evolution of AdpA Family Master Regulators of Morphological Differentiation and Secondary Metabolism in <italic>Streptomyces</italic>.
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- Journal of Molecular Evolution, 2018, v. 86, n. 3/4, p. 204, doi. 10.1007/s00239-018-9834-z
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- Article
Positive and Negative Selection in the β- Esterase Gene Cluster of the Drosophila melanogaster Subgroup.
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- Journal of Molecular Evolution, 2006, v. 62, n. 4, p. 496, doi. 10.1007/s00239-005-0140-1
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- Article
Molecular Evolution of the Hepatitis Delta Virus Antigen Gene: Recombination or Positive Selection?
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- Journal of Molecular Evolution, 2004, v. 59, n. 6, p. 815, doi. 10.1007/s00239-004-0112-x
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- Article
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites.
- Published in:
- Genetics, 2003, v. 164, n. 3, p. 1229, doi. 10.1093/genetics/164.3.1229
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- Article
Short tandem repeat mutations regulate gene expression in colorectal cancer.
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- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-53739-0
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- Article
The Use of the Rare TTA Codon in Streptomyces Genes: Significance of the Codon Context?
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- Indian Journal of Microbiology, 2021, v. 61, n. 1, p. 24, doi. 10.1007/s12088-020-00902-6
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- Article
DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).
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- BMC Genetics, 2016, v. 17, p. 1, doi. 10.1186/s12863-016-0374-5
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- Article
Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.
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- BMC Evolutionary Biology, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12862-015-0352-y
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- Article