Andrew D. Fernandes

Works (4)

Updated: July 5th, 2023 15:57

2008 article

Biochemical and Functional Evidence of p53 Homology Is Inconsistent with Molecular Phylogenetics for Distant Sequences

Fernandes, A. D., & Atchley, W. R. (2008, June 16). Journal of Molecular Evolution.

By: A. Fernandes n & W. Atchley n

author keywords: p53; p63; p73; beta-Sandwich; transcription factor; p731
MeSH headings : Animals; Arthropods / genetics; DNA-Binding Proteins / classification; Evolution, Molecular; Genes, p53; Mollusca / genetics; Nematoda / genetics; Nuclear Proteins / classification; Phylogeny; Sequence Homology, Amino Acid; Tumor Protein p73; Tumor Suppressor Protein p53 / chemistry; Tumor Suppressor Protein p53 / classification; Tumor Suppressor Proteins / classification; Urochordata / genetics
topics (OpenAlex): Cancer-related Molecular Pathways; RNA modifications and cancer; Molecular Biology Techniques and Applications
TL;DR: The study shows that the biochemical and functional evidence of p53 homology for nematodes, arthropods, and protists is inconsistent with their implied phylogenetic relationship within the overall family, and suggests that p63 is a far more appropriate protein for comparison. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2008 article

Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative

Fernandes, A. D., & Atchley, W. R. (2008, July 28). Bioinformatics.

By: A. Fernandes n & W. Atchley n

MeSH headings : Algorithms; Animals; Basic-Leucine Zipper Transcription Factors / chemistry; Basic-Leucine Zipper Transcription Factors / genetics; Computational Biology; Databases, Protein; Evolution, Molecular; Genes, myc; Humans; Proteins / chemistry; Proteins / genetics; Sequence Alignment; Tumor Suppressor Protein p53 / chemistry; Tumor Suppressor Protein p53 / genetics
topics (OpenAlex): Genomics and Phylogenetic Studies; Machine Learning in Bioinformatics; Genetic diversity and population structure
TL;DR: An algorithm to simultaneously infer the set of n-1 relative rates that parameterize the likelihood of an n-site alignment is described, allowing for the first time coherent simultaneous inference of branch-lengths and site-specific evolutionary rates. (via Semantic Scholar)
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15. Life on Land (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2005 article

Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network

Atchley, W. R., & Fernandes, A. D. (2005, April 25). Proceedings of the National Academy of Sciences.

By: W. Atchley n & A. Fernandes n

author keywords: Myc; predictive motif; transcription factor; oncoprotein; molecular evolution
MeSH headings : Amino Acid Sequence / genetics; Basic-Leucine Zipper Transcription Factors; Computational Biology / methods; DNA-Binding Proteins / genetics; Fuzzy Logic; Genetic Variation; Genomics / methods; Helix-Loop-Helix Motifs / genetics; Molecular Sequence Data; Protein Conformation; Proto-Oncogene Proteins c-myc / genetics; Repressor Proteins / genetics; Sequence Alignment; Sequence Homology; Transcription Factors / genetics
topics (OpenAlex): Bioinformatics and Genomic Networks; Protein Structure and Dynamics; RNA and protein synthesis mechanisms
TL;DR: A small set of amino acid sites from the N-terminal portion of the basic helix-loop-helix (bHLH) domain are described that provide very accurate sequence signatures for the Myc-Max-Mad transcription factor network and three of its member proteins. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2005 article

Solving the protein sequence metric problem

Atchley, W. R., Zhao, J., Fernandes, A. D., & Drüke, T. (2005, April 25). Proceedings of the National Academy of Sciences.

By: W. Atchley n, J. Zhao n, A. Fernandes n & T. Drüke n

author keywords: basic helix-loop-helix; molecular evolution; multivariate statistics; amino acid attributes; factor analysis
MeSH headings : Amino Acid Sequence / genetics; Analysis of Variance; Cluster Analysis; Codon / genetics; Computational Biology / methods; Discriminant Analysis; Genetic Variation; Models, Genetic; Multivariate Analysis; Phylogeny; Protein Conformation; Static Electricity; Statistics as Topic / methods
topics (OpenAlex): RNA and protein synthesis mechanisms; Machine Learning in Bioinformatics; Genomics and Phylogenetic Studies
TL;DR: Multivariate statistical analyses on almost 500 amino acid attributes are used to produce a small set of highly interpretable numeric patterns of amino acid variability that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge. (via Semantic Scholar)
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10. Reduced Inequalities (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

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