Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA) [PDF]
, 2011 Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes.
Jingjie Hu +7 more
core +1 more source
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison [PDF]
, 2006 Non-coding DNA comprises ∼80% of the euchromatic portion of the Drosophila melanogaster genome. Non-coding sequences are known to contain functionally important elements controlling gene expression, but the proportion of sites that are selectively ...
Keightley, Peter, Halligan, Daniel
core +1 more source
FEBS Letters, EarlyView.Inositol pyrophosphates are energy‐rich signaling molecules that perform critical functions in cells. Three different families of phosphatases hydrolyze the β phosphate of the inositol pyrophosphate molecules: two have narrow specificities and one is promiscuous.
Ronda J. Rolfes
wiley +1 more source
Replication independent formation of extrachromosomal circular DNA in mammalian cell-free system.
PLoS ONE, 2009 Extrachromosomal circular DNA (eccDNA) is a pool of circular double stranded DNA molecules found in all eukaryotic cells and composed of repeated chromosomal sequences. It was proposed to be involved in genomic instability, aging and alternative telomere
Zoya Cohen, Sara Lavi
doaj +1 more source
Statistical Models of the Protein Fitness Landscape: Applications to Protein Evolution and Engineering [PDF]
, 2012 Understanding the protein fitness landscape is important for describing how natural proteins evolve and for engineering new proteins with useful properties.
Romero, Philip Anthony
core +1 more source
FEBS Letters, EarlyView.CT10 regulator of kinase (CRK) and CRK‐Like (CRKL) are signaling adaptors driving cell adhesion, motility, differentiation, and proliferation. SH2‐domain containing (SH) proteins are enriched in YXXP motifs which when phosphorylated create preferred binding sites for CRK family SH2 domains.
Phoebe M. Cousens +8 more
wiley +1 more source
An in silico study of the differential effect of oxidation on two biologically relevant G-quadruplexes: Possible implications in oncogene expression [PDF]
, 2012 G-quadruplex structures, formed from guanine rich sequences, have previously been shown to be involved in various physiological processes including cancer-related gene expression.
William J D Stebbeds +14 more
core +1 more source
Reconstructing enzyme evolution by protein engineering
FEBS Letters, EarlyView.Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler +2 more
wiley +1 more source
The role of highly conserved non-coding DNA sequences in vertebrate development and evolution [PDF]
, 2010 PhDComparisons between vertebrate genome sequences, from mammals to fishes, have revealed thousands of conserved non-coding elements (CNEs) that are associated with developmental genes.
Parker, Hugo
core
Investigating transcription factor dynamics in health and disease using FRAP
FEBS Letters, EarlyView.FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj +3 more
wiley +1 more source