The evolutionary origin of orphan genes
Gene evolution has long been thought to be primarily driven by duplication and
rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes …
rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes …
Machine learning on protein–protein interaction prediction: models, challenges and trends
Protein–protein interactions (PPIs) carry out the cellular processes of all living organisms.
Experimental methods for PPI detection suffer from high cost and false-positive rate, hence …
Experimental methods for PPI detection suffer from high cost and false-positive rate, hence …
Proto-genes and de novo gene birth
Novel protein-coding genes can arise either through re-organization of pre-existing genes or
de novo,. Processes involving re-organization of pre-existing genes, notably after gene …
de novo,. Processes involving re-organization of pre-existing genes, notably after gene …
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
The population genetic perspective is that the processes sha** genomic variation can be
revealed only through simultaneous investigation of sequence polymorphism and …
revealed only through simultaneous investigation of sequence polymorphism and …
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica
MC Schatz, LG Maron, JC Stein, AH Wences… - Genome biology, 2014 - Springer
Background The use of high throughput genome-sequencing technologies has uncovered a
large extent of structural variation in eukaryotic genomes that makes important contributions …
large extent of structural variation in eukaryotic genomes that makes important contributions …
Protein length in eukaryotic and prokaryotic proteomes
L Brocchieri, S Karlin - Nucleic acids research, 2005 - academic.oup.com
We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to
function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes …
function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes …
Physical limits of cells and proteomes
What are the physical limits to cell behavior? Often, the physical limitations can be
dominated by the proteome, the cell's complement of proteins. We combine known protein …
dominated by the proteome, the cell's complement of proteins. We combine known protein …
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
Background Sequencing the expressed genetic information of an ecosystem
(metatranscriptome) can provide information about the response of organisms to varying …
(metatranscriptome) can provide information about the response of organisms to varying …
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
Lineage-specific gene loss, to a large extent, accounts for the differences in gene repertoires
between genomes, particularly among eukaryotes. We derived a parsimonious scenario …
between genomes, particularly among eukaryotes. We derived a parsimonious scenario …
Phylogenetic patterns of emergence of new genes support a model of frequent de novoevolution
Background New gene emergence is so far assumed to be mostly driven by duplication and
divergence of existing genes. The possibility that entirely new genes could emerge out of the …
divergence of existing genes. The possibility that entirely new genes could emerge out of the …