-
Article
Open AccessSRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs
Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs fo...
-
Article
Open AccessDifferential DNA methylation of vocal and facial anatomy genes in modern humans
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challeng...
-
Article
Open AccessIdentification of introns harboring functional sequence elements through positional conservation
Many human introns carry out a function, in the sense that they are critical to maintain normal cellular activity. Their identification is fundamental to understanding cellular processes and disease. However, ...
-
Article
Open AccessThe role of nucleotide composition in premature termination codon recognition
It is not fully understood how a termination codon is recognized as premature (PTC) by the nonsense-mediated decay (NMD) machinery. This is particularly true for transcripts lacking an exon junction complex (E...
-
Article
ApoB-containing lipoproteins regulate angiogenesis by modulating expression of VEGF receptor 1
High concentrations of some types of plasma lipoproteins, such as low-density lipoprotein, promote atherosclerosis and a wide range of vascular-related diseases. These pathogenic lipoproteins have in common th...
-
Article
Open AccessOrigin and evolution of spliceosomal introns
Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were inter...
-
Protocol
A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure
Spliceosomal introns are one of the principal distinctive features of eukaryotes. Nevertheless, different large-scale studies disagree about even the most basic features of their evolution. In order to come up...
-
Article
Open AccessHomoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
Rare genomic changes (RGCs) that are thought to comprise derived shared characters of individual clades are becoming an increasingly important class of markers in genome-wide phylogenetic studies. Recently, we...
-
Article
Open AccessPatterns of intron gain and conservation in eukaryotic genes
The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction ...
-
Chapter
Correlations between Quantitative Measures of Genome Evolution, Expression and Function
In addition to multiple, complete genome sequences, genome-wide data on biological properties of genes, such as knockout effect, expression levels, protein-protein interactions, and others, are rapidly accumul...
-
Chapter and Conference Paper
An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes
We propose a detailed model of evolution of exon-intron structure of eukaryotic genes that takes into account gene-specific intron gain and loss rates, branch-specific gain and loss coefficients, invariant sit...
-
Chapter and Conference Paper
Drawing Directed Graphs Using One-Dimensional Optimization
We present an algorithm for drawing directed graphs, which is based on rapidly solving a unique one-dimensional optimization problem for each of the axes. The algorithm results in a clear description of the hi...
-
Article
Estimating the size of the olfactory repertoire
The concept of shape space, which has been successfully implemented in immunology, is used here to construct a model for the discrimination power of the olfactory system. Using reasonable assumptions on the be...
