Related papers: A Quantitative Understanding of Human Sex Chromoso…
Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…
Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation…
The paternally inherited Y chromosome has been widely used in population genetic studies to understand relationships among human populations. Our interpretation of Y chromosomal evidence about population history and genetics has rested on…
In this the first of an anticipated four paper series, fundamental results of quantitative genetics are presented from a first principles approach. While none of these results are in any sense new, they are presented in extended detail to…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
All genes on the human Y-chromosome were studied using fractal dimension and Shannon entropy. Clear outlier clusters were identified. Among these were 6 sequences that have since been withdrawn as CDSs and 1 additional sequence that is not…
To test whether X-chromosome has unique genomic characteristics, X-chromosome and 22 autosomes were compared for RNA binding density. Nucleotide sequences on the chromosomes were divided into 50kb per segment that was recoded as a set of…
The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of…
The human genome remains incomplete, with multi-megabase sized gaps representing the endogenous centromeres and other heterochromatic regions. These regions are commonly enriched with long arrays of near-identical tandem repeats, known as…
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
A series of studies have revealed the among-population components of genetic variation are higher for the paternal Y chromosome than for the maternal mitochondrial DNA (mtDNA), which indicates sex-biased migrations in human populations.…
Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…
The X-chromosome is often excluded from genome-wide association studies because of analytical challenges. Some of the problems, such as the random, skewed or no X-inactivation model uncertainty, have been investigated. Other considerations…
Sex chromosomes have independently evolved in species with separate sexes in most lineages across the tree of life. However, the well-accepted canonical model of sex chromosome evolution is not universally supported. There is no single…