Taras K Oleksyk

Taras K Oleksyk
University of Puerto Rico at Mayagüez | UPRM · Departamento de Biología

Ph.D.

About

122
Publications
34,963
Reads
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15,997
Citations
Introduction
Draft Genome Sequence Assembly of the Puerto Rican Parrot (Amazona vittata): a Genome Project Funded by the Local Community
Additional affiliations
August 2013 - present
Saint Petersburg State University
Position
  • Fellow
January 2010 - present
University of Puerto Rico - Mayaguez
January 2009 - present
University of Puerto Rico at Mayagüez
Position
  • Professor (Assistant)

Publications

Publications (122)
Article
Full-text available
Documenting genome diversity is important for the local biomedical communities and instrumental in developing precision and personalized medicine. Currently, tens of thousands of whole-genome sequences from Europe are publicly available, but most of these represent populations of developed countries of Europe. The uneven distribution of the availab...
Article
Full-text available
Advances in both morphological and molecular techniques have uncovered many lineages across the tree of life, and Neotropical vertebrates are no exception. Sphaerodactylus geckos (Sphaerodactylidae) are abundant and important components of the Neotropical herpetofauna, but few studies have thoroughly investigated them using a combination of morphol...
Article
Full-text available
The availability of genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information, providing a pathway for a better understanding of major evolutionary questions [...]
Article
Circulating vitamin D levels and the risk of osteoporosis have significant inheritance. Single nucleotide polymorphisms (SNPs) in the GC, DHCR7/NADSYN1, CYP2R1, CYP24A1, and SEC23A genes have shown significant association with these conditions in previous genome-wide association studies (GWAS). Objective: to study the frequency of alleles associate...
Article
Full-text available
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, end...
Article
Full-text available
Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaf...
Article
Full-text available
Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full...
Article
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Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented ind...
Article
The parrots (Psittaciformes, Aves) are a group of colorful, intelligent, long-lived birds with a wide range of body sizes and plumage colors and patterns. One third of the parrot species is threatened with extinction due to habitat loss and the pet trade, a larger percentage than any other comparable bird order. We present the complete genome seque...
Preprint
Full-text available
The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals re...
Article
Full-text available
Вітамін D бере участь у різноманітних біологічних процесах, включаючи кістковий метаболізм, модуляцію імунної відповіді та регуляцію проліферації й диференціювання клітин. Дефіцит вітаміну D пов’язують із впливом на виникненням таких нескелетних захворювань, як цукровий діабет 1-го та 2-го типів, рак, серцево-судинні захворювання, що підтверджує пл...
Article
The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome se...
Article
Full-text available
Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activi...
Article
Full-text available
Breast cancer is the most common cause of cancer diagnosis in women and is responsible for considerable mortality among the women of Puerto Rico. However, there are few studies in Puerto Rico on the genetic factors influencing risk. To determine the contribution of pathogenic mutations in BRCA1 and BRCA2, we sequenced these genes in 302 cases from...
Article
Full-text available
Solenodons are insectivores living in Hispaniola and Cuba that form an isolated branch in the tree of placental mammals highly divergent from other eulipothyplan insectivores The history, unique biology and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data, but a whole genome assembly for soleno...
Article
Mobile element insertions (MEIs) represent ~25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases,...
Preprint
Full-text available
Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly f...
Article
The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in...
Article
Full-text available
Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm...
Article
We report the sequence sof �244 human Y chromosomes randomly ascertained from 26 worldwide populations by the �1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants con...
Article
Full-text available
Solenodons are insectivores found only in Hispaniola and Cuba, with a Mesozoic divergence date versus extant mainland mammals. Solenodons are the oldest lineage of living eutherian mammal for which a mitogenome sequence has not been reported. We determined complete mitogenome sequences for six Hispaniolan solenodons (Solenodon paradoxus) using next...
Article
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Background Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DN...
Article
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We are witnessing the great era of genome exploration of the world, as genetic variation in people is being detailed across multiple varied world populations in an effort unprecedented since the first human genome sequence appeared in 2001. However, these efforts have yet to produce a comprehensive mapping of humankind, because important regions of...
Article
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In the News story “Who has your DNA—or wants it” (25 September, p. [1475][1]), J. Kaiser listed 17 projects that aim to chart human genetic diversity across the globe in the context of a dozen ongoing national genome sequencing initiatives ([ 1 ][2]). Yet Russia—a country with 1/10th of
Article
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The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-covera...
Article
Full-text available
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-covera...
Article
Full-text available
A third of African Americans with sporadic focal segmental glomerulosclerosis (FSGS) or HIV-associated nephropathy (HIVAN) do not carry APOL1 renal risk genotypes. This raises the possibility that other APOL1 variants may contribute to kidney disease. To address this question, we sequenced all APOL1 exons in 1437 Americans of African and European d...
Article
Full-text available
Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pattern is compared to another population with no history of selection, a rise in variance of allele frequencies between populations is observed...
Article
Full-text available
Background As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. Findings Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidem...
Conference Paper
Full-text available
Native to the headwaters of the Amazon River, cacao (Theobroma cacao L.) is an important agricultural tree crop produced in tropical regions around the world. Its raw product, the seed or ‘beans’, is the source for the multi-billion dollar chocolate industry. The USDA-ARS Tropical Agriculture Research Station in Mayaguez, PR maintains a diverse, re...
Article
Full-text available
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to bui...
Article
Full-text available
The Puerto Rican parrot (Amazona vittata) is one of the most endangered avian species in the world. Its dramatic decline to near extinction in 1975 was thwarted only by the establishment of two captive breeding pro- grams. To date, conservation efforts resulted in a signifi- cant population recovery with over 400 living birds either at the two capt...
Article
Full-text available
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of th...
Article
Full-text available
Little is known about the natural history of the Sphaerodactylus species endemic to the three islands located in the Mona Passage separating the Greater Antillean islands of Hispaniola and Puerto Rico. In this study, parts of two mitochondrial genes, 16S rRNA and 12S rRNA, were sequenced to determine the relationships between the sphaerodactylids t...
Article
Full-text available
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of th...
Article
Full-text available
Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three divers...
Article
Full-text available
Purple sea urchins (Strongylocentrotus purpuratus) express a highly variable set of immune genes called Sp185/333 by two subtypes of coelomocytes: the polygonal and small phagocytes. We report that the Sp185/333 genes and their encoded proteins are also expressed in all of the major organs in the adult sea urchin, including the axial organ, pharynx...