A5079764042- Genetic diversity and population structure
- Fish Ecology and Management Studies
- Genetic and phenotypic traits in livestock
- Animal Behavior and Reproduction
- Bioinformatics and Genomic Networks
- Evolution and Genetic Dynamics
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Veterinary Equine Medical Research
- Wildlife Ecology and Conservation
- Avian ecology and behavior
- Environmental DNA in Biodiversity Studies
- Cancer-related Molecular Pathways
- Epigenetics and DNA Methylation
- Ginseng Biological Effects and Applications
- Genomics and Phylogenetic Studies
- Plant and animal studies
- Molecular Biology Techniques and Applications
- Agriculture, Soil, Plant Science
- HIV Research and Treatment
- Ubiquitin and proteasome pathways
- Machine Learning in Bioinformatics
- Genetic Associations and Epidemiology
- Advanced biosensing and bioanalysis techniques
- Autophagy in Disease and Therapy
Cornell University
2015-2024
Amgen (United States)
2013-2016
Boston University
2007-2010
Many Microbe Microarrays Database (M 3D ) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M contains over a thousand Affymetrix microarrays for Escherichia coli , Saccharomyces cerevisiae Shewanella oneidensis . The uniformly normalized make generated by different laboratories researchers more comparable. To computational analyses, provides raw (CEL file) downloads each compendium. In addition, web-based...
A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes-variation in individual survival, reproductive success, movement-are often difficult quantify. Fully understanding requires pedigree, set relationships among all individuals Here, we use extensive pedigree genomic information from a long-studied Florida Scrub-Jays (Aphelocoma coerulescens)...
Abstract The Arabian horse, one of the world’s oldest breeds any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result its development in arid Middle East, ability to thrive hot, dry environment. Here we studied 378 horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing examine hypotheses about genomic diversity, population structure, relationship other horse breeds. We...
The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses determine relationship Arabians with other Iranian horse breeds. We evaluated 71 from 8 matrilineal strains tracing 47 mares the mid late 19th century, using equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed expected heterozygosity (0.43) (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs homozygosity...
// Anne Y. Saiki 1 , Sean Caenepeel Elissa Cosgrove 2, 5 Cheng Su 3 Michael Boedigheimer 4 Jonathan D. Oliner Oncology Research, Amgen, Inc., Thousand Oaks, California, USA 2 Genome Analysis Unit, South San Francisco, Biostatistics, Seattle, Washington, Molecular Sciences, Department of Biology and Genetics, Cornell University, Ithaca, New York, Correspondence to: Oliner, e-mail: jonoliner@hotmail.com Keywords: TP53 MDM2 amplification Received: October 28, 2014 ...
Abstract Motivation: DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from hundreds of that indirectly affected. Here, we developed a sparse simultaneous equation model (SSEM) mRNA expression data and Lasso regression estimate parameters, thus constructing network gene interaction effects. This inferred was then used filter given experimental condition interest...
Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies demographic consequences isolation are critical understand how populations persist through changing conditions. We used a 34-year and environmental dataset from population cooperatively-breeding Florida Scrub-Jays (
Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies demographic consequences isolation are critical understand how populations persist through changing conditions. We used a 34-year and environmental dataset from population cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) create mechanistic...
ABSTRACT A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes - variation in individual survival, reproductive success, movement are often difficult quantify. Fully understanding requires pedigree, set relationships among all individuals Here, we use extensive pedigree genomic information from a long-studied Florida Scrub-Jays ( Aphelocoma...
Abstract Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about changes in populations early stages decline, especially those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data 288 Florida scrub jays ( Aphelocoma coerulescens ; FSJ) sampled 2000 2008 compare levels genetic diversity, inbreeding, relatedness, lengths runs...
Abstract Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well effective population size, transmission modes, strength mode selection. Here, demonstrate role that history played shaping short-term evolutionary dynamics We used a 25-year pedigree genomic dataset from...
Abstract Background Transcriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)-gene interactions at the genome-wide level. In correlation-based TRNI, edges can in principle be evaluated using standard statistical tests. However, while such tests nominally assume independent microarray experiments, we expect dependency between experiments compendia, due to both project-specific factors...
ABSTRACT The composition of the gut microbiome is impacted by a complex array factors, from nutrient and availability, to physical factors like temperature, pH, flow rate, as well interactions among members microbial community. Many these are affected host, raising question how host genetic variation impacts composition. Though human studies confirm this type role for genetics, its overall importance still subject debate remains difficult study. mouse model, allowing strict control...
Abstract Inbreeding, or breeding with close relatives, often decreases individual fitness, but mate choice in many species can increase inbreeding risk. Inbreeding is more likely limited dispersal, such as cooperative breeders where non-parental individuals—often offspring from previous broods—provide parental care and frequently breed to home. We leverage 32 years of data a population Florida Scrub-Jays ( Aphelocoma coerulescens ), an avian breeder, investigate whether choice, its lifetime...
Summary Whole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in context endangered species, it can provide a quantification genetic risk posed by reduced diversity inbreeding. Prior 1920, Florida scrub-jay ( Aphelocoma coerulescens ) had been widespread across Florida, but with expansion agriculture human habitation, its population has declined 95%, resulting fragmentation into semi-isolated subpopulations. By sequencing 241...
ABSTRACT Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well effective population size, transmission modes, strength mode selection. Here, demonstrate role that history played shaping short-term evolutionary dynamics We used a 25-year pedigree genomic dataset from...
Abstract USP8 and the ESCRT pathway (endosomal sorting complex required for transport) are cellular homeostasis through key functions in shuttling ubiquitinated proteins towards lysosomal degradation, regulating maturation of autophagosomal structures. In large-scale siRNA screens, vast majority cancer cell lines do not demonstrate dependency on or components viability. However, we identified three (HCC70, HCC1954 PFSK1) that acutely dependent other (HGS, TSG101) Using a transcriptome-wide...
Abstract The interpretation of RNAi knockdown experiments can be challenging due to the extensive off-target effects exhibited by siRNAs and shRNAs. This has led reporting results that cannot independently verified, or identification putative cancer targets are insufficiently robust support industrial drug discovery efforts. problems associated with off target particularly acute in high throughput screens, whose often differ wildly between laboratories using different experimental platforms....