Fereydoun Hormozdiari
A5005747594- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- Genetic Associations and Epidemiology
- Genetics and Neurodevelopmental Disorders
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Autism Spectrum Disorder Research
- Gene Regulatory Network Analysis
- Genetic factors in colorectal cancer
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Bioinformatics
- Algorithms and Data Compression
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Genetic diversity and population structure
- RNA Research and Splicing
- MicroRNA in disease regulation
- Nutrition, Genetics, and Disease
- Genetic Mapping and Diversity in Plants and Animals
University of California, Davis
2016-2024
University of Washington
2010-2019
Howard Hughes Medical Institute
2010-2016
Seattle University
2013-2014
Simon Fraser University
2007-2012
BC Cancer Agency
2008-2011
Stanford University
2010
Tel Aviv University
2008
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set eight structural variant classes comprising both balanced unbalanced variants, which constructed using short-read DNA sequencing data statistically phased onto haplotype blocks 26 populations. Analysing this set, identify gene-intersecting exhibiting population stratification naturally occurring homozygous gene knockouts that suggest...
High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into genetic variation evolutionary history enabling comparison with human diversity. In an effort to provide insights variation, the authors sequence wild- captive-born from across seven subspecies. Their data analyses shed light on population structure gene flow, inbreeding, inferred dynamics...
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies human genetic diversity and disease association. Here, we apply a suite long-read, short-read, strand-specific technologies, optical mapping, variant discovery algorithms to comprehensively analyze three trios define the full spectrum variation in haplotype-resolved manner. We identify 818,054 indel (<50 bp) 27,622 SVs (≥50 per genome. also discover 156 inversions genome 58 intersect...
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. final, phase 3 release 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS resource, which now includes 602 complete trios, sequenced to depth 30X using Illumina. We performed single-nucleotide variant (SNV) short...
Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers, such as lymphomas sarcomas. RNA-Seq (whole transcriptome shotgun sequencing) is proving be a useful tool for discovery novel gene cancer transcriptomes. However, algorithmic methods using data remain underdeveloped. We have developed deFuse, computational method fusion tumor data. Unlike existing that use only unique best-hit alignments consider boundaries...
A spotlight on great ape genomes Most nonhuman primate generated to date have been “humanized” owing their many gaps and the reliance guidance by reference human genome. To remove this humanizing effect, Kronenberg et al. assembled long-read of a chimpanzee, an orangutan, two humans compared them with previously gorilla This analysis recognized genomic structural variation specific particular lineages. Comparisons between chimpanzee cerebral organoids showed down-regulation expression genes...
Duplications and deletions in the human genome can lead to variation copy number for genes genomic loci among humans. Such variants reveal evolutionary patterns have implications health. Sudmant et al. examined copy-number across 236 individual genomes from 125 populations. Deletions were under more selection, whereas duplications showed population-specific structure. Interestingly, Oceanic populations retain large postulated originated an ancient Denisovan lineage. Science , this issue...
Recent studies show that along with single nucleotide polymorphisms and small indels, larger structural variants among human individuals are common. The Human Genome Structural Variation Project aims to identify classify deletions, insertions, inversions (>5 Kbp) in a number of normal fosmid-based paired-end sequencing approach using traditional technologies. realization new ultra-high-throughput platforms now makes it feasible detect the full spectrum genomic variation many individual...
Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed computational method, termed MAGI ( m erging ffected g enes into i ntegrated networks), simultaneously integrates protein–protein interactions and RNA-seq expression profiles during brain development discover “modules” enriched for de novo mutations in probands. applied this method...
Abstract Recent years have witnessed an increase in research activity for the detection of structural variants (SVs) and their association to human disease. The advent next-generation sequencing technologies make it possible extend scope variation studies a point previously unimaginable as exemplified by 1000 Genomes Project. Although various computational methods been described SVs, no such algorithm is yet fully capable discovering transposon insertions, very important class SVs study...
Protein-protein interaction (PPI) networks of many organisms share global topological features such as degree distribution, k-hop reachability, betweenness and closeness. Yet, some these can differ significantly from the others in terms local structures: e.g. number specific network motifs vary among PPI networks. Counting provides a major challenge to compare biomolecular Recently developed algorithms have been able count induced occurrences subgraphs with k < or = 7 vertices. Yet no...
The current paradigm of cancer care relies on predictive nomograms which integrate detailed histopathology with clinical data. However, when predictions fail, the consequences for patients are often catastrophic, especially in prostate where influence decision to therapeutically intervene. We hypothesized that high dimensional data afforded by massively parallel sequencing (MPS) is not only capable providing biological insights, but may aid molecular pathology tumours. assembled a cohort six...
Small insertions and deletions (indels) large structural variations (SVs) are major contributors to human genetic diversity disease. However, mutation rates characteristics of de novo indels SVs in the general population have remained largely unexplored. We report 332 validated changes identified whole genomes 250 families, including complex indels, retrotransposon insertions, interchromosomal events. These data indicate a rate 2.94 (1–20 bp) 0.16 (>20 per generation. De affect on average...
Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection. However, it is not known whether affect fitness independently, so that cumulative loss depends exponentially on number alleles, or synergistically, each additional allele results in a larger decrease relative fitness. with synergistic epistasis should produce negative linkage disequilibrium between and, therefore, an underdispersed...
Abstract Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority studies provide neither global view full spectrum these variants nor integrate them into reference panels genetic variation. Here, we analyse whole genome sequencing data 769 individuals from 250 Dutch families, haplotype-resolved map 1.9 million across 9 different variant classes, including novel forms complex indels,...