Patrick G. S. Grady
A5088905168- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Biosensors and Analytical Detection
- Genetic Mapping and Diversity in Plants and Animals
- Plant Molecular Biology Research
- Genetic diversity and population structure
- Legume Nitrogen Fixing Symbiosis
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Evolution and Paleontology Studies
- Genomic variations and chromosomal abnormalities
- Advanced biosensing and bioanalysis techniques
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
- Immune responses and vaccinations
- Identification and Quantification in Food
- Biomedical Text Mining and Ontologies
- Hymenoptera taxonomy and phylogeny
- RNA modifications and cancer
- Sperm and Testicular Function
- Plant responses to water stress
University of Connecticut
2021-2025
University of Minnesota
2020-2025
Institute for Systems Biology
2021-2023
Seven Bridges Genomics (United States)
2018
University of Illinois Urbana-Champaign
2016-2017
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
Mobile elements and repetitive genomic regions are sources of lineage-specific innovation uniquely fingerprint individual genomes. Comprehensive analyses such repeat elements, including those found in more complex the genome, require a complete, linear genome assembly. We present de novo discovery annotation T2T-CHM13 human reference genome. identified previously unknown satellite arrays, expanded catalog variants families for repeats mobile characterized classes composite repeats, located...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology...
Abstract A data set comprising DNA sequences from 388 loci and >99,000 aligned nucleotide positions, generated using anchored hybrid enrichment, was used to estimate relationships among 138 leafhoppers treehoppers representative of all major lineages Membracoidea, the most diverse superfamily hemipteran insects. Phylogenetic analysis concatenated sequence maximum likelihood produced a tree with branches receiving high support. separate coalescent gene same generally recovered strongly...
Abstract Background The global COVID-19 pandemic has led to an urgent need for scalable methods clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands isolates are being sequenced around the world deposited in public data repositories. A number using both short- long-read currently applied sequencing, including amplicon approaches, metagenomic methods, sequence capture or enrichment methods....
Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living (Canis lupus), dire have yet be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dating > 13,000 72,000 years ago, estimated consensus species trees for these 10 species. Our results revealed that ~2/3 wolf ancestry is derived a lineage sister clade comprising gray wolf, coyote, dhole, remaining ~1/3 near...
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently most commonly used phylogenomic approaches involve some form genome reduction. While these make assembling more economical for organisms with large genomes, they reduce genomic coverage and thereby long-term utility data. Currently, moderate small genomes ($<$1000 Mbp) it is feasible sequence entire at modest ($10-30\times$). Computational challenges handling...
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, segmental duplications 1–3 . As a result, more than half the is missing from GRCh38 reference it remains last be finished 4, 5 Here, Telomere-to-Telomere (T2T) consortium presents complete 62,460,029 base pair HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y adds over 30 million pairs reference, revealing ampliconic...
Abstract Apes possess two sex chromosomes—the male-specific Y and the X shared by males females. The chromosome is crucial for male reproduction, with deletions linked to infertility. carries genes vital reproduction cognition. Variation in mating patterns brain function among great apes suggests corresponding differences their structure evolution. However, due highly repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using state-of-the-art...
Abstract Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural established populations. These provide a window into contemporary patterns of diversity, structure relatedness that can guide managers in how best source animals their translocation programmes. The inclusion historical samples, where possible, strengthens monitoring allowing assessment changes diversity over time providing benchmark future...
The marsupial moles are arguably Australia’s most enigmatic marsupials. Almost indistinguishable from placental (eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome southern mole, we insights into its unusual biology. We show definitively by retrophylogenomic analysis that closely related to bandicoots and bilbies (order Peramelemorphia). find evidence marked decline in mole effective population size, likely preceding arrival humans regions near...
Abstract The COVID-19 global pandemic is an unprecedented health emergency. Insufficient access to testing has hampered effective public interventions and patient care management in a number of countries. Furthermore, the availability regulatory-cleared reagents challenged widespread implementation testing. We rapidly developed qRT-PCR SARS-CoV-2 detection assay using 384-well format tested its analytic performance across multiple nucleic acid extraction kits. Our data shows robust accuracy...
Abstract The publication of the first complete, haploid telomere-to-telomere (T2T) human genome revealed new insights into structure and function heretofore “invisible” parts including centromeres, tandem repeat arrays, segmental duplications. Refinement T2T processes now enables comparative analyses complete genomes across entire clades to gain a broader understanding evolution chromosome function. project involved unique ad hoc effort involving many researchers laboratories, serving as...
Abstract DNA methylation is critical to the regulation of transposable elements and gene expression can play an important role in adaptation stress response mechanisms plants. Traditional methods quantification rely on bisulfite conversion that compromise accuracy. Recent advances long‐read sequencing technologies allow for detection real time. The associated algorithms interpret these modifications have evolved from strictly statistical approaches Hidden Markov Models and, recently, deep...
Abstract The publication of the first complete, haploid telomere-to-telomere (T2T) human genome revealed new insights into structure and function heretofore “invisible” parts including centromeres, tandem repeat arrays, segmental duplications. Refinement T2T processes now enables comparative analyses complete genomes across entire clades to gain a broader understanding evolution chromosome function. project involved unique ad hoc effort involving many researchers laboratories, serving as...
X chromosome inactivation (XCI) is an epigenetic process that results in the transcriptional silencing of one somatic cells females. This phenomenon common to both eutherian and marsupial mammals, but there are fundamental differences. In eutherians, chosen for random. DNA methylation on inactive high at transcription start sites (TSSs) their flanking regions, resulting universally methylation. contrasts XCI marsupials where paternally derived always silenced, which low TSSs regions. Here,...
Abstract Motivation Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B play an important role in basic cellular processes and associated with instability, gene regulation, oncogenesis. Experimental methods low-throughput can detect only a limited set of non-B structures, while computational rely on base motifs, which necessary but not sufficient indicators structures. Oxford Nanopore sequencing is efficient...
Abstract The global COVID-19 pandemic has led to an urgent need for scalable methods clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands isolates are being sequenced around the world deposited in public data repositories. A number using both short- long-read currently applied sequencing, including amplicon approaches, metagenomic methods, sequence capture or enrichment methods. Given small...
Abstract Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific innovation fingerprint individual genomes. Comprehensive analyses large, composite or arrayed repeat those found in more complex the genome require a complete, linear assembly. Here we present first de novo discovery annotation complete human reference genome, T2T-CHM13v1.0. We identified novel satellite arrays, expanded catalog variants families for known repeats mobile elements,...
The MAPK genes are critical for gonadal differentiation in eutherian mammals, but their role marsupial mammals is unknown. Characterisation and phylogenetic analyses of the tammar wallaby show these highly conserved with orthologues mammalian non-mammalian species.