LaDeana Hillier
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View article: Genomic resources for comparative analyses of obligate avian brood parasitism
Genomic resources for comparative analyses of obligate avian brood parasitism Open
Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental …
View article: Lineage-resolved analysis of embryonic gene expression evolution in <i>C. elegans</i> and <i>C. briggsae</i>
Lineage-resolved analysis of embryonic gene expression evolution in <i>C. elegans</i> and <i>C. briggsae</i> Open
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous cells. The conserved invariant embryoni…
View article: Binding profiles for 961<i>Drosophila</i>and<i>C. elegans</i>transcription factors reveal tissue-specific regulatory relationships
Binding profiles for 961<i>Drosophila</i>and<i>C. elegans</i>transcription factors reveal tissue-specific regulatory relationships Open
A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and mod…
View article: The Caenorhabditis RNA-seq Browser: a web-based application for on-demand analysis of publicly available Caenorhabditis spp. bulk RNA-sequencing data.
The Caenorhabditis RNA-seq Browser: a web-based application for on-demand analysis of publicly available Caenorhabditis spp. bulk RNA-sequencing data. Open
The Caenorhabditis RNA-seq Browser is an open-source Shiny web app that enables on-demand visualization and quantification of bulk RNA-sequencing data for five Caenorhabditis species: C. elegans, C. briggsae,
View article: Lineage-resolved analysis of embryonic gene expression evolution in<i>C. elegans</i>and<i>C. briggsae</i>
Lineage-resolved analysis of embryonic gene expression evolution in<i>C. elegans</i>and<i>C. briggsae</i> Open
What constraints govern the evolution of gene expression patterns across development remains a fundamental question of evolutionary biology. The advent of single-cell sequencing opens the possibility of learning these constraints by system…
View article: Binding profiles for 954 Drosophila and<i>C. elegans</i>transcription factors reveal tissue specific regulatory relationships
Binding profiles for 954 Drosophila and<i>C. elegans</i>transcription factors reveal tissue specific regulatory relationships Open
SUMMARY A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the modERN (model organism Encyclopedia of Regulatory Networks) consortium …
View article: Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution
Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution Open
View article: A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference Open
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis‐assemblies and a larger tha…
View article: High resolution genomes of multiple<i>Xiphophorus</i>species provide new insights into microevolution, hybrid incompatibility, and epistasis
High resolution genomes of multiple<i>Xiphophorus</i>species provide new insights into microevolution, hybrid incompatibility, and epistasis Open
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence …
View article: A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference
A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference Open
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger tha…
View article: An integrated analysis tool reveals intrinsic biases in gene set enrichment
An integrated analysis tool reveals intrinsic biases in gene set enrichment Open
Generating meaningful interpretations of gene lists remains a challenge for all large-scale studies. Many approaches exist, often based on evaluating gene enrichment among pre-determined gene classes. Here, we conceived and implemented yet…
View article: A high-quality bonobo genome refines the analysis of hominid evolution
A high-quality bonobo genome refines the analysis of hominid evolution Open
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation 1,2 . Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference geno…
View article: A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution
A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution Open
View article: Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility Open
A high-quality rhesus macaque genome Genome technology has improved substantially since the first full organismal genomes were generated. Applying new technology, Warren et al. refined the genome of the rhesus macaque, a model nonhuman pri…
View article: Author Correction: Elephant shark genome provides unique insights into gnathostome evolution
Author Correction: Elephant shark genome provides unique insights into gnathostome evolution Open
View article: Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster Open
Many animal species use a chromosome-based mechanism of sex determination, which has led to the coordinate evolution of dosage-compensation systems. Dosage compensation not only corrects the imbalance in the number of X chromosomes between…
View article: A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism Open
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is li…
View article: A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.
A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Open
Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves,…
View article: A chromosome level genome of<i>Astyanax mexicanus</i>surface fish for comparing population-specific genetic differences contributing to trait evolution
A chromosome level genome of<i>Astyanax mexicanus</i>surface fish for comparing population-specific genetic differences contributing to trait evolution Open
Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves,…
View article: The quail genome: insights into social behaviour, seasonal biology and infectious disease response
The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
View article: A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism Open
The domestic cat ( Felis catus ) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is …
View article: Additional file 16 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 16 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Viral read presence in quail samples
View article: Additional file 10 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 10 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Pathway analysis from photoperiod study
View article: Additional file 12 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 12 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
List of differentially expressed genes, FDR 1.6 in infection study
View article: Additional file 8 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 8 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
List of selection signatures detected from the HSR / LSR lines
View article: Additional file 11 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 11 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Sequences of cathelicidins and defensin genes identified in quail genome
View article: Additional file 3 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 3 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Location of breakpoints between chicken and quail chromosomes
View article: Additional file 9 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 9 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Statistics from photoperiod differential expression study
View article: Additional file 13 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 13 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Overrepresented GO terms in differentially expressed genes in infection study
View article: Additional file 4 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response
Additional file 4 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response Open
Percent of quail genes with orthologs identified in related bird genomes