Dr. O'Neill's research projects use molecular genetic approaches to study centromere function and evolution; small RNA biogenesis; epigenetics, transcriptional control and chromatin modifiers; and whole genome and transcriptome sequencing in several model systems, including human, non-human primates, mouse, and marsupials. Using techniques such as in situ hybridization, microarray screening, cell assays, and next-generation sequencing (Illumina, 454 pyrosequencing, SOLiD 5500xl, Ion Torrent Proton), she is addressing the hypothesis that epigenetic modifiers (DNA methylation, histone modifications and small RNAs) mediate transcriptional controls and genome stability. She is lead PI on four de novo eukaryotic genome sequencing projects. Dr. O'Neill has produced next generation sequence for draft assemblies and her lab has written novel scripts for improving genome assemblies with data from multiple next generation sequencing platforms. The lab has been actively sequencing the unfinished portions of both the human and tammar wallaby (a marsupial model) genome using a combination of paired end sequencing, whole genome shotgun, BAC deep sequencing and FISH techniques. Moreover, Dr. O'Neill is involved in several different integrated genomics projects that include RNA-seq (small and whole transcriptome), ChIP-seq, RIP- seq, methyl-seq, and paired end sequencing targeting a Peromyscus disease model, a mouse model for Autism, human samples and patient-derived iPS cells, and several wallaby, primate, and marine species. She has worked with genomics techniques on several grants and research projects over the last 20 years focusing on genome stability and function. As Director of the Center for Genome Innovation within the Institute for Systems Genomics, she oversees the ABI SOLiD 5500xl, 454+ Genome Analyzer, Illumina NextSeq, Illumina Miseq and Ion Torrent Proton.
Areas of Expertise (3)
La Trobe University: Ph.D.
Media Appearances (1)
UConn Teams With JAX to Study Single Cell Genomics
"Jackson Lab’s arrival in Connecticut introduced many people to the concept of genomic medicine — the development of techniques that will allow medical treatments to be personalized to individual patients. And its a science that’s still rapidly evolving, said Dr. Rachel O'Neill of UConn’s Center for Genome Innovation..."
The Southern Ocean salp, Salpa thompsoni (Tunicata, Thaliacea), is a pivotal species in the pelagic ecosystem of the Western Antarctic Peninsula (WAP), one of the fastest warming regions of the world oceans. This study produced a complete reference transcriptome for S. thompsoni containing 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) ...
Supernumerary chromosomes have been studied in many species of eukaryotes, including the cichlid fish, Astatotilapia latifasciata. However, there are many unanswered questions about the maintenance, inheritance, and functional aspects of supernumerary chromosomes. The cichlid family has been highlighted as a model for evolutionary studies, including those that focus on mechanisms ...
Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked ...
The maintenance of a proper gene dosage is essential in cellular networks. To resolve the dosage imbalance between eutherian females (XX) and male (XY), X chromosome inactivation (XCI) occurs in females, while X-chromosome dosage compensation up-regulates the active X to balance its expression with that of autosome pairs [Ohno’s hypothesis; Ohno 1967 Sex Chromosomes and Sex-linked ...
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate ...