Geoffrey J. Faulkner
A5040882194- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Medical Imaging Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Immunotherapy and Immune Responses
- Pluripotent Stem Cells Research
- Genetics and Neurodevelopmental Disorders
- Cell Adhesion Molecules Research
- Cancer-related molecular mechanisms research
- Plant Virus Research Studies
- Immune Response and Inflammation
- Ubiquitin and proteasome pathways
- Virus-based gene therapy research
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- NF-κB Signaling Pathways
- interferon and immune responses
- Glycosylation and Glycoproteins Research
The University of Queensland
2016-2025
Mater Research
2016-2025
Allen Institute for Brain Science
2021-2025
Translational Research Institute
2014-2023
Roslin Institute
2009-2017
University of Edinburgh
2009-2017
Institute of Biomedical Science
2017
Genomics (United Kingdom)
2016
In-Q-Tel
2013
QIMR Berghofer Medical Research Institute
2013
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
Abstract Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. was specifically developed to detect 16S rRNA gene chimeras PCR-clone libraries environmental samples but can be applied other nucleotide alignments. Availability: available as interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl
For 10,000 years pigs and humans have shared a close complex relationship. From domestication to modern breeding practices, shaped the genomes of domestic pigs. Here we present assembly analysis genome sequence female Duroc pig (Sus scrofa) comparison with wild from Europe Asia. Wild emerged in South East Asia subsequently spread across Eurasia. Our results reveal deep phylogenetic split between European Asian boars ∼1 million ago, selective sweep indicates selection on genes involved RNA...
Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets genes has not been previously studied en masse. Exploiting the fact active are transcribed, we simultaneously measured their activity in 19 human 14 mouse time courses covering a wide range cell types biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated earliest responses....
Somatic LINE-1 (L1) retrotransposition during neurogenesis is a potential source of genotypic variation among neurons. As neurogenic niche, the hippocampus supports pronounced L1 activity. However, basal parameters and biological impact L1-driven mosaicism remain unclear. Here, we performed single-cell retrotransposon capture sequencing (RC-seq) on individual human hippocampal neurons glia, as well cortical An estimated 13.7 somatic insertions occurred per neuron carried sequence hallmarks...
Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies the transcriptional responses primary human and mouse macrophages Toll-like receptor (TLR)–4 agonist lipopolysaccharide (LPS). By using custom platform permitting cross-species interrogation coupled with deep sequencing mRNA 5′ ends, we identified extensive divergence LPS-regulated orthologous...
L1 retrotransposons comprise 17% of the human genome and are its only autonomous mobile elements. Although L1-induced insertional mutagenesis causes Mendelian disease, their mutagenic load in cancer has been elusive. Using L1-targeted resequencing 16 colorectal tumor matched normal DNAs, we found that certain cancers were excessively mutagenized by human-specific L1s, while no verifiable insertions present tissues. We confirmed de novo malignancy both validating sequencing 69/107...
Abstract In the FANTOM5 project, transcription initiation events across human and mouse genomes were mapped at a single base-pair resolution their frequencies monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands samples, consisting variety primary cells, tissues, cell lines, time series samples during activation development, subjected to uniform pipeline data production. The analysis started measuring RNA extracts assess...
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS and embryonic (hES) differ significantly, which affects cell function1-8. These differences include epigenetic memory aberrations that emerge during reprogramming, for mechanisms remain unknown. Here we characterized persistence emergence these by performing genome-wide DNA methylation profiling throughout primed naive reprogramming somatic...
ASXL transcriptional regulator 1 (ASXL1) is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), alongside DNA methyltransferase 3 alpha (DNMT3A) and Tet methylcytosine dioxygenase 2 ( TET2) . CH can progress to myeloid malignancies including chronic monomyelocytic leukemia (CMML) also strongly associated with inflammatory cardiovascular disease all-cause mortality humans. DNMT3A TET2 regulate methylation demethylation pathways, respectively,...