A5077384369- Cancer Genomics and Diagnostics
- Ovarian cancer diagnosis and treatment
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Pancreatic and Hepatic Oncology Research
- Gene expression and cancer classification
- Genomics and Rare Diseases
- Cancer-related molecular mechanisms research
- BRCA gene mutations in cancer
- CRISPR and Genetic Engineering
- Organ Transplantation Techniques and Outcomes
- Biomedical and Engineering Education
- Renal cell carcinoma treatment
- Scientific Computing and Data Management
- RNA and protein synthesis mechanisms
- Gallbladder and Bile Duct Disorders
- Genomic variations and chromosomal abnormalities
- Intraperitoneal and Appendiceal Malignancies
- Liver Disease Diagnosis and Treatment
- Trypanosoma species research and implications
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
University of Limerick
2023-2024
Peter MacCallum Cancer Centre
2013-2023
The University of Melbourne
2010-2023
Washington University in St. Louis
2009-2023
Biocon (India)
2023
University College Dublin
2007-2020
Barnes-Jewish Hospital
2020
Royal Women's Hospital
2015
University of Vienna
2002
Abstract Motivation: In light of the increasing adoption targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, robust method for copy number variation (CNV) analysis is needed maximize value this promising technology. Results: We present CNV detection TR data, including whole-exome capture data. Our calls gains and losses each target region based on normalized depth coverage. key strategies include use base-level log-ratios remove GC-content bias,...
Abstract Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public services by platform stability, tool and reference dataset diversity, training, support integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements accessibility, discoverability...
There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas the natural sciences. As a result, life sciences have become increasingly computational nature, and bioinformatics has taken central role research studies. However, basic skills, data analysis, stewardship are still rarely taught science educational programs, resulting skills gap researchers tasked with analysing these big datasets. In order to address this empower...
Abstract Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and underlying biology clinical features, but there is significant lag development downstream analysis methods benchmarking tools. Here we present SPIAT (spatial image tissues), a spatial-platform agnostic toolkit with suite spatial algorithms, spaSim simulator), simulator data. includes multiple colocalization, neighborhood heterogeneity metrics to...
Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing thirty-three individuals from 15 to identify potential predisposing genes. Our analysis identified heterozygous, deleterious mutations in DNA repair genes FANCC BLM, which are responsible autosomal recessive disorders Fanconi Anemia Bloom syndrome. total, screening...
Low grade serous ovarian tumours are a rare and under-characterised histological subtype of epithelial tumours, with little known the molecular drivers facilitators tumorigenesis beyond classic oncogenic RAS/RAF mutations. With move towards targeted therapies due to chemoresistant nature this subtype, it is pertinent more fully characterise genetic events driving tumour type, some which may influence response therapy and/or development drug resistance. We performed genome-wide...
Background The increased sequencing of pathogen genomes and the subsequent availability genome-scale functional datasets are expected to guide experimental work necessary for target-based drug discovery. However, a major bottleneck in this has been difficulty capturing integrating relevant information an easily accessible format identifying prioritizing potential targets. open-access resource TDRtargets.org facilitates target prioritization tropical disease pathogens such as mycobacteria...
Mucinous ovarian tumors are an unusual group of rare neoplasms with apparently clear progression from benign to borderline carcinoma, yet a controversial cell origin in the surface epithelium. They thought be molecularly distinct other but there have been no exome-level sequencing studies performed date. To understand genetic etiology mucinous and assess presence novel therapeutic targets or pathways, we undertook exome 24 encompassing (5), (8) carcinoma (11) histologies also assessed...
CDK12 and CDK13 regulate POLII elongation rate processivity influence the selection of transcription termination sites.
Loss of heterozygosity (LOH) is a common genetic event in cancer development, and known to be involved the somatic loss wild-type alleles many inherited syndromes. The wider involvement LOH assumed relate unmasking somatically mutated tumour suppressor gene through wild type allele. We analysed 86 ovarian carcinomas for mutations 980 genes selected on basis their location regions LOH. identified 36 significantly genes, but these could only partly account quanta samples. Using our own TCGA...
Abstract Mucinous carcinomas represent a distinct morphological subtype which can arise from several organ sites, including the ovary, and their genetic characteristics are largely under‐described. Exome sequencing of 12 primary mucinous ovarian tumours identified RNF43 as most frequently somatically mutated novel gene, secondary to KRAS at frequency equal that TP53 BRAF . Further screening in larger cohort additional mutations, with total 2/22 (9%) borderline 6/29 (21%) carcinomas. Seven...
Abstract Motivation Seurat is one of the most popular software suites for analysis single-cell RNA sequencing data. Considering popularity tidyverse ecosystem, which offers a large set data display, query, manipulation, integration and visualization utilities, great opportunity exists to interface object with tidyverse. This gives science community users possibility operate familiar grammar. Results To provide tidyverse-oriented without compromising efficiency, we developed tidyseurat,...
New drug targets are urgently needed for parasites of socio-economic importance. Genes that essential parasite survival highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns difficult to perform in many species parasites. We examined the applicability large-scale essentiality from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, discover each their genomes. Parasite lack...
Background The blood-feeding hookworm Necator americanus infects hundreds of millions people worldwide. In order to elucidate fundamental molecular biological aspects this hookworm, the transcriptome adult stage was explored using next-generation sequencing and bioinformatic analyses. Methodology/Principal Findings A total 19,997 contigs were assembled from sequence data; 6,771 these had known orthologues in free-living nematode Caenorhabditis elegans, most them encoded proteins with WD40...
Abstract Background Leishmania spp. are sandfly transmitted protozoan parasites that cause a spectrum of diseases in more than 12 million people worldwide. Much research is now focusing on how these adapt to the distinct nutrient environments they encounter digestive tract vector and phagolysosome compartment mammalian macrophages. While data mining annotation genomes three species has provided an initial inventory predicted metabolic components associated pathways, resources for integrating...
Multiple myeloma (MM) is an incurable malignancy with unmet need for innovative treatment options. Histone deacetylase inhibitors (HDACi) are a new class of anticancer agent that have demonstrated activity in hematological malignancies. Here, we investigated the efficacy and safety HDACi (vorinostat, panobinostat, romidepsin) novel combination therapies using vitro human MM cell lines vivo preclinical screening utilizing syngeneic transplanted Vk*MYC MM. were combined ABT-737, which targets...
Abstract Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using concept tidiness, to facilitate modularisation. We present tidybulk, a modular framework for bulk transcriptional analyses that introduces tidy structure paradigm analysis grammar. Tidybulk covers wide variety procedures integrates large ecosystem publicly available algorithms under common framework. decreases coding burden, facilitates reproducibility, increases...
Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - open-source software community focused on omics analysis. This guide serves as valuable reference both learners educators field.