Team
Computational Biology projects
Featured Research
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
An atlas of active enhancers across human cell types and tissues
A promoter-level mammalian expression atlas
An integrated encyclopedia of DNA elements in the human genome
Landscape of transcription in human cells
Reports and Findings
Trends in prenatal diagnosis of congenital anomalies in Western Australia between 1980 and 2020: A population-based study
Advances in screening and diagnostics have changed the way in which we identify and diagnose congenital anomalies.
Published research Child Disability Computational Biology Child disabilityHospitalizations from Birth to 28 Years in a Population Cohort of Individuals Born with Five Rare Craniofacial Anomalies in Western Australia
To describe trends, age-specific patterns, and factors influencing hospitalizations for 5 rare craniofacial anomalies.
Published research Human Capability Child Disability Computational Biology Child disabilitySAMStat 2: quality control for next generation sequencing data
SAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and mapping error profiles split by mapping quality. This allows users to rapidly identify reasons for poor mapping including the presence of untrimmed adapters or poor sequencing quality at individual read positions.
Published research Computational BiologyCD4+ T cells drive an inflammatory, TNF-α/IFN-rich tumor microenvironment responsive to chemotherapy
While chemotherapy remains the first-line treatment for many cancers, it is still unclear what distinguishes responders from non-responders. Here, we characterize the chemotherapy-responsive tumor microenvironment in mice, using RNA sequencing on tumors before and after cyclophosphamide, and compare the gene expression profiles of responders with progressors.
Children's Cancers Published research Computational Biology Sarcoma Translational Research Translational Genetics