Institution
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
Recent research
- BiologyOpen access
pileup-hi: an ultra-high-throughput, customizable alignment pileup program for large datasets
Abstract Motivation Recent advancements in next-generation sequencing have combined massive data throughput with high read accuracy to facilitate large-scale, rapid, and sensitive analysis of genetic variation. High-depth, high-quality platforms such as the Illumina NovaSeq X and...
- Health & MedicineOpen access
Tumor microbial biodiversity and microsatellite instability in colorectal cancer
Background Growing evidence links the gut microbiome to colorectal cancer (CRC) progression, with certain bacterial species enriched in specific molecular tumor subtypes. DNA mismatch repair deficiency in CRC, evidenced by the presence of microsatellite instability (MSI), has bee...
- Climate & Environment
Abstract Epidemiologic studies of PFAS and liver cancer risk have produced conflicting results with no strong or clear associations for pre-diagnostic perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA), and perfluorohexanesulfonate (PFHxS). We now report analyses of nine...
- Health & MedicineOpen access
Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line
ABSTRACT Anelloviruses are highly diverse, ubiquitous single-stranded DNA viruses whose replication, cellular reservoirs, and mechanisms of persistence remain poorly understood. Here, we identify and characterize a Alphatorquevirus homin 29 genome stably integrated into an rDNA l...
- BiologyOpen access
Assessing the Validity of the Fixed Tree Topology Assumption in Phylodynamic Inference
Abstract Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology strategies on phylogenetic and phy...
- Health & Medicine
PURPOSE: Immune checkpoint inhibitors have limited activity as monotherapy in biliary cancers. Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a pleiotropic immune cell growth factor which achieved prolonged survival when combined with ipilimumab in melanoma. We cond...