A5085566500- Single-cell and spatial transcriptomics
- HIV Research and Treatment
- Neonatal Respiratory Health Research
- Mosquito-borne diseases and control
- Cell Image Analysis Techniques
- Viral Infections and Vectors
- HIV/AIDS drug development and treatment
- Evolution and Genetic Dynamics
- Tuberculosis Research and Epidemiology
- Genomics and Phylogenetic Studies
- HIV/AIDS Research and Interventions
- Mycobacterium research and diagnosis
- Acute Myeloid Leukemia Research
- Immune cells in cancer
- Infectious Diseases and Tuberculosis
- Congenital Diaphragmatic Hernia Studies
- Immune Cell Function and Interaction
- Data Visualization and Analytics
- Microbial Community Ecology and Physiology
- Cancer Genomics and Diagnostics
- Material Dynamics and Properties
- Birth, Development, and Health
- Surfactants and Colloidal Systems
- Genetic Mapping and Diversity in Plants and Animals
- Zebrafish Biomedical Research Applications
UNSW Sydney
2019-2025
Avenir Health
2024
Ecologie & Evolution
2024
Environmental Earth Sciences
2024
Stanford University
2016-2023
Cancer Institute of New South Wales
2020-2023
Garvan Institute of Medical Research
2020-2022
Genomics (United Kingdom)
2022
Prince of Wales Hospital
2021
Pancreatic Cancer Action Network
2021
HTSeq 2.0 provides a more extensive API including new representation for sparse genomic data, enhancements in htseq-count to suit single cell omics, script data using and molecular barcodes, improved documentation, testing deployment, bug fixes, Python 3 support.HTSeq is released as an open-source software under the GNU General Public License available from Package Index at https://pypi.python.org/pypi/HTSeq. The source code on Github https://github.com/htseq/htseq.Supplementary are...
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare are essential. We performed whole-genome deep sequencing of HIV-1 9 untreated patients, 6-12 longitudinal samples per patient spanning 5-8 years infection. show that patterns minor diversity reproducible between patients mirror global diversity, suggesting a universal...
Dengue and Zika viral infections affect millions of people annually can be complicated by hemorrhage shock or neurological manifestations, respectively. However, a thorough understanding the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach probe transcriptome together with intracellular RNA at level. applied monitor dengue infection...
Dengue virus (DENV) infection can result in severe complications. However, the understanding of molecular correlates severity is limited, partly due to difficulties defining peripheral blood mononuclear cells (PBMCs) that contain DENV RNA vivo. Accordingly, there are currently no biomarkers predictive progression dengue (SD). Bulk transcriptomics data difficult interpret because consists multiple cell types may react differently infection. Here, we applied virus-inclusive single-cell RNA-seq...
HIV-1 infection cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). In a previous paper (Zanini et al, 2015) we documented evolution 10 untreated patients. Here characterize establishment, turnover, and viral reservoirs same patients after 3-18 ART. A median 14% (range 0-42%) sequences were defective due to G-to-A hypermutation. Remaining showed no evidence over Most from very similar viruses...
Abstract Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation the dynamics genetic variation. At approximately neutral sites, accumulate with rate 1.2 × 10−5 per site day, agreement measured cell cultures. We G A be largest, followed by other transitions C T, T C, G, while...
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 belonging to expanded and hypermutated clonal families identified by transcriptomic analysis single plasmablasts from DENV-infected individuals. Among these, J9 J8, two somatically related bNAbs potently neutralized DENV1-4. Mutagenesis studies showed major recognition...
At birth, the lungs rapidly transition from a pathogen-free, hypoxic environment to pathogen-rich, rhythmically distended air-liquid interface. Although many studies have focused on adult lung, perinatal lung remains unexplored. Here, we present an atlas of murine immune compartment during early postnatal development. We show that late embryonic is dominated by specialized proliferative macrophages with surprising physical interaction developing vasculature. These disappear after birth and...
We report on a joint experimental-theoretical study of collective diffusion in, and static shear viscosity solutions bovine serum albumin (BSA) proteins, focusing the dependence protein salt concentration. Data obtained from dynamic light scattering rheometric measurements are compared to theoretical calculations based an analytically treatable spheroid model BSA with isotropic screened Coulomb plus hard-sphere interactions. The only input dynamics is structure factor consistent fit...
The formation of protein clusters as precursors for crystallization and phase separation is fundamental practical interest in science. Using multivalent ions, the strengths both long-range Coulomb repulsion short-range attraction can be tuned solutions, representing a well-controlled model system to study static dynamic properties clustering during transition from charge-stabilized an aggregate regime. Here, we compressibility, diffusion, size solutes by means (SLS) light scattering (DLS)...
The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well temperature. We present comprehensive study on nanosecond time nanometer length scales below, at, above denaturation temperature Td. Our experimental data evidence dynamical processes protein solutions three distinct scales. suggest consistent physical picture dynamics: (i) self-diffusion entire molecule confirmed to agree with colloid theory for all temperatures where its...
The Tabula Muris Consortium We have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells 20 organs and tissues. These represent new resource for biology, revealing gene expression in poorly characterized populations allowing direct controlled comparison types shared between tissues, such as T-lymphocytes endothelial distinct anatomical locations. Two technical approaches were used most tissues: one approach,...
package for Mathematica (Wolfram Research, Inc., 2022).IGraph/M serves as the Wolfram Language interfaces to igraph C library (Csárdi et al.,
Whole-organism cell atlases have painted the cellular landscapes of individual species, however comparing cells across tree life remains challenging. Most cross-species analyses are restricted to orthologous genes, while complexity atlas data constitutes an access barrier for many researchers. We developed a computational strategy accelerate exploration identities at scale. integrated 30 detailing expression 861,013 genes by 2,645,508 animal and plant trained universal model transcriptomes...
Network models are widely applied to describe connectivity and flow in diverse systems. In contrast, the fact that many connected systems move through space as result of dynamic restructuring has received little attention. Therefore, we introduce concept 'traveling networks', analyze a tree-based model where leaves stochastically manipulated grow, branch, retract. We derive how these rates determine key attributes network structure motion, enabling compact understanding higher-level...
Mechanisms by which HIV affects the thymus are multiple and only partially known, role of thymic dysfunction in HIV/AIDS immunopathogenesis remains poorly understood. To evaluate effects infection on intra-thymic precursors T cells HIV-infected adults, we conducted a detailed immunophenotypic study tissue isolated from 7 10 HIV-negative adults who were to undergo heart surgery. We found that thymuses individuals characterized relative depletion CD4+ single positive corresponding enrichment...
The analysis of the evolutionary dynamics a population with many polymorphic loci is challenging, as large number possible genotypes needs to be tracked. In absence analytical solutions, forward computer simulations are an important tool in multi-locus genetics. run time standard algorithms simulate sexual populations increases 8(L) L, or square size N.We have developed arbitrary genetic maps, including multiple crossovers, that scales 3(L). If crossovers restricted at most one, reduced...
Intrapatient HIV-1 evolution is dominated by selection on the protein level in arms race with adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies target a new epitope, virus often escapes via nonsynonymous mutations that impair recognition. Synonymous do not affect this interplay and are assumed to be neutral. We analyze longitudinal intrapatient data from C2-V5 part of envelope gene (env) observe synonymous derived alleles rarely fix even though they reach high...
At birth, the lung is still immature, heightening susceptibility to injury but enhancing regenerative capacity. Angiogenesis drives postnatal development. Therefore, we profiled transcriptional ontogeny and sensitivity of pulmonary endothelial cells (EC) during early life. Although subtype speciation was evident at immature EC exhibited transcriptomes distinct from mature counterparts, which progressed dynamically over time. Gradual, temporal changes in aerocyte capillary (CAP2) contrasted...