Paul A. Bates
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View article: Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer
Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer Open
The evolution of cancer undermines the long-term efficacy of therapy. In this study, we combine experimental, computational, and clinical data analysis to investigate factors influencing the competition of subclones in lung cancer. Lineage…
View article: Testing T2K's Bayesian constraints with priors in alternate parameterisations
Testing T2K's Bayesian constraints with priors in alternate parameterisations Open
Bayesian analysis results require a choice of prior distribution. In long-baseline neutrino oscillation physics, the usual parameterisation of the mixing matrix induces a prior that privileges certain neutrino mass and flavour state symmet…
View article: Impact of <scp>AlphaFold</scp> on structure prediction of protein complexes: The <scp>CASP15‐CAPRI</scp> experiment
Impact of <span>AlphaFold</span> on structure prediction of protein complexes: The <span>CASP15‐CAPRI</span> experiment Open
We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7…
View article: Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment
Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment Open
We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homo-dimers, 3 homo-trimers, 13 hetero-dimers including 3 antibody-antigen complexes, and…
View article: Tomorrow’s Country: Practice‐oriented principles for Indigenous cultural fire research in south‐east Australia
Tomorrow’s Country: Practice‐oriented principles for Indigenous cultural fire research in south‐east Australia Open
First Nations peoples are revitalising diverse cultural fire practices and knowledge. Institutional and societal recognition of these practices is growing. Yet there has been little academic research on these fire practices in south‐east A…
View article: Robust 3D modeling reveals spatiosyntenic properties of animal genomes
Robust 3D modeling reveals spatiosyntenic properties of animal genomes Open
Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (synteny). Using versatile chromosomal modeling, we infer three-dimensional topology of genomes from rep…
View article: Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma Open
Cancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organised in a variety of ways, ranging from thin discontinuous strands to thick ‘pushing’ collectives. Here we employ…
View article: Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes Open
Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, th…
View article: Author response: Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
Author response: Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Cancers, such as squam…
View article: Application of deep learning methods: From molecular modelling to patient classification
Application of deep learning methods: From molecular modelling to patient classification Open
We are now well into the information driven age with complex, heterogeneous, datasets in the biological sciences continuing to grow at a rapid pace. Moreover, distilling of such datasets, to find new governing principles, are underway. Lea…
View article: Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization
Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization Open
Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations re…
View article: Spatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study
Spatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study Open
View article: Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma Open
Cancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organized in a variety of ways, ranging from thin discontinuous strands to thick ‘pushing’ collectives. Here we employ…
View article: Prediction of protein assemblies, the next frontier: The <scp>CASP14‐CAPRI</scp> experiment
Prediction of protein assemblies, the next frontier: The <span>CASP14‐CAPRI</span> experiment Open
We present the results for CAPRI Round 50, the fourth joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher‐order oligomers. Four of the…
View article: Robust 3D modelling reveals spatiosyntenic properties of animal genomes
Robust 3D modelling reveals spatiosyntenic properties of animal genomes Open
Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (macrosynteny). We developed a novel three-dimensional chromosomal modelling approach to show that synte…
View article: Author response for "Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment"
Author response for "Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment" Open
View article: Toward Patient-Specific Prediction of Ablation Strategies for Atrial Fibrillation Using Deep Learning
Toward Patient-Specific Prediction of Ablation Strategies for Atrial Fibrillation Using Deep Learning Open
Atrial fibrillation (AF) is a common cardiac arrhythmia that affects 1% of the population worldwide and is associated with high levels of morbidity and mortality. Catheter ablation (CA) has become one of the first line treatments for AF, b…
View article: Selection of metastasis competent subclones in the tumour interior
Selection of metastasis competent subclones in the tumour interior Open
View article: Spatial patterns of tumour growth impact clonal diversification: computational modelling and evidence in the TRACERx Renal study
Spatial patterns of tumour growth impact clonal diversification: computational modelling and evidence in the TRACERx Renal study Open
Intra-tumour genetic heterogeneity (ITH) fuels cancer evolution. The role of clonal diversity and genetic complexity in the progression of clear-cell renal cell carcinomas (ccRCCs) has been characterised, but the ability to predict clinica…
View article: A FIJI macro for quantifying pattern in extracellular matrix
A FIJI macro for quantifying pattern in extracellular matrix Open
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously…
View article: Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast
Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast Open
Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely underst…
View article: Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage
Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage Open
Background Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions i…
View article: Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology Open
The CAPRI and CASP prediction experiments have demonstrated the power of community wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure pre…
View article: Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast
Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast Open
Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely underst…
View article: Selection of metastasis competent subclones in the tumour interior: TRACERx renal
Selection of metastasis competent subclones in the tumour interior: TRACERx renal Open
While the genetic evolutionary features of solid tumour growth are becoming increasingly described, the spatial and physical nature of subclonal growth remains unclear. Here we utilise 102 macroscopic whole tumour images from clear cell re…
View article: A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9
A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9 Open
We present a novel combination of generative and predictive machine learning models for discovering unique protein inhibitors. The new method is assessed on its ability to generate unique inhibitors for the cancer associated protein kinase…
View article: Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing
Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing Open
View article: Additional file 2 of Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage
Additional file 2 of Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage Open
Additional file 2. Table S2, Hi-C library sequencing read statistics. (CSV 1 kb)
View article: A FIJI Macro for quantifying pattern in extracellular matrix
A FIJI Macro for quantifying pattern in extracellular matrix Open
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously…
View article: Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock
Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock Open
The formation of specific protein‐protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small …