A5044908269- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Evolutionary Game Theory and Cooperation
- Evolution and Genetic Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Mathematical and Theoretical Epidemiology and Ecology Models
- Epigenetics and DNA Methylation
- Multiple Myeloma Research and Treatments
- Genomics and Phylogenetic Studies
- Advanced Thermodynamics and Statistical Mechanics
- Protein Degradation and Inhibitors
- Spacecraft Design and Technology
- Ubiquitin and proteasome pathways
- Functional Brain Connectivity Studies
- Structural Analysis of Composite Materials
- Biomedical Text Mining and Ontologies
- Time Series Analysis and Forecasting
- Genomic variations and chromosomal abnormalities
- Scientific Computing and Data Management
- Testicular diseases and treatments
- PI3K/AKT/mTOR signaling in cancer
- Mass Spectrometry Techniques and Applications
University of Missouri–St. Louis
2012-2022
Washington University in St. Louis
2015-2021
James S. McDonnell Foundation
2015-2019
Saint Louis University
2018
University of Missouri
2013
Mind Research Network
2011
University of New Mexico
2011
CO2CRC
2006
Commonwealth Scientific and Industrial Research Organisation
2006
Geoscience Australia
2006
Highlights•871 predisposition variants/CNVs discovered in 8% of 10,389 cases 33 cancers•Pan-cancer approach identified shared variants and genes across cancers•33 affecting activating domains oncogenes showed high expression•47 VUSs prioritized using cancer enrichment, LOH, expression other evidenceSummaryWe conducted the largest investigation to date, discovering 853 pathogenic or likely from types. Twenty-one single cross-cancer associations, including novel associations SDHA melanoma...
The availability of well-characterized neuroimaging data with large numbers subjects, especially for clinical populations, is critical to advancing our understanding the healthy and diseased brain. Such enables questions be answered in a much more generalizable manner also has potential yield solutions derived from novel methods that were conceived after original studies' implementation. Though there currently growing interest sharing, community been struggling years how best encourage...
Abstract Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast patient-derived xenograft (PDX) models. Integrated proteogenomic shows positive correlation between measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal markers. Proteogenomic also validates a number...
Abstract Summary CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity germline variants. gathers evidence from databases annotations, provided by local tools files or via ReST APIs, classifies variants according to ACMG guidelines assessing variant pathogenicity. User-designed criteria can be incorporated into CharGer’s flexible framework, thereby allowing users create customized classification protocol. Availability...
We describe the systematic approach to incidental findings (IFs) used at Mind Research Network (MRN) where all MRI scans receive neuroradiologist interpretation and participants are provided results.From 2004 2011, 8,545 were acquired by 45 researchers. As mandated MRN's external institutional review board, structural sequences evaluated a clinical who generated report that included recommendations for referral if indicated. Investigators received copy of their participants' reports, which...
A database of curated genomic variants with clinically supported drug therapies and other oncological annotations is described. The accompanying web portal provides a search engine two modes: one that allows users to query gene, cancer type, variant type or position for druggable mutations, another visualize, on three-dimensional protein structures, putative sites cluster known mutations.http://dinglab.wustl.edu/depo.
Identifying genomic variants is a fundamental first step toward the understanding of role inherited and acquired variation in disease. The accelerating growth corpus sequencing data that underpins such analysis making data-download bottleneck more evident, placing substantial burdens on research community to keep pace. As result, search for alternative approaches traditional “download analyze” paradigm local computing resources has led rapidly growing demand cloud-computing solutions...
Aberrant phospho-signaling is a hallmark of cancer. We investigated kinase-substrate regulation 33,239 phosphorylation sites (phosphosites) in 77 breast tumors and 24 cancer xenografts. Our search discovered 2134 quantitatively correlated kinase-phosphosite pairs, enriching for extending experimental or binding-motif predictions. Among the 91 kinases with auto-phosphorylation, elevated EGFR, ERBB2, PRKG1, WNK1 phosphosignaling were enriched basal, HER2-E, Luminal A, B cancers, respectively,...
Abstract Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering phosphosites cancer mutations on protein structures. identifies 474 such hybrid clusters 1255 phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, IDH1 p.Y139/IDH2 p.Y179 are adjacent to...
Recent computational studies have shown that speciation can occur under neutral conditions, i.e., when the simulated organisms all identical fitness. These works bear comparison with mathematical of clustering on landscapes in context branching and coalescing random walks. Here, we show sympatric clustering/speciation a landscape whose dimensions specify only organisms' phenotypes. We demonstrate occurs not case assortative mating, but also asexual fission; it is observed control mating....
Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection—neutral evolution—in which organisms defined only by phenotype. Universal dynamics has previously been demonstrated in related model on neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional condition of (where is number offspring each...
Abstract G-protein coupled receptors (GPCRs) account for about 4% of all encoded genes in the human genome with over 800 different types. They activate signal transduction pathways inside cell that regulate a wide variety cellular responses and physiological processes. GPCRs are known to play role disease progression target 40% drugs on market. However, implication tumor initiation and/or has not been extensively studied remains unknown. Due being major drug targets, identifying functional...
Abstract A significant fraction of cancers have a heritable component, and require an interplay between somatic germline variants. Common rare variants been investigated by previous GWAS family based studies. However, comprehensive analysis both in cancer using high throughput sequencing data to discover genetic functional relevance is lacking. Herein, we the potential role from over 20 major types large-scale studies such as TCGA ICGC discovered thousands genomes. To link these phenotypes,...