Allison P. Heath
A5058890056- Cancer Genomics and Diagnostics
- Glioma Diagnosis and Treatment
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Neuroblastoma Research and Treatments
- Epigenetics and DNA Methylation
- Biomedical and Engineering Education
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Nutrition, Genetics, and Disease
- Research Data Management Practices
- Radiomics and Machine Learning in Medical Imaging
- Microbial Metabolic Engineering and Bioproduction
- Biomedical Text Mining and Ontologies
- Evolution and Genetic Dynamics
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Pancreatic and Hepatic Oncology Research
- Cancer-related molecular mechanisms research
- Health and Medical Research Impacts
- Chromosomal and Genetic Variations
- Metabolomics and Mass Spectrometry Studies
Children's Hospital of Philadelphia
2017-2025
Alex's Lemonade Stand Foundation
2022
University of Chicago
2012-2017
Health Alliance International
2013-2014
University of Illinois Chicago
2012
Rice University
2005-2011
Baylor College of Medicine
2010
University of North Texas Health Science Center
2007
University of North Texas
2007
The Genomic Data Commons will initially house raw genomic data and diagnostic, histologic, clinical outcome from National Cancer Institute–funded projects. A harmonization process align sequencing to the genome identify mutations alterations.
Abstract International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international registry collecting from 19 centers, makes >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional longitudinal data, including treatment outcome are being collected by GENIE Biopharma Collaborative using PRISSMM curation...
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA and proteomics phosphoproteomics profiling, of 218 tumors across 7 histological types childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span boundaries, suggesting treatments used for one type may be applied...
Abstract The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide cancer research community with a data repository uniformly processed genomic and associated clinical that enables sharing collaborative analysis in support precision medicine. initial GDC dataset include genomic, epigenomic, proteomic, other from NCI TCGA TARGET programs. production for started June, 2015 using an OpenStack-based private cloud. By June 2016, had analyzed more than 50,000 raw...
Pediatric brain tumors are the leading cause of cancer-related death in children United States and contribute a disproportionate number potential years life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary The Children's Brain Tumor Network (CBTN) is multi-institutional international clinical research consortium created advance therapeutic development through collection rapid distribution biospecimens data via open-science...
Data-driven basic, translational, and clinical research has resulted in improved outcomes for children, adolescents, young adults (AYAs) with pediatric cancers. However, challenges sharing data between institutions, particularly research, prevent addressing substantial unmet needs children AYA patients diagnosed certain Systematically collecting from every child can enable greater understanding of cancers, improve survivorship, accelerate development new more effective therapies. To...
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, Children's Brain Tumor Network (CBTN) Pacific Neuro-Oncology Consortium (PNOC) created a systematic process tumor biobanking, model generation, sequencing with immediate access to harmonized data. We leverage data establish OpenPBTA, an open collaborative project over 40 scalable...
Abstract Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time‐scales. The underlying assumption in multiscale simulations is that it possible move reliably between different resolutions. We present method efficiently generates realistic all‐atom structures starting from C α atom positions, obtained for instance extensive coarse‐grain simulations. method, reconstruction algorithm (RACOGS), validated...
As large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, analyze them. One possible approach provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along tools resources it.
Data commons collocate data, storage, and computing infrastructure with core services commonly used tools applications for managing, analyzing, sharing data to create an interoperable resource the research community. An architecture is described, as well some lessons learned from operating several large-scale commons.
Abstract The contribution of rare pathogenic/likely pathogenic (P/LP) germline variants to pediatric central nervous system (CNS) tumor development remains understudied. Here, we characterized the prevalence and clinical significance P/LP in cancer predisposition genes across 830 CNS patients from Pediatric Brain Tumor Atlas (PBTA). We identified 24.2% (201/830) majority (154/201) lacked reporting genetic syndromes. Among carriers, 30.7% had putative somatic second hits or loss function...
Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent new post-genomics technologies, becoming increasingly prevalent; yet full impact these can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, distribution metadata. To...
As the number of cloud platforms supporting scientific research grows, there is an increasing need to support interoperability between two or more platforms. A well accepted core concept make data in Findable, Accessible, Interoperable and Reusable (FAIR). We introduce a companion that applies cloud-based computing environments we call Secure Authorized FAIR Environment (SAFE). SAFE require platform governance structures are designed sensitive controlled access data, such as biomedical data....
Abstract Motivation: Finding novel or non-standard metabolic pathways, possibly spanning multiple species, has important applications in fields such as engineering, network analysis and reconstruction. Traditionally, this been a manual process, but the large volume of data now available created need for computational tools to automatically identify biologically relevant pathways. Results: We present new algorithms finding given desired start target compound, that conserve number atoms by...
Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, procedures for sharing biosamples associated genomic phenotypic data on broadly consented cohorts, across sites of care.Three the nation's leading children's hospitals launched Genomic Research Innovation Network (GRIN), federated information technology infrastructure, harmonized biobanking...
The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic associated clinical data to the research community. This dataset continues grow currently includes 14,500 patients. GDC is an example a biomedical commons, which collocates with storage computing infrastructure commonly used web services, software applications, tools create secure, interoperable, extensible resource for researchers. (i) repository downloading that have been...
The falling costs and increasing fidelity of high-throughput biomedical research data have led to a renaissance in cancer surveillance treatment. Yet, the amount, velocity, complexity these overcome capacity number researchers collecting analyzing this information. By centralizing data, processing power, tools, there is valuable opportunity share resources thus increase efficiency, impact research. Herein, we describe current commons how they operate oncology landscape, including an overview...