A5086627043- Privacy-Preserving Technologies in Data
- Cryptography and Data Security
- Cancer Genomics and Diagnostics
- Blockchain Technology Applications and Security
- Ethics in Clinical Research
- Epigenetics and DNA Methylation
- Caching and Content Delivery
- Law, AI, and Intellectual Property
- DNA Repair Mechanisms
- Genetic Neurodegenerative Diseases
- Bacterial Genetics and Biotechnology
- Micro and Nano Robotics
- Microbial Metabolic Engineering and Bioproduction
- Mitochondrial Function and Pathology
- Forensic and Genetic Research
- Calcium Carbonate Crystallization and Inhibition
- Echinoderm biology and ecology
- Gene Regulatory Network Analysis
- Molecular Biology Techniques and Applications
- Microtubule and mitosis dynamics
- Genomics and Rare Diseases
- Wireless Communication Security Techniques
- Renal Transplantation Outcomes and Treatments
- Paleontology and Stratigraphy of Fossils
- Organ Donation and Transplantation
Stanford University
2022-2024
Yale University
2018-2022
Whitney Museum of American Art
2019-2022
Swiss Federal Institute of Aquatic Science and Technology
2018
ETH Zurich
2018
Abstract Expansion of a single repetitive DNA sequence, termed tandem repeat (TR), is known to cause more than 50 diseases 1,2 . However, expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts TRs, phenomenon microsatellite instability; however, larger have been systematically analysed cancer 3–8 Here we identified TR 2,622 genomes spanning 29 types. seven types, found 160 recurrent (rREs), most which...
Abstract Background As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate storage and sharing protocols need be adopted. One promising option for secure, high-integrity is Ethereum smart contracts. a blockchain platform, contracts are immutable pieces of code running on virtual machines in this platform that can invoked by user or another contract (in the network). The 2019 iDASH (Integrating Data Analysis, Anonymization, Sharing) competition...
There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier these is achieving practical solutions for data ownership and integrity. Blockchain provides challenges in other realms, such as finance. However, its use genomics stymied due the difficulty storing large-scale on-chain, slow transaction speeds, limitations on querying. To overcome roadblocks, we developed private blockchain network store genomic variants reference-aligned reads...
Genotype imputation is the inference of unknown genotypes using known population structure observed in large genomic datasets; it can further our understanding phenotype-genotype relationships and useful for QTL mapping GWASs. However, compute-intensive nature genotype overwhelm local servers computation storage. Hence, many researchers are moving toward cloud services, raising privacy concerns. We address these concerns by developing an efficient, privacy-preserving algorithm called...
Abstract Background With the advent of precision medicine, pharmacogenomics data is becoming increasingly critical to patient care. These describe relationship between a particular variant in genome and response drug by patient. As utilizing this kind becomes more integral medical treatment decisions, appropriate storage sharing will be critical. A potential way securely storing smart contract with Ethereum blockchain. This an open-source blockchain platform for decentralized applications....
Abstract Biomineralization is ubiquitous in both unicellular and multicellular living systems [1, 2] has remained elusive due to a limited understanding of physicochemical biomolecular processes [3]. Echinoderms, identified with diverse architectures calcite-based structures the dermis[4], present an enigma how cellular control shape form individual structures. Specifically, holothurians (sea cucumbers), multi-cellular clusters construct discrete single-crystal calcite ‘ossicles’ ( ∼ 100 µ m...
Abstract The genomic characterization of individuals promises to be immensely useful for biomedical research and healthcare. However, a critical barrier expanding personal genome sequencing is achieving secure, high-integrity storage raw data. While cloud offers solutions access such data from any place device, the vulnerabilities centralized in relation security, integrity, robustness, as single points failure, have not yet been addressed. Blockchain potential alternative these modes....
Abstract The generation of functional genomics datasets is surging, as they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). intention experiments not necessarily to study genetic variants, yet pose privacy concerns due their use next-generation sequencing. Moreover, there a great incentive share raw reads for better analyses general research reproducibility. Thus, we need new modes sharing beyond traditional controlled-access models. Here,...
Abstract Genotype imputation is the statistical inference of unknown genotypes using known population haplotype structures observed in large genomic datasets, such as HapMap and 1000 genomes project. can help further our understanding relationships between traits, extremely useful for analyses genome-wide association studies expression quantitative loci inference. Increasing number genotyped will increase power inferring genotype-phenotype relationships, but amount data required...
Functional genomics data are becoming clinically actionable, raising privacy concerns. However, quantifying leakage via genotyping is difficult due to the heterogeneous nature of sequencing techniques. Thus, we present FANCY, a tool that rapidly estimates number leaking variants from raw RNA-Seq, ATAC-Seq and ChIP-Seq reads, without explicit genotyping. FANCY employs supervised regression using overall statistics as features provides an estimate risk before release.FANCY can predict...
Multicellular organisms utilize thin sheet folding to achieve functional three-dimensional forms. During embryonic development, stereotypical epithelial folds emerge from active cellular and molecular processes including cell shape change differential growth. Active promises be a powerful design technique in the fields of solids, soft robotics, synthetic biology. However, general principles remain poorly understood. Here we discover non-canonical cilia-driven behavior exhibited by basal...
Abstract Functional genomics data is becoming clinically actionable, raising privacy concerns. However, quantifying the leakage by genotyping difficult due to heterogeneous nature of sequencing techniques. Thus, we present FANCY, a tool that rapidly estimates number leaking variants from raw RNA-Seq, ATAC-Seq and ChIP-Seq reads, without explicit genotyping. FANCY employs supervised regression using overall statistics as features provides an estimate risk before release. can predict...
Abstract Expansion of a single repetitive DNA sequence, termed tandem repeat (TR), is known to cause more than 50 diseases. However, expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts TRs (STRs), phenomenon microsatellite instability (MSI); however larger have been systematically analyzed cancer. Here, we identified TR 2,622 cancer genomes, spanning 29 types. 7 types, found 160 recurrent (rREs); most...