A5011659992- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Cell Image Analysis Techniques
- CAR-T cell therapy research
- Autism Spectrum Disorder Research
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Cancer Research and Treatments
- Acute Kidney Injury Research
- Mathematical Biology Tumor Growth
- Genetics and Neurodevelopmental Disorders
- Protein Tyrosine Phosphatases
- CRISPR and Genetic Engineering
- Ocular and Laser Science Research
- Machine Learning in Bioinformatics
- Cancer Immunotherapy and Biomarkers
- Hemodynamic Monitoring and Therapy
- Monoclonal and Polyclonal Antibodies Research
- Cancer Genomics and Diagnostics
- Glioma Diagnosis and Treatment
- Renal and related cancers
- Genetics, Bioinformatics, and Biomedical Research
- Non-Invasive Vital Sign Monitoring
University of California, San Diego
2023-2024
Massachusetts Institute of Technology
2021
Broad Institute
2017-2018
Summary Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved neurogenesis, tubulin biology, transcriptional regulation, chromatin...
Gene set analysis is a mainstay of functional genomics, but it relies on manually curated databases gene functions that are incomplete and unaware biological context. Here we evaluate the ability OpenAI's GPT-4, Large Language Model (LLM), to develop hypotheses about common from its embedded biomedical knowledge. We created GPT-4 pipeline label sets with names summarize their consensus functions, substantiated by text citations. Benchmarking against named in Ontology, generated very similar...
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Abstract Cisplatin is a commonly administrated chemotherapy drug for cancer treatment. Although the direct mechanism of cisplatin largely well-defined, it challenging to comprehensively assess its systemic effects. Cellular responses perturbations are intricate processes involving modifications protein complexes across diverse cellular compartments. Therefore, substantial research endeavors have been directed towards unraveling organization in cells. We recently built multiscale integrated...
Gene set analysis is a mainstay of functional genomics, but it relies on curated databases gene functions that are incomplete. Here we evaluate five Large Language Models (LLMs) for their ability to discover the common biological represented by set, substantiated supporting rationale, citations and confidence assessment. Benchmarking against canonical sets from Ontology, GPT-4 confidently recovered name or more general concept (73% cases), while benchmarking random correctly yielded zero...
Abstract Acute kidney injury (AKI) is common in the intensive care unit, where it associated with increased mortality. AKI often defined using creatinine and urine output criteria. The creatinine-based definition more reliable but less expedient, whereas based rapid reliable. Our goal to examine criterion augment physiological features for better agreement definitions of AKI. objectives are threefold: (1) characterize baseline AKI; (2) refine criteria identify thresholds that best agree...
Abstract Ongoing pre-clinical efforts aim to deploy genome-scale CRISPR/Cas9 technology and large collections of small molecules catalog maps cancer vulnerabilities at scale. However, such in pediatric rare cancers have lagged behind comparable more common types due the dearth cell models. Here, we present an update from our “Cancer Cell Line Factory” project on overcome key laboratory biologistics challenges precluding progress cancers. This effort, now it’s 3rd year, represents industry...
Abstract The development of new cancer therapeutics requires sufficient genetic and phenotypic diversity models. Current collections human cell lines are limited for many rare types, zero models exist that broadly available. Here, we report results from the pilot phase Cancer Cell Line Factory (CCLF) project aims to overcome this obstacle by systematically creating next-generation in vitro adult pediatric patients' specimens making these We first developed a workflow laboratory, genomics...
Tumors involving the central nervous system (CNS) include over 200 primary and metastatic subtypes with major clinical impact. Research on CNS neoplasms has been hampered by lack of appropriate models for many subtypes. We established a robust workflow systematic culturing approach to create cancer cell line from all adult pediatric patients here report results these ongoing efforts. Tumor samples consented cancers were systematically collected 2008–18. grown in different media substrates...