Document text
Principal Investigator: Augustin Luna
Organization: NATIONAL LIBRARY OF MEDICINE
Fiscal Year: 2024
Award: $882,387
Funding agency: National Library of Medicine
1. Computational Analysis of Sarcoma Pharmacogenomics
Sarcomas are a diverse group of rare malignancies composed of multiple different clinical and molecular subtypes. Due to their rarity and heterogeneity, basic, translational, and clinical research in sarcoma has trailed behind that of other cancers. With colleagues, Luna lab group members worked to conduct analyses in the following areas related to sarcomas:
* The biological relevance of sarcoma cell lines as preclinical models based on oncogenic fusions
* The mutation and mutational burden characteristics of sarcoma cell lines
* Predictive biomarkers of drug response using sarcoma cell line pharmacogenomics data
2. Machine Learning Analysis of Single-Cell Perturbation Datasets
Perturbation experiments probe the response of cells or cellular systems to changes in conditions (e.g., drug treatment). Large-scale single-cell perturbation–response screens enable exploration of complex cellular behavior inaccessible in bulk measurements. Reliable analysis of increasingly large perturbation datasets requires efficient statistical tools to harness large numbers of cells and perturbations. There is presently little convention for statistical comparison of response profiles in perturbation studies. Luna lab group members worked to conduct analyses worked to develop a method for quantification of perturbation effects and significance testing as well as a measure between sets of single-cell expression profiles.
3. Graph-Based Computational Analysis for Drug-Target Identification in COVID-19
The COVID-19 global pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 Disease Map project was a large-scale community effort uniting 277 scientists from 130 Institutions that worked to better understand SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Luna lab group members worked as part of this effort to develop C19DMap-Neo4j graph database of SARS-CoV-2-host interactions, as well as understand to analyze this dataset in relation to Clinical Trials (clinicaltrials.gov) data for drug repurposing opportunities.
4. Continued Development of the Systems Biology Graphical Notation (SBGN) for Exchange of Cellular Signaling Knowledge
Systems Biology Graphical Notation project, an effort to standardize the graphical notation used in maps of biological networks and processes from gene regulation, to metabolism, to cellular signaling. The effort enables scientists to visually represent networks of biochemical interactions in a standard, unambiguous way. The SBGN effort is a community effort that draws on ideas from numerous researchers to develop a widely usable representation formalism. Luna lab group members continued to develop SBGN based on community feedback concentrated on remaining areas ambiguities that can arise in some SBGN diagrams; an example of this involves duplication of visual elements and the semantics of these duplications. Additionally, Luna lab group members continued to work on tools to simplify the use of SBGN by the wider research community; these efforts focus on simplifying the generation of SBGN diagrams.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><Address><Area><Basic Research><Basic Science><Biochemical><Biological><Biology><COVID crisis><COVID epidemic><COVID pandemic><COVID-19><COVID-19 crisis><COVID-19 epidemic><COVID-19 era><COVID-19 global health crisis><COVID-19 global pandemic><COVID-19 health crisis><COVID-19 pandemic><COVID-19 period><COVID-19 public health crisis><COVID-19 virus><COVID-19 years><COVID19 virus><CV-19><Cancers><Cell Body><Cell Communication and Signaling><Cell Line><Cell Signaling><CellLine><Cells><Characteristics><Clinical Research><Clinical Study><Clinical Trials><CoV-2><CoV2><Communities><Complex><Computer Analysis><Computer Models><Computerized Models><Coronavirus Infectious Disease 2019><DNA Alteration><DNA Sequence Alteration><DNA mutation><Data><Data Reporting><Data Set><Development><Disease><Disorder><Drug Targeting><Drug Therapy><Drugs><Elements><Feedback><Gene Action Regulation><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Generations><Genetic Alteration><Genetic Change><Genetic defect><Genetic mutation><Goals><Graph><Heterogeneity><Institution><Intermediary Metabolism><Intracellular Communication and Signaling><Investigators><Knowledge><Machine Learning><Malignant Neoplasms><Malignant Soft Tissue Neoplasm><Malignant Tumor><Maps><Measurement><Measures><Medication><Metabolic Processes><Metabolism><Methodology><Methods><Mutation><Oncogenic><Pharmaceutical Preparations><Pharmacogenomics><Pharmacotherapy><Pre-Clinical Model><Preclinical Models><Property><Proteomics><Research><Research Personnel><Researchers><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 epidemic><SARS-CoV-2 global health crisis><SARS-CoV-2 global pandemic><SARS-CoV-2 pandemic><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-coronavirus-2 epidemic><SARS-coronavirus-2 pandemic><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sarcoma><Scientist><Semantics><Sequence Alteration><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome CoV 2 epidemic><Severe Acute Respiratory Syndrome CoV 2 pandemic><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 epidemic><Severe acute respiratory syndrome coronavirus 2 pandemic><Severe acute respiratory syndrome related corona virus 2><Signal Transduction><Signal Transduction Systems><Signaling><Standardization><Strains Cell Lines><System><Systems Biology><Systems Development><Testing><Translational Research><Translational Science><Visual><Work><Wuhan coronavirus><bio-informatics pipeline><bioinformatics pipeline><biologic><biological signal transduction><biological standardization><cancers that are rare><cell behavior><cellular behavior><clinical decision-making><clinical subtypes><computational analyses><computational analysis><computational modeling><computational models><computer analyses><computer based models><computerized modeling><conference><convention><coronavirus disease 2019><coronavirus disease 2019 crisis><coronavirus disease 2019 epidemic><coronavirus disease 2019 global health crisis><coronavirus disease 2019 global pandemic><coronavirus disease 2019 health crisis><coronavirus disease 2019 pandemic><coronavirus disease 2019 public health crisis><coronavirus disease 2019 virus><coronavirus disease crisis><coronavirus disease epidemic><coronavirus disease pandemic><coronavirus disease-19><coronavirus disease-19 global pandemic><coronavirus disease-19 pandemic><coronavirus disease-19 virus><coronavirus infectious disease-19><cultured cell line><data representation><data representations><developmental><drug repositioning><drug repurposing><drug treatment><drug/agent><experiment><experimental research><experimental study><experiments><expression subtypes><genome mutation><genomic alteration><graph database><hCoV19><human disease><improved><interoperability><machine based learning><machine learning based method><machine learning method><machine learning methodologies><malignancy><malignant soft tissue tumor><member><molecular sub-types><molecular subsets><molecular subtypes><nCoV2><neoplasm/cancer><novel><predictive biomarkers><predictive marker><predictive molecular biomarker><rare cancer><rare malignancy><rare tumor><repurposing agent><repurposing medication><response><severe acute respiratory syndrome coronavirus 2 global health crisis><severe acute respiratory syndrome coronavirus 2 global pandemic><single cell analysis><summit><symposia><symposium><tool><translation research><translational investigation><usability>