Amanda Saravia-Butler
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View article: MeDiSumQA: Patient-Oriented Question-Answer Generation from Discharge Letters
MeDiSumQA: Patient-Oriented Question-Answer Generation from Discharge Letters Open
While increasing patients' access to medical documents improves medical care, this benefit is limited by varying health literacy levels and complex medical terminology. Large language models (LLMs) offer solutions by simplifying medical in…
View article: Analyzing the relationship between gene expression and phenotype in space-flown mice using a causal inference machine learning ensemble
Analyzing the relationship between gene expression and phenotype in space-flown mice using a causal inference machine learning ensemble Open
Spaceflight has several detrimental effects on human and rodent health. For example, liver dysfunction is a common phenotype observed in space-flown rodents, and this dysfunction is partially reflected in transcriptomic changes. Studies li…
View article: MeDiSumQA: Patient-Oriented Question-Answer Generation from Discharge Letters
MeDiSumQA: Patient-Oriented Question-Answer Generation from Discharge Letters Open
View article: NASA open science data repository: open science for life in space
NASA open science data repository: open science for life in space Open
Space biology and health data are critical for the success of deep space missions and sustainable human presence off-world. At the core of effectively managing biomedical risks is the commitment to open science principles, which ensure tha…
View article: Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice
Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice Open
Impairment of the central nervous system (CNS) poses a significant health risk for astronauts during long-duration space missions. In this study, we employed an innovative approach by integrating single-cell multiomics (transcriptomics and…
View article: Inspiration4 data access through the NASA Open Science Data Repository
Inspiration4 data access through the NASA Open Science Data Repository Open
The increasing accessibility of commercial and private space travel necessitates a profound understanding of its impact on human health. The NASA Open Science Data Repository (OSDR) provides transparent and FAIR access to biological studie…
View article: Inspiration4 Data Access through the NASA Open Science Data Repository
Inspiration4 Data Access through the NASA Open Science Data Repository Open
The increasing accessibility of commercial and private space travel necessitates a profound understanding of its impact on human health. The NASA Open Science Data Repository (OSDR) provides transparent and FAIR access to biological studie…
View article: Celebrating 30 years of access to NASA Space Life Sciences data
Celebrating 30 years of access to NASA Space Life Sciences data Open
NASA’s space life sciences research programs established a decades-long legacy of enhancing our ability to safely explore the cosmos. From Skylab and the Space Shuttle Program to the NASA Balloon Program and the International Space Station…
View article: Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction.
Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction. Open
Missions into Deep Space are planned this decade. Yet the health consequences of exposure to microgravity and galactic cosmic radiation (GCR) over years-long missions on indispensable visceral organs such as the kidney are largely unexplor…
View article: Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts
Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in …
View article: Batch effect correction methods for NASA GeneLab transcriptomic datasets
Batch effect correction methods for NASA GeneLab transcriptomic datasets Open
Introduction: RNA sequencing (RNA-seq) data from space biology experiments promise to yield invaluable insights into the effects of spaceflight on terrestrial biology. However, sample numbers from each study are low due to limited crew ava…
View article: Spatially resolved multiomics on the neuronal effects induced by spaceflight
Spatially resolved multiomics on the neuronal effects induced by spaceflight Open
Impairment of the central nervous system (CNS) functions in astronauts is a major health risk for long-duration space missions. Here, for the first time, we combine single-cell multiomics (transcriptomics and chromatin accessibility) and s…
View article: Biological research and self-driving labs in deep space supported by artificial intelligence
Biological research and self-driving labs in deep space supported by artificial intelligence Open
Space biology research aims to understand fundamental spaceflight effects on organisms, develop foundational knowledge to support deep space exploration and, ultimately, bioengineer spacecraft and habitats to stabilize the ecosystem of pla…
View article: Biomonitoring and precision health in deep space supported by artificial intelligence
Biomonitoring and precision health in deep space supported by artificial intelligence Open
View article: Analyzing the Relationship Between Gene Expression and Phenotype in Space-Flown Mice Using a Causal Inference Machine Learning Ensemble
Analyzing the Relationship Between Gene Expression and Phenotype in Space-Flown Mice Using a Causal Inference Machine Learning Ensemble Open
Spaceflight has several detrimental effects on human and rodent health. For example, liver dysfunction is a common phenotype observed in space-flown rodents, and this dysfunction is partially reflected in transcriptomic changes. Studies li…
View article: GL4U-Intro-2023
GL4U-Intro-2023 Open
This zip file contains the lecture slides and jupyter notebooks used in the 2023 GeneLab for Colleges and Universities (GL4U) Introduction module.
View article: Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients
Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients Open
View article: The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response
The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response Open
SUMMARY Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggere…
View article: Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection
Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection Open
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasophar…
View article: System-wide transcriptome damage and tissue identity loss in COVID-19 patients
System-wide transcriptome damage and tissue identity loss in COVID-19 patients Open
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndro…
View article: Betacoronavirus-specific alternate splicing
Betacoronavirus-specific alternate splicing Open
View article: The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response
The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response Open
Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanism…
View article: Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients
Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients Open
We analyzed RNA sequencing data from nasal swabs used for SARS-CoV-2 testing. 13% of 317 PCR-negative samples contained over 100 reads aligned to multiple regions of the SARS-CoV-2 genome. Differential gene expression analysis compares the…
View article: The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response
The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response Open
Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms trigg…
View article: System-wide transcriptome damage and tissue identity loss in COVID-19 patients
System-wide transcriptome damage and tissue identity loss in COVID-19 patients Open
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndro…
View article: Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health Open
Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-…
View article: Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs Open
Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of p…
View article: Role of miR-2392 in driving SARS-CoV-2 infection
Role of miR-2392 in driving SARS-CoV-2 infection Open
To evaluate the role of a circulating microRNA, miR-2392, as a potential biomarker for COVID-19 and to develop a potential COVID-19 therapeutic and antiviral to inhibit miR2392.
View article: Betacoronavirus-specific alternate splicing
Betacoronavirus-specific alternate splicing Open
Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 S…
View article: The Great Deceiver: miR-2392’s Hidden Role in Driving SARS-CoV-2 Infection
The Great Deceiver: miR-2392’s Hidden Role in Driving SARS-CoV-2 Infection Open
Summary MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic dat…