About

Paul Avery is a professor in the Department of Physics at the University of Florida, holding a PhD from the University of Illinois obtained in 1980. His research interests include experimental high energy physics, with active participation in the CLEO experiment at Cornell University and the CMS experiment at CERN in Geneva, Switzerland. Dr. Avery's work also encompasses the study of decays of heavy quarks, and he has a strong focus on software development, including object-oriented methods and fitting algorithms. Additionally, he is involved in computing, particularly distributed computing and Computational Grids, and is currently engaged in a major grid initiative called GriPhyN. He is affiliated with the Institute for High Energy Physics and Astrophysics (IHEPA), where his office is located at 2029 NPB 352, and can be contacted via phone at 352.392.9264 or email at avery@ufl.edu.

Research topics

• Biology
• Cell biology
• Genetics
• Geology
• Environmental science
• Astronomy
• Astrobiology
• Ecology
• Earth science
• Neuroscience
• Physics

Selected publications

• GLARE: discovering hidden patterns in spaceflight transcriptome using representation learning

  npj Microgravity · 2025-10-28

  articleOpen access

  Spaceflight studies present novel insights into biological processes through exposure to stressors outside the evolutionary path of terrestrial organisms. Despite limited access to space environments, numerous transcriptomic datasets from spaceflight experiments are now available through NASA's GeneLab data repository, which allows public access, encouraging further analysis. While various computational pipelines and methods have been used to process these transcriptomic datasets, learning-model-driven analyses have yet to be applied to a broad array of such spaceflight-related datasets. In this study, we present an open-source pipeline, GLARE: GeneLAb Representation learning pipelinE, which consists of training different representation learning approaches from manifold learning to self-supervised learning that enhance the performance of downstream analytical tasks. We illustrate the utility of GLARE by applying it to gene-level transcriptional values from the results of the CARA spaceflight experiment, an Arabidopsis root tip transcriptome dataset that spanned light, dark, and microgravity treatments. We show that GLARE not only substantiated the findings of the original study concerning cell wall remodeling but also revealed additional patterns of gene expression affected by the treatments, including evidence of hypoxic response. This work suggests there is great potential to supplement the insights drawn from initial studies on spaceflight omics-level data through further machine-learning-enabled analyses.

  PublisherOA PDFDOI

• Application of Open‐Source Digital Resources for <scp>3D</scp> Visualization of Clustered Transcriptomic Data

  Physiologia Plantarum · 2025-09-01

  articleOpen access

  As datasets grow in size with the increased accessibility of high-throughput transcriptome sequencing, methods of dimensionality reduction have become invaluable for data analysis. The methods of dimensionality reduction, including t-distributed stochastic neighbor embedding or Uniform Manifold Approximation and Projection, are utilized to create figures and projections of the high-dimensional data into a set of lower dimensions, 2D or 3D, which are more well-suited for human comprehension. These methods of dimensionality reduction have continually grown in popularity and widespread use. Despite this popularity, creating engaging and visually attractive features remains an issue for many users without significant coding experience. To remediate this issue, an HTML-based digital resource was created that utilizes publicly available scripts from JsDelivr and GitHub, and Blender, an open-source modeling software. We have generated two open-source digital data visualization resources that can be applied to the transcriptomic data processed using the aforementioned methods of dimensionality reduction. The first, HTMLview, utilizes a provided HTML file template to create an interactive and engaging 3D model in digital space. The second method, Blenderview, utilizes the open-source modeling software, Blender, to create and animate high-quality models and videos of processed datapoints. The two methods were tested with transcriptomic data processed via dimensionality reduction algorithms. The methods provided create two distinct paths for researchers to better visualize, examine, and share their data, while also utilizing open-source technologies that are readily available to most potential users.

  PublisherOA PDFDOI

• Simulated Microgravity Enhances Germ Tube Elongation by <i>Golovinomyces cichoracearum</i> on <i>Cucurbita pepo</i> and <i>Arabidopsis thaliana</i> Leaves

  Phytopathology · 2025-12-15

  article

  Bioregenerative life support systems (BLSS) are proposed for the production of food crops, water recycling, and air revitalization in future microgravity, Moon, and Mars habitats. The alternative hypothesis ( Ha) for the current study was that simulated microgravity would increase phytopathogen growth rates, potentially leading to increased levels of disease in space-based BLSS modules. Squash cotyledon leaf discs and full canopies of Arabidopsis thaliana ( At) plants were dusted with conidia from 14-day-old colonies of Golovinomyces cichoracearum ( Gc). Leaves were positioned into one of five gravity treatments: (i) adaxial leaf surfaces pointed upward ( 1g-up control), (ii) adaxial surface oriented 90° to Earth's 1g down vector ( 1g-90° control), (iii) adaxial surfaces pointed down ( 1g-down control), (iv) rotated on a 2D clinostat, or (v) randomly rotated on a 3D random positioning machine ( RPM). Inoculated squash leaf discs and At canopies were incubated on agar media for 2 or 3 days postinoculation (dpi), fixed with 3% glutaraldehyde, and imaged with SEM. The fastest growth rates on squash leaf discs were observed for germ tubes on squash leaf discs exposed to the 2D clinostat (mean = 94.2 µm at 3 dpi) and 3D RPM system (65.3 µm at 3 dpi); all three 1g controls were similar (approximately 38 to 45 µm long). The growth rates of germ tubes on At leaves under similar gravity treatments were approximately 33% of the growth rates observed on squash leaves. The results suggest that Gc conidia may germinate more rapidly and grow faster in altered gravity conditions compared with 1g controls, supporting the Ha.

  PublisherDOI

• Maiden isolation and molecular confirmation of lumpy skin disease virus from cattle in West Bengal

  Indian Journal of Animal Health · 2025-04-10

  articleOpen access

  To investigate the presence of lumpy skin disease virus (LSDV) in some suspected cattle of West Bengal (WB), the nodules and scabs were collected and virological/ molecular confirmation was performed.The skin biopsies (n=6) were collected from the representative animals (n=3) in virus transport medium and stored at 4 o C. Latter, LSDV-specific polymerase chain reaction (PCR), recommended by World Organization for Animal Health (WOAH, previously OIE), was performed.Chorioallantoic membrane (CAM) of sample inoculated embryonated chicken egg (ECE) showing pock lesions was triturated and inoculated into vero cell lines.Clear cytopathic effect (CPE) of virus was observed at 72 hours post inoculation.Capripox virus specific PCR confirmed the presence of LSD virus in the cell supernatant.We report LSDV isolation from field outbreaks using ECE and vero cell lines first time in WB.LSD cases of WB need urgent attention to formulate control strategies as the state shares international borders.

  PublisherDOI

• Spaceflight impacts xyloglucan oligosaccharide abundance in Arabidopsis thaliana root cell walls

  Life Sciences in Space Research · 2024-02-16 · 1 citations

  articleOpen accessCorresponding

  Over the course of more than a decade, space biology investigations have consistently indicated that cell wall remodeling occurs in a variety of spaceflight-grown plants. Here, we describe a mass spectrometric method to study the fundamental composition of xyloglucan, the most abundant hemicellulose in dicot cell walls, in space-grown plants. Four representative Arabidopsis root samples, from a previously conducted spaceflight experiment - Advanced Plant EXperiment - 04 (APEX-04), were used to investigate changes in xyloglucan oligosaccharides abundances in spaceflight-grown plants compared to ground controls. In situ localized enzymatic digestions and surface sampling mass spectrometry analysis provided spatial resolution of the changes in xyloglucan oligosaccharides abundances. Overall, the results showed that oligosaccharide XXLG/XLXG and XXFG branching patterns were more abundant in the lateral roots of spaceflight-grown plants, while XXXG, XLFG, and XLFG/XLFG were more abundant in the lateral roots of ground control plants. In the primary roots, XXFG had a higher abundance in ground controls than in spaceflight plants. This methodology of analyzing the basic components of the cell wall in this paper highlights two important findings. First, that are differences in the composition of xyloglucan oligosaccharides in spaceflight root cell walls compared to ground controls and, second, most of these differences are observed in the lateral roots. Thus, the methodology described in this paper provides insights into spaceflight cell wall modifications for future investigations.

  PublisherDOI

• Light has a principal role in the Arabidopsis transcriptomic response to the spaceflight environment

  npj Microgravity · 2024-08-06 · 3 citations

  articleOpen accessSenior author

  The Characterizing Arabidopsis Root Attractions (CARA) spaceflight experiment provides comparative transcriptome analyses of plants grown in both light and dark conditions within the same spaceflight. CARA compared three genotypes of Arabidopsis grown in ambient light and in the dark on board the International Space Station (ISS); Col-0, Ws, and phyD, a phytochrome D mutant in the Col-0 background. In all genotypes, leaves responded to spaceflight with a higher number of differentially expressed genes (DEGs) than root tips, and each genotype displayed distinct light / dark transcriptomic patterns that were unique to the spaceflight environment. The Col-0 leaves exhibited a substantial dichotomy, with ten-times as many spaceflight DEGs exhibited in light-grown plants versus dark-grown plants. Although the total number of DEGs in phyD leaves is not very different from Col-0, phyD altered the manner in which light-grown leaves respond to spaceflight, and many genes associated with the physiological adaptation of Col-0 to spaceflight were not represented. This result is in contrast to root tips, where a previous CARA study showed that phyD substantially reduced the number of DEGs. There were few DEGs, but a series of space-altered gene categories, common to genotypes and lighting conditions. This commonality indicates that key spaceflight genes are associated with signal transduction for light, defense, and oxidative stress responses. However, these key signaling pathways enriched from DEGs showed opposite regulatory direction in response to spaceflight under light and dark conditions, suggesting a complex interaction between light as a signal, and light-signaling genes in acclimation to spaceflight.

  PublisherOA PDFDOI

• GLARE: Discovering hidden patterns in spaceflight transcriptome using representation learning

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-06-06

  preprintOpen access

  ABSTRACT Spaceflight studies present novel insights into biological processes through exposure to stressors outside the evolutionary path of terrestrial organisms. Despite limited access to space environments, numerous transcriptomic datasets from spaceflight experiments are now available through NASA’s GeneLab data repository, which allows public access to these datasets, encouraging further analysis. While various computational pipelines and methods have been used to process these transcriptomic datasets, learning-model-driven analyses have yet to be applied to a broad array of such spaceflight-related datasets. In this study, we propose an open-source framework, GLARE: GeneLAb Representation learning pipelinE, which consists of training different representation learning approaches from manifold learning to self-supervised learning that enhances the performance of downstream analytical tasks such as pattern recognition. We illustrate the utility of GLARE by applying it to gene-level transcriptional values from the results of the CARA spaceflight experiment, an Arabidopsis root tip transcriptome dataset that spanned light, dark, and microgravity treatments. We show that GLARE not only substantiated the findings of the original study concerning cell wall remodeling but also revealed additional patterns of gene expression affected by the treatments, including evidence of hypoxia. This work suggests there is great potential to supplement the insights drawn from initial studies on spaceflight omics-level data through further machine-learning-enabled analyses.

  PublisherOA PDFDOI

• Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight

  Biology Direct · 2024-04-30 · 3 citations

  articleOpen accessSenior author

  BACKGROUND: The Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana, wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to explore specific space-altered methylation at single-molecule resolution to associate specific changes over large regions of spaceflight related genes. To date, tools of multiplexed targeted DNA methylation sequencing remain limited for plant genomes. RESULTS: To provide methylation data at single-molecule resolution, Flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation in genic regions of interest. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets with space-altered distributions of the proportion of methylated cytosines per molecule were identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and loss-of-function mutants of two of these genes (named as EMO1 and EMO2 for ELP2-regulated Methylation in Orbit 1 and 2) showed enhanced root growth rate. CONCLUSIONS: FENGC simplifies and reduces the cost of multiplexed, targeted, single-molecule profiling of methylation in plants, providing additional resolution along each DNA molecule that is not seen in population-based short-read data such as WGBS. This case study has revealed spaceflight-altered regional modification of cytosine methylation occurring within single DNA molecules of cell subpopulations, which were not identified by WGBS. The single-molecule survey by FENGC can lead to identification of novel functional genes. The newly identified EMO1 and EMO2 are root growth regulators which may be epigenetically involved in plant adaptation to spaceflight.

  PublisherOA PDFDOI

• Light has a principal role in the physiological adaptation of plants to the spaceflight environment

  Research Square · 2024-03-20

  preprintOpen access1st authorCorresponding
  PublisherOA PDFDOI

• Transcriptomic dynamics in the transition from ground to space are revealed by Virgin Galactic human-tended suborbital spaceflight

  npj Microgravity · 2023-12-20 · 3 citations

  articleOpen accessSenior author

  The Virgin Galactic Unity 22 mission conducted the first astronaut-manipulated suborbital spaceflight experiment. The experiment examined the operationalization of Kennedy Space Center Fixation Tubes (KFTs) as a generalizable approach to preserving biology at various phases of suborbital flight. The biology chosen for this experiment was Arabidopsis thaliana, ecotype Col-0, because of the plant history of spaceflight experimentation within KFTs and wealth of comparative data from orbital experiments. KFTs were deployed as a wearable device, a leg pouch attached to the astronaut, which proved to be operationally effective during the course of the flight. Data from the inflight samples indicated that the microgravity period of the flight elicited the strongest transcriptomic responses as measured by the number of genes showing differential expression. Genes related to reactive oxygen species and stress, as well as genes associated with orbital spaceflight, were highly represented among the suborbital gene expression profile. In addition, gene families largely unaffected in orbital spaceflight were diversely regulated in suborbital flight, including stress-responsive transcription factors. The human-tended suborbital experiment demonstrated the operational effectiveness of the KFTs in suborbital flight and suggests that rapid transcriptomic responses are a part of the temporal dynamics at the beginning of physiological adaptation to spaceflight.

  PublisherOA PDFDOI

Frequent coauthors

• Robert J. Ferl

  University of Florida

  157 shared

• Mingqi Zhou

  University of Florida

  21 shared

• Natasha Sng

  21 shared

• Agata K. Żupańska

  Search for Extraterrestrial Intelligence

  18 shared

• Jordan Callaham

  University of Florida

  15 shared

• Andrew C. Schuerger

  University of Florida

  14 shared

• Eric R. Schultz

  University of Minnesota

  11 shared

• Collin LeFrois

  9 shared