About

Professor Rhonda Bacher leads a research group focused on developing computational methods and software for analyzing genomic data, with a particular emphasis on single-cell data and high-parameter immune data. Her group includes graduate students and research assistants working on advancing accessibility and interpretability of computational tools for single-cell -omics data, as well as developing models for identifying marker genes and genetic perturbations in complex experimental designs. She actively mentors students at various levels, including master's, PhD, and undergraduate researchers, fostering their development in biostatistics, biomedical sciences, and computational biology. Professor Bacher encourages prospective graduate students interested in genomic data analysis to contact her, noting the requirement for admission to the Department of Biostatistics PhD program at the University of Florida.

Research topics

• Biology
• Immunology
• Genetics
• Medicine
• Internal medicine
• Cell biology
• Pathology
• Endocrinology
• Cancer research

Selected publications

• Divergent chromatin remodeling trajectories in CD66b ⁺ MDSCs distinguishes recovery from chronic critical illness after sepsis

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-23

  articleOpen access

  ABSTRACT Sepsis remains a leading cause of morbidity and mortality worldwide, with survivors often following divergent trajectories: rapid recovery (RAP) or progression to chronic critical illness (CCI). CCI is characterized by persistent organ dysfunction, recurrent infections, and immune dysregulation. Myeloid-derived suppressor cells (MDSCs), which expand in number after sepsis, are implicated in this maladaptive state, yet their epigenetic regulation remains poorly understood. Here, we applied an Omni-ATAC protocol optimized to profile chromatin accessibility in CD66b + MDSCs from healthy participants (HPs) and sepsis patients across time points (day 4, day 14–21, and 6 months) and clinical outcomes (RAP, CCI, and Deceased). Dimensionality reduction analyses of genome-wide chromatin accessibility showed clear separation of sepsis and HP samples. Furthermore, these analyses revealed distinct trajectories post-sepsis diagnosis: RAP samples progressively regained HP-like chromatin states, whereas CCI samples remained epigenetically “locked” in aberrant states. Differential accessibility analysis identified thousands of promoter regions with altered accessibility, including immune checkpoint and inflammatory genes (e.g., ARG1, CD274, S100A8 / 9 ). Pathway analyses predicted global suppression of immune, metabolic, and chromatin remodeling programs in CCI, contrasting with restoration in RAP. These findings from patient-derived CD66b + MDSCs suggest that epigenetic chromatin remodeling underlies divergent recovery trajectories and highlight chromatin-modifying pathways as potential therapeutic targets to restore immune competence in sepsis patients with CCI.

  PublisherOA PDFDOI

• C-754-01. Burn Injury Drives Biphasic Macrophage Immune Reprogramming Through Locus-Specific Epigenetic Remodeling

  Journal of Burn Care & Research · 2026-03-01

  articleOpen access

  Abstract Introduction Severe burn injury is followed by immune dysfunction marked by early hyperinflammation and later immunosuppression. The underlying epigenetic mechanisms remain incompletely understood. We hypothesized that burn injury induces coordinated chromatin remodeling in macrophages that governs this biphasic immune phenotype. Methods Female C57BL/6 mice (n = 6) underwent 20% TBSA full-thickness scald injury or sham procedure. Splenic F4/80+ macrophages were isolated on days 2, 9, and 14 post-injury. Cytokine secretion was measured following TLR2 (peptidoglycan) or TLR4 (LPS) stimulation. Targeted transcriptomic profiling of >1300 immune/metabolic genes was performed by nanoString. Epigenetic remodeling of 180 immune loci was assessed using single-molecule Methyltransferase accessibility protocol for individual templates combined with flap-enabled next-generation capture (MAPit-FENGC) to simultaneously measure DNA methylation and chromatin accessibility. Results Macrophages from burn mice demonstrated a biphasic trajectory. At day 2, TLR-stimulated IL-6, MCP-1, and TNFα secretion were increased versus sham (p<.05). By day 14, MCP-1 and TNFα responses were suppressed, while IL-10 secretion increased (p<.05). Transcriptomic profiling confirmed dynamic regulation of Il10, Socs3, and cell-cycle genes, with persistent repression of Nfkb1, Traf6, and Stat3. MAPit-FENGC revealed early chromatin accessibility gains at proinflammatory loci (Cxcl15, Ccl7) and progressive repression of Stat3, Tgfb1, and Nfkb1 promoters. Nucleosome repositioning at the Il10 promoter preceded transcriptional upregulation, suggesting epigenetic priming for tolerance. Conclusions Burn injury induces temporally coordinated transcriptomic and epigenetic remodeling in macrophages, shifting from hyperinflammation to immune tolerance. Locus-specific chromatin remodeling underlies this transition, highlighting mechanistic drivers of post-burn immune paralysis. Applicability of Research to Practice These findings identify macrophage epigenetic reprogramming as a targetable mechanism of burn-induced immune dysfunction. Therapeutic interventions that recalibrate macrophage chromatin states may restore balanced immunity and reduce infection risk in burn survivors. Funding for the study Supported by NIH NIGMS.

  PublisherOA PDFDOI

• scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-11

  articleOpen accessSenior authorCorresponding

  Single-cell RNA-seq studies of viral infection are limited by sparse viral reads, under-labeled infected cells, and bystander responses that confound differential expression (DE) analysis. We introduce scDEcrypter, a penalized two-way mixture model that leverages partial labels for infection status and additional variables such as cell type. Our approach employs data-splitting to avoid double-dipping and enables fast, likelihood-based inference for DE analysis. Through simulations and applications on two different viral infection datasets, scDEcrypter demonstrated improved recovery of infected cell states and identified more biologically coherent infection-associated genes and enriched pathways.

  PublisherOA PDFDOI

• Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes

  Cell Reports · 2026-03-23

  articleOpen access

  This study explores the inflammatory response observed in the pancreas and pancreatic lymph nodes (pLNs) during the natural history of type 1 diabetes (T1D). Using multicell-resolution spatial transcriptomics (ST), we profile individuals without diabetes (ND), at-risk autoantibody-positive (AAb+) individuals, and T1D donors. In the T1D pancreas, we observed global upregulation of inflammation-associated transcripts, including REG family genes, C3, SOD2, and OLFM4. In the T1D pLN, LTB was significantly upregulated within the lymphoid follicles. Using an orthogonal subcellular-resolution ST platform on an independent donor set, we identified follicular B cells as the primary source of LTB in the pLN and observed increased LTB expression in lymphocytes in insulitic lesions proximal to CCL19/CCL21-expressing endothelium. Collectively, these findings highlight lymphotoxin-β and downstream chemokine signatures in the pancreatic lymphatics as well as within the insulitic lesion, which can inform future therapeutic interventions.

  PublisherDOI

• Physiologically relevant 3D CRISPR screening enhances mechanistic insight into chemical toxicity compared to 2D screening

  Toxicology · 2026-02-03 · 1 citations

  articleOpen access

  CRISPR-based approaches can complement other genomics-based toxicology studies by enabling causal interrogation of gene function modulating chemical-induced toxicity. Moreover, CRISPR screens enable scalable and systematic identification of functional pathways involved in cellular response to chemical exposure. Cell-based functional toxicogenomics approaches using CRISPR provide a potential powerful tool for the development of mechanism-driven new approach methodologies (NAMs) for toxicodynamic and toxicokinetic hazard screening to enable more effective risk assessment. To improve the physiological relevance of in vitro functional toxicogenomics, we developed a three-dimensional (3D) CRISPR screening platform using HepG2/C3A spheroids cultured in a continuously rotating bioreactor (ClinoStar). We evaluated the potential utility of a 3D CRISPR screen as compared to conventional 2D screen using a custom CRISPR sgRNA library representing common loss-of-function genetic variants in the human population and exposure to the well characterized DNA damaging toxicant, doxorubicin. The 3D platform identified more genes and pathways in which variants have previously been associated with doxorubicin toxicity in clinical studies than the 2D system. These results support the utility of 3D CRISPR screening to identify physiologically relevant genetic determinants underlying chemical toxicity.

  PublisherDOI

• Identification of functional genetic components modulating toxicity response to PFOS using genome-wide CRISPR screens in HepG2/C3A cells

  Archives of Toxicology · 2026-01-27 · 1 citations

  articleOpen access

  Abstract Perfluorooctane sulfonate (PFOS) poses significant health and environmental risks due to its persistence and widespread use and has been linked to various adverse outcomes, such as liver toxicity. Although the molecular responses and toxicity effects of PFOS exposure have been extensively studied, considerable uncertainty remains regarding the causal mechanisms leading to PFOS-associated adverse effects. To help bridge this gap, we conducted CRISPR screens in HepG2/C3A human liver cells exposed to IC 25 (170 µM) of PFOS to identify genes and pathways influencing PFOS-induced cytotoxicity. Using a genome-wide CRISPR knockout library targeting 18,819 genes, we identified 340 candidate genes that modulate PFOS-induced cytotoxicity when genetically disrupted (189 gene disruptions increased sensitivity and 151 gene disruptions increased resistance). From these candidate genes, we individually disrupted two candidate genes, SLC6A9 which encodes the glycine transporter GlyT1, and CPSF2 , and confirmed increased resistance to PFOS exposure. Further, molecular docking analysis predicts that PFOS directly binds to GlyT1 and functional inhibition of GlyT1 also increases resistance to PFOS exposure. Gene-Disease outcome association analysis using the Comparative Toxicogenomics Database (CTD) indicated an enrichment of candidate genes associated with cancer-related and liver disease phenotypes. KEGG and STRING enrichment analyses found over representation of several biological pathways including DNA damage response and cell cycle. Lastly, cross-species conservation analysis using the top two validated gene targets found that their pathways were highly conserved in several environmentally relevant species. These findings provide new mechanistic and functional insights into PFOS-induced cytotoxicity, highlight potential molecular targets for toxicity mitigation, and establish a foundation for cross-species toxicogenomic modeling of PFOS health effects.

  PublisherOA PDFDOI

• Physiologically Relevant 3D CRISPR Screening Enhances Mechanistic Insight into Chemical Toxicity Compared to 2D Screening

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-19

  articleOpen access

  Abstract Many omics-based approaches in toxicology research primarily rely on correlative data, often lacking functional relationships or causal links between genotypes and phenotypes. CRISPR-based approaches can overcome this limitation by establishing direct causal connections between genes and toxicological phenotypes. Moreover, CRISPR screens enable scalable and systematic interrogation of gene function and associated mechanisms following chemical exposure, predominantly using in vitro models. In line with the paradigm of new approach methodologies (NAMs) in toxicology research, CRISPR screens hold promise to provide an in vitro cell-based functional toxicogenomics approach. One of the main limitations of conventional in vitro assays is their compromised physiological relevance to humans due to their inability to fully recapitulate in vivo physiology. To improve the functional and physiological relevance of the toxicogenomics approach, we developed a 3D CRISPR screening system using HepG2/C3A spheroids generated and cultivated in a continuously rotating bioreactor (ClinoStar). We first performed time-course 3D CRISPR screens to identify genes that confer growth disadvantage or advantage, influencing spheroid development compared to 2D cultures. We then applied this approach to a chemical toxicity study using doxorubicin, comparing the performance of the 3D and 2D systems in identifying chemical-specific mechanisms. The results showed that the 3D system captured more candidate genetic determinants and biological pathways related to DNA damage processes—a known toxicity mechanism of doxorubicin—demonstrating improved performance in identifying chemical-specific pathways over the 2D counterpart. In our screens, we employed custom CRISPR sgRNA libraries representing common human loss-of-function genetic variants (mean allele frequency > 0.1% in all individuals catalogued in the genome aggregation database), which potentially affect toxicity responses. By comparing our CRISPR screen results with previously reported genetic associations for doxorubicin response, we found that the 3D system identified more known associated genes than the 2D system. Together, the 3D CRISPR screening system demonstrated its feasibility and utility for physiologically relevant functional toxicogenomics. This platform enables in vitro NAMs, by providing a scalable and effective approach to identify causal genetic determinants and biological pathways that modulate chemical-induced toxicity.

  PublisherDOI

• Interpretable trajectory inference with single-cell linear adaptive negative-binomial expression (scLANE) testing

  Nucleic Acids Research · 2025-12-19

  articleOpen accessSenior author

  The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to identify genes exhibiting changes in expression significantly associated with progression through the trajectory. While a few techniques for trajectory differential expression exist, most rely on generalized additive models to account for the inherent nonlinearity of gene expression dynamics. As such, the results can be difficult to interpret, and biological conclusions rely on subjective visual inspections. To address this challenge, we propose single-cell linear adaptive negative-binomial expression (scLANE) testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several simulation scenarios, we applied it to a set of diverse biological datasets and demonstrated its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods. scLANE is freely available as an R package through Bioconductor at https://bioconductor.org/packages/scLANE/, and is also accessible via a web server leveraging high-performance computing resources at https://sclane.rc.ufl.edu/.

  PublisherDOI

• Chromatin Remodeling and Transcriptional Silencing Define the Dynamic Innate Immune Response of Tissue Resident Macrophages After Burn Injury

  Shock · 2025-10-22 · 1 citations

  article

  Severe burn injury induces prolonged immune dysfunction, but the underlying molecular mechanisms remain poorly defined. We hypothesized that burn injury causes epigenetic and transcriptional training of innate immune cells. Splenic F4/80⁺ macrophages were isolated from mice at 2, 9, and 14 days after 20% total body surface area contact burn. Targeted transcriptomics and chromatin profiling revealed a biphasic response: early transcriptional silencing of inflammatory genes (e.g., Stat3 , Traf6 , and Nfkb1 ), followed by increased accessibility and expression of anti-inflammatory loci ( Il-10 and Socs3 ). Metabolic genes showed persistent suppression of mitochondrial and oxidative phosphorylation programs. Canonical pathway analysis indicated early interleukin-10 signaling activation and long-term repression of classical macrophage activation. Chromatin remodeling included nucleosome repositioning events, supporting dynamic, and locus-specific regulation. These findings challenge the notion that burn-induced immune suppression is solely due to systemic inflammation and instead suggest durable, epigenetically programmed alterations in macrophage function.

  PublisherDOI

• Serological markers of exocrine pancreatic function are differentially informative for distinguishing individuals progressing to type 1 diabetes

  BMJ Open Diabetes Research & Care · 2025-01-01

  articleOpen access

  INTRODUCTION: Altered serum levels of growth hormones, adipokines, and exocrine pancreas enzymes have been individually linked with type 1 diabetes (T1D). We collectively evaluated seven such biomarkers, combined with islet autoantibodies (AAb) and genetic risk score (GRS2), for their utility in predicting AAb/T1D status. RESEARCH DESIGN AND METHODS: Cross-sectional serum samples (n=154 T1D, n=56 1AAb+, n=77 ≥2AAb+, n=256 AAb-) were assessed for IGF1, IGF2, adiponectin, leptin, amylase, lipase, and trypsinogen (n=543, age range 2.7-30.0 years) using random forest modeling. RESULTS: GRS2, age, lipase, trypsinogen, and AAb against ZnT8, GAD65, and insulin were the most informative markers. Notably, these variables were differentially informative according to AAb/T1D status. Higher GRS2 (p<0.001) and lower lipase levels (p=0.002) favored ≥2AAb+ versus AAb- classification. AAb against ZnT8 (p<0.01), GAD65 (p=0.021), or insulin (p=0.01) each independently favored ≥2AAb+ versus 1AAb+ classification. Reduced trypsinogen (p<0.001) and increased lipase levels (p<0.001) favored recent-onset T1D versus ≥2AAb+ classification. CONCLUSIONS: Among the serological markers tested, lipase and trypsinogen levels were the most informative for differentiating among clinical groups, with the utility of each enzyme varying according to GRS2 and AAb/T1D status. These data support exocrine pancreas enzymes as candidates for longitudinal follow-up.

  PublisherOA PDFDOI

Recent grants

• Resolving single-cell analysis challenges via data-driven decision frameworks and novel statistical methods

  NIH · $1.5M · 2022–2027

Frequent coauthors

• Todd M. Brusko

  38 shared

• Philip A. Efron

  University of Florida

  34 shared

• Maigan A. Brusko

  Florida College

  31 shared

• Lyle L. Moldawer

  Florida College

  29 shared

• Michael P. Kladde

  University of Florida

  28 shared

• Dijoia B. Darden

  Florida College

  27 shared

• Tyler J. Loftus

  University of Florida

  27 shared

• Marvin L. Dirain

  Florida College

  26 shared

Education

• PhD, Statistics

  University of Wisconsin-Madison

  2017