Rhonda L Bacher,
Associate Professor
About Rhonda L Bacher
Rhonda Bacher is an Associate Professor of Biostatistics at the University of Florida. She leads the Bacher Group in developing relevant statistical methods and computational software addressing important challenges in genomics, epigenomics, and biomedical research. Her research group is dedicated to ensuring accessibility of their software and contributing to the larger research community through open-source platforms. In their collaborations with scientists and clinicians, they use statistical models and machine learning to better understand how molecular phenotypes change in response to environmental stressors, age, and disease.
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Teaching Profile
Courses Taught
2020-2025
PHC7979 Advanced Research
2019-2020
PHC6601 Seminar in Contemporary Public Health Issues
2020,2022-2025
PHC6088 Statistical Analysis of Genetic Data
2020
HSC4913 Supervised Research Experience
2019-2020
PHC6946 Public Health Internship
2018-2019
PHC6937 Special Topics in Public Health
2023-2024
PHC6905 Independent Study
2023-2025
PHC7980 Research for Doctoral Dissertation
Research Profile
Areas of Interest
- Biostatistics
- Genomics
- Statistical Genetics
Publications
Academic Articles
2025
Inhibition of CD226 co-stimulation suppresses diabetes development in the NOD mouse by augmenting regulatory T cells and diminishing effector T cell function
Diabetologia.
68(2):397-418
[DOI] 10.1007/s00125-024-06329-8.
[PMID] 39636437.
2025
Serological markers of exocrine pancreatic function are differentially informative for distinguishing individuals progressing to type 1 diabetes.
BMJ open diabetes research & care.
13(1)
[DOI] 10.1136/bmjdrc-2024-004655.
[PMID] 39755561.
2024
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Briefings in Bioinformatics.
25(3)
[DOI] 10.1093/bib/bbae216.
[PMID] 38725155.
2024
Home-Based Digital Exercise Training Program to Improve Physical Function of Older Sepsis Survivors: Protocol of the HEAL Sepsis Randomized Clinical Trial.
JMIR research protocols.
13
[DOI] 10.2196/60270.
[PMID] 39418096.
2024
Inhibition of CD226 Co-Stimulation Suppresses Diabetes Development in the NOD Mouse by Augmenting Tregs and Diminishing Effector T Cell Function.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2024.07.16.603756.
[PMID] 39071293.
2024
Serum exocrine pancreas enzymes are biomarkers of immunotherapy response in new-onset type 1 diabetes.
Frontiers in endocrinology.
15
[DOI] 10.3389/fendo.2024.1497373.
[PMID] 39678192.
2024
The post-septic peripheral myeloid compartment reveals unexpected diversity in myeloid-derived suppressor cells.
Frontiers in immunology.
15
[DOI] 10.3389/fimmu.2024.1355405.
[PMID] 38720891.
2024
Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroids and its toxicological implications.
Toxicology letters.
401:125-138
[DOI] 10.1016/j.toxlet.2024.10.004.
[PMID] 39368564.
2024
TRANSCRIPTOMIC DIFFERENCES IN PERIPHERAL MONOCYTE POPULATIONS IN SEPTIC PATIENTS BASED ON OUTCOME.
Shock (Augusta, Ga.).
62(2):208-216
[DOI] 10.1097/SHK.0000000000002379.
[PMID] 38713581.
2024
Unique lymphocyte transcriptomic profiles in septic patients with chronic critical illness.
Frontiers in immunology.
15
[DOI] 10.3389/fimmu.2024.1478471.
[PMID] 39691721.
2023
Analysis of Single-Cell RNA-seq Data.
Methods in molecular biology (Clifton, N.J.).
2629:95-114
[DOI] 10.1007/978-1-0716-2986-4_6.
[PMID] 36929075.
2023
Biomaterials-based nanoparticles conjugated to regulatory T cells provide a modular system for localized delivery of pharmacotherapeutic agents.
Journal of biomedical materials research. Part A.
111(2):185-197
[DOI] 10.1002/jbm.a.37442.
[PMID] 36082558.
2023
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.12.18.572214.
[PMID] 38187768.
2023
Human immune phenotyping reveals accelerated aging in type 1 diabetes
JCI Insight.
8(17)
[DOI] 10.1172/jci.insight.170767.
[PMID] 37498686.
2023
Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.12.19.572477.
[PMID] 38187622.
2023
Leveraging remeasured samples in biomedical studies
Nature Computational Science.
3(8):669-670
[DOI] 10.1038/s43588-023-00491-6.
2023
Responders to low-dose ATG induce CD4+ T cell exhaustion in type 1 diabetes
JCI Insight.
8(16)
[DOI] 10.1172/jci.insight.161812.
[PMID] 37432736.
2022
Data-driven assessment of dimension reduction quality for single-cell omics data.
Patterns (New York, N.Y.).
3(3)
[DOI] 10.1016/j.patter.2022.100465.
[PMID] 35510193.
2022
Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization
Nucleic Acids Research.
50(2):e12-e12
[DOI] 10.1093/nar/gkab1071.
[PMID] 34850101.
2022
Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients.
JAMA network open.
5(7)
[DOI] 10.1001/jamanetworkopen.2022.21520.
[PMID] 35819783.
2021
A Novel Single Cell RNA-seq Analysis of Non-Myeloid Circulating Cells in Late Sepsis.
Frontiers in immunology.
12
[DOI] 10.3389/fimmu.2021.696536.
[PMID] 34484194.
2021
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells
Nature Communications.
12(1)
[DOI] 10.1038/s41467-021-26091-4.
[PMID] 34599187.
2021
Chronic Critical Illness Elicits a Unique Circulating Leukocyte Transcriptome in Sepsis Survivors.
Journal of clinical medicine.
10(15)
[DOI] 10.3390/jcm10153211.
[PMID] 34361995.
2021
Exocrine Pancreatic Enzymes Are a Serological Biomarker for Type 1 Diabetes Staging and Pancreas Size.
Diabetes.
70(4):944-954
[DOI] 10.2337/db20-0995.
[PMID] 33441381.
2021
Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis.
Diabetes.
70(4):932-943
[DOI] 10.2337/db20-0937.
[PMID] 33419759.
2021
Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation
Journal of Clinical Investigation.
131(21)
[DOI] 10.1172/jci144833.
2021
Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
Bioinformatics.
37(24):4857-4859
[DOI] 10.1093/bioinformatics/btab438.
[PMID] 34125875.
2021
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data.
Bioinformatics (Oxford, England).
37(22):4123-4128
[DOI] 10.1093/bioinformatics/btab450.
[PMID] 34146085.
2021
Overlapping but Disparate Inflammatory and Immunosuppressive Responses to SARS-CoV-2 and Bacterial Sepsis: An Immunological Time Course Analysis.
Frontiers in immunology.
12
[DOI] 10.3389/fimmu.2021.792448.
[PMID] 34956225.
2021
Single-Cell RNA-seq of Human Myeloid-Derived Suppressor Cells in Late Sepsis Reveals Multiple Subsets With Unique Transcriptional Responses: A Pilot Study.
Shock (Augusta, Ga.).
55(5):587-595
[DOI] 10.1097/SHK.0000000000001671.
[PMID] 33021571.
2021
TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes.
Cell.
184(3):827-839.e14
[DOI] 10.1016/j.cell.2020.11.035.
[PMID] 33545036.
2020
Human Regulatory T Cells From Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood.
Frontiers in immunology.
11
[DOI] 10.3389/fimmu.2020.00611.
[PMID] 32351504.
2020
Identification of Unique mRNA and miRNA Expression Patterns in Bone Marrow Hematopoietic Stem and Progenitor Cells After Trauma in Older Adults.
Frontiers in immunology.
11
[DOI] 10.3389/fimmu.2020.01289.
[PMID] 32670283.
2020
Insulin-Like Growth Factor Dysregulation Both Preceding and Following Type 1 Diabetes Diagnosis.
Diabetes.
69(3):413-423
[DOI] 10.2337/db19-0942.
[PMID] 31826866.
2020
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
PLOS ONE.
15(9)
[DOI] 10.1371/journal.pone.0239711.
[PMID] 32986734.
2019
An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells.
Cell reports.
28(9):2247-2255.e5
[DOI] 10.1016/j.celrep.2019.07.090.
[PMID] 31461642.
2019
Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
PLOS Computational Biology.
15(12)
[DOI] 10.1371/journal.pcbi.1007543.
[PMID] 31815944.
2019
Normalization for Single-Cell RNA-Seq Data Analysis.
Methods in molecular biology (Clifton, N.J.).
1935:11-23
[DOI] 10.1007/978-1-4939-9057-3_2.
[PMID] 30758817.
2018
Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes.
Developmental biology.
439(1):30-41
[DOI] 10.1016/j.ydbio.2018.04.007.
[PMID] 29678445.
2018
Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.
BMC bioinformatics.
19(1)
[DOI] 10.1186/s12859-018-2405-x.
[PMID] 30326833.
2017
An Examination of Brain Abnormalities and Mobility in Individuals with Mild Cognitive Impairment and Alzheimer’s Disease
Frontiers in Aging Neuroscience.
9
2017
SCnorm: robust normalization of single-cell RNA-seq data
Nature Methods.
14(6):584-586
[DOI] 10.1038/nmeth.4263.
[PMID] 28418000.
2017
SCnorm: robust normalization of single-cell RNA-seq data
.
14(6):584-586
2017
Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
PLoS Biology.
15(12)
2017
Species-Specific Developmental Timing is Maintained by Pluripotent Stem Cells Ex Utero
.
423(2):101-110
2017
Statistical Methods for Latent Class Quantitative Trait Loci Mapping
Genetics.
208(2)
2016
Design and computational analysis for single-cell RNA-sequencing experiments
Genome Biology.
17
Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization
.
[DOI] 10.1101/2020.10.05.326553.
methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
.
[DOI] 10.1101/2020.11.13.382465.
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data
.
[DOI] 10.1101/2020.10.28.359901.
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
.
[DOI] 10.1101/764191.
SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data
.
[DOI] 10.1101/090167.
Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments
.
[DOI] 10.1101/185413.
Grants
Sep 2024
ACTIVE
Artificial Intelligence Passport for Biomedical Research (AIPassportBMR ): Digital Experiential Learning Community for Upskilling in Artificial Intelligence for Biomedical, Behavioral and Clinical Research
Role: Project Manager
Funding: NATL INST OF HLTH NIGMS
Sep 2024
ACTIVE
Restoration of immune regulation in type 1 diabetes through the synergistic action of insulin-like growth factor-1 and interleukin-2
Role: Co-Investigator
Funding: BREAKTHROUGH T1D – formerly JDRF Intl
Dec 2023
ACTIVE
Establishing immune, endocrine, and exocrine signatures of type 1 diabetes progression in longitudinally sampled peripheral blood from the ENDIA nested case control study
Role: Co-Investigator
Funding: BREAKTHROUGH T1D – formerly JDRF Intl
via HELMSLEY CHARITABLE TRUST, LEONA & HARRY
Jun 2023
ACTIVE
Immune Function and the Progression to Type 1 Diabetes
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Feb 2023
ACTIVE
The CD226 costimulatory axis in type 1 diabetes
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDDK
Sep 2022
ACTIVE
Resolving single-cell analysis challenges via data-driven decision frameworks and novel statistical methods
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Aug 2022
ACTIVE
Histone fold Mutations in Cancer Pathogenesis
Role: Faculty
Funding: NATL INST OF HLTH NCI
Mar 2022
– Feb 2025
Home-based digital exercise training program to improve physical function of older sepsis survivorsHEAL Sepsis Trial
Role: Co-Investigator
Funding: NATL INST OF HLTH NIA
Feb 2022
ACTIVE
CRISPR screens of population relevant genes governing toxicant resilience
Role: Co-Investigator
Funding: NATL INST OF HLTH NIEHS
Jun 2021
ACTIVE
Pathological Myeloid Activation After Sepsis and Trauma
Role: Co-Investigator
Funding: NATL INST OF HLTH NIGMS
May 2021
ACTIVE
Dysfunctional Myelopoiesis and Myeloid-Derived Suppressor Cells in Sepsis Pathobiology
Role: Co-Investigator
Funding: NATL INST OF HLTH NIGMS
Jan 2021
– Dec 2024
Developing a Novel PROTAC-Based NR4A1 Degrader for Breast Cancer Therapy
Role: Co-Investigator
Funding: US ARMY MED RES ACQUISITION
Aug 2019
ACTIVE
Engineering a Human Microphysiological System for the Characterization of Islet-Immune Interactions
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDDK
Aug 2019
– Jul 2021
Engineering a Human Microphysiological System for the Characterization of Islet-Immune Interactions
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDDK
Jun 2019
– Aug 2020
Single cell sequencing for islet-reactive T cell clonotype and transcript signatures
Role: Co-Investigator
Funding: BREAKTHROUGH T1D – formerly JDRF Intl
Apr 2019
– Mar 2020
A Composite Serological Risk Score to Predict Type 1 Diabetes Progression and Clinical Diagnosis
Role: Co-Investigator
Funding: BREAKTHROUGH T1D – formerly JDRF Intl
Aug 2018
– Aug 2019
Uncovering the Life Clock of Red Blood Cells Using Single-Cell Analysis
Role: Principal Investigator
Funding: JAYNE KOSKINAS TED GIOVANIS FOU
Jun 2018
– May 2023
Immune Function and the Progression to Type 1 Diabetes
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Jun 2018
– May 2022
Characterization of SLE-susceptibility loci on mouse chromosome 1
Role: Project Manager
Funding: NATL INST OF HLTH NIAID
Aug 2016
– Aug 2022
Development of Brassica as a low dose radiation biosensor
Role: Co-Investigator
Funding: DEFENSE THREAT REDUCTION AGENCY
Education
PhD/Statistics
2017
·
University of Wisconsin-Madison
BS/Mathematics
2012
·
University of Florida
BS/Statistics
2012
·
University of Florida
Contact Details
Phones:
- Business:
- (352) 294-5914
Emails:
- Business:
- rbacher@ufl.edu
Addresses:
- Business Mailing:
-
P.O. BOX 117450
GAINESVILLE FL 326110001 - Business Street:
-
2004 MOWRY RD
GAINESVILLE FL 32610