Rhonda L Bacher,
Assistant Professor
About Rhonda L Bacher
Related Links:
Teaching Profile
Courses Taught
2020-2024
PHC7979 Advanced Research
2019-2020
PHC6601 Seminar in Contemporary Public Health Issues
2020,2022-2024
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
2023-2024
PHC7980 Research for Doctoral Dissertation
Research Profile
Open Researcher and Contributor ID (ORCID)
0000-0001-5787-476X
Areas of Interest
- Biostatistics
- Genomics
- Statistical Genetics
Publications
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
.
14(6):584-586
2017
SCnorm: robust normalization of single-cell RNA-seq data
Nature Methods.
14(6):584-586
[DOI] 10.1038/nmeth.4263.
[PMID] 28418000.
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
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: JDRF
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
ACTIVE
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
ACTIVE
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: JDRF
Apr 2019
– Mar 2020
A Composite Serological Risk Score to Predict Type 1 Diabetes Progression and Clinical Diagnosis
Role: Co-Investigator
Funding: JDRF
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
2017
·
University of Wisconsin-Madison
BS
2008
·
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