Rhonda L Bacher

Rhonda L Bacher,

Assistant Professor

Department: PHHP-COM BIOSTATISTICS
Business Phone: (352) 294-5914
Business Email: rbacher@ufl.edu

About Rhonda L Bacher

Teaching Profile

Courses Taught
2020-2023
PHC7979 Advanced Research
2019-2020
PHC6601 Seminar in Contemporary Public Health Issues
2020,2022
PHC6088 Statistical Analysis of Genetic Data
2020
HSC4913 Supervised Resrch Exp
2019-2020
PHC6946 Public Health Internship
2018-2019
PHC6937 Special Topics in Public Health

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0001-5787-476X

Areas of Interest
  • Biostatistics
  • Genomics
  • Statistical Genetics

Publications

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):4123-8 [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.
Experimental design for large scale omic studies
. [DOI] 10.1101/532580.
Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation
. [DOI] 10.1101/2022.11.08.515732.
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 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
Aug 2022 ACTIVE
Pathologic Myeloid Activation in Pediatric Burn Injury
Role: Other
Funding: NATL INST OF HLTH NICHD
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 ACTIVE
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

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