Rhonda L. Bacher

发表

Chronic Critical Illness Elicits a Unique Circulating Leukocyte Transcriptome in Sepsis Survivors

H. Baker, L. Moldawer, P. Efron, 2021, Journal of clinical medicine.

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics

Brian E. McIntosh, Christina Kendziorski, Cara Argus, 2019, PLoS Comput. Biol..

Species-specific developmental timing is maintained by pluripotent stem cells ex utero.

Brian E. McIntosh, Jennifer M. Bolin, Ron Stewart, 2017, Developmental biology.

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells

R. Stewart, Rhonda Bacher, Li-Fang Chu, 2019, Cell reports.

Exocrine Pancreatic Enzymes Are a Serological Biomarker for Type 1 Diabetes Staging and Pancreas Size

Rhonda Bacher, D. Perry, M. Atkinson, 2021, Diabetes.

Overlapping but Disparate Inflammatory and Immunosuppressive Responses to SARS-CoV-2 and Bacterial Sepsis: An Immunological Time Course Analysis

R. Hotchkiss, Rhonda Bacher, L. Moldawer, 2021, Frontiers in Immunology.

Design and computational analysis of single-cell RNA-sequencing experiments

Rhonda Bacher, C. Kendziorski, Rhonda L. Bacher, 2016, Genome Biology.

SCnorm: robust normalization of single-cell RNA-seq data

M. Newton, R. Stewart, A. Gasch, 2017, Nature Methods.

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

Megan N. McClean, Christina Kendziorski, Stephen R Quake, 2017, PLoS biology.

Human Regulatory T Cells From Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood

Rhonda Bacher, H. Baker, M. C. López, 2020, Frontiers in Immunology.

Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

Megan N. McClean, S. Quake, A. Gasch, 2017, bioRxiv.

A Novel Single Cell RNA-seq Analysis of Non-Myeloid Circulating Cells in Late Sepsis

Marie-Pierre L. Gauthier, Rhonda Bacher, L. Moldawer, 2021, Frontiers in Immunology.

Binned multinomial logistic regression for integrative cell type annotation

Rhonda Bacher, Aaron J. Molstad, Keshav Motwani, 2021, 2111.12149.

Genetic Drivers of Pancreatic Islet Function

B. Yandell, G. Churchill, K. Broman, 2018, Genetics.

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

R. Stewart, Li-Fang Chu, Ning Leng, 2018, BMC Bioinformatics.

Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation

Jeremy R. B. Newman, Marie-Pierre L. Gauthier, A. Conesa, 2022, bioRxiv.

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data

Rhonda Bacher, Parker Knight, Carolina E. Pardo, 2020, bioRxiv.

Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation

Jeremy R. B. Newman, Marie-Pierre L. Gauthier, A. Conesa, 2022, bioRxiv.

Human immune phenotyping reveals accelerated aging in type 1 diabetes

C. Mathews, P. Concannon, D. Perry, 2023, bioRxiv.

CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells

Andrew P. Voigt, S. Zheng, Rhonda Bacher, 2021, Nature Communications.

Single-Cell RNA-seq of Human Myeloid-Derived Suppressor Cells in Late Sepsis Reveals Multiple Subsets With Unique Transcriptional Responses: A Pilot Study

Marie-Pierre L. Gauthier, Rhonda Bacher, L. Moldawer, 2020, Shock.

Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes.

James A. Thomson, Li-Fang Chu, Ron Stewart, 2018, Developmental biology.

Identification of direct transcriptional targets of NFATC2 that promote β-cell proliferation.

S. Keleş, Rhonda Bacher, C. Kendziorski, 2021, The Journal of clinical investigation.

Insulin-Like Growth Factor Dysregulation Both Preceding and Following Type 1 Diabetes Diagnosis

W. Hagopian, Rhonda Bacher, M. Atkinson, 2019, Diabetes.

Experimental design for large scale omic studies

Lauren M. McIntyre, Funda Ogut, Jeremy R. B. Newman, 2019, bioRxiv.

Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis

D. Perry, M. Atkinson, S. Chamala, 2021, Diabetes.

Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization

James A. Thomson, Christina Kendziorski, Rhonda Bacher, 2020, bioRxiv.

Analysis of Single-Cell RNA-seq Data.

Rhonda L. Bacher, Xiaoru Dong, 2023, Methods in molecular biology.

Biomaterials‐based nanoparticles conjugated to regulatory T cells provide a modular system for localized delivery of pharmacotherapeutic agents

Rhonda Bacher, B. Keselowsky, A. Posgai, 2022, Journal of biomedical materials research. Part A.

Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients

Rhonda Bacher, L. Moldawer, T. Sweeney, 2022, JAMA network open.

Identification of Unique mRNA and miRNA Expression Patterns in Bone Marrow Hematopoietic Stem and Progenitor Cells After Trauma in Older Adults

B. Brumback, H. Baker, P. Efron, 2020, Frontiers in Immunology.

SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data

Ning Leng, James A. Thomson, Christina Kendziorski, 2016, bioRxiv.

Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis

Bret Duffin, James A. Thomson, Christina Kendziorski, 2019, PloS one.

TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes

Aaron M. Rosenfeld, K. Kaestner, M. Betts, 2021, Cell.

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data

Christina Kendziorski, Rhonda Bacher, Zijian Ni, 2020, bioRxiv.

Statistical Methods for Latent Class Quantitative Trait Loci Mapping

C. Kendziorski, A. Attie, M. Keller, 2017, Genetics.

Normalization for Single-Cell RNA-Seq Data Analysis.

Rhonda Bacher, Rhonda L. Bacher, 2019, Methods in molecular biology.

Responders to low-dose ATG induce CD4+ T cell exhaustion in type 1 diabetes

P. Linsley, C. Mathews, V. Gersuk, 2023, JCI insight.

Responders to low-dose ATG induce CD4 + T cell exhaustion in type 1 diabetes

P. Linsley, C. Mathews, V. Gersuk, 2023 .

Human immune phenotyping reveals accelerated aging in type 1 diabetes

C. Wasserfall, D. Schatz, L. Jacobsen, 2023, JCI insight.

Design and computational analysis of single-cell RNA-sequencing experiments

Rhonda Bacher, C. Kendziorski, Rhonda L. Bacher, 2016, Genome Biology.

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

Ning Leng, James A. Thomson, Christina Kendziorski, 2018, BMC Bioinformatics.

Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments

R. Stewart, Li-Fang Chu, Ning Leng, 2017, bioRxiv.

The post-septic peripheral myeloid compartment reveals unexpected diversity in myeloid-derived suppressor cells

Marie-Pierre L. Gauthier, P. Efron, J. Rincon, 2024, medRxiv.

Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference

Maigan A. Brusko, Rhonda L. Bacher, Xiaoru Dong, 2024, Briefings in bioinformatics.

Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing

Rhonda L. Bacher, Jack R. Leary, 2023, bioRxiv.

Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference

Maigan A. Brusko, Rhonda L. Bacher, Xiaoru Dong, 2023, bioRxiv.

Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis

Bret Duffin, James A. Thomson, Christina Kendziorski, 2020, PloS one.

Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule

Jennifer M. Bolin, Angela L. Elwell, R. Stewart, 2019, bioRxiv.

Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule

Jennifer M. Bolin, Angela L. Elwell, Li-Fang Chu, 2019, bioRxiv.