Zhu Z*, Dong X*, Kim C, Maugee C, Barbazuk WB, Vulpe CD, Bacher R. (2026). simCRISPR: Modeling Experimental Complexity in Pooled CRISPR Screens. bioRxiv.
Zhong L, Ensberg K, Tibbetts S, Molstad AJ, Bacher R. (2026). scDEcrypter: Uncertainty-aware differential expression analysis for viral infection in scRNA-seq. bioRxiv.
Brant JO, Gauthier MP, Rodhouse CE, Wu R, Hernandez-Rios M, Zeumer-Spataro L, Dirain ML, Ungaro RF, Rocha IL, Wiggins WB, Charles AM, Xiao F, Bible LE, Mohr AM, Larson SD, Rincon JC, Wallet SM, Brusko MA, Loftus TJ, Moldawer LL, Mathews CE, Bacher R, Cai G, Maile R, Efron PA, Kladde MP. (2026). Divergent chromatin remodeling trajectories in CD66b+ MDSCs distinguishes recovery from chronic critical illness after sepsis. bioRxiv.
Dong X, Goyal A, Liang M, Brusko MA, Brusko TM, Bacher R. (2025). Penalized Linear Models for Highly Correlated High-Dimensional Immunophenotyping Data. arXiv.
Kim C, Tagmount A, Zhu Z, Barbazuk WB, Bacher R, Vulpe CD. (2025). Genome-wide CRISPR screens identified C18orf32 as a novel regulator of lipid metabolism that mediates PFOA-induced toxicity. bioRxiv.
Peters LD, Brusko MA, Seay HR, Posgai AL, Wasserfall CH, Atkinson MA, Bacher R, Brusko TM. (2025). Aberrant immune regulation and enrichment of stem-like CD8+ T cells in the pancreatic lymph node during type 1 diabetes development. bioRxiv.
Leary JR, Dong X, Bacher R. (2026). Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. Nucleic Acids Research, 54(2), p. gkaf1494.
Kim C, Zhu Z, Tagmount A, Barbazuk WB, Bacher R, Stuchal LD, Martyniuk CJ, Vulpe CD. (2025). Characterizing common loss-of-function genes and their potential utility in assessing population variability and chemical susceptibility. NAM Journal, 2, p. 100103.
Medina-Serpas MA, Brusko M, Golden GJ, Campbell-Thompson M, Rogers T, Reardon S, Posgai AL, Bacher R, Luning Prak ET, Liu C, Kaestner KH, Naji A, Betts MR, McIntyre LM, Atkinson MA, Brusko TM. (2026). Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-beta signature in human type 1 diabetes. Cell Reports, 45(4), p. 117144.
Kim C, Zhu Z, Tagmount A, Barbazuk WB, Bacher R, Vulpe CD. (2026). Physiologically relevant 3D CRISPR screening enhances mechanistic insight into chemical toxicity compared to 2D screening. Toxicology, 522, p. 154422.
Kim C, Tagmount A, Zhu Z, Wilson F, Li D, Ostrov DA, Barbazuk BW, Bacher R, Vulpe CD. (2026). Identification of functional genetic components modulating toxicity response to PFOS using genome-wide CRISPR screens in HepG2/C3A cells. Archives of Toxicology, 100, pp. 1391–1410.
Kim HG, Gauthier MPL, Higgs A, Hernandez DA, Zhou M, Brant JO, Bacher R, Darden DB, Wallet SM, Mathews CE, Moldawer LL, Efron PA, Kladde MP, Maile R. (2026). Chromatin remodeling and transcriptional silencing define the dynamic innate immune response of tissue resident macrophages after burn injury. Shock, 65(3), pp. 538-550.
Drotar DM, Vazquez Ramos GJA, Williams MD, David ST, Luce C, Smith JA, Posgai AL, Bacher R, Campbell-Thompson M, Kusmartseva I, Brusko MA, Atkinson MA, Wasserfall CH. (2025). Loss of Insulin-Positive Cell Clusters Precedes the Decrease in Islet Frequency and β-Cell Area in Type 1 Diabetes. Diabetes, 74(11), pp. 2008-2015.
Brown ME, Thirawatananond P, Peters LD, Kern EJ, Vijay S, Sachs LK, Posgai AL, Brusko MA, Shapiro MR, Mathews CE, Bacher R, Brusko TM. (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), pp. 397-418.
Williams MD, Grace CR, Posgai AL, McGrail KM, Brusko MA, Haller MJ, Jacobsen LM, Schatz DA, Brusko TM, Atkinson MA, Bacher R, Wasserfall CH. (2025). Serological markers of exocrine pancreatic function are differentially informative for distinguishing individuals progressing to type 1 diabetes. BMJ Open Diabetes Research and Care, 13(1), p. e004655.
Dong X, Leary JR, Yang C, Brusko MA, Brusko TM, Bacher R. (2024). Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference. Briefings in Bioinformatics, 25(3), p. bbae216.
Kim C, Zhu Z, Barbazuk BW, Bacher R, Vulpe CD. (2024). Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroids and its toxicological implications. Toxicology Letters, 401, pp. 125-138.
Bruggeman BS, Gornisiewicz S, Bacher R, McGrail K, Campbell-Thompson M, Wasserfall C, Jacobsen LM, Atkinson M, Haller MJ, Schatz DA. (2024). Serum exocrine pancreas enzymes are biomarkers of immunotherapy response in new-onset type 1 diabetes. Frontiers in Endocrinology, 15, p. 1497373.
Barrios EL*, Leary JR*, Darden DB, Rincon JC, Willis M, Polcz VE, Gillies GS, Munley JA, Dirain ML, Ungaro R, Nacionales DC, Gauthier ML, Larson SD, Morel L, Loftus TJ, Mohr AM, Maile R, Kladde MP, Mathews CE, Brusko MA, Brusko TM, Moldawer LL, Bacher R†, Efron PA†. (2024). The post-septic peripheral myeloid compartment reveals unexpected diversity in myeloid-derived suppressor cells. Frontiers in Immunology, 15, p. 1355405.
Motwani K, Bacher R, Molstad AJ. (2023). Binned multinomial logistic regression for integrative cell-type annotation. Biometrics, 79(4), pp. 3485-3496.
Shapiro MR*, Dong X*, Perry D*, McNichols JM, Thirawatananond P, Posgai AL, Peters L, Motwani K, Musca RS, Muir A, Concannon P, Jacobsen LM, Mathews CE, Wasserfall CH, Haller MJ, Schatz DA, Atkinson MA, Brusko MA, Bacher R†, Brusko TM†. (2023). Human immune phenotyping reveals accelerated aging in type 1 diabetes. JCI Insight, 8(17), p. e170767.
Jacobsen LM, Diggins K, Blanchfield L, McNichols JA, Perry DJ, Brant J, Dong X, Bacher R, Gersuk VH, Schatz DA, Atkinson MA, Mathews CE, Haller MJ, Long SA, Linsley PS, Brusko TM. (2023). Responders to low-dose ATG induce CD4 T cell exhaustion in type 1 diabetes. JCI Insight, 8(16), p. e161812.
Marshall GP, Cserny J, Wang CW, Looney B, Posgai AL, Bacher R, Keselowsky B, Brusko TM. (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), pp. 185-197.
Bacher R†, Chu LF, Argus C, Bolin JM, Knight, P, Thomson JA, Stewart R, Kendziorski C†. (2022). Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization. Nucleic Acids Research, 50(2), p. e12.
Brakenridge SC, Chen UI, Loftus T, Ungaro R, Dirain M, Kerr A, Zhong L, Bacher R, Starostik P, Ghita G, Midic U, Darden D, Fenner B, Wacker J, Efron PA, Liesenfeld O, Sweeney TE, Moldawer LL. (2022). Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients. JAMA Network Open, 5(7), p. e2221520.
Brown J, Ni Z, Mohanty C, Bacher R, Kendziorski C. (2021). Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. Bioinformatics, 37(22), pp. 4123-4128.
Knight, P, Gauthier MPL, Pardo CE, Darst RP, Kapadia, K, Browder, H, Morton, E, Riva A, Kladde MP, Bacher R. (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), pp. 4857-4859.
Loftus TJ, Ungaro R, Dirain M, Efron PA, Mazer MB, Remy KE, Hotchkiss RS, Zhong L, Bacher R, Starostik P, Moldawer LL, Brakenridge SC. (2021). Overlapping but disparate inflammatory and immunosuppressive responses to SARS-CoV-2 and bacterial sepsis: an immunological time course analysis. Frontiers in Immunology, 12, p. 792448.
Simonett SP, Shin S, Herring JA, Bacher R, Smith LA, Dong C, Rabaglia ME, Stapleton DS, Schueler KL, Choi J, Bernstein MN, Turkewitz DR, Perez-Cervantes C, Spaeth J, Stein, R, Tessem JS, Kendziorski C, Keles S, Moskowitz IP, Keller MP, Attie AD. (2021). Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. The Journal of Clinical Investigation, 131(21), p. e144833.
Kim MC, Borcherding N, Ahmed KK, Voigt AP, Vishwakarma A, Kolb R, Kluz PN, Pandey G, De U, Drashansky T, Helm EY, Zhang X, Gibson-Corley KN, Klesney-Tait J, Zhu Y, Lu J, Lu J, Huang X, Xiang H, Cheng J, Wang D, Wang Z, Tang J, Hu J, Wang Z, Liu H, Li M, Zhuang H, Avram D, Zhou D, Bacher R, Zheng SG, Wu X, Zakharia Y, Zhang W. (2021). CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Nature Communications, 12(1), p. 5764.
Darden DB, Dong X, Brusko MA, Kelly L, Fenner B, Rincon JC, Dirain ML, Ungaro R, Nacionales DC, Gauthier MPL, Kladde M, Brusko TM, Bihorac A, Moore FA, Loftus T, Bacher R, Moldawer LL, Mohr AM, Efron PA. (2021). A novel single cell RNA-seq analysis of non-myeloid circulating cells in late sepsis. Frontiers in Immunology, 12, p. 696536.
Darden DB, Bacher R, Brusko MA, Knight, P, Hawkins RB, Cox MC, Dirain ML, Ungaro R, Nacionales DC, Rincon JC, Gauthier MPL, Kladde M, Bihorac A, Brusko TM, Moore FA, Brakenridge SC, Mohr AM, Moldawer LL, Efron PA. (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, 55(5), p. 587.
Ross JJ, Wasserfall CH, Bacher R, Perry DJ, McGrail K, Posgai AL, Dong X, Muir A, Li X, Campbell-Thompson M, Brusko TM, Schatz DA, Haller MJ, Atkinson MA. (2021). Exocrine Pancreatic Enzymes Are a Serological Biomarker for Type 1 Diabetes Staging and Pancreas Size. Diabetes, 70(4), pp. 944-954.
Williams MD, Bacher R, Perry DJ, Grace CR, McGrail KM, Posgai AL, Muir A, Chamala S, Haller MJ, Schatz DA, Brusko TM, Atkinson MA, Wasserfall CH. (2021). Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis. Diabetes, 70(4), pp. 932-943.
Japp AS, Meng W, Rosenfeld AM, Perry DJ, Thirawatananond P, Bacher R, Liu C, Gardner JS, HPAP Consortium, Atkinson MA, Kaestner KH, Brusko TM, Naji A, Luning Prak ET, Betts MR. (2021). TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes. Cell, 184(3), pp. 827-839.
Seirup M, Chu LF, Sengupta S, Leng N, Browder, H, Kapadia, K, Shafer CM, Duffin B, Elwell AL, Bolin JM, Swanson S, Stewart R, Kendziorski C, Thomson JA†, Bacher R†. (2020). Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. PLOS One, 15(9), p. e0239711.
Motwani K, Peters LD, Vliegen WH, Gomaa El-sayed A, Seay HR, Cecilia Lopez M, Baker HV, Posgai AL, Brusko MA, Perry DJ, Bacher R, Larkin J, Haller MJ, Brusko TM. (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, 611.
Shapiro MR, Wasserfall CH, McGrail SM, Posgai AL, Bacher R, Muir A, Haller MJ, Schatz DA, Wesley JD, von Herrath M, Hagopian WA, Speake C, Atkinson MA, Brusko TM. (2020). Insulin-Like Growth Factor Dysregulation Both Preceding and Following Type 1 Diabetes Diagnosis. Diabetes, 69(3), pp. 413-423.
Barry C†, Schmitz MT, Argus C, Bolin JM, Probasco MD, Leng N, Duffin B, Steill J, Swanson S, McIntosh BE, Stewart R, Kendziorski C, Thomson JA, Bacher R†. (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), p. e1007543.
Chu LF, Mamott D, Ni Z, Bacher R, Liu C, Swanson S, Kendziorski C, Stewart RM, Thomson JA. (2019). An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells. Cell Reports, 28(9), pp. 2247-2255.
Bacher R†, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart RM†. (2018). Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. BMC Bioinformatics, 19, pp. 1-10.
Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu, LF, Stewart RM, Thomson JA, Vereide DT. (2018). Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Developmental Biology, 439(1), pp. 30-41.
Keller MP, Gatti DM, Schueler KL, Rabaglia ME, Stapleton DS, Simecek P, Vincent M, Allen S, Broman AT, Bacher R, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD. (2018). Genetic drivers of pancreatic islet function. Genetics, 209(1), pp. 335-356.
Bacher R*, Chu LF*, Leng N, Thomson JA, Gasch A, Thomson JA, Stewart RM, Newton M, Kendziorski C. (2017). SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods, 14(6), pp. 584-586.
Bacher R, Kendziorski, C. (2016). Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biology, 17, pp. 1-14.
Gasch AP, Yu B, Hose J, Escalante L, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriyev IV, Kendziorski C, Quake SR, McClean MN. (2017). Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLOS Biology, 15(12), p. e2004050.
Barry C, Schmit MT, Jiang P, Schwarz MP, Duffin BM, Swanson S, Bacher R, Bolin JM, Elwell AL, McIntosh BE, Stewart R, Thomson JA. (2017). Species-Specific Developmental Timing is Maintained by Pluripotent Stem Cells Ex Utero. Developmental Biology, 423(2), pp. 101-110.
Zhong L and Bacher R. (2023). Leveraging remeasured samples in biomedical studies. Nature Computational Science, 3(8), 669-670.
Dong X and Bacher R. (2022). Data-driven assessment of dimension reduction quality for single-cell omics data. Patterns, 3(3), 100465.
Dong X and Bacher R. (2023). Analysis of Single-Cell RNA-seq Data. In Methods in Molecular Biology, Fridley B & Wang X (Eds.). Statistical Genomics. pp. 95–114.
Bacher R. (2019). Normalization for single-cell RNA-seq data analysis. In Computational methods for single-cell data analysis, Guo-Cheng Yuan (Ed.). Methods in Molecular Biology. pp. 11–23.