Key: * indicates co-first authors; \(\dagger\) indicates corresponding authors; students/trainees are underlined
Motwani K, Bacher, Rhonda, Molstad AJ. Binned multinomial logistic regression for integrative cell type annotation. arXiv preprint arXiv:2111.12149 (accepted at The Annals of Applied Statistics) (2023).
Jacobsen LM, Diggins K, Blanchfield L, McNichols JA, Perry DJ, Brant J, Dong, Xiaoru, Bacher, Rhonda, Gersuk VH, Schatz DA, Atkinson MA, Mathews CE, Haller MJ, Long SA, Linsley PS, Brusko TM. Responders to low-dose ATG induce CD4 T cell exhaustion in type 1 diabetes. JCI Insight, e161812 (2023).
Marshall GP, Cserny J, Wang CW, Looney B, Posgai AL, Bacher, Rhonda, Keselowsky B, Brusko TM. 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 (2023).
Bacher, Rhonda\(^\dagger\), Chu LF, Argus C, Bolin JM, Knight, Parker, Thomson JA, Stewart R, Kendziorski C\(^\dagger\). Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization. Nucleic Acids Research, 50(2), e12-e12 (2022).
Brakenridge SC, Chen UI, Loftus T, Ungaro R, Dirain M, Kerr A, Zhong, Luer, Bacher, Rhonda, Starostik P, Ghita G, Midic U, Darden D, Fenner B, Wacker J, Efron PA, Liesenfeld O, Sweeney TE, Moldawer LL. Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients. JAMA Network Open, 5(7), e2221520-e2221520 (2022).
Brown J, Ni Z, Mohanty C, Bacher, Rhonda, Kendziorski C. Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. Bioinformatics, 37(22), 4123-4128 (2021).
Knight, Parker, Gauthier MPL, Pardo CE, Darst RP, Kapadia, Kevin, Browder, Hadley, Morton, Eliza, Riva A, Kladde MP, Bacher, Rhonda\(^\dagger\). 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 (2021).
Loftus TJ, Ungaro R, Dirain M, Efron PA, Mazer MB, Remy KE, Hotchkiss RS, Zhong, Luer, Bacher, Rhonda, Starostik P, Moldawer LL, Brakenridge SC. Overlapping but disparate inflammatory and immunosuppressive responses to SARS-CoV-2 and bacterial sepsis: an immunological time course analysis. Frontiers in Immunology, 12, 792448 (2021).
Simonett SP, Shin S, Herring JA, Bacher, Rhonda, 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. Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. The Journal of clinical investigation, 131(21) (2021).
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, Rhonda, Zheng SG, Wu X, Zakharia Y, Zhang W. CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Nature communications, 12(1), 5764 (2021).
Darden DB, Dong, Xiaoru, 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, Rhonda, Moldawer LL, Mohr AM, Efron PA. A novel single cell RNA-seq analysis of non-myeloid circulating cells in late sepsis. Frontiers in Immunology, 12, 696536 (2021).
Darden DB, Ghita GL, Wang Z, Stortz JA, Lopez MC, Cox MC, Hawkins RB, Rincon JC, Kelly LS, Fenner BP, Ozrazgat-Baslanti T, Leeuwenburgh C, Bihorac A, Loftus TJ, Moore FA, Brakenridge SC, Baker HV, Bacher, Rhonda, Mohr AM, Moldawer LL, Efron PA. Chronic Critical Illness Elicits a Unique Circulating Leukocyte Transcriptome in Sepsis Survivors. Journal of Clinical Medicine, 10(15), 3211 (2021).
Darden DB, Bacher, Rhonda, Brusko MA, Knight, Parker, 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. 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), 587 (2021).
Ross JJ, Wasserfall CH, Bacher, Rhonda, Perry DJ, McGrail K, Posgai AL, Dong, Xiaoru, Muir A, Li X, Campbell-Thompson M, Brusko TM, Schatz DA, Haller MJ, Atkinson MA. Exocrine Pancreatic Enzymes Are a Serological Biomarker for Type 1 Diabetes Staging and Pancreas Size. Diabetes, 70(4), 944-954 (2021).
Williams MD, Bacher, Rhonda, Perry DJ, Grace CR, McGrail KM, Posgai AL, Muir A, Chamala S, Haller MJ, Schatz DA, Brusko TM, Atkinson MA, Wasserfall CH. Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis. Diabetes, 70(4), 932-943 (2021).
Japp AS, Meng W, Rosenfeld AM, Perry DJ, Thirawatananond P, Bacher, Rhonda, Liu C, Gardner JS, HPAP Consortium, Atkinson MA, Kaestner KH, Brusko TM, Naji A, Luning Prak ET, Betts MR. TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes. Cell, 184(3), 827-839 (2021).
Seirup M\(^\dagger\), Chu LF, Sengupta S, Leng N, Browder, Hadley, Kapadia, Kevin, Shafer CM, Duffin B, Elwell AL, Bolin JM, Swanson S, Stewart R, Kendziorski C, Thomson JA\(^\dagger\), Bacher, Rhonda\(^\dagger\). Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. Plos one, 15(9), e0239711 (2020).
Darden DB, Stortz JA, Hollen MK, Cox MC, Apple CG, Hawkins RB, Rincon JC, Lopez M, Wang Z, Navarro E, Hagen JE, Parvataneni HK, Brusko MA, Kladde M, Bacher, Rhonda, Brumback BA, Brakenridge SC, Baker HV, Cogle CR, Mohr AM, Efron PA. 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, 1289 (2020).
Motwani K*, Peters LD*, Vliegen WH, Gomaa El-sayed A, Seay HR, Cecilia Lopez M, Baker HV, Posgai AL, Brusko MA, Perry DJ, Bacher, Rhonda, Larkin J, Haller MJ, Brusko TM. 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 (2020).
Shapiro MR, Wasserfall CH, McGrail SM, Posgai AL, Bacher, Rhonda, Muir A, Haller MJ, Schatz DA, Wesley JD, von Herrath M, Hagopian WA, Speake C, Atkinson MA, Brusko TM. Insulin-Like Growth Factor Dysregulation Both Preceding and Following Type 1 Diabetes Diagnosis. Diabetes, 69(3), 413-423 (2020).
Barry C\(^\dagger\), 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,Rhonda\(^\dagger\). 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), e1007543 (2019).
Chu LF, Mamott D, Ni Z, Bacher, Rhonda, Liu C, Swanson S, Kendziorski C, Stewart RM, Thomson JA. An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells. Cell Reports, 28(9), 2247-2255 (2019).
Seirup, M., Chu, L.F., Sengupta, S., Leng, N., Browder, H., Kapadia, K., Shafer, C.M., Duffin, B., Elwell, A.L., Bolin, J.M., Swanson, S., Stewart, R., Kendziorski, C., Thomson, J.A., Bacher, R\(\dagger\). Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. PLOS ONE. (2020).
Williams, M.D., Bacher, R., Perry, D.J., Grace, C.R., McGrail, K.M., Posgai, A.L., Muir, A., Chamala, S., Haller, M.J., Schatz, D.A. and Brusko, T.M., Atkinson, M.A., Wasserfall, C.H. Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis. Diabetes. (2021).
Ross, J.J., Wasserfall, C.H., Bacher, R., Perry, D.J., McGrail, K., Posgai, A.L., Dong, X., Muir, A., Li, X., Campbell-Thompson, M. and Brusko, T.M. Exocrine Pancreatic Enzymes Are a Serological Biomarker for Type 1 Diabetes Staging and Pancreas Size. Diabetes. (2021).
Darden, D.B., Bacher, R., Brusko, M.A., Knight, P., Hawkins, R.B., Cox, M.C., Dirain, M.L., Ungaro, R., Nacionales, D.C., Rincon, J.C., Gauthier, M.-P.L., Kladde, M., Bihorac, A., Brusko, T.M., Moore, F.A., Brakenridge, S.C., Mohr, A.M., Moldawer, L.L., Efron, P.A. Single Cell RNA-SEQ of Human Myeloid Derived Suppressor Cells in Late Sepsis Reveals Multiple Subsets with Unique Transcriptional Responses: A Pilot Study. Shock. (2021).
Darden, D.B., Ghita, G.L., Wang, Z., Stortz, J.A., Lopez, M.C., Cox, M.C., Hawkins, R.B., Rincon, J.C., Kelly, L.S., Fenner, B.P., Ozrazgat-Baslanti, T., Leeuwenburgh C., Bihorac A., Loftus T.J., Moore F.A., Brakenridge S.C., Baker H.V., Bacher R., Mohr A.M., Moldawer L.L., Efron P.A. Chronic Critical Illness Elicits a Unique Circulating Leukocyte Transcriptome in Sepsis Survivors. Journal of Clinical Medicine, 10(15), p.3211. (2021).
Darden, D.B., Dong, X., Brusko, M.A., Kelly, L., Fenner, B., Rincon, J.C., Dirain, M.L., Ungaro, R., Nacionales, D.C., Gauthier, M., Kladde, M., Brusko T.M., Bihorac A., Moore F.A., Loftus T., Bacher R., Moldawer L.L., Mohr A.M., Efron, P.A. A novel single cell RNA-seq analysis of non-myeloid circulating cells in late sepsis. Frontiers in Immunology, 12, p.696536. (2021).
Kim, M.C., Borcherding, N., Ahmed, K.K., Voigt, A.P., Vishwakarma, A., Kolb, R., Kluz, P.N., Pandey, G., De, U., Drashansky, T., Helm, E.Y., Zhang X., Gibson-Corley K.N., 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 S.G., Wu X., Zakharia Y., Zhang W. CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Nature Communications, 12(1), pp.1-13. (2021).
Simonett, S.P., Shin, S., Herring, J.A., Bacher, R., Smith, L.A., Dong, C., Rabaglia, M.E., Stapleton, D.S., Schueler, K.L., Choi, J., Bernstein, M.N., Turkewitz D.R., Perez-Cervantes C., Spaeth J., Stein, R., Tessem J.S., Kendziorski C., Keles S., Moskowitz I.P., Keller M.P., Attie, A.D. Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. The Journal of Clinical Investigation, 131(21). (2021).
Loftus, T.J., Ungaro, R., Dirain, M., Efron, P.A., Mazer, M.B., Remy, K.E., Hotchkiss, R.S., Zhong, L., Bacher, R., Starostik, P., Moldawer, L.L., Brakenridge, S. C. 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. (2021).
Brown, J., Ni, Z., Mohanty, C., Bacher, R., Kendziorski, C. Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. Bioinformatics, 37(22), pp.4123-4128. (2021).
Brakenridge, S. C., Chen, U. I., 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 P.A., Liesenfeld O., Sweeney T.E., Moldawer L.L. Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients. JAMA Network Open, 5(7), e2221520-e2221520. (2022).
Bacher, Rhonda*\(^\dagger\), Leng N*, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart RM\(^\dagger\). Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. BMC bioinformatics 19, 1-10 (2018).
Vermillion KL, Bacher, Rhonda, Tannenbaum AP, Swanson S, Jiang P, Chu, LF, Stewart RM, Thomson JA, Vereide DT. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Developmental biology, 439(1), 30-41 (2018).
Keller MP, Gatti DM, Schueler KL, Rabaglia ME, Stapleton DS, Simecek P, Vincent M, Allen S, Broman AT, Bacher, Rhonda, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD. Genetic drivers of pancreatic islet function. Genetics, 209(1), 335-356 (2018).
Bacher, Rhonda*, Chu LF*, Leng N, Thomson JA, Gasch A, Thomson JA, Stewart RM, Newton M, Kendziorski C. SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods, 14(6), 584-586 (2017).
Gasch AP*, Yu B*, Hose J, Escalante L, Place M, Bacher, Rhonda, Kanbar J, Ciobanu D, Sandor L, Grigoriyev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS biology, 15(12),e2004050 (2017).
Ye S, Bacher, Rhonda, Keller MP, Attie AD, Kendziorski C. Statistical Methods for Latent Class Quantitative Trait Loci Mapping. Genetics, 206(3), 1309-1317 (2017).
Barry C, Schmit MT, Jiang P, Schwarz MP, Duffin BM, Swanson S, Bacher, Rhonda, Bolin JM, Elwell AL, McIntosh BE, Stewart R, Thomson JA. Species-Specific Developmental Timing is Maintained by Pluripotent Stem Cells Ex Utero. Developmental biology, 423(2), 101-110 (2017).
Fischer BL, Bacher, Rhonda, Bendlin BB, Birdsill AC, Ly M, Hoscheidt SM, Chappell RJ, Mahoney JE, Gleason CE. An Examination of Brain Abnormalities and Mobility in Individuals with Mild Cognitive Impairment and Alzheimer’s Disease. Frontiers in aging neuroscience, 9, 86 (2017).
Shapiro MR*, Dong, Xiaoru*, 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 Rhonda\(^\dagger\), Brusko TM\(^\dagger\). Human immune phenotyping reveals accelerated aging in type 1 diabetes. bioRxiv, (2023).
Zhou M, Nabilsi NH, Wang A, Gauthier MPL, Murray KO, Azari H, Owens WS, Newman JRB, Pardo-Palacios FJ, Conesa A, Riva A, Clanton TL, Reynolds BA, Concannon P, Brant JO, Bacher, Rhonda, Kladde MP. Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation. bioRxiv, (2022).
Ogut F, Newman JRB, Bacher, Rhonda, Concannon PJ, Verhoeven KJF, McIntyre LM. Experimental design for large scale omic studies. bioRxiv, (2019).
Dong, Xiaoru and Bacher, Rhonda\(^\dagger\). Data-driven assessment of dimension reduction quality for single-cell omics data. Patterns, 3(3), p.100465, (2022).
Dong, Xiaoru and Bacher, Rhonda. Analysis of Single-Cell RNA-seq Data. In Methods in Molecular Biology, Fridley B & Wang X (Eds.). Statistical Genomics. DOI 10.1007/978-1-0716-2986-4_6, (2023).
Bacher, Rhonda. Normalization for single-cell RNA-seq data analysis. In Computational methods for single-cell data analysis, Guo-Cheng Yuan (Ed.). Methods in Molecular Biology. DOI 10.1007/978-1-4939-9057-3, (2019).