• I am a bioinformatics scientist with industry and academic experience. Currently, I engage in collaborative research on projects primarily in immunology and infectious disease. These collaborations serve as an opportunity for requirements gathering that my group can use for developing bioinformatics tools which can be used more broadly in the community. I serve as director of the Data Analytics and Bioinformatics Core for the UAB Cooperative Centers on Human Immunology U19 award as well as co-PI on the Bioinformatics, Data Management and Integration project for the Global Team Science Award by the Lupus Research Alliance, a multi-site program.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2023 Single cell analysis of human nasal mucosal IgE antibody secreting cells reveals a newly minted phenotypeMucosal Immunology2023
    2023 Mixed Origins: HIV gp120-specific memory develops from pre-existing memory and naïve B cells following vaccination in humans.AIDS Research and Human Retroviruses2023
    2023 Spatiotemporal immune atlas of the first clinical-grade, gene-edited pig-to-human kidney xenotransplant. 2023
    2022 HLA-II-Associated HIV-1 Adaptation Decreases CD4+ T-Cell Responses in HIV-1 Vaccine RecipientsJournal of Virology.  96. 2022
    2022 Circulating Tregs Accumulate in Omental Tumors and Acquire Adipose-Resident FeaturesCancer Immunology Research.  10:641-655. 2022
    2022 A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic cryptsImmunity.  55:494-511.e11. 2022
    2021 GM-CSF production by non-classical monocytes controls antagonistic LPS-driven functions in allergic inflammationCell Reports.  37. 2021
    2021 CD4+ T Cells Are Dispensable for Induction of Broad Heterologous HIV Neutralizing Antibodies in Rhesus MacaquesFrontiers in Immunology.  12. 2021
    2021 Lung dendritic cells migrate to the spleen to prime long-lived TCF1hi memory CD8+ T cell precursors after influenza infectionScience Immunology.  6. 2021
    2021 Extrafollicular IgD+ B cells generate IgE antibody secreting cells in the nasal mucosa.Mucosal Immunology.  14:1144-1159. 2021
    2021 Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn's DiseaseGastroenterology.  161:522-535.e6. 2021
    2020 Neonatal Exposure to Commensal-Bacteria-Derived Antigens Directs Polysaccharide-Specific B-1 B Cell Repertoire DevelopmentImmunity.  53:172-186.e6. 2020
    2020 Persistence of HIV-1 Env-Specific Plasmablast Lineages in Plasma Cells after Vaccination in HumansCell Reports Medicine.  1. 2020
    2020 GM-CSF Availability Determines LPS-Mediated Functions in Allergic Inflammation 2020
    2019 T-bet Transcription Factor Promotes Antibody-Secreting Cell Differentiation by Limiting the Inflammatory Effects of IFN-γ on B CellsImmunity.  50:1172-1187.e7. 2019
    2019 Ifnγ induces epigenetic programming of human t-bethi b cells and promotes tlr7/8 and il-21 induced differentiationeLife.  8. 2019
    2019 Exercise promotes a cardioprotective gene program in resident cardiac fibroblasts.JCI Insight.  4. 2019
    2019 Broad and protective influenza B virus neuraminidase antibodies in humans after vaccination and their clonal persistence as plasma cellsmBio.  10:1-17. 2019
    2019 Complex responses to hydrogen peroxide and hypochlorous acid by the probiotic bacterium lactobacillus reuterimSystems.  4. 2019
    2019 Differential transcriptome and development of human peripheral plasma cell subsetsJCI Insight.  4. 2019
    2018 B cells inhibit bone formation in rheumatoid arthritis by suppressing osteoblast differentiation.Nature Communications.  9:5127. 2018
    2018 A highly potent and broadly neutralizing H1 influenza-specific human monoclonal antibodyScientific Reports.  8. 2018
    2018 Visualizing nationwide variation in medicare Part D prescribing patternsPeerJ.  18. 2018
    2018 Understanding B-cell activation and autoantibody repertoire selection in systemic lupus erythematosus: A B-cell immunomics approachImmunological Reviews.  284:120-131. 2018
    2018 Small proline-rich protein 2B drives stress-dependent p53 degradation and fibroblast proliferation in heart failure. 2018
    2018 Identification of GB1, a gene whose constitutive overexpression increases glycinebetaine content in maize and soybeanPlant Direct.  2. 2018
    2017 Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory IllnessScientific Reports.  7. 2017
    2017 Pre-existing neutralizing antibody mitigates B cell dysregulation and enhances the Envspecific antibody response in SHIV-infected rhesus macaquesPLoS One.  12. 2017
    2017 Properties of healthcare teaming networks as a function of network construction algorithms.PLoS One.  12:e0175876. 2017
    2016 Increased Steady-State Memory B Cell Subsets among High-Risk Participants in an HIV Vaccine TrialAIDS Research and Human Retroviruses.  32:1143-1148. 2016
    2016 Regulatory T Cell Numbers in Inflamed Skin Are Controlled by Local Inflammatory Cues That Upregulate CD25 and Facilitate Antigen-Driven Local Proliferation.Journal of Immunology.  197:2208-2218. 2016
    2016 Humoral dysregulation associated with increased systemic inflammation among injection heroin usersPLoS One.  11. 2016
    2016 Follicular lymphoma tregs have a distinct transcription profile impacting their migration and retention in the malignant lymph nodePLoS One.  11. 2016
    2016 Competitive SWIFT cluster templates enhance detection of aging changes. 2016
    2016 Expression of the Long Non-Coding RNA HOTAIR Correlates with Disease Progression in Bladder Cancer and Is Contained in Bladder Cancer Patient Urinary Exosomes.PLoS One.  11:e0147236. 2016
    2016 Identification of significant B cell associations with undetected observations using a Tobit modelStatistics and its Interface.  9:79-91. 2016
    2015 Longitudinal studies of a B cell-derived signature of tolerance in renal transplant recipients.American Journal of Transplantation.  15:2908-2920. 2015
    2015 A Diagnostic Serum Antibody Test for Patients With Staphylococcus aureus OsteomyelitisClinical Orthopaedics and Related Research.  473:2735-2749. 2015
    2015 Long-Lived Plasma Cells Are Contained within the CD19-CD38hiCD138+ Subset in Human Bone MarrowImmunity.  43:132-145. 2015
    2015 Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosusNature Immunology.  16:755-765. 2015
    2014 Primary Sjögren's syndrome is characterized by distinct phenotypic and transcriptional profiles of IgD+ unswitched memory B cells.Arthritis and Rheumatology.  66:2558-2569. 2014
    2014 Neutrophil-mediated IFN activation in the bone marrow alters B cell development in human and murine systemic lupus erythematosus.Journal of Immunology.  192:906-918. 2014
    2014 Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy.PLoS One.  9:e110657. 2014
    2013 Inflammation-induced interstitial migration of effector CD4+ T cells is dependent on integrin α vNature Immunology.  14:949-958. 2013
    2013 IL-4 Attenuates Th1-Associated Chemokine Expression and Th1 Trafficking to Inflamed Tissues and Limits Pathogen ClearancePLoS One.  8. 2013
    2013 9G4+ antibodies isolated from HIV-infected patients neutralize HIV-1 and have distinct autoreactivity profilesPLoS One.  8. 2013
    2012 Advances in human B cell phenotypic profilingFrontiers in Immunology.  3. 2012
    2012 9G4 autoreactivity is increased in HIV-infected patients and correlates with HIV broadly neutralizing serum activityPLoS One.  7. 2012
    2012 Syk inhibition with fostamatinib leads to transitional B lymphocyte depletionClinical Immunology.  142:237-242. 2012
    2012 Multiparameter flow cytometry and bioanalytics for B cell profiling in systemic lupus erythematosusMethods in Molecular Biology.  900:109-134. 2012
    2011 Decreased influenza-specific B cell responses in rheumatoid arthritis patients treated with anti-tumor necrosis factorArthritis Research and Therapy.  13. 2011
    2011 Follicular lymphoma tumor-infiltrating T-helper (TH) cells have the same polyfunctional potential as normal nodal TH cells despite skewed differentiationBlood.  118:3591-3602. 2011
    2011 Multifaceted intervention by the hsp90 inhibitor ganetespib (sta-9090) in cancer cells with activated jak/stat signalingPLoS One.  6. 2011
    1998 Analysis of direction-tuning curves of neurons in the turtle's accessory optic systemExperimental Brain Research.  121:361-370. 1998
    1996 A model for optokinetic eye movements in turtles that incorporates properties of retinal-slip neuronsVisual Neuroscience.  13:375-383. 1996
    1993 Visual-response properties of units in the turtle cerebellar granular layer in vitroJournal of Neurophysiology.  69:1314-1322. 1993
    1991 Effects Of Synaptic Drugs On Turtle Optokinetic Nystagmus And The Spike Responses Of The Basal Optic NucleusVisual Neuroscience.  7:431-440. 1991
    1991 Electrophysiological evidence for a direct projection of direction-sensitive retinal ganglion cells to the turtle's accessory optic systemJournal of Neurophysiology.  65:1022-1033. 1991
    1990 Retinal direction-sensitive input to the accessory optic system: an in vitro approach with behavioral relevanceBrain Research.  522:161-164. 1990
    1990 Visual-response properties of neurons in turtle basal optic nucleus in vitroJournal of Neurophysiology.  63:1033-1045. 1990

    Research Overview

  • My research interests cover broad areas of bioinformatics, from data modeling, databases and software pipeline development for high-throughput workflows, through analysis and innovative visualization approaches for complex biological data sets. In particular, I am interested in developing tools for facilitating the study of adaptive immunity, including a workflow and toolbox for studying B cell receptor repertoires by next generation sequencing, and a fully automated pipeline for analyzing antibody reactivity profiles by cytometric bead array.
  • Investigator On

  • B Cells and Plasma Cells in Black SLE, Mechanisms of Disease Heterogeneity  awarded by Emory University
  • Distinct Glycophenotypes and Abnormal Signaling Define a Subpopulation of B cells Responsible for Production of Autoantigen in IgA Nephropathy  awarded by National Institute of Diabetes and Digestive and Kidney Diseases/NIH/DHHS
  • Dynamics of the Protective Vaccine-Induced Human Influenza Neuraminidase B Cell Response  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Functional Implications of Tfh Cell Heterogeneity After Infection  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Functional Implications of Tfh Cell Heterogeneity After Infection  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Identification and Characterization of Effector Memory B Cell Populations That Dominate Memory Responses to Subsequent Influenza Infection and Vaccination  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Molecular Analysis and Lineage Tracing of Influenza-Specific, Lung-Resident Memory B Cells  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Origin and Function of Double Negative T Cells in Lupus  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Origin and Function of Double Negative T Cells in Lupus  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Pathogenic Autoantibodies with Specificity for Aberrant Glycoproteins: Assessment of a Therapeutic Target in an Autoimmune Disease  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Plasma Cells in Health and Disease - Project 1: Epigenetic and Metabolic Mechanisms Governing Commitment to the Long-lived Plasma Cell Pool  awarded by Emory University
  • Regulation of T Cell Responses to Allergens and Environmental Microbes  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Resident Cardiac Macrophage Dysfunction and Pneumonia-Associated Adverse Cardiac Events  awarded by American Heart Association
  • TLR7 and TLR9-Directed Plasma Cell Formation: Dissecting the Molecular Basis for their Differential Dependence on IFN-Induced Signals  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Targeting IgM Memory to Establish Protective B Cell Responses to HIV  awarded by University of Rochester Medical Center
  • Targeting Tonsillar B Cells for the Induction of Effective Mucosal Immunity to HIV  awarded by National Institute of Dental and Craniofacial Research/NIH/DHHS
  • The Origin and Future Protective Activity of SARS-CoV-2 RBD Specific Neutralizing Antibodies  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Tissue and Organ Specific Human B Cell Immunity  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Tissue and Organ Specific Human B Cell Immunity - Project 2: Characterization of Virus-Specific Human B Cell Subsets in Lymphoid and Non-Lymphoid Tissues  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Tissue and Organ Specific Human B Cell Immunity - Supplement - Metabolic Risk Factors and Inflammation in PASC Development  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Virus-Induced Cell Fate Decisions in Anti-Viral Immunity  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Virus-induced Cell Fate Decisions in Anti-Viral Immunity - Administrative Supplement  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Teaching Overview

  • I am the course director for INFO 610/710 Programming with Biological Data - offered yearly in the summer session. This course provides students necessary bioinformatics programming and data skills using Linux, MySQL and Python or R. Emphasis will be placed on best practices for conduct of reproducible research. The focus will be on practical computing, programming and data management concepts that can be applied to bioinformatics and data analysis problems. This course assumes no computational background and a primary learning goal is to learn how to learn about computational tools and approaches to foster independence in students working in an increasingly complex landscape of data.
  • Education And Training

  • Doctor of Philosophy in Neuroscience, University of Pittsburgh 1993
  • Bachelor of Engineering in Electrical, Electronics and Communications Engineering, University of Delaware 1987
  • Full Name

  • Alexander Rosenberg