S. T. Reddy

Deep learning-guided selection of antibody therapies with enhanced resistance to current and prospective SARS-CoV-2 Omicron variants

This study uses deep learning to identify antibodies resistant to SARS-CoV-2 Omicron variants by predicting their binding and escape from mutations.

Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer

This study uses multimodal single-cell profiling to analyze T cell specificity and reactivity in lung cancer patients, identifying tumor- and virus-reactive T cells and their functional states.

Meta Learning Improves Robustness and Performance in Machine Learning-Guided Protein Engineering

This study applies meta learning to protein engineering to improve performance with limited labeled data, showing significant gains over baselines.

A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell therapy applications

The paper introduces a method for CRISPR-targeted genome integration of a barcoded gene into antigen-specific T cells to enhance traceability and monitoring in adoptive cell therapy.

ePlatypus: an ecosystem for computational analysis of immunogenomics data

ePlatypus provides a computational ecosystem for immunogenomics data analysis, integrating diverse modalities and tools to study adaptive immunity and computational immunology.

Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies

The paper evaluates neutralisation resistance of Omicron sublineages BA.2.75.2, BA.4.6, and BA.2.10.4, finding BA.2.75.2 shows extensive escape from neutralising antibodies.

Persistent virus-specific and clonally expanded antibody secreting cells respond to induced self antigen in the CNS

The paper identifies virus-specific, clonally expanded antibody-secreting cells in the CNS that persist and respond to induced self-antigen, with parallels in multiple sclerosis patients.

Evasion of neutralizing antibodies by Omicron sublineage BA.2.75

This study evaluates the neutralization sensitivity of the SARS-CoV-2 BA.2.75 sublineage to monoclonal antibodies and sera from individuals infected with earlier variants.

Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity

The paper profiles clonal selection of B and T cells in murine models of infection and autoimmunity using single-cell sequencing, linking repertoire features to cell phenotypes.

A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron

This paper describes a synthetic bispecific antibody that neutralizes SARS-CoV-2 Delta and Omicron variants with picomolar affinity.

Variable loss of antibody potency against SARS-CoV-2 B.1.1.529 (Omicron)

This study assesses neutralizing antibody responses against the SARS-CoV-2 Omicron variant, showing reduced potency compared to the pandemic founder but with some cross-neutralizing capacity in vaccinated individuals.

Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen-specificity

The paper generates a single-cell B cell atlas to link antibody repertoires, transcriptomes, and antigen specificity in murine immunization models.

The Physiological Landscape and Specificity of Antibody Repertoires

This study analyzes antibody repertoires across multiple lymphoid organs in immunized mice, finding that strong humoral responses lead to consolidated, overlapping B-cell clones and a uniform but redundant physiological landscape.

Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes

Echidna simulates single-cell immune receptor repertoires and transcriptomes, enabling benchmarking of clonotyping and phylogenetic analysis tools.

Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells

This study investigates whether clonal expansion of plasma cells is deterministic or stochastic by analyzing antigen-specificity, affinity, and epitope convergence in antibody repertoires.

Clonally expanded virus-specific CD8 T cells acquire diverse transcriptional phenotypes during acute, chronic, and latent infections

This study examines clonal expansion and transcriptional diversity in virus-specific CD8 T cells across different infection stages using single-cell sequencing and a new bioinformatic tool.

A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients

This study uses single-cell sequencing to analyze immune repertoires and transcriptomes in convalescent COVID-19 patients, revealing age-related differences in T and B cell responses.

Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2

Single-cell sequencing and screening identify expanded plasma cell clones in COVID-19 patients producing SARS-CoV-2-specific neutralizing antibodies.

Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes

Platypus integrates single-cell immune repertoires with transcriptomes to analyze lymphocyte features and transcriptional profiles in convalescent COVID-19 patients.

CRISPR-targeted display of functional T cell receptors enables engineering of enhanced specificity and prediction of cross-reactivity

The paper introduces a CRISPR-based platform to engineer TCRs with enhanced specificity and predict cross-reactivity by profiling mutational landscapes and screening TCR libraries.

Quantification of proteins, protein complexes and mRNA in single cells by proximity-sequencing

This paper introduces Prox-seq, a method to measure proteins, protein complexes, and mRNA in single cells, demonstrating its ability to detect 91 protein complexes and thousands of mRNAs in T-cells and B-cells.

Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice

This study uses single-cell sequencing to show that aged mouse brains have clonally expanded and transcriptionally distinct lymphocytes, potentially contributing to neuroinflammation.

A functional screening platform for engineering chimeric antigen receptors with reduced on-target, off-tumour activation

This study develops a functional screening platform to engineer CARs with reduced on-target, off-tumour activation by selecting for variants that respond only to high antigen expression.

Profiling virus-specific Tcf1+ T cell repertoires during acute and chronic viral infection

The paper analyzes Tcf1+ and Tcf1- T cell repertoires during acute and chronic LCMV infection, finding they are not clonally distinct and show minor differences in repertoire parameters.

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

This study compares IgM antibody repertoires in blood and bone marrow plasma cells of mice after viral infection, finding that they are mouse-specific but not infection-specific.

Convergent selection in antibody repertoires is revealed by deep learning

This study uses deep learning to identify convergent antibody sequences in mice, showing their antigen-specificity and potential for immunodiagnostics.

Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow

The paper identifies discrete populations of isotype-switched memory B cells in murine spleen and bone marrow, with distinct locations and characteristics.

Molecular design, optimization and genomic integration of chimeric B cell receptors in murine B cells

The paper designs, optimizes, and genomically integrates chimeric B cell receptors (CBCRs) in murine B cells using CRISPR-Cas9, demonstrating robust surface expression and antigen recognition.

Exploring Structural Aspects of the Human Golgi Matrix Protein GRASP55 in Solution

This study investigates the structural properties of human GRASP55 in solution, revealing its disordered regions, monomeric state, and aggregation behavior during denaturation.