Benjamin D. Greenbaum

This paper introduces CloneSearch, a method to identify expanding and contracting T cell clones from longitudinal TCR sequencing without requiring antigen-specific information.

The paper identifies TIE CD8+ T cell clonotypes associated with prolonged survival in pancreatic cancer patients and links resistance to stromal and immune barriers.

The paper introduces enFoldX, a structure-based method for predicting TCR:pMHC binding using AlphaFold3 ensembles, achieving high accuracy for cognate vs. non-cognate classification.

This study compares genomic and immunologic features of germline TP53-driven breast cancers to sporadic breast cancers, finding distinct patterns of genomic instability and immune infiltration.

This study uses spatial transcriptomics and single-cell analysis to reveal how MDS bone marrow microenvironments are altered, showing TGFβ dysregulation in malignant cells and immune escape mechanisms.

This study shows mutant p53 uses its C-terminal domain to reprogram PARP activity, enabling replication stress adaptation and metastasis in TNBC, and identifies mtp53 as a biomarker for PARP inhibitor and DNA-damaging therapy.

The paper identifies MDF, a repair scar linked to POLQ-driven error-prone repair, as a marker of immune-responsive HRD pancreatic cancer with increased neoantigens and favorable clinical outcomes.

The paper analyzes how neoantigenic properties of TP53 variants correlate with cancer risk and presentation in Li-Fraumeni syndrome carriers.

The paper quantifies viral mimicry in genomes across species and shows how repetitive elements maintain pathogen-like features under selection.

The paper maps T cell epitopes in SARS-CoV-2, showing that immunodominant regions are conserved across variants and important for immune surveillance.

GeneVector uses mutual information-based dimensionality reduction to identify transcriptional programs and classify cell types across single-cell RNA-seq datasets.

This paper introduces TCRi, an information theoretic framework to analyze TCR and gene expression data from cancer patients, showing improved characterization of clonotypes and their phenotypic changes post-therapy.

This study identifies molecular and immune features associated with response to anti-PD-(L)1 therapy in NSCLC using a cohort of 393 patients.

sgDI-tector detects and quantifies subgenomic RNAs in SARS-CoV-2 NGS data, identifying a ranked set of sgRNAs and comparing their levels to defective interfering viral genomes.

This paper develops a probabilistic machine learning model to identify antigen-specific TCRs using sequence data and clone abundance, enabling personalized discrimination of specific versus non-specific T-cell responses.

This study identifies HNRNPM as a splicing factor critical for prostate cancer cell growth by regulating splicing fidelity and circRNA biogenesis, suggesting it as a therapeutic target.

The paper analyzes CpG dinucleotide distribution in SARS-CoV-2, finding low average CpG content with fluctuations linked to immune evasion and replication strategies.