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.

This paper introduces a method to decode host and viral family fingerprints in nucleotide usage, showing it outperforms deep learning for classification and enables manipulation of nucleotide composition in viral sequences.

This study shows that SMARCA4 mutations in ovarian cancer increase immunogenicity through interferon response and epigenetic changes, enhancing T cell and NK cell activity in the tumor microenvironment.

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.

The paper identifies host-virus chimeric proteins, called UFOs, generated during influenza virus infection through the translation of viral 5UTRs using host transcripts.