Jason Perera
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View article: HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields
HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields Open
We introduce HyperDiffusionFields (HyDiF), a framework that models 3D molecular conformers as continuous fields rather than discrete atomic coordinates or graphs. At the core of our approach is the Molecular Directional Field (MDF), a vect…
View article: Virtual CRISPR: Can LLMs Predict CRISPR Screen Results?
Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? Open
View article: 1202 An NGS-based workflow to estimate allele-specific HLA loss of heterozygosity
1202 An NGS-based workflow to estimate allele-specific HLA loss of heterozygosity Open
View article: Pep2Vec: An Interpretable Model for Peptide-MHC Presentation Prediction and Contaminant Identification in Ligandome Datasets
Pep2Vec: An Interpretable Model for Peptide-MHC Presentation Prediction and Contaminant Identification in Ligandome Datasets Open
As personalized cancer vaccines advance, precise modeling of antigen presentation by MHC class I and II is crucial. High-quality training data is essential for clinical models. Existing deep learning models focus on prediction performance …
View article: Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity
Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity Open
Antigen presentation on MHC class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an…
View article: Graph-pMHC: Graph Neural Network Approach to MHC Class II Peptide Presentation and Antibody Immunogenicity
Graph-pMHC: Graph Neural Network Approach to MHC Class II Peptide Presentation and Antibody Immunogenicity Open
Antigen presentation on MHC Class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an…
View article: 491 BASECAMP-1: an observational study to identify relapsed solid tumor patients with human leukocyte antigen (HLA) loss of heterozygosity (LOH) and leukapheresis for future CAR T-cell therapy
491 BASECAMP-1: an observational study to identify relapsed solid tumor patients with human leukocyte antigen (HLA) loss of heterozygosity (LOH) and leukapheresis for future CAR T-cell therapy Open
Background Solid tumors comprise >90% of cancers. Metastatic colorectal cancer, non-small cell lung cancer, and pancreatic cancer are among the leading causes of cancer-related mortality (5-year overall survival: 14%, 6%, and 3%, respectiv…
View article: 73 Characterization of tumor-infiltrating T-cell repertoire in human cancers
73 Characterization of tumor-infiltrating T-cell repertoire in human cancers Open
Background TCR and BCR repertoire profiling is a promising technique that can provide a clinically useful window into the complex interactions between tumor cells and infiltrating lymphocytes. Despite recent advances in repertoire sequenci…
View article: 68 Rapid detection of somatic variants in human leukocyte antigen class 1 genes from solid tumor samples
68 Rapid detection of somatic variants in human leukocyte antigen class 1 genes from solid tumor samples Open
Background Human Leukocyte Antigens (HLA) class 1 proteins are important for recognizing tumor specific mutations (neoantigens) and presenting them to CD8+ T-cells. Somatic mutations in HLA genes can potentially reduce the set of neoantige…
View article: Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA
Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA Open
Liquid biopsy is a valuable precision oncology tool that is increasingly used as a non-invasive approach to identify biomarkers, detect resistance mutations, monitor disease burden, and identify early recurrence. The Tempus xF liquid biops…
View article: A pan-cancer organoid platform for precision medicine
A pan-cancer organoid platform for precision medicine Open
Patient-derived tumor organoids (TOs) are emerging as high-fidelity models to study cancer biology and develop novel precision medicine therapeutics. However, utilizing TOs for systems-biology-based approaches has been limited by a lack of…
View article: Metadata record for the manuscript: Analytical validation of a targeted liquid biopsy assay with comprehensive molecular and clinical profiling of circulating tumor DNA from 1,000 patients
Metadata record for the manuscript: Analytical validation of a targeted liquid biopsy assay with comprehensive molecular and clinical profiling of circulating tumor DNA from 1,000 patients Open
Summary This metadata record provides details of the data supporting the claims of the related manuscript: “Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA”. The related study prese…
View article: Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction Open
View article: Clinical validation of the tempus xT next-generation targeted oncology sequencing assay
Clinical validation of the tempus xT next-generation targeted oncology sequencing assay Open
We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations and microsatellite instability in solid tumors and hematologic malignancies. This targeted oncology assay utilizes tumor-…
View article: Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance
Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance Open
View article: The development and function of thymic B cells
The development and function of thymic B cells Open