NLM DIR Seminar Schedule
UPCOMING SEMINARS
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July 3, 2025 Matthew Diller
Using Ontologies to Make Knowledge Computable -
July 15, 2025 Noam Rotenberg
Cell phenotypes in the biomedical literature: a systematic analysis and the NLM CellLink text mining corpus
RECENT SEMINARS
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July 3, 2025 Matthew Diller
Using Ontologies to Make Knowledge Computable -
July 1, 2025 Yoshitaka Inoue
Graph-Aware Interpretable Drug Response Prediction and LLM-Driven Multi-Agent Drug-Target Interaction Prediction -
June 10, 2025 Aleksandra Foerster
Interactions at pre-bonding distances and bond formation for open p-shell atoms: a step toward biomolecular interaction modeling using electrostatics -
June 3, 2025 MG Hirsch
Interactions among subclones and immunity controls melanoma progression -
May 29, 2025 Harutyun Sahakyan
In silico evolution of globular protein folds from random sequences
Scheduled Seminars on April 25, 2024
Contact NLMDIRSeminarScheduling@mail.nih.gov with questions about this seminar.
Abstract:
Transcriptome analysis is a key tool allowing to investigate healthy and diseased tissues at the molecular level. While single-cell RNA sequencing offers valuable insights into cell types and states, complex sample preparation procedures and higher cost restrict its widespread adoption compared to the older bulk RNA sequencing, which is already widely established, has lower cost, and exhaustive population-level data collections available. In addition, newer technology in form of spatial transcriptomics, which offers locality-based insights, essentially produces data from many thousands of localized bulk mixtures. However, bulk expression data comprise a mixture of heterogeneous cell types and capture average expression. Thus, deconvolving bulk mixtures and inferring cell type populations from bulk expression, remains indispensable.
Many computational methods have been developed to infer cell type proportions from bulk data, generally with the use of reference data based on single-cell sequencing, which guides the process. However, technological inconsistencies between the bulk mixtures and the reference affect the accuracy of such approaches. Moreover, medical conditions are also associated with tissue reprogramming, possibly resulting in changes in cell type composition.
In this talk, a new model for cell type deconvolution is introduced; to our knowledge the first one to offer condition-aware cell type deconvolution. It allows both the incorporation of a quantitative condition that may have a sample-specific effect on expression of certain genes in certain cell types, as well as an implicit mechanism of correction for inconsistencies between the reference and the bulk mixtures. We give an efficient method to solve the model, inferring both cell type proportions as well as the trend of the influence of the quantitative condition on genes expression in cell type populations. Our benchmarks demonstrate the increased accuracy of this model over more basic models, and increased resilience to inconsistencies between the reference and the bulk expression.