Ruth Dannenfelser
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View article: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
Interpretable phenotype decoding from multicondition sequencing data with ALPINE Open
As sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has become available, encompassing a wide range of phenotypic features and biological perturbations. Unfortunately, …
View article: Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell types
Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell types Open
A bstract DNA methylation (DNAm) is a core gene regulatory mechanism that captures cellular responses to short- and long-term stimuli such as environmental exposures, aging, and cellular differentiation. Although DNAm has proven valuable a…
View article: Interpretable phenotype decoding from multi-condition sequencing data with ALPINE
Interpretable phenotype decoding from multi-condition sequencing data with ALPINE Open
As sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has become available, encompassing a wide range of phenotypic features and biological perturbations. Unfortunately, …
View article: Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks
Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks Open
Accurate, data-driven representations of genes are critical for interpreting high-throughput biological data, yet no consensus exists on the most effective embedding strategy for common functional prediction tasks. Here, we present a syste…
View article: A best-match approach for gene set analyses in embedding spaces
A best-match approach for gene set analyses in embedding spaces Open
Embedding methods have emerged as a valuable class of approaches for distilling essential information from complex high-dimensional data into more accessible lower-dimensional spaces. Applications of embedding methods to biological data ha…
View article: Disentangling associations between complex traits and cell types with<i>seismic</i>
Disentangling associations between complex traits and cell types with<i>seismic</i> Open
A bstract Integrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific biological processes underlying com…
View article: Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer Open
Protein-protein interactions play an essential role in nearly all biological processes, and it has become increasingly clear that in order to better understand the fundamental processes that underlie disease, we must develop a strong under…
View article: ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces
ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces Open
A bstract Embedding methods have emerged as a valuable class of approaches for distilling essential information from complex high-dimensional data into more accessible lower-dimensional spaces. Applications of embedding methods to biologic…
View article: Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer Open
Protein-protein interactions play an essential role in nearly all biological processes, and it has become increasingly clear that in order to better understand the fundamental processes that underlie disease, we must develop a strong under…
View article: Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts
Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts Open
Many of the most commonly explored natural language processing (NLP) information extraction tasks can be thought of as evaluations of declarative knowledge, or fact-based information extraction. Procedural knowledge extraction, i.e., break…
View article: Joint embedding of biological networks for cross-species functional alignment
Joint embedding of biological networks for cross-species functional alignment Open
Motivation Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, …
View article: Data from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i>
Data from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i> Open
Lymphocytic infiltration is associated with better prognosis in several epithelial malignancies including breast cancer. The tumor suppressor TP53 is mutated in approximately 30% of breast adenocarcinomas, with varying frequency across mol…
View article: Supplementary Figures S1-S5, Tables 1-3 from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i>
Supplementary Figures S1-S5, Tables 1-3 from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i> Open
Supplementary Figures S1-S5, Tables 1-3. S1: Distributions of P values from interaction analysis of Discovery (a) and Validation (c) cohorts. Comparison of Permutation P values and parametric P values for interaction analysis in Discovery …
View article: Supplementary Figures S1-S5, Tables 1-3 from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i>
Supplementary Figures S1-S5, Tables 1-3 from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i> Open
Supplementary Figures S1-S5, Tables 1-3. S1: Distributions of P values from interaction analysis of Discovery (a) and Validation (c) cohorts. Comparison of Permutation P values and parametric P values for interaction analysis in Discovery …
View article: Data from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i>
Data from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type <i>TP53</i> Open
Lymphocytic infiltration is associated with better prognosis in several epithelial malignancies including breast cancer. The tumor suppressor TP53 is mutated in approximately 30% of breast adenocarcinomas, with varying frequency across mol…
View article: Joint embedding of biological networks for cross-species functional alignment
Joint embedding of biological networks for cross-species functional alignment Open
Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this transfer, sequence similarity does not imply functional similarity, and thus, several current approache…
View article: SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma
SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma Open
SynNotch-CAR T cells durably clear glioblastoma xenografts, overcoming dual challenges of antigen heterogeneity and specificity common to solid tumors.
View article: IMMU-33. MULTI-ANTIGEN RECOGNITION CIRCUITS OVERCOME CHALLENGES OF SPECIFICITY, HETEROGENEITY, AND DURABILITY IN T-CELL THERAPY FOR GLIOBLASTOMA
IMMU-33. MULTI-ANTIGEN RECOGNITION CIRCUITS OVERCOME CHALLENGES OF SPECIFICITY, HETEROGENEITY, AND DURABILITY IN T-CELL THERAPY FOR GLIOBLASTOMA Open
Treatment of solid cancers with chimeric antigen receptor (CAR) T-cells is challenging because of a lack of target antigens that are both tumor-specific and homogenously expressed. While epidermal growth factor receptor (EGFR)vIII represen…
View article: Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab
Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab Open
A high concentration of circulating vascular endothelial growth factor (VEGF) in cancer patients is associated with an aggressive tumor phenotype. Here, serum levels of 27 cytokines and blood cell counts were assessed in breast cancer pati…
View article: Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity
Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity Open
The tumor microenvironment is now widely recognized for its role in tumor progression, treatment response, and clinical outcome. The intratumoral immunological landscape, in particular, has been shown to exert both pro-tumorigenic and anti…