Tara Eicher
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View article: BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops
BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops Open
Summary In analyzing gene regulatory network models, a common question is how members of a particular set of genes are connected. For example, one might want to explore network relationship between a set of differentially expressed genes, …
View article: Finding Salient Multi-Omic Interactomes Relevant to Multiple Biomedical Outcomes using Graph Ensemble Neural Networks
Finding Salient Multi-Omic Interactomes Relevant to Multiple Biomedical Outcomes using Graph Ensemble Neural Networks Open
Although multi-omics integration relevant to patient outcome is typically characterized by an analyte interactome, current multi-omic integration methods either (1) model outcome without directly including associations between analytes, (2…
View article: Consistent Multi-Omic Relationships Uncover Molecular Basis of Pediatric Asthma IgE Regulation
Consistent Multi-Omic Relationships Uncover Molecular Basis of Pediatric Asthma IgE Regulation Open
Serum total immunoglobulin E levels (total IgE) capture the state of the immune system in relation to allergic sensitization. High levels are associated with airway obstruction and poor clinical outcomes in pediatric asthma. Inconsistent p…
View article: IntLIM 2.0: identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements
IntLIM 2.0: identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements Open
Motivation IntLIM uncovers phenotype-dependent linear associations between two types of analytes (e.g. genes and metabolites) in a multi-omic dataset, which may reflect chemically or biologically relevant relationships. Results The new Int…
View article: RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes Open
Motivation Functional interpretation of high-throughput metabolomic and transcriptomic results is a crucial step in generating insight from experimental data. However, pathway and functional information for genes and metabolites are distri…
View article: PATH-13. IMAGE-BASED PHENOTYPING OF GLIOMAS FOR CLINICAL USE
PATH-13. IMAGE-BASED PHENOTYPING OF GLIOMAS FOR CLINICAL USE Open
Adult-type diffuse gliomas have been classified according to histopathological characteristics only. Based on molecular profiles, the World Health Organization (WHO) classification defines three distinct biologic and prognostic types of di…
View article: RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites Open
RaMP-DB 2.0 is a web interface, API, relational database and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. Since its first release in 2018, RaMP-DB 2.0 has been upgra…
View article: Additional file 1 of Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements
Additional file 1 of Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements Open
Additional file 1. Supplementary Tables. This file contains Supplementary Tables 1–7.
View article: An OpenData portal to share COVID-19 drug repurposing data in real time
An OpenData portal to share COVID-19 drug repurposing data in real time Open
The National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign – named OpenData – with the goal of making data across a range of SARS-CoV-2 relat…
View article: Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources Open
As researchers are increasingly able to collect data on a large scale from multiple clinical and omics modalities, multi-omics integration is becoming a critical component of metabolomics research. This introduces a need for increased unde…
View article: Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge Open
Background Proteomic measurements, which closely reflect phenotypes, provide insights into gene expression regulations and mechanisms underlying altered phenotypes. Further, integration of data on proteome and transcriptome levels can vali…
View article: MOESM1 of Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
MOESM1 of Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge Open
Additional file 1. Supplementary Figures
View article: PO-389 Epigenomic and mutation determinants of carcinogen-driven primary epithelial cell immortalization
PO-389 Epigenomic and mutation determinants of carcinogen-driven primary epithelial cell immortalization Open
Introduction Based on cancer genome sequencing, almost 600 genes have been implicated in cancer development to date, and recently, chromatin structural changes have emerged as a key mechanism for translating exogenous cues, such as carcin…