FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis

Y Zhang, DJ Topham, J Thakar, X Qiu - Bioinformatics, 2017 - academic.oup.com
Motivation Gene set enrichment analyses (GSEAs) are widely used in genomic research to
identify underlying biological mechanisms (defined by the gene sets), such as Gene …

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

A Niarakis, J Thakar, M Barberis, M Rodríguez Martínez… - 2022 - academic.oup.com
Abstract Summary The Community of Special Interest (COSI) in Computational Modelling of
Biological Systems (SysMod) brings together interdisciplinary scientists interested in …

Meta-analysis of cell-specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes

A Khan, D Katanic, J Thakar - BMC bioinformatics, 2017 - Springer
Background Despite advances in the gene-set enrichment analysis methods; inadequate
definitions of gene-sets cause a major limitation in the discovery of novel biological …

Potential genes and pathways of neonatal sepsis based on functional gene set enrichment analyses

YX Meng, XH Cai, LP Wang - Computational and Mathematical …, 2018 - Wiley Online Library
Background. Neonatal sepsis (NS) is considered as the most common cause of neonatal
deaths that newborns suffer from. Although numerous studies focus on gene biomarkers of …

[HTML][HTML] Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein

J Thakar, Y Qian, L Benoodt, D Roumanes, X Qiu… - Vaccine: X, 2020 - Elsevier
Respiratory syncytial virus (RSV) is the most important cause of respiratory tract illness
especially in young infants that develop severe disease requiring hospitalization, and …

Network analysis of large-scale data and its application to immunology

L Benoodt, J Thakar - Immunoinformatics, 2020 - Springer
Diseases and infections elicit a multilayered immune response which consists of molecular
and cellular interaction cascades. Recent advances in high-throughput technologies have …

[图书][B] Executable Models of Signaling Pathways and Application to HIV

R Palli - 2020 - search.proquest.com
Executable models of signaling pathways enable transforming static pictures of signaling
pathways into models that can be used for in-silico experimentation, thereby facilitating …

Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases

R Palli, J Thakar - Computational Cell Biology: Methods and Protocols, 2018 - Springer
Complex interactions involved in host response to infections and diseases require advanced
analytical tools to infer drivers of the response in order to develop strategies for intervention …

[图书][B] Novel Statistical Methods for Gene Set Enrichment Analysis with Empirical Memberships for Overlapping Genes

Y Zhang - 2018 - search.proquest.com
Abstract Gene Set Enrichment Analysis (GSEA) is a powerful inferential tool that incor-
porates knowledge of a priori defined gene sets (eg molecular pathways) into the high …