Computational tools for inferring transcription factor activity

D Hecker, M Lauber, F Behjati Ardakani… - …, 2023 - Wiley Online Library
Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in
cells. Still, their exact modes of action and dependencies on other regulatory aspects remain …

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells

WKM Lai, L Mariani, G Rothschild, ER Smith… - Genome …, 2021 - genome.cshlp.org
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu.
However, antibody availability and reliability can be problematic, whereas epitope tagging …

Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data

CZ Ma, MR Brent - Bioinformatics, 2021 - academic.oup.com
Motivation The activity of a transcription factor (TF) in a sample of cells is the extent to which
it is exerting its regulatory potential. Many methods of inferring TF activity from gene …

REMIND-Cancer: A Recurrence-Agnostic Workflow for Identifying and Prioritizing Functional Promoter Single Nucleotide Variants

NAB Abad - 2024 - archiv.ub.uni-heidelberg.de
The discovery of functional cancer drivers has traditionally focused on mutations within
coding regions of DNA, despite these regions comprising only about 2% of the entire …

TFA inference: Using mathematical modeling of gene expression data to infer the activity of transcription factors

C Ma - 2022 - search.proquest.com
Transcription factors (TFs) are a set of proteins that play a key role in the information
processing system that enables a cell to respond to changes in internal and external state …

A ChIP-exo screen of 887 PCRP transcription factor antibodies in human cells

WKM Lai, L Mariani, G Rothschild, ER Smith… - bioRxiv, 2020 - biorxiv.org
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu.
However, antibody availability and reliability are problematic and epitope tagging can be …

[PDF][PDF] Inaugural dissertation for obtaining the doctoral degree of the Combined Faculty of Mathematics

NAB Abad - d-nb.info
The discovery of functional cancer drivers has traditionally focused on mutations within
coding regions of DNA, despite these regions comprising only about 2% of the entire …

Estimating Gene Regulatory Activity using Mathematical Optimization

S Trescher - 2020 - edoc.hu-berlin.de
Gene regulation is one of the most important cellular processes and closely interlinked
pathogenesis. The elucidation of regulatory mechanisms can be approached by many …

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R Cao, J Wang, P Brunner, JT Willie, X Li… - …, 2024 - digitalcommons.wustl.edu
Recognizing familiar faces and learning new faces play an important role in social cognition.
However, the underlying neural computational mechanisms remain unclear. Here, we …