Abigail D Bellis

Northwestern University | NU · Department of Chemical and Biological Engineering

Tissue development and disease progression are multi-stage processes controlled by an evolving set of key regulatory factors, and identifying these factors necessitates a dynamic analysis spanning relevant time scales. Current omics approaches depend on incomplete biological databases to identify critical cellular processes. Herein, we present TRAC...

Identifying the dynamic activity of critical signaling pathways that lead to a given phenotype and inferring the relationships between those critical signaling pathways are still challenges for the systems biology community. In this work we present a new alternative. Our lab has recently established a technique for large-scale analysis of dynamic s...

Live-cell assays to measure cellular function performed within 3D cultures have the potential to elucidate the underlying processes behind disease progression and tissue formation. Cells cultured in 3D interact and remodel their microenvironment and can develop into complex structures. We have developed a transcription factor (TF) activity array th...

Identifying molecular mechanisms or therapeutic targets is typically based on large-scale cellular analysis that measures the abundance of mRNA or protein; however, abundance does not necessarily correlate with activity. We report a method for direct large-scale quantification of active pathways that employs a cellular array with parallel gene deli...

Euclidian clustering of large-scale array data. Means of log2 transformed normalized TF activities from three replicates across three arrays were clustered. Data are denoted as described in Fig. S1. Replicates within arrays clustered together, indicating data could be blocked by array. (0.04 MB DOC)

TF reporters used in large-scale transfected cell arrays. (0.05 MB DOC)

Box plot of replicates from large-scale arrays. Means of log2 transformed normalized TF activities from three replicates across three arrays are shown. ‘1.1’ denotes array 1, replicate 1 and ‘2.3’ denotes array 2, replicate 3, etc. Means and standard deviations were consistent within arrays, with some variability between arrays. No outliers were pr...

Pairwise comparisons of replicates from large-scale arrays. Means of log2 transformed normalized TF activities from three replicates across three arrays were compared. The correlation factor is represented in the bottom right corner of each graph. Comparisons within arrays showed good correlation (R2>0.96), and correlations across arrays were weake...

Extracellular activation of signal transduction pathways and their downstream target transcription factors (TFs) are critical regulators of cellular processes and tissue development. The intracellular signaling network is complex, and techniques that quantify the activities of numerous pathways and connect their activities to the resulting phenotyp...

Many molecular markers have been inadequate for identifying therapeutic targets or predicting patient outcomes, which has motivated the development of cell-based assays that provide the physiological context in which to investigate molecular function. Gene delivery, in particular, is being employed with these assays to manipulate a specific factor...

Transfected cell arrays offer a high-throughput method that allows for the parallel analysis of multiple pathways or genes within a physiological context. We have developed a transfected cell array that employs a dual-plasmid system that gives the ability to normalize for spot-to-spot variation in transfection efficiency. Each spot within the array...

Transfected cell arrays (TCAs) represent a high-throughput technique to correlate gene expression with functional cell responses. Despite advances in TCAs, improvements are needed for the widespread application of this technology. We have developed a TCA that combines a two-plasmid system and dual-bioluminescence imaging to quantitatively normalize...

The cellular microenvironment impacts how signals are transduced by cells and plays a key role in tissue homeostasis. Although pH is generally well regulated, there are a number of situations where acidosis occurs and our work addresses how low pH impacts cell association of insulin-like growth factor-I (IGF-I) in the presence of IGF binding protei...