@article {79,
	title = {BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models},
	journal = {PLoS One},
	volume = {11},
	year = {2016},
	month = {2016},
	pages = {e0148379},
	abstract = {<p>BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.</p>},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0148379},
	author = {Bilgin, Cemal Cagatay and Fontenay, Gerald and Cheng, Qingsu and Hang Chang and Ju Han and Parvin, Bahram}
}
@article {241,
	title = {Stiffness of the microenvironment upregulates ERBB2 expression in 3D cultures of MCF10A within the range of mammographic density.},
	journal = {Sci Rep},
	volume = {6},
	year = {2016},
	month = {2016},
	pages = {28987},
	abstract = {<p>The effects of the stiffness of the microenvironment on the molecular response of 3D colony organization, at the maximum level of mammographic density (MD), are investigated. Phenotypic profiling reveals that 3D colony formation is heterogeneous and increased stiffness of the microenvironment, within the range of the MD, correlates with the increased frequency of aberrant 3D colony formation. Further integrative analysis of the genome-wide transcriptome and phenotypic profiling hypothesizes overexpression of ERBB2 in the premalignant MCF10A cell lines at a stiffness value that corresponds to the collagen component at high mammographic density. Subsequently, ERBB2 overexpression has been validated in the same cell line. Similar experiments with a more genetically stable cell line of 184A1 also revealed an increased frequency of aberrant colony formation with the increased stiffness; however, 184A1 did not demonstrate overexpression of ERBB2 at the same stiffness value of the high MD. These results suggest that stiffness exacerbates premalignant cell line of MCF10A.</p>},
	issn = {2045-2322},
	doi = {10.1038/srep28987},
	author = {Cheng, Qingsu and Bilgin, Cemal Cagatay and Fonteney, Gerald and Hang Chang and Henderson, Matthew and Han, Ju and Parvin, Bahram}
}
