Biomedical Informatics Hub

The Cancer Genome Atlas (TCGA) has been one of the clearing houses of genome-wide array data for the understanding of the molecular basis of cancer from large cohorts. These analyses are intrinsically from bulk measurements of mixed cell types, derived from frozen biopsy sections that include tissues with mixed histopathology and/or microanatomies (e.g., tumor, stroma). While bulk array profiling may provide insights into molecular aberrations, it provides only an average genome-wide measurement for a biopsy and fails to reveal inherent cellular composition and heterogeneity of a tumor. On the other hand, histology sections do not provide standardized measurements, but they are rich in content and continue to be the gold standard for the assessment of tissue neoplasm.

In this project, we aims to provide univariate cellular morphoetric summarization for TCGA Kidney Renal Clear Cell Carcinoma (KIRC) Cohort, which can be further utilized for various end points, such as,

• integrated analysis with OMIC data;
• construction of predictive models of clinical outcome

Examples can be found in our previous publication:

• Hang Chang, Ju Han, Alexander Borowsky, Leandro Loss, Jow W. Gray, Paul T. Spellman and Bahram Parvin. "Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association." IEEE Trans. on Medical Imaging, 32 4 (2013): 670-682.

Visualization Tool:  KIRC Whole Slide Images (WSI) and the corresponding segmentation results.

The Cancer Genome Atlas (TCGA) has been one of the clearing houses of genome-wide array data for the understanding of the molecular basis of cancer from large cohorts. These analyses are intrinsically from bulk measurements of mixed cell types, derived from frozen biopsy sections that include tissues with mixed histopathology and/or microanatomies (e.g., tumor, stroma). While bulk array profiling may provide insights into molecular aberrations, it provides only an average genome-wide measurement for a biopsy and fails to reveal inherent cellular composition and heterogeneity of a tumor. On the other hand, histology sections do not provide standardized measurements, but they are rich in content and continue to be the gold standard for the assessment of tissue neoplasm.

In this project, we aims to provide joint cellular morphometric context summarization for TCGA Glioblastoma (GBM) and lower grade glioma (LGG) cohorts, which can be further utilized for various end points, such as,

• integrated analysis with OMIC data; and
• construction of predictive models of clinical outcome.

Examples can be found in our previous publication:

• Hang Chang, Ju Han, Alexander Borowsky, Leandro Loss, Jow W. Gray, Paul T. Spellman and Bahram Parvin. "Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association." IEEE Trans. on Medical Imaging, 32 4 (2013): 670-682.

Visualization Tool:  GBM Whole Slide Images (WSI) and the corresponding segmentation results.

Visualization Tool:  LGG Whole Slide Images (WSI) and the corresponding segmentation results.

We used gene transcript profiling to gain a deeper understanding of the role of FBXW7 in tumor development and to determine the influence of mTOR inhibition by rapamycin on tumor transcriptome and biological functions. In comparison to tumors from p53 single heterozygous (p53+/-) mice, we find that tumors from Fbxw7/p53 double heterozygous (Fbxw7+/-p53+/-) mice show significant deregulation of cholesterol metabolic processes independent of rapamycin treatment, while cell cycle related genes were upregulated in tumors from placebo treated Fbxw7+/-p53+/- mice, but not in tumors from rapamycin treated Fbxw7+/-p53+/- mice. On the other hand, tumors from rapamycin treated Fbxw7+/-p53+/- mice were enriched for genes involved in the integrated stress response, an adaptive mechanism to survive in stressful environments.

Iterrative Radial Voting is an advanced image processing algorithm, initially developed by the Imaing and Informatics Lab at Lawrence Berkeley National Laboratory for the inference of structural saliency and characterization of subcellular events. An example of kernel topology and radial object localization is illustrated as follows,

Multispectral Convolutional Sparse Coding is a machine learning algorithm that was initially developed for the classification of distinct regions of microanatomy and histopathology. This project contains the source code (matlab) for Multispectral Convolutional Sparse Coding that is described in the publication as follows,

• Yin Zhou*, Hang Chang*, Kenneth Barner, Paul Spellman, and Bahram Parvin. “Classification of Histology Sections via Multispectral Convolutional Sparse Coding.” IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2014), Columbus, Ohio, U.S, June 2014. (*Co-First Authors)

The Cancer Genome Atlas (TCGA) has been one of the clearing houses of genome-wide array data for the understanding of the molecular basis of cancer from large cohorts. These analyses are intrinsically from bulk measurements of mixed cell types, derived from frozen biopsy sections that include tissues with mixed histopathology and/or microanatomies (e.g., tumor, stroma). While bulk array profiling may provide insights into molecular aberrations, it provides only an average genome-wide measurement for a biopsy and fails to reveal inherent cellular composition and heterogeneity of a tumor. On the other hand, histology sections do not provide standardized measurements, but they are rich in content and continue to be the gold standard for the assessment of tissue neoplasm.

In this project, we aims to provide univariate cellular morphoetric summarization for TCGA lower grade glioma (LGG) Cohort, which can be further utilized for various end points, such as,

• integrated analysis with OMIC data;
• construction of predictive models of clinical outcome

Examples can be found in our previous publication:

• Hang Chang, Ju Han, Alexander Borowsky, Leandro Loss, Jow W. Gray, Paul T. Spellman and Bahram Parvin. "Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association." IEEE Trans. on Medical Imaging, 32 4 (2013): 670-682.

Visualization Tool:  LGG Whole Slide Images (WSI) and the corresponding segmentation results.