Abstract: Compositions, methods, and kits are provided for diagnosing hepatocellular carcinoma in patients. In particular, methylated cell-free DNA biomarkers and methods of using them to determine if a patient has hepatocellular carcinoma are provided. Additionally, the methylated cell-free DNA biomarkers can be used to distinguish between patients with a chronic liver disease such as cirrhosis who do not have hepatocellular carcinoma and those patients with a chronic liver disease who have hepatocellular carcinoma. The identified biomarkers can be used alone or in combination with one or more additional biomarkers or relevant clinical parameters in prognosis, diagnosis, therapy selection, or monitoring treatment of hepatocellular carcinoma.

Abstract: Systems and methods for targeted therapy based on single-cell stimulus perturbation response. In one embodiment, a method for optimizing stimulus combinations for therapy includes receiving a cell sample, treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli, labeling the cell sample with a plurality of metal-conjugated probes, analyzing the cell sample using a mass spectrometer, obtaining mass spectrometry data from the mass spectrometer, identifying subpopulations within the cell sample using the mass spectrometry data, computing stimulus effects, generating a nested-effects model using the mass spectrometry data, and scoring stimuli combinations using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli.

Abstract: An example method for analyzing quantitative information obtained from radiological images includes identifying a ROI or a VOI in a radiological image, segmenting the ROI or the VOI from the radiological image and extracting quantitative features that describe the ROI or the VOI. The method also includes creating a radiological image record including the quantitative features, imaging parameters of the radiological image and clinical parameters and storing the radiological image record in a data structure containing a plurality of radiological image records. In addition, the method includes receiving a request with the patient's radiological image or information related thereto, analyzing the data structure to determine a statistical relationship between the request and the radiological image records and generating a patient report with a diagnosis, a prognosis or a recommended treatment regimen for the patient's disease based on a result of analyzing the data structure.

Abstract: Methods and systems for determining progression and other characteristics of microarray expression levels and similar information, alternatively using a network or communications medium or tangible storage medium or logic processor.

Abstract: An example method for analyzing quantitative information obtained from radiological images includes identifying a ROI or a VOI in a radiological image, segmenting the ROI or the VOI from the radiological image and extracting quantitative features that describe the ROI or the VOI. The method also includes creating a radiological image record including the quantitative features, imaging parameters of the radiological image and clinical parameters and storing the radiological image record in a data structure containing a plurality of radiological image records. In addition, the method includes receiving a request with the patient's radiological image or information related thereto, analyzing the data structure to determine a statistical relationship between the request and the radiological image records and generating a patient report with a diagnosis, a prognosis or a recommended treatment regimen for the patient's disease based on a result of analyzing the data structure.

Abstract: Systems and methods for targeted therapy based on single-cell stimulus perturbation response. In one embodiment, a method for optimizing stimulus combinations for therapy includes receiving a cell sample, treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli, labeling the cell sample with a plurality of metal-conjugated probes, analyzing the cell sample using a mass spectrometer, obtaining mass spectrometry data from the mass spectrometer, identifying subpopulations within the cell sample using the mass spectrometry data, computing stimulus effects, generating a nested-effects model using the mass spectrometry data, and scoring stimuli combinations using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli.

Abstract: An example method for analyzing quantitative information obtained from radiological images includes identifying a ROI or a VOI in a radiological image, segmenting the ROI or the VOI from the radiological image and extracting quantitative features that describe the ROI or the VOI. The method also includes creating a radiological image record including the quantitative features, imaging parameters of the radiological image and clinical parameters and storing the radiological image record in a data structure containing a plurality of radiological image records. In addition, the method includes receiving a request with the patient's radiological image or information related thereto, analyzing the data structure to determine a statistical relationship between the request and the radiological image records and generating a patient report with a diagnosis, a prognosis or a recommended treatment regimen for the patient's disease based on a result of analyzing the data structure.

Abstract: An example method for analyzing quantitative information obtained from radiological images includes identifying a ROI or a VOI in a radiological image, segmenting the ROI or the VOI from the radiological image and extracting quantitative features that describe the ROI or the VOI. The method also includes creating a radiological image record including the quantitative features, imaging parameters of the radiological image and clinical parameters and storing the radiological image record in a data structure containing a plurality of radiological image records. In addition, the method includes receiving a request with the patient's radiological image or information related thereto, analyzing the data structure to determine a statistical relationship between the request and the radiological image records and generating a patient report with a diagnosis, a prognosis or a recommended treatment regimen for the patient's disease based on a result of analyzing the data structure.

Abstract: Methods and systems for determining progression and other characteristics of microarray expression levels and similar information, alternatively using a network or communications medium or tangible storage medium or logic processor.