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BACKGROUND The interrogation of proteomes ("proteomics") in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine. METHODOLOGY/PRINCIPAL FINDINGS We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes(More)
BACKGROUND Lung cancer is the leading cause of cancer deaths worldwide. New diagnostics are needed to detect early stage lung cancer because it may be cured with surgery. However, most cases are diagnosed too late for curative surgery. Here we present a comprehensive clinical biomarker study of lung cancer and the first large-scale clinical application of a(More)
CT screening for lung cancer is effective in reducing mortality, but there are areas of concern, including a positive predictive value of 4% and development of interval cancers. A blood test that could manage these limitations would be useful, but development of such tests has been impaired by variations in blood collection that may lead to poor(More)
BACKGROUND Malignant pleural mesothelioma (MM) is an aggressive, asbestos-related pulmonary cancer that is increasing in incidence. Because diagnosis is difficult and the disease is relatively rare, most patients present at a clinically advanced stage where possibility of cure is minimal. To improve surveillance and detection of MM in the high-risk(More)
Lung cancer remains the most common cause of cancer-related mortality. We applied a highly multiplexed proteomic technology (SOMAscan) to compare protein expression signatures of non small-cell lung cancer (NSCLC) tissues with healthy adjacent and distant tissues from surgical resections. In this first report of SOMAscan applied to tissues, we highlight 36(More)
Identifying interpretable discriminative high-order feature interactions given limited training data in high dimensions is challenging in both machine learning and data mining. In this paper, we propose a factorization based sparse learning framework termed FHIM for identifying high-order feature interactions in linear and logistic regression models, and(More)
Disrupted or abnormal biological processes responsible for cancers often quantitatively manifest as disrupted additive and multiplicative interactions of gene/protein expressions correlating with cancer progression. However, the examination of all possible combinatorial interactions between gene features in most case-control studies with limited training(More)
Graphical models have gained a lot of attention recently as a tool for learning and representing dependencies among variables in multivariate data. Often, domain scientists are looking specifically for differences among the dependency networks of different conditions or populations (e.g. differences between regulatory networks of different species, or(More)
  • Sanjay Purushotham, Martin Renqiang, Min, C.-C Jay Kuo, Rachel Ostroff
  • 2014
Identifying interpretable discriminative high-order feature interactions given limited training data in high dimensions is challenging in both machine learning and data mining. In this paper, we propose a factorization based sparse learning framework termed FHIM for identifying high-order feature interactions in linear and logistic regression models, and(More)
Motivation: Responsible for many complex human diseases including cancers, disrupted or abnormal gene interactions can be identified through their expression changes correlating with the progression of a disease. However, the examination of all possible combinatorial interactions between gene features in a genome-wide case-control study is computationally(More)
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