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Network component analysis: Reconstruction of regulatory signals in biological systems
We develop a method, called network component analysis, for uncovering hidden regulatory signals from outputs of networked systems, when only a partial knowledge of the underlying network topology is available. Expand
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Cell autonomous role of PTEN in regulating castration-resistant prostate cancer growth.
Alteration of the PTEN/PI3K pathway is associated with late-stage and castrate-resistant prostate cancer (CRPC). However, how PTEN loss is involved in CRPC development is not clear. Here, we showExpand
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Pten loss and RAS/MAPK activation cooperate to promote EMT and metastasis initiated from prostate cancer stem/progenitor cells.
PTEN loss or PI3K/AKT signaling pathway activation correlates with human prostate cancer progression and metastasis. However, in preclinical murine models, deletion of Pten alone fails to mimic theExpand
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Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli
Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense, microorganisms possess a complex network to copeExpand
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Ensemble modeling of metabolic networks.
Complete modeling of metabolic networks is desirable, but it is difficult to accomplish because of the lack of kinetics. As a step toward this goal, we have developed an approach to build an ensembleExpand
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Identification of CD166 as a Surface Marker for Enriching Prostate Stem/Progenitor and Cancer Initiating Cells
New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining unique properties and pathways of cell sub-populations capable of sustaining the net growth of theExpand
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Organoid cystogenesis reveals a critical role of microenvironment in human polycystic kidney disease
Polycystic kidney disease (PKD) is a life-threatening disorder, commonly caused by defects in polycystin-1 (PC1) or polycystin-2 (PC2), in which tubular epithelia form fluid-filled cysts 1, 2. AExpand
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High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping.
Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-throughput screening (HTS), but the complexity of organoid cultures poses a significant challenge forExpand
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gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation.
Network Component Analysis (NCA) is a network structure-driven framework for deducing regulatory signal dynamics. In contrast to classical approaches such as principal component analysis orExpand
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Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer
Purpose: To carry out an integrative profile of human pancreatic ductal adenocarcinoma (PDAC) to identify prognosis-significant genes and their related pathways. Experimental Design: A concordantExpand
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