The Experts below are selected from a list of 440148 Experts worldwide ranked by ideXlab platform
Ralph Weissleder - One of the best experts on this subject based on the ideXlab platform.
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Use of Magnetic Nanoparticles as Nanosensors to Probe for Molecular Interactions
ChemBioChem, 2004Co-Authors: J. Manuel Perez, Lee Josephson, Ralph WeisslederAbstract:Biocompatible magnetic nanosensors have been designed to detect Molecular Interactions in biological media. Upon target binding, these nanosensors cause changes in the spin–spin relaxation times of neighboring water molecules, which can be detected by magnetic resonance (NMR/MRI) techniques. These magnetic nanosensors have been designed to detect specific mRNA, proteins, enzymatic activity, and pathogens (e.g., virus) with sensitivity in the low femtomole range (0.5–30 fmol).
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA–DNA, protein–protein, protein–small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogenous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
Manuel J Perez - One of the best experts on this subject based on the ideXlab platform.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA–DNA, protein–protein, protein–small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogenous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
Lee Josephson - One of the best experts on this subject based on the ideXlab platform.
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Use of Magnetic Nanoparticles as Nanosensors to Probe for Molecular Interactions
ChemBioChem, 2004Co-Authors: J. Manuel Perez, Lee Josephson, Ralph WeisslederAbstract:Biocompatible magnetic nanosensors have been designed to detect Molecular Interactions in biological media. Upon target binding, these nanosensors cause changes in the spin–spin relaxation times of neighboring water molecules, which can be detected by magnetic resonance (NMR/MRI) techniques. These magnetic nanosensors have been designed to detect specific mRNA, proteins, enzymatic activity, and pathogens (e.g., virus) with sensitivity in the low femtomole range (0.5–30 fmol).
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA–DNA, protein–protein, protein–small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogenous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
Jimeng Sun - One of the best experts on this subject based on the ideXlab platform.
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skipgnn predicting Molecular Interactions with skip graph networks
Scientific Reports, 2020Co-Authors: Kexin Huang, Cao Xiao, Lucas M Glass, Marinka Zitnik, Jimeng SunAbstract:Molecular interaction networks are powerful resources for Molecular discovery. They are increasingly used with machine learning methods to predict biologically meaningful Interactions. While deep learning on graphs has dramatically advanced the prediction prowess, current graph neural network (GNN) methods are mainly optimized for prediction on the basis of direct similarity between interacting nodes. In biological networks, however, similarity between nodes that do not directly interact has proved incredibly useful in the last decade across a variety of interaction networks. Here, we present SkipGNN, a graph neural network approach for the prediction of Molecular Interactions. SkipGNN predicts Molecular Interactions by not only aggregating information from direct Interactions but also from second-order Interactions, which we call skip similarity. In contrast to existing GNNs, SkipGNN receives neural messages from two-hop neighbors as well as immediate neighbors in the interaction network and non-linearly transforms the messages to obtain useful information for prediction. To inject skip similarity into a GNN, we construct a modified version of the original network, called the skip graph. We then develop an iterative fusion scheme that optimizes a GNN using both the skip graph and the original graph. Experiments on four interaction networks, including drug-drug, drug-target, protein-protein, and gene-disease Interactions, show that SkipGNN achieves superior and robust performance. Furthermore, we show that unlike popular GNNs, SkipGNN learns biologically meaningful embeddings and performs especially well on noisy, incomplete interaction networks.
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skipgnn predicting Molecular Interactions with skip graph networks
arXiv: Molecular Networks, 2020Co-Authors: Kexin Huang, Cao Xiao, Lucas M Glass, Marinka Zitnik, Jimeng SunAbstract:Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful Interactions. While deep learning on graphs has dramatically advanced the prediction prowess, current graph neural network (GNN) methods are optimized for prediction on the basis of direct similarity between interacting nodes. In biological networks, however, similarity between nodes that do not directly interact has proved incredibly useful in the last decade across a variety of interaction networks. Here, we present SkipGNN, a graph neural network approach for the prediction of Molecular Interactions. SkipGNN predicts Molecular Interactions by not only aggregating information from direct Interactions but also from second-order Interactions, which we call skip similarity. In contrast to existing GNNs, SkipGNN receives neural messages from two-hop neighbors as well as immediate neighbors in the interaction network and non-linearly transforms the messages to obtain useful information for prediction. To inject skip similarity into a GNN, we construct a modified version of the original network, called the skip graph. We then develop an iterative fusion scheme that optimizes a GNN using both the skip graph and the original graph. Experiments on four interaction networks, including drug-drug, drug-target, protein-protein, and gene-disease Interactions, show that SkipGNN achieves superior and robust performance, outperforming existing methods by up to 28.8\% of area under the precision recall curve (PR-AUC). Furthermore, we show that unlike popular GNNs, SkipGNN learns biologically meaningful embeddings and performs especially well on noisy, incomplete interaction networks.
Terrence Oloughlin - One of the best experts on this subject based on the ideXlab platform.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA–DNA, protein–protein, protein–small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogenous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
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magnetic relaxation switches capable of sensing Molecular Interactions
Nature Biotechnology, 2002Co-Authors: Manuel J Perez, Terrence Oloughlin, Dagmar Hogemann, Lee Josephson, Ralph WeisslederAbstract:Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect Molecular Interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of Molecular Interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these Interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.
