Search Results - "Hoff, Bruce"

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges by Ellrott, Kyle, Buchanan, Alex, Creason, Allison, Mason, Michael, Schaffter, Thomas, Hoff, Bruce, Eddy, James, Chilton, John M, Yu, Thomas, Stuart, Joshua M, Saez-Rodriguez, Julio, Stolovitzky, Gustavo, Boutros, Paul C, Guinney, Justin

“…Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are…”
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Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer by Margolin, Adam A, Bilal, Erhan, Huang, Erich, Norman, Thea C, Ottestad, Lars, Mecham, Brigham H, Sauerwine, Ben, Kellen, Michael R, Mangravite, Lara M, Furia, Matthew D, Vollan, Hans Kristian Moen, Rueda, Oscar M, Guinney, Justin, Deflaux, Nicole A, Hoff, Bruce, Schildwachter, Xavier, Russnes, Hege G, Park, Daehoon, Vang, Veronica O, Pirtle, Tyler, Youseff, Lamia, Citro, Craig, Curtis, Christina, Kristensen, Vessela N, Hellerstein, Joseph, Friend, Stephen H, Stolovitzky, Gustavo, Aparicio, Samuel, Caldas, Carlos, Børresen-Dale, Anne-Lise

“…Although molecular prognostics in breast cancer are among the most successful examples of translating genomic analysis to clinical applications, optimal…”
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Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models by Karr, Jonathan R, Williams, Alex H, Zucker, Jeremy D, Raue, Andreas, Steiert, Bernhard, Timmer, Jens, Kreutz, Clemens, Wilkinson, Simon, Allgood, Brandon A, Bot, Brian M, Hoff, Bruce R, Kellen, Michael R, Covert, Markus W, Stolovitzky, Gustavo A, Meyer, Pablo

“…Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even…”
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How dietary arachidonic- and docosahexaenoic- acid rich oils differentially affect the murine hepatic transcriptome by Berger, Alvin, Roberts, Matthew A, Hoff, Bruce

“…Herein, we expand our previous work on the effects of long chain polyunsaturated fatty acids (LC-PUFA) on the murine hepatic transcriptome using novel…”
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DREAMTools: a Python package for scoring collaborative challenges [version 2; peer review: 1 approved, 2 approved with reservations] by Cokelaer, Thomas, Bansal, Mukesh, Bare, Christopher, Bilal, Erhan, Bot, Brian M, Chaibub Neto, Elias, Eduati, Federica, de la Fuente, Alberto, Gönen, Mehmet, Hill, Steven M, Hoff, Bruce, Karr, Jonathan R, Küffner, Robert, Menden, Michael P, Meyer, Pablo, Norel, Raquel, Pratap, Abhishek, Prill, Robert J, Weirauch, Matthew T, Costello, James C, Stolovitzky, Gustavo, Saez-Rodriguez, Julio

“…DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational…”
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Bayesian network reconstruction using systems genetics data: comparison of MCMC methods by Tasaki, Shinya, Sauerwine, Ben, Hoff, Bruce, Toyoshiba, Hiroyoshi, Gaiteri, Chris, Chaibub Neto, Elias

“…Reconstructing biological networks using high-throughput technologies has the potential to produce condition-specific interactomes. But are these reconstructed…”
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Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database by Clayton, Ashley, DeFelice, Mialy, Zalmanek, Brynn, Hodgson, Jay, Morin, Caroline, Simon, Stockard, Bletz, Julie A, Eddy, James A, Nikolov, Milen, Banerjee, Jineta, Vinnakota, Kalyan, Marasca, Marco, Boske, Kevin J, Hoff, Bruce, Bradic, Ljubomir, Kim, YooRi, Goss, James R, Allaway, Robert J

“…Abstract Experimental tools and resources, such as animal models, cell lines, antibodies, genetic reagents and biobanks, are key ingredients in biomedical…”
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AGORA: A PLATFORM FOR THE DEMOCRATIZATION OF ALZHEIMER’S DISEASE TARGET EVIDENCE by Greenwood, Anna K., Daily, Kenneth, Mukherjee, Sumit, Perumal, Thanneer M., Woo, Kara H., Sieberts, Solveig K., Simon, Stockard, Dembogurski, Renan, Ferreyra, Diego, Peters, Mette A., Do, Khai, Hoff, Bruce, Doerr, Megan, MacDuffie Woodburn, John, Omberg, Larsson, Mangravite, Lara M., Logsdon, Benjamin A.

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P4‐113: AGORA: A PLATFORM FOR THE DEMOCRATIZATION OF ALZHEIMER'S DISEASE TARGET EVIDENCE by Greenwood, Anna K., Daily, Kenneth, Mukherjee, Sumit, Perumal, Thanneer M., Woo, Kara H., Sieberts, Solveig K., Simon, Stockard, Dembogurski, Renan, Ferreyra, Diego, Peters, Mette A., Do, Khai, Hoff, Bruce, Doerr, Megan, MacDuffie Woodburn, John, Omberg, Larsson, Mangravite, Lara M., Logsdon, Benjamin A.

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Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models: e1004096 by Karr, Jonathan R, Williams, Alex H, Zucker, Jeremy D, Raue, Andreas, Steiert, Bernhard, Timmer, Jens, Kreutz, Clemens, Wilkinson, Simon, Allgood, Brandon A, Bot, Brian M, Hoff, Bruce R, Kellen, Michael R, Covert, Markus W, Stolovitzky, Gustavo A, Meyer, Pablo, Consortium, Parameter EstimationChallenge

“…Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even…”
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Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays by DRAGHICI, Sorin, KULAEVA, Olga, HOFF, Bruce, PETROV, Anton, SHAMS, Soheil, TAINSKY, Michael A

“…A crucial step in microarray data analysis is the selection of subsets of interesting genes from the initial set of genes. In many cases, especially when…”
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An effective personalized approach to a rare tumor: prolonged survival in metastatic pancreatic acinar cell carcinoma based on genetic analysis and cell line development by Armstrong, Matthew D, Von Hoff, Daniel, Barber, Bruce, Marlow, Laura A, von Roemeling, Christina, Cooper, Simon J, Travis, Patrick, Campbell, Elizabeth, Paz-Fumagalli, Ricardo, Copland, John A, Colon-Otero, Gerardo

“…Acinar cell carcinoma of the pancreas is an uncommon malignancy, accounting for less than 1% of all pancreatic neoplasms. Because of its rarity, only a few…”
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DREAMTools: a Python package for scoring collaborative challenges by Cokelaer, Thomas, Bansal, Mukesh, Bare, Christopher, Bilal, Erhan, Bot, Brian M, Chaibub Neto, Elias, Eduati, Federica, de la Fuente, Alberto, Gönen, Mehmet, Hill, Steven M, Hoff, Bruce, Karr, Jonathan R, Küffner, Robert, Menden, Michael P, Meyer, Pablo, Norel, Raquel, Pratap, Abhishek, Prill, Robert J, Weirauch, Matthew T, Costello, James C, Stolovitzky, Gustavo, Saez-Rodriguez, Julio

“…DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational…”
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A model of duration in normal and perturbed reaching movement by Hoff, Bruce

“…In modeling human and primate motor behavior, optimization has been used to mathematically describe hand trajectories during reaching movement, with the…”
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Noise sampling method: an ANOVA approachallowing robust selection of differentially regulatedgenes measured by DNA microarrays by Draghici, Sorin, Kulaeva, Olga, Hoff, Bruce, Petrov, Anton, Shams, Soheil, Tainsky, Michael A.

“…Motivation: A crucial step in microarray data analysis is the selection of subsets of interesting genes from the initial set of genes. In many cases,…”
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Reducing overfitting in challenge-based competitions by Neto, Elias Chaibub, Hoff, Bruce R, Bare, Chris, Bot, Brian M, Yu, Thomas, Magravite, Lara, Trister, Andrew D, Norman, Thea, Meyer, Pablo, Saez-Rodrigues, Julio, Costello, James C, Guinney, Justin, Stolovitzky, Gustavo

“…Over-fitting is a dreaded foe in challenge-based competitions. Because participants rely on public leaderboards to evaluate and refine their models, there is…”
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A computational description of the organization of human reaching and prehension by Hoff, Bruce Richard

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