Search Results - "Woolf, Peter J"

GAGE: generally applicable gene set enrichment for pathway analysis by Luo, Weijun, Friedman, Michael S, Shedden, Kerby, Hankenson, Kurt D, Woolf, Peter J

“…Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has…”
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A gene regulatory network for root epidermis cell differentiation in Arabidopsis by Bruex, Angela, Kainkaryam, Raghunandan M, Wieckowski, Yana, Kang, Yeon Hee, Bernhardt, Christine, Xia, Yang, Zheng, Xiaohua, Wang, Jean Y, Lee, Myeong Min, Benfey, Philip, Woolf, Peter J, Schiefelbein, John

“…The root epidermis of Arabidopsis provides an exceptional model for studying the molecular basis of cell fate and differentiation. To obtain a systems-level…”
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A mechanistic model of PCR for accurate quantification of quantitative PCR data by Boggy, Gregory J, Woolf, Peter J

“…Quantitative PCR (qPCR) is a workhorse laboratory technique for measuring the concentration of a target DNA sequence with high accuracy over a wide dynamic…”
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Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection by Huang, Yongsheng, Zaas, Aimee K, Rao, Arvind, Dobigeon, Nicolas, Woolf, Peter J, Veldman, Timothy, Øien, N Christine, McClain, Micah T, Varkey, Jay B, Nicholson, Bradley, Carin, Lawrence, Kingsmore, Stephen, Woods, Christopher W, Ginsburg, Geoffrey S, Hero, 3rd, Alfred O

“…Exposure to influenza viruses is necessary, but not sufficient, for healthy human hosts to develop symptomatic illness. The host response is an important…”
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vProtein: identifying optimal amino acid complements from plant-based foods by Woolf, Peter J, Fu, Leeann L, Basu, Avik

“…Indispensible amino acids (IAAs) are used by the body in different proportions. Most animal-based foods provide these IAAs in roughly the needed proportions,…”
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RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples by Alvarez, Angel, Woolf, Peter J

“…A central question in cancer biology is what changes cause a healthy cell to form a tumor. Gene expression data could provide insight into this question, but…”
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Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information by Luo, Weijun, Hankenson, Kurt D, Woolf, Peter J

“…Probability based statistical learning methods such as mutual information and Bayesian networks have emerged as a major category of tools for reverse…”
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poolMC: smart pooling of mRNA samples in microarray experiments by Kainkaryam, Raghunandan M, Bruex, Angela, Gilbert, Anna C, Schiefelbein, John, Woolf, Peter J

“…Typically, pooling of mRNA samples in microarray experiments implies mixing mRNA from several biological-replicate samples before hybridization onto a…”
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A fuzzy logic approach to analyzing gene expression data by WOOLF, PETER J, WANG, YIXIN

“…1 Bioinformatics, Department of Molecular Biology, Parke-Davis Pharmaceutical Research, Warner-Lanbert, Ann Arbor 48105 2 Department of Chemical Engineering,…”
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poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening by Kainkaryam, Raghunandan M, Woolf, Peter J

“…A key goal of drug discovery is to increase the throughput of small molecule screens without sacrificing screening accuracy. High-throughput screening (HTS) in…”
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Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway by Shah, Abhik, Tenzen, Toyoaki, McMahon, Andrew P, Woolf, Peter J

“…The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression…”
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Self organization of membrane proteins via dimerization by Woolf, Peter J, Linderman, Jennifer J

“…Protein–protein dimerization is ubiquitous in biology, but its role in self-organization remains unexplored. Here we use Monte Carlo simulations to demonstrate…”
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A Nonadaptive Combinatorial Group Testing Strategy to Facilitate Health Care Worker Screening during the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Outbreak by McDermott, John H., Stoddard, Duncan, Woolf, Peter J., Ellingford, Jamie M., Gokhale, David, Taylor, Algy, Demain, Leigh A.M., Newman, William G., Black, Graeme

“…Routine testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in health care workers (HCWs) is critical. Group testing strategies to…”
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Tissue-Specific Profiling Reveals Transcriptome Alterations in Arabidopsis Mutants Lacking Morphological Phenotypes by Simon, Marissa, Bruex, Angela, Kainkaryam, Raghunandan M., Zheng, Xiaohua, Huang, Ling, Woolf, Peter J., Schiefelbein, John

“…Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences…”
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Bayesian analysis of signaling networks governing embryonic stem cell fate decisions by Woolf, Peter J., Prudhomme, Wendy, Daheron, Laurence, Daley, George Q., Lauffenburger, Douglas A.

“…Motivation: Signaling events that direct mouse embryonic stem (ES) cell self-renewal and differentiation are complex and accordingly difficult to understand in…”
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Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks by Alvarez, Angel, Woolf, Peter J

“…Messenger RNA expression is regulated by a complex interplay of different regulatory proteins. Unfortunately, directly measuring the individual activity of…”
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computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging by Mehta, Khamir, Hoppe, Adam D, Kainkaryam, Raghunandan, Woolf, Peter J, Linderman, Jennifer J

“…Fluorescence resonance energy transfer (FRET) microscopy can measure the spatial distribution of protein interactions inside live cells. Such experiments give…”
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Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization by Luo, Weijun, Friedman, Michael S, Hankenson, Kurt D, Woolf, Peter J

“…BMP6 mediated osteoblast differentiation plays a key role in skeletal development and bone disease. Unfortunately, the signaling pathways regulated by BMP6 are…”
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miniTUBA: medical inference by network integration of temporal data using Bayesian analysis by Xiang, Zuoshuang, Minter, Rebecca M., Bi, Xiaoming, Woolf, Peter J., He, Yongqun

“…Motivation: Many biomedical and clinical research problems involve discovering causal relationships between observations gathered from temporal events. Dynamic…”
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Alterations in dihydropyridine receptors in dystrophin-deficient cardiac muscle by Woolf, Peter J, Lu, Sai, Cornford-Nairn, Renee, Watson, Michael, Xiao, Xiao-Hui, Holroyd, Sean M, Brown, Lindsay, Hoey, Andrew J

“…The deficiency of dystrophin, a critical membrane stabilizing protein, in the mdx mouse causes an elevation in intracellular calcium in myocytes. One mechanism…”
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