Search Results - "Savage, Sara R"

caAtlas: An immunopeptidome atlas of human cancer by Yi, Xinpei, Liao, Yuxing, Wen, Bo, Li, Kai, Dou, Yongchao, Savage, Sara R., Zhang, Bing

“…Comprehensive characterization of tumor antigens is essential for the design of cancer immunotherapies, and mass spectrometry (MS)-based immunopeptidomics…”
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RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα by Savage, Sara R, Bretz, Colin A, Penn, John S

“…TNFα has been identified as playing an important role in pathologic complications associated with diabetic retinopathy and retinal inflammation, such as…”
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Deep Learning in Proteomics by Wen, Bo, Zeng, Wen‐Feng, Liao, Yuxing, Shi, Zhiao, Savage, Sara R., Jiang, Wen, Zhang, Bing

“…Proteomics, the study of all the proteins in biological systems, is becoming a data‐rich science. Protein sequences and structures are comprehensively…”
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Hypoxia-induced expression of VEGF splice variants and protein in four retinal cell types by Watkins, William M., McCollum, Gary W., Savage, Sara R., Capozzi, Megan E., Penn, John S., Morrison, David G.

“…The purpose of this study was to investigate the hypoxia-induced Vegf120, Vegf164 and Vegf188 mRNA expression profiles in rat Müller cells (MC), astrocytes,…”
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Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources by Savage, Sara R, Zhang, Bing

“…Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources…”
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A highly annotated database of genes associated with platinum resistance in cancer by Huang, Dongqing, Savage, Sara R., Calinawan, Anna P., Lin, Chenwei, Zhang, Bing, Wang, Pei, Starr, Timothy K., Birrer, Michael J., Paulovich, Amanda G.

“…Platinum-based chemotherapy, including cisplatin, carboplatin, and oxaliplatin, is prescribed to 10-20% of all cancer patients. Unfortunately, platinum…”
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Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results by Savage, Sara R., Shi, Zhiao, Liao, Yuxing, Zhang, Bing

“…Weighted set cover and affinity propagation algorithms are used to combine results from multiple enrichment analyses. Weighted set cover first condenses…”
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Correction to: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources by Savage, Sara R, Zhang, Bing

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IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining by Savage, Sara R., Zhang, Yaoyun, Jaehnig, Eric J., Liao, Yuxing, Shi, Zhiao, Pham, Huy Anh, Xu, Hua, Zhang, Bing

“…Global phosphoproteomics experiments quantify tens of thousands of phosphorylation sites. However, data interpretation is hampered by our limited knowledge on…”
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Fluorescent probe dyes for metabolic-ion sensing under high hydrostatic pressures by Urayama, Paul, Frey, Eric W., Savage, Sara R.

“…Fluorescence spectroscopy and microscopy imaging are widely used at ambient pressure for analytical studies on biological systems. Before using…”
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Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis by Zille, Marietta, Oses-Prieto, Juan A, Savage, Sara R, Karuppagounder, Saravanan S, Chen, Yingxin, Kumar, Amit, Morris, John H, Scheidt, Karl A, Burlingame, Alma L, Ratan, Rajiv R

“…Ferroptosis is a caspase-independent, iron-dependent form of regulated necrosis extant in traumatic brain injury, Huntington disease, and hemorrhagic stroke…”
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Correction: Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results by Savage, Sara R., Shi, Zhiao, Liao, Yuxing, Zhang, Bing

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Pan-cancer proteogenomics expands the landscape of therapeutic targets by Savage, Sara R, Yi, Xinpei, Lei, Jonathan T, Wen, Bo, Zhao, Hongwei, Liao, Yuxing, Jaehnig, Eric J, Somes, Lauren K, Shafer, Paul W, Lee, Tobie D, Fu, Zile, Dou, Yongchao, Shi, Zhiao, Gao, Daming, Hoyos, Valentina, Gao, Qiang, Zhang, Bing

“…Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug Administration (FDA). We integrate Clinical Proteomic Tumor Analysis…”
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Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors by Lv, Xiangdong, Lu, Xuan, Cao, Jin, Luo, Qin, Ding, Yao, Peng, Fanglue, Pataer, Apar, Lu, Dong, Han, Dong, Malmberg, Eric, Chan, Doug W, Wang, Xiaoran, Savage, Sara R, Mao, Sufeng, Yu, Jingjing, Peng, Fei, Yan, Liang, Meng, Huan, Maneix, Laure, Han, Yumin, Chen, Yiwen, Yao, Wantong, Chang, Eric C, Catic, Andre, Lin, Xia, Miles, George, Huang, Pengxiang, Sun, Zheng, Burt, Bryan, Wang, Huamin, Wang, Jin, Yao, Qizhi Cathy, Zhang, Bing, Roth, Jack A, O'Malley, Bert W, Ellis, Matthew J, Rimawi, Mothaffar F, Ying, Haoqiang, Chen, Xi

“…Despite substantial advances in targeting mutant KRAS, tumor resistance to KRAS inhibitors (KRASi) remains a major barrier to progress. Here, we report…”
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Inside Front Cover: Deep Learning in Proteomics by Wen, Bo, Zeng, Wen‐Feng, Liao, Yuxing, Shi, Zhiao, Savage, Sara R., Jiang, Wen, Zhang, Bing

“…DOI: 10.1002/pmic.201900335 Deep learning holds great potential in proteomics research. In article number 1900335, Bo Wen et al. provide a comprehensive…”
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A proteogenomics data-driven knowledge base of human cancer by Liao, Yuxing, Savage, Sara R, Dou, Yongchao, Shi, Zhiao, Yi, Xinpei, Jiang, Wen, Lei, Jonathan T, Zhang, Bing

“…By combining mass-spectrometry-based proteomics and phosphoproteomics with genomics, epi-genomics, and transcriptomics, proteogenomics provides comprehensive…”
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The peroxisome proliferator-activated receptor-β/δ antagonist GSK0660 mitigates retinal cell inflammation and leukostasis by Capozzi, Megan E., Savage, Sara R., McCollum, Gary W., Hammer, Sandra S., Ramos, Carla J., Yang, Rong, Bretz, Colin A., Penn, John S.

“…Diabetic retinopathy (DR) is triggered by retinal cell damage stimulated by the diabetic milieu, including increased levels of intraocular free fatty acids…”
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RNA-seq identifies a role for the PPARβ/δ inverse agonist GSK0660 in the regulation of TNFα-induced cytokine signaling in retinal endothelial cells by Savage, Sara R, McCollum, Gary W, Yang, Rong, Penn, John S

“…The peroxisome proliferator-activated receptor beta/delta (PPARβ/δ) is a transcription factor with roles in metabolism, angiogenesis, and inflammation. It has…”
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NFAT isoforms play distinct roles in TNFα-induced retinal leukostasis by Bretz, Colin A., Savage, Sara R., Capozzi, Megan E., Suarez, Sandra, Penn, John S.

“…The objective of this study was to determine the role of individual NFAT isoforms in TNFα-induced retinal leukostasis. To this end, human retinal microvascular…”
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Peroxisome proliferator-activated receptor-β/δ regulates angiogenic cell behaviors and oxygen-induced retinopathy by Capozzi, Megan E, McCollum, Gary W, Savage, Sara R, Penn, John S

“…To develop new therapies against ocular neovascularization (NV), we tested the effect of peroxisome proliferator-activated receptor-β/δ (PPAR-β/δ) agonism and…”
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