Search Results - "Ross, Karen E."

miRTex: A Text Mining System for miRNA-Gene Relation Extraction by Li, Gang, Ross, Karen E, Arighi, Cecilia N, Peng, Yifan, Wu, Cathy H, Vijay-Shanker, K

“…MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally…”
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Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer by Ross, Karen E, Zhang, Guolin, Akcora, Cuneyt, Lin, Yu, Fang, Bin, Koomen, John, Haura, Eric B, Grimes, Mark

“…We analyzed large-scale post-translational modification (PTM) data to outline cell signaling pathways affected by tyrosine kinase inhibitors (TKIs) in ten lung…”
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KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases by Anandakrishnan, Manju, Ross, Karen E, Chen, Chuming, Shanker, Vijay, Cowart, Julie, Wu, Cathy H

“…Aberrant protein kinase regulation leading to abnormal substrate phosphorylation is associated with several human diseases. Despite the promise of therapies…”
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Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer by Çelen, İrem, Ross, Karen E, Arighi, Cecilia N, Wu, Cathy H

“…Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to…”
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Tunable synthetic extracellular matrices to investigate breast cancer response to biophysical and biochemical cues by Sawicki, Lisa A., Ovadia, Elisa M., Pradhan, Lina, Cowart, Julie E., Ross, Karen E., Wu, Cathy H., Kloxin, April M.

“…The extracellular matrix (ECM) is thought to play a critical role in the progression of breast cancer. In this work, we have designed a photopolymerizable,…”
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iPTMnet: an integrated resource for protein post-translational modification network discovery by Huang, Hongzhan, Arighi, Cecilia N, Ross, Karen E, Ren, Jia, Li, Gang, Chen, Sheng-Chih, Wang, Qinghua, Cowart, Julie, Vijay-Shanker, K, Wu, Cathy H

“…Abstract Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We…”
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COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases by Chen, Chuming, Ross, Karen E, Gavali, Sachin, Cowart, Julie E, Wu, Cathy H

“…Abstract Summary The global response to the COVID-19 pandemic has led to a rapid increase of scientific literature on this deadly disease. Extracting knowledge…”
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Alterations in the Global Proteome and Phosphoproteome in Third Generation EGFR TKI Resistance Reveal Drug Targets to Circumvent Resistance by Zhang, Xu, Maity, Tapan K, Ross, Karen E, Qi, Yue, Cultraro, Constance M, Bahta, Meriam, Pitts, Stephanie, Keswani, Meghana, Gao, Shaojian, Nguyen, Khoa Dang P, Cowart, Julie, Kirkali, Fatos, Wu, Cathy, Guha, Udayan

“…Lung cancer is the leading cause of cancer mortality worldwide. The treatment of patients with lung cancer harboring mutant EGFR with orally administered EGFR…”
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iPTMnet RESTful API for Post-translational Modification Network Analysis by Gavali, Sachin, Ross, Karen E, Cowart, Julie, Chen, Chuming, Wu, Cathy H

“…iPTMnet is a resource that combines rich information about protein post-translational modifications (PTM) from curated databases as well as text mining tools…”
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The Spindle Midzone Microtubule-Associated Proteins Ase1p and Cin8p Affect the Number and Orientation of Astral Microtubules in Saccharomyces cerevisiae by de Gramont, Armand, Barbour, Leslie, Ross, Karen E., Cohen-Fix, Orna

“…The nucleus of the budding yeast S. cerevisiae has to move to the bud neck during mitosis in order for proper DNA segregation to take place. This movement is…”
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Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII by Chatr-Aryamontri, Andrew, Hirschman, Lynette, Ross, Karen E, Oughtred, Rose, Krallinger, Martin, Dolinski, Kara, Tyers, Mike, Korves, Tonia, Arighi, Cecilia N

“…The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical…”
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The Role of Cdh1p in Maintaining Genomic Stability in Budding Yeast by Ross, Karen E, Cohen-Fix, Orna

“…Cdh1p, a substrate specificity factor for the cell cycle-regulated ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C), promotes exit from…”
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Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint by Ross, Karen E, Arighi, Cecilia N, Ren, Jia, Natale, Darren A, Huang, Hongzhan, Wu, Cathy H

“…As a member of the Open Biomedical Ontologies (OBO) foundry, the Protein Ontology (PRO) provides an ontological representation of protein forms and complexes…”
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Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources by Huang, Liang-Chin, Ross, Karen E., Baffi, Timothy R., Drabkin, Harold, Kochut, Krzysztof J., Ruan, Zheng, D’Eustachio, Peter, McSkimming, Daniel, Arighi, Cecilia, Chen, Chuming, Natale, Darren A., Smith, Cynthia, Gaudet, Pascale, Newton, Alexandra C., Wu, Cathy, Kannan, Natarajan

“…Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources…”
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iPTMnet: Integrative Bioinformatics for Studying PTM Networks by Ross, Karen E, Huang, Hongzhan, Ren, Jia, Arighi, Cecilia N, Li, Gang, Tudor, Catalina O, Lv, Mengxi, Lee, Jung-Youn, Chen, Sheng-Chih, Vijay-Shanker, K, Wu, Cathy H

“…Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are…”
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Protein ontology on the semantic web for knowledge discovery by Chen, Chuming, Huang, Hongzhan, Ross, Karen E., Cowart, Julie E., Arighi, Cecilia N., Wu, Cathy H., Natale, Darren A.

“…The Protein Ontology (PRO) provides an ontological representation of protein-related entities, ranging from protein families to proteoforms to complexes…”
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ISSN Is for Black, White, and Many Shades of Grey by Reynolds, Regina Romano, Ross, Karen E. A.

“…The International Standard Serial Number (ISSN) is a unique identifier most often associated with popular magazines, scholarly journals, and newspapers. The…”
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DEXTER: Disease-Expression Relation Extraction from Text by Gupta, Samir, Dingerdissen, Hayley, Ross, Karen E, Hu, Yu, Wu, Cathy H, Mazumder, Raja, Vijay-Shanker, K

“…Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research,…”
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Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature by Wang, Qinghua, Ross, Karen E, Huang, Hongzhan, Ren, Jia, Li, Gang, Vijay-Shanker, K, Wu, Cathy H, Arighi, Cecilia N

“…Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein…”
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RESTful API for iPTMnet: a resource for protein post-translational modification network discovery by Gavali, Sachin, Cowart, Julie, Chen, Chuming, Ross, Karen E, Arighi, Cecilia, Wu, Cathy H

“…Abstract iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and…”
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