Search Results - "Becnel, B"

The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways by Ochsner, Scott A., Abraham, David, Martin, Kirt, Ding, Wei, McOwiti, Apollo, Kankanamge, Wasula, Wang, Zichen, Andreano, Kaitlyn, Hamilton, Ross A., Chen, Yue, Hamilton, Angelica, Gantner, Marin L., Dehart, Michael, Qu, Shijing, Hilsenbeck, Susan G., Becnel, Lauren B., Bridges, Dave, Ma’ayan, Avi, Huss, Janice M., Stossi, Fabio, Foulds, Charles E., Kralli, Anastasia, McDonnell, Donald P., McKenna, Neil J.

“…Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored…”
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Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways by Becnel, Lauren B, Darlington, Yolanda F, Ochsner, Scott A, Easton-Marks, Jeremy R, Watkins, Christopher M, McOwiti, Apollo, Kankanamge, Wasula H, Wise, Michael W, DeHart, Michael, Margolis, Ronald N, McKenna, Neil J

“…Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including…”
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Transcriptomine, a web resource for nuclear receptor signaling transcriptomes by Ochsner, Scott A, Watkins, Christopher M, McOwiti, Apollo, Xu, Xueping, Darlington, Yolanda F, Dehart, Michael D, Cooney, Austin J, Steffen, David L, Becnel, Lauren B, McKenna, Neil J

“…The nuclear receptor (NR) superfamily of ligand-regulated transcription factors directs ligand- and tissue-specific transcriptomes in myriad developmental,…”
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Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates by Swick, Michelle C, Evangelista, Michael A, Bodine, Truston J, Easton-Marks, Jeremy R, Barth, Patrick, Shah, Minita J, Bormann Chung, Christina A, Stanley, Sarah, McLaughlin, Stephen F, Lee, Clarence C, Sheth, Vrunda, Doan, Quynh, Hamill, Richard J, Steffen, David, Becnel, Lauren B, Sucgang, Richard, Zechiedrich, Lynn

“…Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies…”
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A FAIR-Based Approach to Enhancing the Discovery and Re-Use of Transcriptomic Data Assets for Nuclear Receptor Signaling Pathways by Ochsner, Scott A, Darlington, Yolanda F, McOwiti, Apollo, Kankanamge, Wasula H, Naumov, Alexey, Becnel, Lauren B, McKenna, Neil J

“…Public transcriptomic assets in the nuclear receptor (NR) signaling field hold considerable collective potential for exposing underappreciated aspects of NR…”
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FAIR data sharing: The roles of common data elements and harmonization by Kush, R.D., Warzel, D., Kush, M.A., Sherman, A., Navarro, E.A., Fitzmartin, R., Pétavy, F., Galvez, J., Becnel, L.B., Zhou, F.L., Harmon, N., Jauregui, B., Jackson, T., Hudson, L.

“…The value of robust and responsible data sharing in clinical research and healthcare is recognized by patients, patient advocacy groups, researchers, journal…”
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Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine by Becnel, Lauren B, Ochsner, Scott A, Darlington, Yolanda F, McOwiti, Apollo, Kankanamge, Wasula H, Dehart, Michael, Naumov, Alexey, McKenna, Neil J

“…We previously developed a web tool, Transcriptomine, to explore expression profiling data sets involving small-molecule or genetic manipulations of nuclear…”
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Use of EHRs data for clinical research: Historical progress and current applications by Nordo, Amy Harris, Levaux, Hugh P., Becnel, Lauren B., Galvez, Jose, Rao, Prasanna, Stem, Komathi, Prakash, Era, Kush, Rebecca Daniels

“…The benefits of reusing EHR data for clinical research studies are numerous. They portend the opportunity to bring new therapies to patients sooner,…”
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Acquire: an open-source comprehensive cancer biobanking system by Dowst, Heidi, Pew, Benjamin, Watkins, Chris, McOwiti, Apollo, Barney, Jonathan, Qu, Shijing, Becnel, Lauren B

“…The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable…”
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BRIDG: a domain information model for translational and clinical protocol-driven research by Becnel, Lauren B, Hastak, Smita, Ver Hoef, Wendy, Milius, Robert P, Slack, MaryAnn, Wold, Diane, Glickman, Michael L, Brodsky, Boris, Jaffe, Charles, Kush, Rebecca, Helton, Edward

“…Abstract Background: It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however,…”
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Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART by Barbosa-Silva, Adriano, Bratfalean, Dorina, Gu, Wei, Satagopam, Venkata, Houston, Paul, Becnel, Lauren B, Eifes, Serge, Richard, Fabien, Tielmann, Andreas, Herzinger, Sascha, Rege, Kavita, Balling, Rudi, Peeters, Paul, Schneider, Reinhard

“…Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC…”
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Improving the discoverability, accessibility, and citability of omics datasets: a case report by Darlington, Yolanda F, Naumov, Alexey, McOwiti, Apollo, Kankanamge, Wasula H, Becnel, Lauren B, McKenna, Neil J

“…Although omics datasets represent valuable assets for hypothesis generation, model testing, and data validation, the infrastructure supporting their reuse…”
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Minireview: Progress and Challenges in Proteomics Data Management, Sharing, and Integration by Becnel, Lauren B, McKenna, Neil J

“…The proteome represents the identity, expression levels, interacting partners, and posttranslational modifications of proteins expressed within any given cell…”
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Global Standards to Expedite Learning From Medical Research Data by Hudson, Lynn D., Kush, Rebecca D., Navarro Almario, Eileen, Seigneuret, Nathalie, Jackson, Tammy, Jauregui, Barbara, Jordan, David, Fitzmartin, Ronald, Zhou, F. Liz, Malone, James K., Galvez, Jose, Becnel, Lauren B.

“…CDISC standards support the gamut of medical research (including nutrition, public health, epidemiology, outcomes, and interventional research) and apply to…”
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An open access pilot freely sharing cancer genomic data from participants in Texas by Becnel, Lauren B., Pereira, Stacey, Drummond, Jennifer A., Gingras, Marie-Claude, Covington, Kyle R., Kovar, Christie L., Doddapaneni, Harsha Vardhan, Hu, Jianhong, Muzny, Donna, McGuire, Amy L., Wheeler, David A., Gibbs, Richard A.

“…Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting…”
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CDISC SHARE, a Global, Cloud-based Resource of Machine-Readable CDISC Standards for Clinical and Translational Research by Hume, Samuel, Chow, Anthony, Evans, Julie, Malfait, Frederik, Chason, Julie, Wold, J Darcy, Kubick, Wayne, Becnel, Lauren B

“…The Clinical Data Interchange Standards Consortium (CDISC) is a global non-profit standards development organization that creates consensus-based standards for…”
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Correction: Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates by Swick, Michelle C., Evangelista, Michael A., Bodine, Truston J., Easton-Marks, Jeremy R., Barth, Patrick, Shah, Minita J., Bormann Chung, Christina A., Stanley, Sarah, McLaughlin, Stephen F., Lee, Clarence C., Sheth, Vrunda, Doan, Quynh, Hamill, Richard J., Steffen, David, Becnel, Lauren B., Sucgang, Richard, Zechiedrich, Lynn

“…The following sentence should be included with the Funding Statement: "RJH was supported in part by resources provided by the Department of Veterans Affairs."…”
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Research Resource: dkCOIN, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) Consortium Interconnectivity Network: A Pilot Program to Aggregate Research Resources Generated by Multiple Research Consortia by McKenna, Neil J, Howard, Christopher L, Aufiero, Michael, Easton-Marks, Jeremy, Steffen, David L, Becnel, Lauren B, Magnuson, Mark A, McIndoe, Richard A, Cartailler, Jean-Philippe

“…The National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) supports multiple basic science consortia that generate high-content datasets,…”
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Stone Interlayer Pavement Design by Rasoulian, Masood, Becnel, Byron, Keel, Gary

“…A project was initiated to evaluate the pavement performance of an alternative pavement design, referred to here as stone interlayer or inverted pavement. The…”
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Long-Term Performance of Stone Interlayer Pavement by Titi, Hani, Rasoulian, Masood, Martinez, Mark, Becnel, Byron, Keel, Gary

“…This paper presents an evaluation of long-term performance of an alternative flexible pavement design referred to here as stone interlayer pavement. This…”
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