Search Results - "Jenkins, Sherry L"

Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing by Clarke, Daniel J B, Rebman, Alison W, Bailey, Allison, Wojciechowicz, Megan L, Jenkins, Sherry L, Evangelista, John E, Danieletto, Matteo, Fan, Jinshui, Eshoo, Mark W, Mosel, Michael R, Robinson, William, Ramadoss, Nitya, Bobe, Jason, Soloski, Mark J, Aucott, John N, Ma'ayan, Avi

“…Although widely prevalent, Lyme disease is still under-diagnosed and misunderstood. Here we followed 73 acute Lyme disease patients and uninfected controls…”
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Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network by Ma'ayan, Avi, Jenkins, Sherry L, Neves, Susana, Hasseldine, Anthony, Grace, Elizabeth, Dubin-Thaler, Benjamin, Eungdamrong, Narat J, Weng, Gehzi, Ram, Prahlad T, Rice, J. Jeremy, Kershenbaum, Aaron, Stolovitzky, Gustavo A, Blitzer, Robert D, Iyengar, Ravi

“…We developed a model of 545 components (nodes) and 1259 interactions representing signaling pathways and cellular machines in the hippocampal CA1 neuron. Using…”
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Toxicology knowledge graph for structural birth defects by Evangelista, John Erol, Clarke, Daniel J. B., Xie, Zhuorui, Marino, Giacomo B., Utti, Vivian, Jenkins, Sherry L., Ahooyi, Taha Mohseni, Bologa, Cristian G., Yang, Jeremy J., Binder, Jessica L., Kumar, Praveen, Lambert, Christophe G., Grethe, Jeffrey S., Wenger, Eric, Taylor, Deanne, Oprea, Tudor I., de Bono, Bernard, Ma’ayan, Avi

“…Background Birth defects are functional and structural abnormalities that impact about 1 in 33 births in the United States. They have been attributed to…”
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update by Kuleshov, Maxim V, Jones, Matthew R, Rouillard, Andrew D, Fernandez, Nicolas F, Duan, Qiaonan, Wang, Zichen, Koplev, Simon, Jenkins, Sherry L, Jagodnik, Kathleen M, Lachmann, Alexander, McDermott, Michael G, Monteiro, Caroline D, Gundersen, Gregory W, Ma'ayan, Avi

“…Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools…”
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Gene Set Knowledge Discovery with Enrichr by Xie, Zhuorui, Bailey, Allison, Kuleshov, Maxim V, Clarke, Daniel J B, Evangelista, John E, Jenkins, Sherry L, Lachmann, Alexander, Wojciechowicz, Megan L, Kropiwnicki, Eryk, Jagodnik, Kathleen M, Jeon, Minji, Ma'ayan, Avi

“…Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of…”
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Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data by Koleti, Amar, Terryn, Raymond, Stathias, Vasileios, Chung, Caty, Cooper, Daniel J, Turner, John P, Vidović, Dušica, Forlin, Michele, Kelley, Tanya T, D'Urso, Alessandro, Allen, Bryce K, Torre, Denis, Jagodnik, Kathleen M, Wang, Lily, Jenkins, Sherry L, Mader, Christopher, Niu, Wen, Fazel, Mehdi, Mahi, Naim, Pilarczyk, Marcin, Clark, Nicholas, Shamsaei, Behrouz, Meller, Jarek, Vasiliauskas, Juozas, Reichard, John, Medvedovic, Mario, Ma'ayan, Avi, Pillai, Ajay, Schürer, Stephan C

“…Abstract The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and…”
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SigCom LINCS: data and metadata search engine for a million gene expression signatures by Evangelista, John Erol, Clarke, Daniel J B, Xie, Zhuorui, Lachmann, Alexander, Jeon, Minji, Chen, Kerwin, Jagodnik, Kathleen M, Jenkins, Sherry L, Kuleshov, Maxim V, Wojciechowicz, Megan L, Schürer, Stephan C, Medvedovic, Mario, Ma’ayan, Avi

“…Abstract Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are…”
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Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd by Wang, Zichen, Monteiro, Caroline D., Jagodnik, Kathleen M., Fernandez, Nicolas F., Gundersen, Gregory W., Rouillard, Andrew D., Jenkins, Sherry L., Feldmann, Axel S., Hu, Kevin S., McDermott, Michael G., Duan, Qiaonan, Clark, Neil R., Jones, Matthew R., Kou, Yan, Goff, Troy, Woodland, Holly, Amaral, Fabio M R., Szeto, Gregory L., Fuchs, Oliver, Schüssler-Fiorenza Rose, Sophia M., Sharma, Shvetank, Schwartz, Uwe, Bausela, Xabier Bengoetxea, Szymkiewicz, Maciej, Maroulis, Vasileios, Salykin, Anton, Barra, Carolina M., Kruth, Candice D., Bongio, Nicholas J., Mathur, Vaibhav, Todoric, Radmila D, Rubin, Udi E., Malatras, Apostolos, Fulp, Carl T., Galindo, John A., Motiejunaite, Ruta, Jüschke, Christoph, Dishuck, Philip C., Lahl, Katharina, Jafari, Mohieddin, Aibar, Sara, Zaravinos, Apostolos, Steenhuizen, Linda H., Allison, Lindsey R., Gamallo, Pablo, de Andres Segura, Fernando, Dae Devlin, Tyler, Pérez-García, Vicente, Ma’ayan, Avi

“…Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new…”
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Appyters: Turning Jupyter Notebooks into data-driven web apps by Clarke, Daniel J.B., Jeon, Minji, Stein, Daniel J., Moiseyev, Nicole, Kropiwnicki, Eryk, Dai, Charles, Xie, Zhuorui, Wojciechowicz, Megan L., Litz, Skylar, Hom, Jason, Evangelista, John Erol, Goldman, Lucas, Zhang, Serena, Yoon, Christine, Ahamed, Tahmid, Bhuiyan, Samantha, Cheng, Minxuan, Karam, Julie, Jagodnik, Kathleen M., Shu, Ingrid, Lachmann, Alexander, Ayling, Sam, Jenkins, Sherry L., Ma'ayan, Avi

“…Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text,…”
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Connectivity Mapping: Methods and Applications by Keenan, Alexandra B, Wojciechowicz, Megan L, Wang, Zichen, Jagodnik, Kathleen M, Jenkins, Sherry L, Lachmann, Alexander, Ma'ayan, Avi

“…Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form…”
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Systems biology--biomedical modeling by Sobie, Eric A, Lee, Young-Seon, Jenkins, Sherry L, Iyengar, Ravi

“…Because of the complexity inherent in biological systems, many researchers frequently rely on a combination of global analysis and computational approaches to…”
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Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop by Jagodnik, Kathleen M., Koplev, Simon, Jenkins, Sherry L., Ohno-Machado, Lucila, Paten, Benedict, Schurer, Stephan C., Dumontier, Michel, Verborgh, Ruben, Bui, Alex, Ping, Peipei, McKenna, Neil J., Madduri, Ravi, Pillai, Ajay, Ma'ayan, Avi

“…[Display omitted] •The NIH BD2K initiative facilitates digitally enabled biomedical research.•The BD2K Commons Framework Pilots Working Group met to clarify…”
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FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources by Clarke, Daniel J B, Wang, Lily, Jones, Alex, Wojciechowicz, Megan L, Torre, Denis, Jagodnik, Kathleen M, Jenkins, Sherry L, McQuilton, Peter, Flamholz, Zachary, Silverstein, Moshe C, Schilder, Brian M, Robasky, Kimberly, Castillo, Claris, Idaszak, Ray, Ahalt, Stanley C, Williams, Jason, Schurer, Stephan, Cooper, Daniel J, de Miranda Azevedo, Ricardo, Klenk, Juergen A, Haendel, Melissa A, Nedzel, Jared, Avillach, Paul, Shimoyama, Mary E, Harris, Rayna M, Gamble, Meredith, Poten, Rudy, Charbonneau, Amanda L, Larkin, Jennie, Brown, C Titus, Bonazzi, Vivien R, Dumontier, Michel J, Sansone, Susanna-Assunta, Ma'ayan, Avi

“…As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic…”
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Systems pharmacology meets predictive, preventive, personalized and participatory medicine by Jenkins, Sherry L, Ma'ayan, Avi

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Gene and drug landing page aggregator by Clarke, Daniel J B, Kuleshov, Maxim V, Xie, Zhuorui, Evangelista, John E, Meyers, Marilyn R, Kropiwnicki, Eryk, Jenkins, Sherry L, Ma'ayan, Avi

“…Many biological and biomedical researchers commonly search for information about genes and drugs to gather knowledge from these resources. For the most part,…”
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Getting Started with LINCS Datasets and Tools by Xie, Zhuorui, Kropiwnicki, Eryk, Wojciechowicz, Megan L, Jagodnik, Kathleen M, Shu, Ingrid, Bailey, Allison, Clarke, Daniel J B, Jeon, Minji, Evangelista, John Erol, V Kuleshov, Maxim, Lachmann, Alexander, Parigi, Abhijna A, Sanchez, Jose M, Jenkins, Sherry L, Ma'ayan, Avi

“…The Library of Integrated Network-based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular…”
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Network analysis of FDA approved drugs and their targets by Ma'ayan, Avi, Jenkins, Sherry L., Goldfarb, Joseph, Iyengar, Ravi

“…The global relationship between drugs that are approved for therapeutic use and the human genome is not known. We employed graph‐theory methods to analyze the…”
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Systems approach to explore components and interactions in the presynapse by Abul-Husn, Noura S, Bushlin, Ittai, Morón, José A, Jenkins, Sherry L, Dolios, Georgia, Wang, Rong, Iyengar, Ravi, Ma'ayan, Avi, Devi, Lakshmi A

“…The application of proteomic techniques to neuroscientific research provides an opportunity for a greater understanding of nervous system structure and…”
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Genes2WordCloud: a quick way to identify biological themes from gene lists and free text by Baroukh, Caroline, Jenkins, Sherry L, Dannenfelser, Ruth, Ma'ayan, Avi

“…Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in…”
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SNAVI: Desktop application for analysis and visualization of large-scale signaling networks by Ma'ayan, Avi, Jenkins, Sherry L, Webb, Ryan L, Berger, Seth I, Purushothaman, Sudarshan P, Abul-Husn, Noura S, Posner, Jeremy M, Flores, Tony, Iyengar, Ravi

“…Studies of cellular signaling indicate that signal transduction pathways combine to form large networks of interactions. Viewing protein-protein and…”
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