Search Results - "Stoeckert, Christian J."

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies by Jackson, Rebecca, Matentzoglu, Nicolas, Overton, James A, Vita, Randi, Balhoff, James P, Buttigieg, Pier Luigi, Carbon, Seth, Courtot, Melanie, Diehl, Alexander D, Dooley, Damion M, Duncan, William D, Harris, Nomi L, Haendel, Melissa A, Lewis, Suzanna E, Natale, Darren A, Osumi-Sutherland, David, Ruttenberg, Alan, Schriml, Lynn M, Smith, Barry, Stoeckert, Jr, Christian J, Vasilevsky, Nicole A, Walls, Ramona L, Zheng, Jie, Mungall, Christopher J, Peters, Bjoern

“…Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when…”
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Chronic Endoplasmic Reticulum Stress Activates Unfolded Protein Response in Arterial Endothelium in Regions of Susceptibility to Atherosclerosis by Civelek, Mete, Manduchi, Elisabetta, Riley, Rebecca J, Stoeckert, Christian J, Davies, Peter F

“…RATIONALE:Endothelial function and dysfunction are central to the focal origin and regional development of atherosclerosis; however, an in vivo endothelial…”
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PlasmoDB: a functional genomic database for malaria parasites by Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P, Dommer, Jennifer, Fischer, Steve, Gajria, Bindu, Gao, Xin, Gingle, Alan, Grant, Greg, Harb, Omar S, Heiges, Mark, Innamorato, Frank, Iodice, John, Kissinger, Jessica C, Kraemer, Eileen, Li, Wei, Miller, John A, Nayak, Vishal, Pennington, Cary, Pinney, Deborah F, Roos, David S, Ross, Chris, Stoeckert, Christian J. Jr, Treatman, Charles, Wang, Haiming

“…PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a…”
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FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes by Basenko, Evelina Y, Pulman, Jane A, Shanmugasundram, Achchuthan, Harb, Omar S, Crouch, Kathryn, Starns, David, Warrenfeltz, Susanne, Aurrecoechea, Cristina, Stoeckert, Jr, Christian J, Kissinger, Jessica C, Roos, David S, Hertz-Fowler, Christiane

“…FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the…”
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Propagation of adipogenic signals through an epigenomic transition state by Steger, David J, Grant, Gregory R, Schupp, Michael, Tomaru, Takuya, Lefterova, Martina I, Schug, Jonathan, Manduchi, Elisabetta, Stoeckert, Jr, Christian J, Lazar, Mitchell A

“…The transcriptional mechanisms by which temporary exposure to developmental signals instigates adipocyte differentiation are unknown. During early…”
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OrthoMCL: identification of ortholog groups for eukaryotic genomes by Li, Li, Stoeckert, Jr, Christian J, Roos, David S

“…The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of…”
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Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo by Jiang, Yi-Zhou, Manduchi, Elisabetta, Stoeckert, Jr, Christian J, Davies, Peter F

“…Atherosclerosis is a heterogeneously distributed disease of arteries in which the endothelium plays an important central role. Spatial transcriptome profiling…”
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Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) by GRANT, Gregory R, FARKAS, Michael H, PIZARRO, Angel D, LAHENS, Nicholas F, SCHUG, Jonathan, BRUNK, Brian P, STOECKERT, Christian J, HOGENESCH, John B, PIERCE, Eric A

“…A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing…”
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Ontogeny of erythroid gene expression by Kingsley, Paul D., Greenfest-Allen, Emily, Frame, Jenna M., Bushnell, Timothy P., Malik, Jeffrey, McGrath, Kathleen E., Stoeckert, Christian J., Palis, James

“…Erythroid ontogeny is characterized by overlapping waves of primitive and definitive erythroid lineages that share many morphologic features during terminal…”
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ToxoDB: an integrated Toxoplasma gondii database resource by Gajria, Bindu, Bahl, Amit, Brestelli, John, Dommer, Jennifer, Fischer, Steve, Gao, Xin, Heiges, Mark, Iodice, John, Kissinger, Jessica C, Mackey, Aaron J, Pinney, Deborah F, Roos, David S, Stoeckert, Christian J. Jr, Wang, Haiming, Brunk, Brian P

“…ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and…”
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EuPathDB: the eukaryotic pathogen genomics database resource by Aurrecoechea, Cristina, Barreto, Ana, Basenko, Evelina Y, Brestelli, John, Brunk, Brian P, Cade, Shon, Crouch, Kathryn, Doherty, Ryan, Falke, Dave, Fischer, Steve, Gajria, Bindu, Harb, Omar S, Heiges, Mark, Hertz-Fowler, Christiane, Hu, Sufen, Iodice, John, Kissinger, Jessica C, Lawrence, Cris, Li, Wei, Pinney, Deborah F, Pulman, Jane A, Roos, David S, Shanmugasundram, Achchuthan, Silva-Franco, Fatima, Steinbiss, Sascha, Stoeckert, Jr, Christian J, Spruill, Drew, Wang, Haiming, Warrenfeltz, Susanne, Zheng, Jie

“…The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists &…”
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EuPathDB: a portal to eukaryotic pathogen databases by Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P, Fischer, Steve, Gajria, Bindu, Gao, Xin, Gingle, Alan, Grant, Greg, Harb, Omar S, Heiges, Mark, Innamorato, Frank, Iodice, John, Kissinger, Jessica C, Kraemer, Eileen T, Li, Wei, Miller, John A, Nayak, Vishal, Pennington, Cary, Pinney, Deborah F, Roos, David S, Ross, Chris, Srinivasamoorthy, Ganesh, Stoeckert, Christian J. Jr, Thibodeau, Ryan, Treatman, Charles, Wang, Haiming

“…EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania,…”
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OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups by Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.

“…The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes…”
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Defining the mammalian CArGome by Sun, Qiang, Chen, Guang, Streb, Jeffrey W, Long, Xiaochun, Yang, Yumei, Stoeckert, Jr, Christian J, Miano, Joseph M

“…Serum response factor (SRF) binds a 1216-fold degenerate cis element known as the CArG box. CArG boxes are found primarily in muscle- and…”
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Coexisting Proinflammatory and Antioxidative Endothelial Transcription Profiles in a Disturbed Flow Region of the Adult Porcine Aorta by Passerini, Anthony G., Polacek, Denise C., Shi, Congzhu, Francesco, Nadeene M., Manduchi, Elisabetta, Grant, Gregory R., Pritchard, William F., Powell, Steven, Chang, Gary Y., Stoeckert, Christian J., Davies, Peter F., Ignarro, Louis J.

“…In the arterial circulation, regions of disturbed flow (DF), which are characterized by flow separation and transient vortices, are susceptible to…”
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MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments by Oliveira, Francislon S, Brestelli, John, Cade, Shon, Zheng, Jie, Iodice, John, Fischer, Steve, Aurrecoechea, Cristina, Kissinger, Jessica C, Brunk, Brian P, Stoeckert, Christian J, Fernandes, Gabriel R, Roos, David S, Beiting, Daniel P

“…Abstract MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to…”
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A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development by Osipovich, Anna B, Dudek, Karrie D, Greenfest-Allen, Emily, Cartailler, Jean-Philippe, Manduchi, Elisabetta, Potter Case, Leah, Choi, Eunyoung, Chapman, Austin G, Clayton, Hannah W, Gu, Guoqiang, Stoeckert, Jr, Christian J, Magnuson, Mark A

“…To gain a deeper understanding of pancreatic β-cell development, we used iterative weighted gene correlation network analysis to calculate a gene co-expression…”
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Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming by Clayton, Hannah W., Osipovich, Anna B., Stancill, Jennifer S., Schneider, Judsen D., Vianna, Pedro G., Shanks, Carolyn M., Yuan, Weiping, Gu, Guoqiang, Manduchi, Elisabetta, Stoeckert, Christian J., Magnuson, Mark A.

“…Using a transgenic mouse model to express MafA, Pdx1, and Neurog3 (3TF) in a pancreatic acinar cell- and doxycycline-dependent manner, we discovered that the…”
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Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3 by Osipovich, Anna B, Long, Qiaoming, Manduchi, Elisabetta, Gangula, Rama, Hipkens, Susan B, Schneider, Judsen, Okubo, Tadashi, Stoeckert, Jr, Christian J, Takada, Shinji, Magnuson, Mark A

“…Insulinoma associated 1 (Insm1) plays an important role in regulating the development of cells in the central and peripheral nervous systems, olfactory…”
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Ontodog: a web-based ontology community view generation tool by Zheng, Jie, Xiang, Zuoshuang, Stoeckert, Christian J., He, Yongqun

“…Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end…”
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