OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
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
Published in Database : the journal of biological databases and curation (26.10.2021)
Published in Database : the journal of biological databases and curation (26.10.2021)
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Journal Article
Chronic Endoplasmic Reticulum Stress Activates Unfolded Protein Response in Arterial Endothelium in Regions of Susceptibility to Atherosclerosis
Civelek, Mete, Manduchi, Elisabetta, Riley, Rebecca J, Stoeckert, Christian J, Davies, Peter F
Published in Circulation research (28.08.2009)
Published in Circulation research (28.08.2009)
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Journal Article
PlasmoDB: a functional genomic database for malaria parasites
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
Published in Nucleic acids research (01.01.2009)
Published in Nucleic acids research (01.01.2009)
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Journal Article
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes
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
Published in Journal of fungi (Basel) (20.03.2018)
Published in Journal of fungi (Basel) (20.03.2018)
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Journal Article
Propagation of adipogenic signals through an epigenomic transition state
Steger, David J, Grant, Gregory R, Schupp, Michael, Tomaru, Takuya, Lefterova, Martina I, Schug, Jonathan, Manduchi, Elisabetta, Stoeckert, Jr, Christian J, Lazar, Mitchell A
Published in Genes & development (15.05.2010)
Published in Genes & development (15.05.2010)
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Journal Article
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
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
Published in Bioinformatics (15.09.2011)
Published in Bioinformatics (15.09.2011)
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Journal Article
Ontogeny of erythroid gene expression
Kingsley, Paul D., Greenfest-Allen, Emily, Frame, Jenna M., Bushnell, Timothy P., Malik, Jeffrey, McGrath, Kathleen E., Stoeckert, Christian J., Palis, James
Published in Blood (07.02.2013)
Published in Blood (07.02.2013)
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Journal Article
ToxoDB: an integrated Toxoplasma gondii database resource
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
Published in Nucleic acids research (01.01.2008)
Published in Nucleic acids research (01.01.2008)
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Journal Article
EuPathDB: the eukaryotic pathogen genomics database resource
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
Published in Nucleic Acids Research (04.01.2017)
Published in Nucleic Acids Research (04.01.2017)
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Journal Article
Web Resource
EuPathDB: a portal to eukaryotic pathogen databases
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
Published in Nucleic acids research (01.01.2010)
Published in Nucleic acids research (01.01.2010)
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Journal Article
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
Published in Nucleic acids research (01.01.2006)
Published in Nucleic acids research (01.01.2006)
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Journal Article
Defining the mammalian CArGome
Sun, Qiang, Chen, Guang, Streb, Jeffrey W, Long, Xiaochun, Yang, Yumei, Stoeckert, Jr, Christian J, Miano, Joseph M
Published in Genome Research (01.02.2006)
Published in Genome Research (01.02.2006)
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Journal Article
Coexisting Proinflammatory and Antioxidative Endothelial Transcription Profiles in a Disturbed Flow Region of the Adult Porcine Aorta
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.
Published in Proceedings of the National Academy of Sciences - PNAS (24.02.2004)
Published in Proceedings of the National Academy of Sciences - PNAS (24.02.2004)
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Journal Article
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
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
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development
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
Published in Development (Cambridge) (21.03.2021)
Published in Development (Cambridge) (21.03.2021)
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Journal Article
Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming
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.
Published in Cell reports (Cambridge) (15.11.2016)
Published in Cell reports (Cambridge) (15.11.2016)
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Journal Article
Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3
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
Published in Development (Cambridge) (01.08.2014)
Published in Development (Cambridge) (01.08.2014)
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Journal Article
Ontodog: a web-based ontology community view generation tool
Zheng, Jie, Xiang, Zuoshuang, Stoeckert, Christian J., He, Yongqun
Published in Bioinformatics (01.05.2014)
Published in Bioinformatics (01.05.2014)
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