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7 results on '"Gruaz-Gumowski, Nadine"'

1. The Gene Ontology knowledgebase in 2023

Author

Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Huaiyu, Mi, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Kan Yan Chloe, Li, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin C C, Renzhi, Su, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Li, Ni, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley J F, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte

Subjects
gene annotation, gene function, knowledge graphs, Genetics, gene ontology, Molecular Biology, knowledgebase
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023

2. The Gene Ontology knowledgebase in 2023

Author

Consortium, Gene Ontology, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte

Subjects
Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Cell Biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023
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3. The UniProt-GO Annotation database in 2011

Author

Dimmer, Emily C., Huntley, Rachael P., Alam-Faruque, Yasmin, Sawford, Tony, OʼDonovan, Claire, Martin, Maria J., Bely, Benoit, Browne, Paul, Mun Chan, Wei, Eberhardt, Ruth, Gardner, Michael, Laiho, Kati, Legge, Duncan, Magrane, Michele, Pichler, Klemens, Poggioli, Diego, Sehra, Harminder, Auchincloss, Andrea, Axelsen, Kristian, Blatter, Marie-Claude, Boutet, Emmanuel, Braconi-Quintaje, Silvia, Breuza, Lionel, Bridge, Alan, Coudert, Elizabeth, Estreicher, Anne, Famiglietti, Livia, Ferro-Rojas, Serenella, Feuermann, Marc, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hinz, Ursula, Hulo, Chantal, James, Janet, Jimenez, Silvia, Jungo, Florence, Keller, Guillaume, Lemercier, Phillippe, Lieberherr, Damien, Masson, Patrick, Moinat, Madelaine, Pedruzzi, Ivo, Poux, Sylvain, Rivoire, Catherine, Roechert, Bernd, Schneider, Michael, Stutz, Andre, Sundaram, Shyamala, Tognolli, Michael, Bougueleret, Lydie, Argoud-Puy, Ghislaine, Cusin, Isabelle, Duek- Roggli, Paula, Xenarios, Ioannis, and Apweiler, Rolf

Published
2012
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4. A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.

Author

Breuza, Lionel, Arighi, Cecilia N., Argoud-Puy, Ghislaine, Casals-Casas, Cristina, Estreicher, Anne, Famiglietti, Maria Livia, Georghiou, George, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hinz, Ursula, Hyka-Nouspikel, Nevila, Kramarz, Barbara, Lovering, Ruth C., Lussi, Yvonne, Magrane, Michele, Masson, Patrick, Perfetto, Livia, Poux, Sylvain, Rodriguez-Lopez, Milagros, and Stoeckert, Christian

Subjects
ALZHEIMER'S disease, PUBLIC domain, MOLECULAR interactions, GENE ontology, BIOINFORMATICS, ALZHEIMER'S disease diagnosis, DATABASES, EXPERT systems, RESEARCH, RESEARCH methodology, METABOLISM, MEDICAL cooperation, EVALUATION research, COMPARATIVE studies, PUBLIC sector
Abstract

Background: The analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured biological data described in free-text journal articles and converting this into more structured, computationally-accessible forms. This enables analyses such as functional enrichment of sets of genes/proteins using the Gene Ontology, and makes the searching of data more productive by managing issues such as gene/protein name synonyms, identifier mapping, and data quality.Objective: To undertake a coordinated annotation update of key public-domain resources to better support Alzheimer's disease research.Methods: We have systematically identified target proteins critical to disease process, in part by accessing informed input from the clinical research community.Results: Data from 954 papers have been added to the UniProtKB, Gene Ontology, and the International Molecular Exchange Consortium (IMEx) databases, with 299 human proteins and 279 orthologs updated in UniProtKB. 745 binary interactions were added to the IMEx human molecular interaction dataset.Conclusion: This represents a significant enhancement in the expert curated data pertinent to Alzheimer's disease available in a number of biomedical databases. Relevant protein entries have been updated in UniProtKB and concomitantly in the Gene Ontology. Molecular interaction networks have been significantly extended in the IMEx Consortium dataset and a set of reference protein complexes created. All the resources described are open-source and freely available to the research community and we provide examples of how these data could be exploited by researchers. [ABSTRACT FROM AUTHOR]

Published
2020
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5. Leptin and human reproduction

Author

Aubert, Michel, Pierroz Fuentes, Dominique, Gruaz-Gumowski, Nadine, Sudre, Béatrice, Raposinho, PD, Dubuis, Jean-Michel Marie Maurice, Broqua, Pierre, and Pralong, François Pierre

Subjects
ddc:616, ddc:618, ddc:618.97
Published
2000

7. Metabolic control of sexual function and growth: role of neuropeptide Y and leptin

Author

Aubert, Michel, Pierroz Fuentes, Dominique, Gruaz-Gumowski, Nadine, D'Alleves, Violaine, Vuagnat, Bernard Bruno, Pralong, François Pierre, Blum, WF, and Sizonenko, Pierre-Claude

Subjects
ddc:616, Leptin, Proteins/metabolism/physiology, Sexual Maturation/physiology, ddc:618, Growth Hormone/secretion, digestive, oral, and skin physiology, Neuropeptide Y/physiology, Diabetes Mellitus, Type 1/physiopathology, Rats, ddc:618.97, Animals, Female, Food Deprivation, hormones, hormone substitutes, and hormone antagonists
Abstract

The discovery of leptin has generated an extraordinary interest in the field of obesity but also in the understanding of the relationship between metabolic status and the neuroendocrine system. Following the initial demonstration that leptin administration to fasting mice can 'protect' neuroendocrine secretions and prevent the changes that are associated with fasting, the concept has emerged that a normal leptin secretion is a prerequisite for normal neuroendocrine secretions. Several unfavorable metabolic situations are associated with low plasma leptin, increased secretion of hypothalmic neuropeptide Y (NPY), and hypogonadism, and a causal relationship has been evoked. Severe dietary restriction in juvenile female rats is associated with low plasma leptin and sexual immaturity. Cessation of food restriction leads to immediate increase in plasma leptin followed 4 days later by vaginal opening. If food restriction is maintained, central leptin infusion can induce sexual maturation, thus demonstrating that leptin can act as a signal for the onset of puberty. In untreated type-I diabetic rats, hypogonadism is associated with very low plasma leptin and increased hypothalmic NYP synthesis and oestrous cyclicity. Fasting rapidly inhibits growth hormone (GH) secretion in association with low plasma leptin and elevated hypothalmic NPY. Central infusion of leptin to fasting rats was able to completely prevent the collapse of GH secretion and to maintain a normal low NPY synthesis. In summary, normally elevated plasma levels appear to be a prerequisite for normal GH and gonadotropin secretion in the rat. Degradation of metabolic conditions results in a rapid reduction of circulating leptin that could represent the signal for several alterations of neuroendocrine secretions. At the level of the hypothalamus, leptin could act on NPY neurons to transduce part or all of this 'metabolic' message. The possibility that changing plasma levels for leptin also affect peripheral endocrine targets, such as pituitary, ovary, adrenal or pancreas, is likely since these endocrine organs express functional long-term leptin receptors.

Published
1998

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