31 results on '"Ramachandran, Sridhar"'
Search Results
2. Harmonizing model organism data in the Alliance of Genome Resources
- Author
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Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A, Alexander, Micheal, Anagnostopoulos, Anna V, Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M, Blake, Judith A, Blodgett, Olin, Bradford, Yvonne M, Bult, Carol J, Cain, Scott, Calvi, Brian R, Carbon, Seth, Chan, Juancarlos, Chen, Wen J, Cherry, J Michael, Cho, Jaehyoung, Christie, Karen R, Crosby, Madeline A, Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L, D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E, dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R, Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C, Gondwe, Felix, Goodman, Josh, Gramates, L Sian, Grove, Christian A, Hale, Paul, Harris, Todd, Hayman, G Thomas, Hill, David P, Howe, Douglas G, Howe, Kevin L, Hu, Yanhui, Jha, Sagar, Kadin, James A, Kaufman, Thomas C, Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E, Laulederkind, Stanley JF, Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A, Martin, Ryan, Marygold, Steven J, Matthews, Beverley, McAndrews, Monica S, Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J, Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S, Nash, Robert S, Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E, Gelbart, Susan Russo, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R, Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M, and Smith, Cynthia L
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,1.5 Resources and infrastructure (underpinning) ,1.1 Normal biological development and functioning ,Generic health relevance ,Alleles ,Animals ,Caenorhabditis elegans ,Databases ,Genetic ,Drosophila ,Gene Ontology ,Humans ,Internet ,Mice ,Molecular Sequence Annotation ,Rats ,Saccharomycetales ,Zebrafish ,Alliance of Genome Resources Consortium ,biocuration ,data mining ,gene expression ,gene function ,gene interaction ,genome ,knowledgebase ,phenotype ,variants ,Developmental Biology ,Biochemistry and cell biology - Abstract
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
- Published
- 2022
3. Critical Text Selection for the Elementary Classroom: A Case for Strategically Using the Classroom Library to Open New Spaces for Critical Literacy Engagements
- Author
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Iyer, Ishwarya N. and Ramachandran, Sridhar
- Abstract
The purpose of this research paper is to encourage school teachers (with an emphasis on elementary teachers) to recognize and explore the literacy potential of their classroom libraries as a powerful critical literacy tool/asset that when designed and utilized strategically has the potential to reposition their classroom pedagogy and curriculum design to be empowering, transformative, inclusive and progressive. To that effect, this paper offers/proposes a framework/model for critical text selection' that can be readily adapted by teachers across various grade levels within the K-12 classrooms to identify the specific critical literacy needs of their learners (including the learning environment) and then employ their classroom library as a critical literacy tool that facilitates learner empowerment both inside and outside their learning spaces. The paper also presents interested teachers with an alternate way to traverse the proposed framework in the hope that it will provide an impetus to teacher scholars and educators interested in adapting the framework into their classroom to innovatively modify the framework we have presented to better work with their unique curricular structure and design.
- Published
- 2020
4. Diversity Consciousness in the Classroom: A Case for Opening New Spaces and Generating 'New' Knowledge for Critical Literacy Using Imaginative Practices
- Author
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Iyer, Ishwarya N. and Ramachandran, Sridhar
- Abstract
The purpose of this research paper is to offer/propose a framework/model of specific imaginative practices, classroom engagement ideas, and implementation pathways that can be adapted across various grade levels within the K-12 (preferably language and literacy) classrooms to utilize the inherent diversity (of lived experiences) amongst the learners as a resources for fostering equity, diversity, and inclusion (EDI) in the classroom while simultaneously generating 'new' knowledge for learning and sense-making. Essentially, the framework proposed will afford expressive outlets into the curriculum via imaginative practices that are designed to allow opportunities for critical literacy learning by bringing common experiences and issues to the fore (utilizing dialogic comprehension-as-sensemaking pedagogy) and thus perpetuating diversity consciousness. The paper also includes a mock-up (i.e. present an example for each step in the framework when possible) of the proposed model in the hope that it will provide an impetus to teacher scholars and educators interested in adapting/including the framework into their classroom.
- Published
- 2019
5. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
- Author
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Sweeney, Blake A, Petrov, Anton I, Ribas, Carlos E, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Seemann, Stefan E, Gorodkin, Jan, Cannone, Jamie J, Gutell, Robin R, Kay, Simon, Marygold, Steven, dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M, Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P, Lowe, Todd M, Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Volders, Pieter-Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J, Kalvari, Ioanna, Nawrocki, Eric P, Petrov, Anton S, Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M, Hoksza, David, Lovering, Ruth C, Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, and Weinberg, Zasha
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,2.6 Resources and infrastructure (aetiology) ,Animals ,Apicomplexa ,Base Sequence ,Betacoronavirus ,Databases ,Nucleic Acid ,Fungi ,Gene Ontology ,Humans ,Internet ,Molecular Sequence Annotation ,Nucleic Acid Conformation ,RNA ,Untranslated ,Sequence Analysis ,RNA ,Software ,RNAcentral Consortium ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
- Published
- 2021
6. Bayesian networks and intelligence technology applied to climate change: An application of fuzzy logic based simulation in avalanche simulation risk assessment using GIS in a Western Himalayan region
- Author
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Arumugam, Thangavelu, Ramachandran, Sridhar, Kinattinkara, Sapna, Velusamy, Sampathkumar, Snehmani, Shanmugamoorthy, Manoj, and Shanmugavadivel, Suthaviji
- Published
- 2022
- Full Text
- View/download PDF
7. The Neglected Case of the 'W': Waste or Wisdom?
- Author
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Ramachandran, Sridhar and Wyandotte, Annette
- Abstract
Institutional withdrawal policies allow students with academic and personal difficulties to avert or minimize damage to the GPA by dropping a course in which they may risk a grade of "D" or "F," or to reduce credit hours to better manage those that remain. Offsetting costs involve lost tuition, delay of progress, and perhaps wasted effort. Yet in the pressures of the moment, how likely are students to weigh competing factors before acting? Do they consider the implications for financial aid, satisfactory academic progress, admission to the major, or timely progress toward a degree? What duties may the institution share with students to promote informed judgments? The authors explore the rewards and risks of dropping a course in view of the literature on the "W." Further, they explicate their own case study of withdrawal behaviors in an introductory course to the Informatics major to address questions raised in light of the growing literature on student retention and persistence. "What ties may exist between dropping a course and dropping out of college?" "How may student success studies guide institutions and faculty to assist students facing 'W' decisions?" "Of what benefit may this kind of intervention be for them?" For example, "How may proactive assistance in the 'W' process encourage students to pursue the competencies of a college degree amid discomfort and frustration likely having both cognitive and affective elements?" "How may students who persist through this challenge be better prepared for the complexities of their lives and work?" (Kuh, Kinzie, Schuh, & Whitt, 2010).
- Published
- 2016
8. The Gene Ontology knowledgebase in 2023
- Author
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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
9. From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes
- Author
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Bradford, Yvonne M, primary, Van Slyke, Ceri E, additional, Howe, Douglas G, additional, Fashena, David, additional, Frazer, Ken, additional, Martin, Ryan, additional, Paddock, Holly, additional, Pich, Christian, additional, Ramachandran, Sridhar, additional, Ruzicka, Leyla, additional, Singer, Amy, additional, Taylor, Ryan, additional, Tseng, Wei-Chia, additional, and Westerfield, Monte, additional
- Published
- 2023
- Full Text
- View/download PDF
10. The Gene Ontology knowledgebase in 2023
- Author
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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
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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
- Full Text
- View/download PDF
11. From Multi-Allele Fish to Non-Standard Environments, How ZFIN Assigns Phenotypes, Human Disease Models, and Gene Expression Annotations to Genes
- Author
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Bradford, Yvonne M., primary, Van Slyke, Ceri E., additional, Howe, Douglas G., additional, Fashena, David, additional, Frazer, Ken, additional, Martin, Ryan, additional, Paddock, Holly, additional, Pich, Christian, additional, Ramachandran, Sridhar, additional, Ruzicka, Leyla, additional, Singer, Amy, additional, Taylor, Ryan, additional, Tseng, Wei-Chia, additional, and Westerfield, Monte, additional
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- 2022
- Full Text
- View/download PDF
12. Spatial data mining using association rules and fuzzy logic for autonomous exploration of geo-referenced cancer data in Western Tamilnadu, India
- Author
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Parasur Babu, Harathi, Selvaraj, Janani, Ramachandran, Sridhar, Marimuthu, Prashanthi Devi, and Somanathan, Balasubramanian
- Published
- 2015
- Full Text
- View/download PDF
13. Time series forecasting using GMDH neural networks for Chikungunya in Mysore district, India
- Author
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K, Stavelin Abhinandithe, primary, B, Madhu, additional, Balasubramanian, Somanathan, additional, and Ramachandran, Sridhar, additional
- Published
- 2022
- Full Text
- View/download PDF
14. Zebrafish information network, the knowledgebase for Danio rerio research
- Author
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Bradford, Yvonne M, primary, Van Slyke, Ceri E, additional, Ruzicka, Leyla, additional, Singer, Amy, additional, Eagle, Anne, additional, Fashena, David, additional, Howe, Douglas G, additional, Frazer, Ken, additional, Martin, Ryan, additional, Paddock, Holly, additional, Pich, Christian, additional, Ramachandran, Sridhar, additional, and Westerfield, Monte, additional
- Published
- 2022
- Full Text
- View/download PDF
15. Harmonizing model organism data in the Alliance of Genome Resources
- Author
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Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A., Alexander, Micheal, Anagnostopoulos, Anna V., Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M., Blake, Judith A., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Christie, Karen R., Crosby, Madeline A., Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L., D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E., dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R., Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C., Gondwe, Felix, Goodman, Josh, Gramates, L. Sian, Grove, Christian A., Hale, Paul, Harris, Todd, Thomas Hayman, G., Hill, David P., Howe, Douglas G., Howe, Kevin L., Hu, Yanhui, Jha, Sagar, Kadin, James A., Kaufman, Thomas C., Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E., Laulederkind, Stanley J. F., Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A., Martin, Ryan, Marygold, Steven J., Matthews, Beverley, McAndrews, Monica S., Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Müller, Hans-Michael, Mungall, Christopher J., Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S., Nash, Robert S., Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E., Russo Gelbart, Susan, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R., Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M., Smith, Cynthia L., Smith, Jennifer R., Stein, Lincoln, Sternberg, Paul W., Tabone, Christopher J., Thomas, Paul D., Thorat, Ketaki, Thota, Jyothi, Toro, Sabrina, Tomczuk, Monika, Trovisco, Vitor, Tutaj, Marek A., Tutaj, Monika, Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Wang, Qinghua, Wang, Shur-Jen, Weng, Shuai, Westerfield, Monte, Williams, Gary, Wilming, Laurens G., Wong, Edith D., Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Zhou, Pinglei, and Zytkovicz, Mark
- Subjects
Internet ,Molecular Sequence Annotation ,Rats ,Mice ,Gene Ontology ,Databases, Genetic ,Saccharomycetales ,Genetics ,Animals ,Humans ,Drosophila ,Caenorhabditis elegans ,Alleles ,Zebrafish - Abstract
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
- Published
- 2021
16. Zebrafish Information Network, the knowledgebase for Danio rerio research
- Author
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Bradford, Yvonne M., primary, Van Slyke, Ceri E., additional, Singer, Amy, additional, Paddock, Holly, additional, Eagle, Anne, additional, Fashena, David, additional, Howe, Douglas G., additional, Frazer, Ken, additional, Martin, Ryan, additional, Pich, Christian, additional, Ramachandran, Sridhar, additional, Ruzicka, Leyla, additional, and Westerfield, Monte, additional
- Published
- 2021
- Full Text
- View/download PDF
17. Forecasting Multivariate time-series data using LSTM Neural Network in Mysore district, Karnataka.
- Author
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Stavelin Abhinandithe, K., Madhu, B., Balasubramanian, Somanathan, and Ramachandran, Sridhar
- Subjects
FORECASTING ,DEEP learning ,TIME series analysis ,DISEASE management ,MACHINE learning - Abstract
Advanced and precise forecasting of infectious diseases plays a critical role in planning and providing resources effectively. Time series forecasting for non-linear issues are accessible using deep learning techniques. The association between climatic parameters and dengue occurrences was investigated in this work, and a forecasting model was constructed using a deep learning approach called long short-term memory (LSTM). Univariate and multivariate LSTM time series forecast models were developed using meteorological and dengue incidence data from January 2006 to December 2019. For univariate data, the Pycharm/Google Colab platform was implemented, as the deep learning framework Keras, which is one of the models in the machine learning library based on Tensorflow. The Pandas Python package with builtin support for time series data was used for multivariate data. The final model was chosen using the mae loss and the Adam optimizer. Once the model had been fixed, predictions were made using the model. The research showed that the meteorological factors such as maximum temperature at lag 3, minimum temperature at lag 3, maximum vapour pressure (lag 0,1 and 2), minimum vapour pressure at lag 1, and vapour pressure daily mean at lag 0,1,4 are all significant predictors of dengue along with RMSE value of 1.121 . The results indicated that LSTM network has higher prediction accuracy than any other traditional forecasting methods. Timely management of seasonal diseases such as dengue along with meteorological parameters can predict epidemics in the future. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
18. RNAcentral 2021:Secondary structure integration, improved sequence search and new member databases
- Author
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Sweeney, Blake A., Petrov, Anton I., Ribas, Carlos E., Finn, Robert D., Bateman, Alex, Szymanski, MacIej, Karlowski, Wojciech M., Seemann, Stefan E., Gorodkin, Jan, Cannone, Jamie J., Gutell, Robin R., Kay, Simon, Marygold, Steven, Dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M., Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P., Lowe, Todd M., Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G., Ma, Lina, Zhang, Zhang, Volders, Pieter Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J., Kalvari, Ioanna, Nawrocki, Eric P., Petrov, Anton S., Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M., Hoksza, David, Lovering, Ruth C., Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, Weinberg, Zasha, Sweeney, Blake A., Petrov, Anton I., Ribas, Carlos E., Finn, Robert D., Bateman, Alex, Szymanski, MacIej, Karlowski, Wojciech M., Seemann, Stefan E., Gorodkin, Jan, Cannone, Jamie J., Gutell, Robin R., Kay, Simon, Marygold, Steven, Dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M., Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P., Lowe, Todd M., Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G., Ma, Lina, Zhang, Zhang, Volders, Pieter Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J., Kalvari, Ioanna, Nawrocki, Eric P., Petrov, Anton S., Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M., Hoksza, David, Lovering, Ruth C., Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, and Weinberg, Zasha
- Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
- Published
- 2021
19. The Zebrafish Information Network: major gene page and home page updates
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Howe, Douglas G, primary, Ramachandran, Sridhar, additional, Bradford, Yvonne M, additional, Fashena, David, additional, Toro, Sabrina, additional, Eagle, Anne, additional, Frazer, Ken, additional, Kalita, Patrick, additional, Mani, Prita, additional, Martin, Ryan, additional, Moxon, Sierra Taylor, additional, Paddock, Holly, additional, Pich, Christian, additional, Ruzicka, Leyla, additional, Schaper, Kevin, additional, Shao, Xiang, additional, Singer, Amy, additional, Van Slyke, Ceri E, additional, and Westerfield, Monte, additional
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- 2020
- Full Text
- View/download PDF
20. English as a Lingua Franca in a Multilingual India
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Iyer, Ishwarya N., primary and Ramachandran, Sridhar, additional
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- 2019
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21. The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources
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Ruzicka, Leyla, primary, Howe, Douglas G, additional, Ramachandran, Sridhar, additional, Toro, Sabrina, additional, Van Slyke, Ceri E, additional, Bradford, Yvonne M, additional, Eagle, Anne, additional, Fashena, David, additional, Frazer, Ken, additional, Kalita, Patrick, additional, Mani, Prita, additional, Martin, Ryan, additional, Moxon, Sierra Taylor, additional, Paddock, Holly, additional, Pich, Christian, additional, Schaper, Kevin, additional, Shao, Xiang, additional, Singer, Amy, additional, and Westerfield, Monte, additional
- Published
- 2018
- Full Text
- View/download PDF
22. Theoretical Wear Rate Prediction and Experimental Validation of Repeatedly Operated Solenoid Valve
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Balasubramaniyan, Sakthivel, primary, Ramachandran, Sridhar, additional, Bashyam, Srinivasan, additional, and Kumar, Suresh, additional
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- 2017
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23. ZFIN, the Zebrafish Model Organism Database: updates and new directions
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Ruzicka, Leyla, Bradford, Yvonne M., Frazer, Ken, Howe, Douglas G., Paddock, Holly, Ramachandran, Sridhar, Singer, Amy, Toro, Sabrina, Van Slyke, Ceri E., Eagle, Anne E., Fashena, David, Kalita, Patrick, Knight, Jonathan, Mani, Prita, Martin, Ryan, Moxon, Sierra A. T., Pich, Christian, Schaper, Kevin, Shao, Xiang, and Westerfield, Monte
- Subjects
Internet ,fungi ,Databases, Genetic ,Models, Animal ,Animals ,Computational Biology ,Genomics ,Zebrafish Proteins ,Article ,Data Curation ,Genetic Association Studies ,Zebrafish - Abstract
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research. ZFIN staff curate detailed information about genes, mutants, genotypes, reporter lines, sequences, constructs, antibodies, knockdown reagents, expression patterns, phenotypes, gene product function, and orthology from publications. Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information. Data can be accessed through topic-specific searches, a new site-wide search, and the data-mining resource ZebrafishMine (http://zebrafishmine.org). Data download and web service options are also available. ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links, and participate in the development of standardized structured vocabularies (ontologies) used for data annotation and searching. ZFIN-curated gene, function, expression, and phenotype data are available for comparative exploration at several multi-species resources. The use of zebrafish as a model for human disease is increasing. ZFIN is supporting this growing area with three major projects: adding easy access to computed orthology data from gene pages, curating details of the gene expression pattern changes in mutant fish, and curating zebrafish models of human diseases.
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- 2015
24. Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN
- Author
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Bradford, Yvonne M., primary, Toro, Sabrina, additional, Ramachandran, Sridhar, additional, Ruzicka, Leyla, additional, Howe, Douglas G., additional, Eagle, Anne, additional, Kalita, Patrick, additional, Martin, Ryan, additional, Taylor Moxon, Sierra A., additional, Schaper, Kevin, additional, and Westerfield, Monte, additional
- Published
- 2017
- Full Text
- View/download PDF
25. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching
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Howe, Douglas G., primary, Bradford, Yvonne M., additional, Eagle, Anne, additional, Fashena, David, additional, Frazer, Ken, additional, Kalita, Patrick, additional, Mani, Prita, additional, Martin, Ryan, additional, Moxon, Sierra Taylor, additional, Paddock, Holly, additional, Pich, Christian, additional, Ramachandran, Sridhar, additional, Ruzicka, Leyla, additional, Schaper, Kevin, additional, Shao, Xiang, additional, Singer, Amy, additional, Toro, Sabrina, additional, Van Slyke, Ceri, additional, and Westerfield, Monte, additional
- Published
- 2016
- Full Text
- View/download PDF
26. The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources.
- Author
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Ruzicka, Leyla, Howe, Douglas G, Ramachandran, Sridhar, Toro, Sabrina, Van Slyke, Ceri E, Bradford, Yvonne M, Eagle, Anne, Fashena, David, Frazer, Ken, Kalita, Patrick, Mani, Prita, Martin, Ryan, Moxon, Sierra Taylor, Paddock, Holly, Pich, Christian, Schaper, Kevin, Shao, Xiang, Singer, Amy, and Westerfield, Monte
- Published
- 2019
- Full Text
- View/download PDF
27. ZFIN, The zebrafish model organism database: Updates and new directions
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Ruzicka, Leyla, primary, Bradford, Yvonne M., additional, Frazer, Ken, additional, Howe, Douglas G., additional, Paddock, Holly, additional, Ramachandran, Sridhar, additional, Singer, Amy, additional, Toro, Sabrina, additional, Van Slyke, Ceri E., additional, Eagle, Anne E., additional, Fashena, David, additional, Kalita, Patrick, additional, Knight, Jonathan, additional, Mani, Prita, additional, Martin, Ryan, additional, Moxon, Sierra A.T., additional, Pich, Christian, additional, Schaper, Kevin, additional, Shao, Xiang, additional, and Westerfield, Monte, additional
- Published
- 2015
- Full Text
- View/download PDF
28. In vitro antibiogram pattern of Staphylococcus aureus isolated from wound infection and molecular analysis of mecA gene and restriction sites in methicillin resistant Staphylococcus aureus
- Author
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Hemamalini, V, primary, Kavitha, V, additional, and Ramachandran, Sridhar, additional
- Published
- 2015
- Full Text
- View/download PDF
29. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching.
- Author
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Howe, Douglas G., Bradford, Yvonne M., Eagle, Anne, Fashena, David, Frazer, Ken, Kalita, Patrick, Mani, Prita, Martin, Ryan, Moxon, Sierra Taylor, Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Schaper, Kevin, Xiang Shao, Singer, Amy, Toro, Sabrina, Van Slyke, Ceri, and Westerfield, Monte
- Published
- 2017
- Full Text
- View/download PDF
30. The Zebrafish Information Network: major gene page and home page updates.
- Author
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Howe DG, Ramachandran S, Bradford YM, Fashena D, Toro S, Eagle A, Frazer K, Kalita P, Mani P, Martin R, Moxon ST, Paddock H, Pich C, Ruzicka L, Schaper K, Shao X, Singer A, Van Slyke CE, and Westerfield M
- Subjects
- Animals, Animals, Genetically Modified, Data Mining methods, Gene Expression, Humans, Internet, Models, Animal, Mutation, Phenotype, Zebrafish Proteins genetics, Computational Biology methods, Databases, Genetic, Genome genetics, Genomics methods, Zebrafish genetics
- Abstract
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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- 2021
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31. Using ZFIN: Data Types, Organization, and Retrieval.
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Van Slyke CE, Bradford YM, Howe DG, Fashena DS, Ramachandran S, and Ruzicka L
- Subjects
- Animals, Gene Ontology, Genes, Genotype, Pseudogenes, Sequence Analysis, DNA, Software, User-Computer Interface, Web Browser, Databases, Genetic, Genome, Genomics methods, Zebrafish genetics
- Abstract
The Zebrafish Model Organism Database (ZFIN; zfin.org) was established in 1994 as the primary genetic and genomic resource for the zebrafish research community. Some of the earliest records in ZFIN were for people and laboratories. Since that time, services and data types provided by ZFIN have grown considerably. Today, ZFIN provides the official nomenclature for zebrafish genes, mutants, and transgenics and curates many data types including gene expression, phenotypes, Gene Ontology, models of human disease, orthology, knockdown reagents, transgenic constructs, and antibodies. Ontologies are used throughout ZFIN to structure these expertly curated data. An integrated genome browser provides genomic context for genes, transgenics, mutants, and knockdown reagents. ZFIN also supports a community wiki where the research community can post new antibody records and research protocols. Data in ZFIN are accessible via web pages, download files, and the ZebrafishMine (zebrafishmine.org), an installation of the InterMine data warehousing software. Searching for data at ZFIN utilizes both parameterized search forms and a single box search for searching or browsing data quickly. This chapter aims to describe the primary ZFIN data and services, and provide insight into how to use and interpret ZFIN searches, data, and web pages.
- Published
- 2018
- Full Text
- View/download PDF
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