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1. Data navigation on the ENCODE portal

Author

Kagda, Meenakshi S., Lam, Bonita, Litton, Casey, Small, Corinn, Sloan, Cricket A., Spragins, Emma, Tanaka, Forrest, Whaling, Ian, Gabdank, Idan, Youngworth, Ingrid, Strattan, J. Seth, Hilton, Jason, Jou, Jennifer, Au, Jessica, Lee, Jin-Wook, Andreeva, Kalina, Graham, Keenan, Lin, Khine, Simison, Matt, Jolanki, Otto, Sud, Paul, Assis, Pedro, Adenekan, Philip, Douglas, Eric, Li, Mingjie, Miyasato, Stuart, Zhong, Weiwei, Luo, Yunhai, Myers, Zachary, Cherry, J. Michael, and Hitz, Benjamin C.

Subjects
Quantitative Biology - Genomics, Computer Science - Databases
Abstract

Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generated by the consortium is shared through a web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth and final phase of the project added a diverse set of new samples (including those associated with human disease), and a wide range of new assays aimed at detection, characterization and validation of functional genomic elements. The ENCODE data portal hosts results from over 23,000 functional genomics experiments, over 800 functional elements characterization experiments (including in vivo transgenic enhancer assays, reporter assays and CRISPR screens) along with over 60,000 results of computational and integrative analyses (including imputations, predictions and genome annotations). The ENCODE Data Coordination Center (DCC) is responsible for development and maintenance of the data portal, along with the implementation and utilisation of the ENCODE uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal. Specifically, we have completely redesigned the home page, improved search interface, added several new pages to highlight collections of biologically related data (deeply profiled cell lines, immune cells, Alzheimer's Disease, RNA-Protein interactions, degron matrix and a matrix of experiments organised by human donors), added single-cell experiments, and enhanced the cart interface for visualisation and download of user-selected datasets.

Published
2023

2. Author Correction: Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

Published
2022

4. Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, Animals, Binding Sites, Chromatin, DNA Methylation, Databases, Genetic, Gene Expression Regulation, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Molecular Sequence Annotation, Quality Control, Regulatory Sequences, Nucleic Acid, Transcription Factors, ENCODE Project Consortium, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

5. Perspectives on ENCODE.

Author

ENCODE Project Consortium, Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, Chromatin, Animals, Humans, Mice, Histones, Transcription Factors, Genomics, DNA Methylation, Gene Expression Regulation, Binding Sites, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Quality Control, Databases, Genetic, Molecular Sequence Annotation, Human Genome, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

6. Deciphering the impact of genomic variation on function.

Author

Engreitz, Jesse M., Lawson, Heather A., Singh, Harinder, Starita, Lea M., Hon, Gary C., Carter, Hannah, Sahni, Nidhi, Reddy, Timothy E., Lin, Xihong, Li, Yun, Munshi, Nikhil V., Chahrour, Maria H., Boyle, Alan P., Hitz, Benjamin C., Mortazavi, Ali, Craven, Mark, Mohlke, Karen L., Pinello, Luca, Wang, Ting, and Kundaje, Anshul

Abstract

Our genomes influence nearly every aspect of human biology—from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanisms of human biology, uncover the basis of genetic predispositions to diseases, and guide the development of new diagnostic tools and therapeutic agents. Yet, understanding how genomic variation alters genome function to influence phenotype has proved challenging. To unlock these insights, we need a systematic and comprehensive catalogue of genome function and the molecular and cellular effects of genomic variants. Towards this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations and predictive modelling to investigate the relationships among genomic variation, genome function and phenotypes. IGVF will create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how such effects connect through gene-regulatory and protein-interaction networks. These experimental data, computational predictions and accompanying standards and pipelines will be integrated into an open resource that will catalyse community efforts to explore how our genomes influence biology and disease across populations.The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The ENCODE Uniform Analysis Pipelines

Author

Hitz, Benjamin C., primary, Lee, Jin-Wook, additional, Jolanki, Otto, additional, Kagda, Meenakshi S., additional, Graham, Keenan, additional, Sud, Paul, additional, Gabdank, Idan, additional, Seth Strattan, J., additional, Sloan, Cricket A., additional, Dreszer, Timothy, additional, Rowe, Laurence D., additional, Podduturi, Nikhil R., additional, Malladi, Venkat S., additional, Chan, Esther T., additional, Davidson, Jean M., additional, Ho, Marcus, additional, Miyasato, Stuart, additional, Simison, Matt, additional, Tanaka, Forrest, additional, Luo, Yunhai, additional, Whaling, Ian, additional, Hong, Eurie L., additional, Lee, Brian T., additional, Sandstrom, Richard, additional, Rynes, Eric, additional, Nelson, Jemma, additional, Nishida, Andrew, additional, Ingersoll, Alyssa, additional, Buckley, Michael, additional, Frerker, Mark, additional, Kim, Daniel S, additional, Boley, Nathan, additional, Trout, Diane, additional, Dobin, Alex, additional, Rahmanian, Sorena, additional, Wyman, Dana, additional, Balderrama-Gutierrez, Gabriela, additional, Reese, Fairlie, additional, Durand, Neva C., additional, Dudchenko, Olga, additional, Weisz, David, additional, Rao, Suhas S. P., additional, Blackburn, Alyssa, additional, Gkountaroulis, Dimos, additional, Sadr, Mahdi, additional, Olshansky, Moshe, additional, Eliaz, Yossi, additional, Nguyen, Dat, additional, Bochkov, Ivan, additional, Shamim, Muhammad Saad, additional, Mahajan, Ragini, additional, Aiden, Erez, additional, Gingeras, Tom, additional, Heath, Simon, additional, Hirst, Martin, additional, James Kent, W., additional, Kundaje, Anshul, additional, Mortazavi, Ali, additional, Wold, Barbara, additional, and Cherry, J. Michael, additional

Published
2023
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8. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Author

Rozowsky, Joel, primary, Gao, Jiahao, additional, Borsari, Beatrice, additional, Yang, Yucheng T., additional, Galeev, Timur, additional, Gürsoy, Gamze, additional, Epstein, Charles B., additional, Xiong, Kun, additional, Xu, Jinrui, additional, Li, Tianxiao, additional, Liu, Jason, additional, Yu, Keyang, additional, Berthel, Ana, additional, Chen, Zhanlin, additional, Navarro, Fabio, additional, Sun, Maxwell S., additional, Wright, James, additional, Chang, Justin, additional, Cameron, Christopher J.F., additional, Shoresh, Noam, additional, Gaskell, Elizabeth, additional, Drenkow, Jorg, additional, Adrian, Jessika, additional, Aganezov, Sergey, additional, Aguet, François, additional, Balderrama-Gutierrez, Gabriela, additional, Banskota, Samridhi, additional, Corona, Guillermo Barreto, additional, Chee, Sora, additional, Chhetri, Surya B., additional, Cortez Martins, Gabriel Conte, additional, Danyko, Cassidy, additional, Davis, Carrie A., additional, Farid, Daniel, additional, Farrell, Nina P., additional, Gabdank, Idan, additional, Gofin, Yoel, additional, Gorkin, David U., additional, Gu, Mengting, additional, Hecht, Vivian, additional, Hitz, Benjamin C., additional, Issner, Robbyn, additional, Jiang, Yunzhe, additional, Kirsche, Melanie, additional, Kong, Xiangmeng, additional, Lam, Bonita R., additional, Li, Shantao, additional, Li, Bian, additional, Li, Xiqi, additional, Lin, Khine Zin, additional, Luo, Ruibang, additional, Mackiewicz, Mark, additional, Meng, Ran, additional, Moore, Jill E., additional, Mudge, Jonathan, additional, Nelson, Nicholas, additional, Nusbaum, Chad, additional, Popov, Ioann, additional, Pratt, Henry E., additional, Qiu, Yunjiang, additional, Ramakrishnan, Srividya, additional, Raymond, Joe, additional, Salichos, Leonidas, additional, Scavelli, Alexandra, additional, Schreiber, Jacob M., additional, Sedlazeck, Fritz J., additional, See, Lei Hoon, additional, Sherman, Rachel M., additional, Shi, Xu, additional, Shi, Minyi, additional, Sloan, Cricket Alicia, additional, Strattan, J Seth, additional, Tan, Zhen, additional, Tanaka, Forrest Y., additional, Vlasova, Anna, additional, Wang, Jun, additional, Werner, Jonathan, additional, Williams, Brian, additional, Xu, Min, additional, Yan, Chengfei, additional, Yu, Lu, additional, Zaleski, Christopher, additional, Zhang, Jing, additional, Ardlie, Kristin, additional, Cherry, J Michael, additional, Mendenhall, Eric M., additional, Noble, William S., additional, Weng, Zhiping, additional, Levine, Morgan E., additional, Dobin, Alexander, additional, Wold, Barbara, additional, Mortazavi, Ali, additional, Ren, Bing, additional, Gillis, Jesse, additional, Myers, Richard M., additional, Snyder, Michael P., additional, Choudhary, Jyoti, additional, Milosavljevic, Aleksandar, additional, Schatz, Michael C., additional, Bernstein, Bradley E., additional, Guigó, Roderic, additional, Gingeras, Thomas R., additional, and Gerstein, Mark, additional

Published
2023
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9. The ENCODE Uniform Analysis Pipelines

Author

Hitz, Benjamin C., Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S., Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, James Kent, W., Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael, Hitz, Benjamin C., Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S., Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, James Kent, W., Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, and Cherry, J. Michael

Abstract

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of theHomo sapiensandMus musculusgenomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and availableviathe ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL;https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environmentsviaCromwell. Access to the pipelines and dataviathe cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE c

Published
2023

10. Annotating and prioritizing human non-coding variants with RegulomeDB

Author

Dong, Shengcheng, primary, Zhao, Nanxiang, additional, Spragins, Emma, additional, Kagda, Meenakshi S., additional, Li, Mingjie, additional, Assis, Pedro, additional, Jolanki, Otto, additional, Luo, Yunhai, additional, Cherry, J Michael, additional, Boyle, Alan P, additional, and Hitz, Benjamin C, additional

Published
2022
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11. Author Correction: Perspectives on ENCODE

Author

ENCODE Project Consortium, Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

Published
2022

14. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Author

Rozowsky, Joel, primary, Drenkow, Jorg, additional, Yang, Yucheng T, additional, Gursoy, Gamze, additional, Galeev, Timur, additional, Borsari, Beatrice, additional, Epstein, Charles B, additional, Xiong, Kun, additional, Xu, Jinrui, additional, Gao, Jiahao, additional, Yu, Keyang, additional, Berthel, Ana, additional, Chen, Zhanlin, additional, Navarro, Fabio, additional, Liu, Jason, additional, Sun, Maxwell S, additional, Wright, James, additional, Chang, Justin, additional, Cameron, Christopher JF, additional, Shoresh, Noam, additional, Gaskell, Elizabeth, additional, Adrian, Jessika, additional, Aganezov, Sergey, additional, Aguet, François, additional, Balderrama-Gutierrez, Gabriela, additional, Banskota, Samridhi, additional, Corona, Guillermo Barreto, additional, Chee, Sora, additional, Chhetri, Surya B, additional, Cortez Martins, Gabriel Conte, additional, Danyko, Cassidy, additional, Davis, Carrie A, additional, Farid, Daniel, additional, Farrell, Nina P, additional, Gabdank, Idan, additional, Gofin, Yoel, additional, Gorkin, David U, additional, Gu, Mengting, additional, Hecht, Vivian, additional, Hitz, Benjamin C, additional, Issner, Robbyn, additional, Kirsche, Melanie, additional, Kong, Xiangmeng, additional, Lam, Bonita R, additional, Li, Shantao, additional, Li, Bian, additional, Li, Tianxiao, additional, Li, Xiqi, additional, Lin, Khine Zin, additional, Luo, Ruibang, additional, Mackiewicz, Mark, additional, Moore, Jill E, additional, Mudge, Jonathan, additional, Nelson, Nicholas, additional, Nusbaum, Chad, additional, Popov, Ioann, additional, Pratt, Henry E, additional, Qiu, Yunjiang, additional, Ramakrishnan, Srividya, additional, Raymond, Joe, additional, Salichos, Leonidas, additional, Scavelli, Alexandra, additional, Schreiber, Jacob M, additional, Sedlazeck, Fritz J, additional, See, Lei Hoon, additional, Sherman, Rachel M, additional, Shi, Xu, additional, Shi, Minyi, additional, Sloan, Cricket Alicia, additional, Strattan, J Seth, additional, Tan, Zhen, additional, Tanaka, Forrest Y, additional, Vlasova, Anna, additional, Wang, Jun, additional, Werner, Jonathan, additional, Williams, Brian, additional, Xu, Min, additional, Yan, Chengfei, additional, Yu, Lu, additional, Zaleski, Christopher, additional, Zhang, Jing, additional, Ardlie, Kristin, additional, Cherry, J Michael, additional, Mendenhall, Eric M, additional, Noble, William S, additional, Weng, Zhiping, additional, Levine, Morgan E, additional, Dobin, Alexander, additional, Wold, Barbara, additional, Mortazavi, Ali, additional, Ren, Bing, additional, Gillis, Jesse, additional, Myers, Richard M, additional, Snyder, Michael P, additional, Choudhary, Jyoti, additional, Milosavljevic, Aleksandar, additional, Schatz, Michael C, additional, Guigó, Roderic, additional, Bernstein, Bradley E, additional, Gingeras, Thomas R, additional, and Gerstein, Mark, additional

Published
2021
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15. Saccharomyces Genome Database: the genomics resource of budding yeast

Author

Cherry, J. Michael, Hong, Eurie L., Amundsen, Craig, Balakrishnan, Rama, Binkley, Gail, Chan, Esther T., Christie, Karen R., Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Karra, Kalpana, Krieger, Cynthia J., Miyasato, Stuart R., Nash, Rob S., Park, Julie, Skrzypek, Marek S., Simison, Matt, Weng, Shuai, and Wong, Edith D.

Published
2012
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16. Saccharomyces Genome Database provides mutant phenotype data

Author

Engel, Stacia R., Balakrishnan, Rama, Binkley, Gail, Christie, Karen R., Costanzo, Maria C., Dwight, Selina S., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Hong, Eurie L., Krieger, Cynthia J., Livstone, Michael S., Miyasato, Stuart R., Nash, Robert, Oughtred, Rose, Park, Julie, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Dolinski, Kara, Botstein, David, and Cherry, J. Michael

Published
2010
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17. Gene Ontology annotations at SGD: new data sources and annotation methods

Author

Hong, Eurie L., Balakrishnan, Rama, Dong, Qing, Christie, Karen R., Park, Julie, Binkley, Gail, Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Krieger, Cynthia J., Livstone, Michael S., Miyasato, Stuart R., Nash, Robert S., Oughtred, Rose, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Zhu, Kathy K., Dolinski, Kara, Botstein, David, and Cherry, J. Michael

Published
2008

18. YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

Author

Balakrishnan, Rama, Park, Julie, Karra, Kalpana, Hitz, Benjamin C, Binkley, Gail, Hong, Eurie L, Sullivan, Julie, Micklem, Gos, Cherry, J Michael, Micklem, Gos [0000-0002-6883-6168], and Apollo - University of Cambridge Repository

Subjects
Internet, User-Computer Interface, Databases, Genetic, Database Management Systems, Saccharomyces cerevisiae, Genome, Fungal, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) provides high-quality curated genomic, genetic, and molecular information on the genes and their products of the budding yeast Saccharomyces cerevisiae. To accommodate the increasingly complex, diverse needs of researchers for searching and comparing data, SGD has implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine (http://yeastmine.yeastgenome.org). YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types. YeastMine offers multiple scenarios in which it can be used such as a powerful search interface, a discovery tool, a curation aid and also a complex database presentation format. DATABASE URL: http://yeastmine.yeastgenome.org.

Published
2018
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19. The ENCODE Portal as an Epigenomics Resource

Author

Jou, Jennifer, primary, Gabdank, Idan, additional, Luo, Yunhai, additional, Lin, Khine, additional, Sud, Paul, additional, Myers, Zachary, additional, Hilton, Jason A., additional, Kagda, Meenakshi S., additional, Lam, Bonita, additional, O'Neill, Emma, additional, Adenekan, Philip, additional, Graham, Keenan, additional, Baymuradov, Ulugbek K., additional, R. Miyasato, Stuart, additional, Strattan, J. Seth, additional, Jolanki, Otto, additional, Lee, Jin‐Wook, additional, Litton, Casey, additional, Y. Tanaka, Forrest, additional, Hitz, Benjamin C., additional, and Cherry, J. Michael, additional

Published
2019
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20. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Author

Luo, Yunhai, primary, Hitz, Benjamin C, primary, Gabdank, Idan, primary, Hilton, Jason A, primary, Kagda, Meenakshi S, primary, Lam, Bonita, primary, Myers, Zachary, primary, Sud, Paul, primary, Jou, Jennifer, primary, Lin, Khine, primary, Baymuradov, Ulugbek K, primary, Graham, Keenan, primary, Litton, Casey, primary, Miyasato, Stuart R, primary, Strattan, J Seth, primary, Jolanki, Otto, primary, Lee, Jin-Wook, primary, Tanaka, Forrest Y, primary, Adenekan, Philip, primary, O’Neill, Emma, primary, and Cherry, J Michael, primary

Published
2019
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21. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.

Author

Luo, Yunhai, Hitz, Benjamin C, Gabdank, Idan, Hilton, Jason A, Kagda, Meenakshi S, Lam, Bonita, Myers, Zachary, Sud, Paul, Jou, Jennifer, Lin, Khine, Baymuradov, Ulugbek K, Graham, Keenan, Litton, Casey, Miyasato, Stuart R, Strattan, J Seth, Jolanki, Otto, Lee, Jin-Wook, Tanaka, Forrest Y, Adenekan, Philip, and O'Neill, Emma

Published
2020
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22. Prevention of data duplication for high throughput sequencing repositories

Author

Gabdank, Idan, primary, Chan, Esther T, additional, Davidson, Jean M, additional, Hilton, Jason A, additional, Davis, Carrie A, additional, Baymuradov, Ulugbek K, additional, Narayanan, Aditi, additional, Onate, Kathrina C, additional, Graham, Keenan, additional, Miyasato, Stuart R, additional, Dreszer, Timothy R, additional, Strattan, J Seth, additional, Jolanki, Otto, additional, Tanaka, Forrest Y, additional, Hitz, Benjamin C, additional, Sloan, Cricket A, additional, and Cherry, J Michael, additional

Published
2018
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23. The Encyclopedia of DNA elements (ENCODE): data portal update

Author

Davis, Carrie A, primary, Hitz, Benjamin C, additional, Sloan, Cricket A, additional, Chan, Esther T, additional, Davidson, Jean M, additional, Gabdank, Idan, additional, Hilton, Jason A, additional, Jain, Kriti, additional, Baymuradov, Ulugbek K, additional, Narayanan, Aditi K, additional, Onate, Kathrina C, additional, Graham, Keenan, additional, Miyasato, Stuart R, additional, Dreszer, Timothy R, additional, Strattan, J Seth, additional, Jolanki, Otto, additional, Tanaka, Forrest Y, additional, and Cherry, J Michael, additional

Published
2017
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24. SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

Author

Hitz, Benjamin C., primary, Rowe, Laurence D., additional, Podduturi, Nikhil R., additional, Glick, David I., additional, Baymuradov, Ulugbek K., additional, Malladi, Venkat S., additional, Chan, Esther T., additional, Davidson, Jean M., additional, Gabdank, Idan, additional, Narayana, Aditi K., additional, Onate, Kathrina C., additional, Hilton, Jason, additional, Ho, Marcus C., additional, Lee, Brian T., additional, Miyasato, Stuart R., additional, Dreszer, Timothy R., additional, Sloan, Cricket A., additional, Strattan, J. Seth, additional, Tanaka, Forrest Y., additional, Hong, Eurie L., additional, and Cherry, J. Michael, additional

Published
2017
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25. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Author

Stunnenberg, Hendrik G., primary, Hirst, Martin, additional, Abrignani, Sergio, additional, Adams, David, additional, de Almeida, Melanie, additional, Altucci, Lucia, additional, Amin, Viren, additional, Amit, Ido, additional, Antonarakis, Stylianos E., additional, Aparicio, Samuel, additional, Arima, Takahiro, additional, Arrigoni, Laura, additional, Arts, Rob, additional, Asnafi, Vahid, additional, Esteller, Manel, additional, Bae, Jae-Bum, additional, Bassler, Kevin, additional, Beck, Stephan, additional, Berkman, Benjamin, additional, Bernstein, Bradley E., additional, Bilenky, Mikhail, additional, Bird, Adrian, additional, Bock, Christoph, additional, Boehm, Bernhard, additional, Bourque, Guillaume, additional, Breeze, Charles E., additional, Brors, Benedikt, additional, Bujold, David, additional, Burren, Oliver, additional, Bussemakers, Marion J., additional, Butterworth, Adam, additional, Campo, Elias, additional, Carrillo-de-Santa-Pau, Enrique, additional, Chadwick, Lisa, additional, Chan, Kui Ming, additional, Chen, Wei, additional, Cheung, Tom H., additional, Chiapperino, Luca, additional, Choi, Nak Hyen, additional, Chung, Ho-Ryun, additional, Clarke, Laura, additional, Connors, Joseph M., additional, Cronet, Philippe, additional, Danesh, John, additional, Dermitzakis, Manolis, additional, Drewes, Gerard, additional, Durek, Pawel, additional, Dyke, Stephanie, additional, Dylag, Tomasz, additional, Eaves, Connie J., additional, Ebert, Peter, additional, Eils, Roland, additional, Eils, Jürgen, additional, Ennis, Catherine A., additional, Enver, Tariq, additional, Feingold, Elise A., additional, Felder, Bärbel, additional, Ferguson-Smith, Anne, additional, Fitzgibbon, Jude, additional, Flicek, Paul, additional, Foo, Roger S.-Y., additional, Fraser, Peter, additional, Frontini, Mattia, additional, Furlong, Eileen, additional, Gakkhar, Sitanshu, additional, Gasparoni, Nina, additional, Gasparoni, Gilles, additional, Geschwind, Daniel H., additional, Glažar, Petar, additional, Graf, Thomas, additional, Grosveld, Frank, additional, Guan, Xin-Yuan, additional, Guigo, Roderic, additional, Gut, Ivo G., additional, Hamann, Alf, additional, Han, Bok-Ghee, additional, Harris, R. Alan, additional, Heath, Simon, additional, Helin, Kristian, additional, Hengstler, Jan G., additional, Heravi-Moussavi, Alireza, additional, Herrup, Karl, additional, Hill, Steven, additional, Hilton, Jason A., additional, Hitz, Benjamin C., additional, Horsthemke, Bernhard, additional, Hu, Ming, additional, Hwang, Joo-Yeon, additional, Ip, Nancy Y., additional, Ito, Takashi, additional, Javierre, Biola-Maria, additional, Jenko, Sasa, additional, Jenuwein, Thomas, additional, Joly, Yann, additional, Jones, Steven J.M., additional, Kanai, Yae, additional, Kang, Hee Gyung, additional, Karsan, Aly, additional, Kiemer, Alexandra K., additional, Kim, Song Cheol, additional, Kim, Bong-Jo, additional, Kim, Hyeon-Hoe, additional, Kimura, Hiroshi, additional, Kinkley, Sarah, additional, Klironomos, Filippos, additional, Koh, In-Uk, additional, Kostadima, Myrto, additional, Kressler, Christopher, additional, Kreuzhuber, Roman, additional, Kundaje, Anshul, additional, Küppers, Ralf, additional, Larabell, Carolyn, additional, Lasko, Paul, additional, Lathrop, Mark, additional, Lee, Daniel H.S., additional, Lee, Suman, additional, Lehrach, Hans, additional, Leitão, Elsa, additional, Lengauer, Thomas, additional, Lernmark, Åke, additional, Leslie, R. David, additional, Leung, Gilberto K.K., additional, Leung, Danny, additional, Loeffler, Markus, additional, Ma, Yussanne, additional, Mai, Antonello, additional, Manke, Thomas, additional, Marcotte, Eric R., additional, Marra, Marco A., additional, Martens, Joost H.A., additional, Martin-Subero, Jose Ignacio, additional, Maschke, Karen, additional, Merten, Christoph, additional, Milosavljevic, Aleksandar, additional, Minucci, Saverio, additional, Mitsuyama, Totai, additional, Moore, Richard A., additional, Müller, Fabian, additional, Mungall, Andrew J., additional, Netea, Mihai G., additional, Nordström, Karl, additional, Norstedt, Irene, additional, Okae, Hiroaki, additional, Onuchic, Vitor, additional, Ouellette, Francis, additional, Ouwehand, Willem, additional, Pagani, Massimiliano, additional, Pancaldi, Vera, additional, Pap, Thomas, additional, Pastinen, Tomi, additional, Patel, Ronak, additional, Paul, Dirk S., additional, Pazin, Michael J., additional, Pelicci, Pier Giuseppe, additional, Phillips, Anthony G., additional, Polansky, Julia, additional, Porse, Bo, additional, Pospisilik, J. Andrew, additional, Prabhakar, Shyam, additional, Procaccini, Dena C., additional, Radbruch, Andreas, additional, Rajewsky, Nikolaus, additional, Rakyan, Vardham, additional, Reik, Wolf, additional, Ren, Bing, additional, Richardson, David, additional, Richter, Andreas, additional, Rico, Daniel, additional, Roberts, David J., additional, Rosenstiel, Philip, additional, Rothstein, Mark, additional, Salhab, Abdulrahman, additional, Sasaki, Hiroyuki, additional, Satterlee, John S., additional, Sauer, Sascha, additional, Schacht, Claudia, additional, Schmidt, Florian, additional, Schmitz, Gerd, additional, Schreiber, Stefan, additional, Schröder, Christopher, additional, Schübeler, Dirk, additional, Schultze, Joachim L., additional, Schulyer, Ronald P., additional, Schulz, Marcel, additional, Seifert, Martin, additional, Shirahige, Katsuhiko, additional, Siebert, Reiner, additional, Sierocinski, Thomas, additional, Siminoff, Laura, additional, Sinha, Anupam, additional, Soranzo, Nicole, additional, Spicuglia, Salvatore, additional, Spivakov, Mikhail, additional, Steidl, Christian, additional, Strattan, J. Seth, additional, Stratton, Michael, additional, Südbeck, Peter, additional, Sun, Hao, additional, Suzuki, Narumi, additional, Suzuki, Yutaka, additional, Tanay, Amos, additional, Torrents, David, additional, Tyson, Frederick L., additional, Ulas, Thomas, additional, Ullrich, Sebastian, additional, Ushijima, Toshikazu, additional, Valencia, Alfonso, additional, Vellenga, Edo, additional, Vingron, Martin, additional, Wallace, Chris, additional, Wallner, Stefan, additional, Walter, Jörn, additional, Wang, Huating, additional, Weber, Stephanie, additional, Weiler, Nina, additional, Weller, Andreas, additional, Weng, Andrew, additional, Wilder, Steven, additional, Wiseman, Sam M., additional, Wu, Angela R., additional, Wu, Zhenguo, additional, Xiong, Jieyi, additional, Yamashita, Yasuhiro, additional, Yang, Xinyi, additional, Yap, Desmond Y., additional, Yip, Kevin Y., additional, Yip, Stephen, additional, Yoo, Jae-Il, additional, Zerbino, Daniel, additional, and Zipprich, Gideon, additional

Published
2016
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26. SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

Author

Hitz, Benjamin C., primary, Rowe, Laurence D., additional, Podduturi, Nikhil R., additional, Glick, David I., additional, Baymuradov, Ulugbek K., additional, Malladi, Venkat S., additional, Chan, Esther T., additional, Davidson, Jean M., additional, Gabdank, Idan, additional, Narayanan, Aditi K., additional, Onate, Kathrina C., additional, Hilton, Jason, additional, Ho, Marcus C., additional, Lee, Brian T., additional, Miyasato, Stuart R., additional, Dreszer, Timothy R., additional, Sloan, Cricket A., additional, Strattan, J. Seth, additional, Tanaka, Forrest Y., additional, Hong, Eurie L., additional, and Cherry, J. Michael, additional

Published
2016
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27. Principles of metadata organization at the ENCODE data coordination center

Author

Hong, Eurie L., primary, Sloan, Cricket A., additional, Chan, Esther T., additional, Davidson, Jean M., additional, Malladi, Venkat S., additional, Strattan, J. Seth, additional, Hitz, Benjamin C., additional, Gabdank, Idan, additional, Narayanan, Aditi K., additional, Ho, Marcus, additional, Lee, Brian T., additional, Rowe, Laurence D., additional, Dreszer, Timothy R., additional, Roe, Greg R., additional, Podduturi, Nikhil R., additional, Tanaka, Forrest, additional, Hilton, Jason A., additional, and Cherry, J. Michael, additional

Published
2016
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28. Integration of new alternative reference strain genome sequences into theSaccharomycesgenome database

Author

Song, Giltae, primary, Balakrishnan, Rama, additional, Binkley, Gail, additional, Costanzo, Maria C., additional, Dalusag, Kyla, additional, Demeter, Janos, additional, Engel, Stacia, additional, Hellerstedt, Sage T., additional, Karra, Kalpana, additional, Hitz, Benjamin C., additional, Nash, Robert S., additional, Paskov, Kelley, additional, Sheppard, Travis, additional, Skrzypek, Marek, additional, Weng, Shuai, additional, Wong, Edith, additional, and Michael Cherry, J., additional

Published
2016
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30. TheSaccharomycesGenome Database Variant Viewer

Author

Sheppard, Travis K., primary, Hitz, Benjamin C., additional, Engel, Stacia R., additional, Song, Giltae, additional, Balakrishnan, Rama, additional, Binkley, Gail, additional, Costanzo, Maria C., additional, Dalusag, Kyla S., additional, Demeter, Janos, additional, Hellerstedt, Sage T., additional, Karra, Kalpana, additional, Nash, Robert S., additional, Paskov, Kelley M., additional, Skrzypek, Marek S., additional, Weng, Shuai, additional, Wong, Edith D., additional, and Cherry, J. Michael, additional

Published
2015
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31. ENCODE data at the ENCODE portal

Author

Sloan, Cricket A., primary, Chan, Esther T., additional, Davidson, Jean M., additional, Malladi, Venkat S., additional, Strattan, J. Seth, additional, Hitz, Benjamin C., additional, Gabdank, Idan, additional, Narayanan, Aditi K., additional, Ho, Marcus, additional, Lee, Brian T., additional, Rowe, Laurence D., additional, Dreszer, Timothy R., additional, Roe, Greg, additional, Podduturi, Nikhil R., additional, Tanaka, Forrest, additional, Hong, Eurie L., additional, and Cherry, J. Michael, additional

Published
2015
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32. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

Author

Benayoun, Bérénice A., primary, Pollina, Elizabeth A., additional, Ucar, Duygu, additional, Mahmoudi, Salah, additional, Karra, Kalpana, additional, Wong, Edith D., additional, Devarajan, Keerthana, additional, Daugherty, Aaron C., additional, Kundaje, Anshul B., additional, Mancini, Elena, additional, Hitz, Benjamin C., additional, Gupta, Rakhi, additional, Rando, Thomas A., additional, Baker, Julie C., additional, Snyder, Michael P., additional, Cherry, J. Michael, additional, and Brunet, Anne, additional

Published
2015
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33. Ontology application and use at the ENCODE DCC

Author

Malladi, Venkat S., primary, Erickson, Drew T., additional, Podduturi, Nikhil R., additional, Rowe, Laurence D., additional, Chan, Esther T., additional, Davidson, Jean M., additional, Hitz, Benjamin C., additional, Ho, Marcus, additional, Lee, Brian T., additional, Miyasato, Stuart, additional, Roe, Gregory R., additional, Simison, Matt, additional, Sloan, Cricket A., additional, Strattan, J. Seth, additional, Tanaka, Forrest, additional, Kent, W. James, additional, Cherry, J. Michael, additional, and Hong, Eurie L., additional

Published
2015
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34. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

Author

Benayoun, Bérénice A., primary, Pollina, Elizabeth A., additional, Ucar, Duygu, additional, Mahmoudi, Salah, additional, Karra, Kalpana, additional, Wong, Edith D., additional, Devarajan, Keerthana, additional, Daugherty, Aaron C., additional, Kundaje, Anshul B., additional, Mancini, Elena, additional, Hitz, Benjamin C., additional, Gupta, Rakhi, additional, Rando, Thomas A., additional, Baker, Julie C., additional, Snyder, Michael P., additional, Cherry, J. Michael, additional, and Brunet, Anne, additional

Published
2014
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35. The Reference Genome Sequence ofSaccharomyces cerevisiae: Then and Now

Author

Engel, Stacia R, primary, Dietrich, Fred S, additional, Fisk, Dianna G, additional, Binkley, Gail, additional, Balakrishnan, Rama, additional, Costanzo, Maria C, additional, Dwight, Selina S, additional, Hitz, Benjamin C, additional, Karra, Kalpana, additional, Nash, Robert S, additional, Weng, Shuai, additional, Wong, Edith D, additional, Lloyd, Paul, additional, Skrzypek, Marek S, additional, Miyasato, Stuart R, additional, Simison, Matt, additional, and Cherry, J Michael, additional

Published
2014
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36. Saccharomycesgenome database provides new regulation data

Author

Costanzo, Maria C., primary, Engel, Stacia R., additional, Wong, Edith D., additional, Lloyd, Paul, additional, Karra, Kalpana, additional, Chan, Esther T., additional, Weng, Shuai, additional, Paskov, Kelley M., additional, Roe, Greg R., additional, Binkley, Gail, additional, Hitz, Benjamin C., additional, and Cherry, J. Michael, additional

Published
2013
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38. ENCODE data at the ENCODE portal.

Author

Sloan, Cricket A., Chan, Esther T., Davidson, Jean M., Malladi, Venkat S., Strattan, J. Seth, Hitz, Benjamin C., Gabdank, Idan, Narayanan, Aditi K., Ho, Marcus, Lee, Brian T., Rowe, Laurence D., Dreszer, Timothy R., Roe, Greg, Podduturi, Nikhil R., Tanaka, Forrest, Hong, Eurie L., and Cherry, J. Michael

Published
2016
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39. The Saccharomyces Genome Database Variant Viewer.

Author

Sheppard, Travis K., Hitz, Benjamin C., Engel, Stacia R., Song, Giltae, Balakrishnan, Rama, Binkley, Gail, Costanzo, Maria C., Dalusag, Kyla S., Demeter, Janos, Hellerstedt, Sage T., Karra, Kalpana, Nash, Robert S., Paskov, Kelley M., Skrzypek, Marek S., Shuai Weng, Wong, Edith D., and Cherry, J. Michael

Published
2016
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40. Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

Author

Song, Giltae, Balakrishnan, Rama, Binkley, Gail, Costanzo, Maria C., Dalusag, Kyla, Demeter, Janos, Engel, Stacia, Hellerstedt, Sage T., Karra, Kalpana, Hitz, Benjamin C., Nash, Robert S., Paskov, Kelley, Sheppard, Travis, Skrzypek, Marek, Shuai Weng, Edith Wong, and Cherry, J. Michael

Subjects
SACCHAROMYCES, GENOMICS, NUCLEOTIDE sequencing, PHENOTYPES, PHENOTYPIC plasticity in plants
Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences. [ABSTRACT FROM AUTHOR]

Published
2016
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41. Annotation of functional variation in personal genomes using RegulomeDB

Author

Boyle, Alan P., primary, Hong, Eurie L., additional, Hariharan, Manoj, additional, Cheng, Yong, additional, Schaub, Marc A., additional, Kasowski, Maya, additional, Karczewski, Konrad J., additional, Park, Julie, additional, Hitz, Benjamin C., additional, Weng, Shuai, additional, Cherry, J. Michael, additional, and Snyder, Michael, additional

Published
2012
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44. The YeastGenome app: the Saccharomyces Genome Database at your fingertips.

Author

Edith D. Wong, Karra, Kalpana, Hitz, Benjamin C., Eurie L. Hong, and Cherry, J. Michael

Subjects
SACCHAROMYCETACEAE, GENETICS, INTERROGATIVE (Grammar), GENOMES, HYPERTEXT systems, GENOTYPE-environment interaction
Abstract

The Saccharomyces Genome Database (SGD) is a scientific database that provides researchers with high-quality curated data about the genes and gene products of Saccharomyces cerevisiae. To provide instant and easy access to this information on mobile devices, we have developed YeastGenome, a native application for the Apple iPhone and iPad. YeastGenome can be used to quickly find basic information about S. cerevisiae genes and chromosomal features regardless of internet connectivity. With or without network access, you can view basic information and Gene Ontology annotations about a gene of interest by searching gene names and gene descriptions or by browsing the database within the app to find the gene of interest. With internet access, the app provides more detailed information about the gene, including mutant phenotypes, references and protein and genetic interactions, as well as provides hyperlinks to retrieve detailed information by showing SGD pages and views of the genome browser. SGD provides online help describing basic ways to navigate the mobile version of SGD, highlights key features and answers frequently asked questions related to the app. The app is available from iTunes (http://itunes.com/apps/yeastgenome). The YeastGenome app is provided freely as a service to our community, as part of SGD's mission to provide free and open access to all its data and annotations. [ABSTRACT FROM AUTHOR]

Published
2013
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45. GRASS: A server for the graphical representation and analysis of structures.

Author

NAYAL, MURAD, HITZ, BENJAMIN C., and HONIG, BARRY

Abstract

GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a World-Wide Web-based, platform-independent, easily used tool for macromolecular visualization and structure analysis. [ABSTRACT FROM PUBLISHER]

Published
1999

46. The ENCODE Uniform Analysis Pipelines.

Author

Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, and Cherry JM

Abstract

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses., Competing Interests: Conflict of interest. None declared

Published
2023
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47. Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

Author

Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, and Michael Cherry J

Subjects
Molecular Sequence Annotation, Reproducibility of Results, Saccharomyces cerevisiae genetics, User-Computer Interface, Databases, Genetic, Genome, Fungal genetics, Genomics methods, Saccharomyces genetics
Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.Database URL: www.yeastgenome.org., (© The Author(s) 2016. Published by Oxford University Press.)

Published
2016
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48. The reference genome sequence of Saccharomyces cerevisiae: then and now.

Author

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, and Cherry JM

Subjects
Chromosome Mapping, Databases, Factual, Internet, Open Reading Frames, Sequence Analysis, DNA, User-Computer Interface, Genome, Fungal, Saccharomyces cerevisiae genetics
Abstract

The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.

Published
2014
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