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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. The Gene Ontology knowledgebase in 2023

Author: Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, 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, and Berardini, Tanya Z
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Gene Ontology, Proteins, Molecular Sequence Annotation, Databases, Genetic, Computational Biology, gene annotation, gene function, knowledgebase, knowledge graphs, Gene Ontology Consortium, Developmental Biology, Biochemistry and 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

3. 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. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author: Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping
Subjects: ENCODE Project Consortium, General Science & Technology
Abstract: In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. 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) are now included in the author list. These errors have been corrected in the online version of the article.
Published: 2022

5. Harmonizing model organism data in the Alliance of Genome Resources

Author: 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
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.5 Resources and infrastructure (underpinning), 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

6. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author: Rehm, Heidi L, Page, Angela JH, Smith, Lindsay, Adams, Jeremy B, Alterovitz, Gil, Babb, Lawrence J, Barkley, Maxmillian P, Baudis, Michael, Beauvais, Michael JS, Beck, Tim, Beckmann, Jacques S, Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K, Boughtwood, Tiffany F, Bourque, Guillaume, Bowers, Sarion R, Brookes, Anthony J, Brudno, Michael, Brush, Matthew H, Bujold, David, Burdett, Tony, Buske, Orion J, Cabili, Moran N, Cameron, Daniel L, Carroll, Robert J, Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P, Chen, Shu Hui, Cherry, J Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L, Cook-Deegan, Robert M, Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M, Denisko, Danielle, Doerr, Megan J, Dolman, Lena I, Dove, Edward S, Dursi, L Jonathan, Dyke, Stephanie OM, Eddy, James A, Eilbeck, Karen, Ellrott, Kyle P, Fairley, Susan, Fakhro, Khalid A, Firth, Helen V, Fitzsimons, Michael S, Fiume, Marc, Flicek, Paul, Fore, Ian M, Freeberg, Mallory A, Freimuth, Robert R, Fromont, Lauren A, Fuerth, Jonathan, Gaff, Clara L, Gan, Weiniu, Ghanaim, Elena M, Glazer, David, Green, Robert C, Griffith, Malachi, Griffith, Obi L, Grossman, Robert L, Groza, Tudor, Auvil, Jaime M Guidry, Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A, Hamosh, Ada, Hansen, David P, Hart, Reece K, Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M, Ho, Calvin WL, Hobb, Ashley E, Hoffman, Michael M, Hofmann, Oliver M, Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E, Husami, Ammar, Jacobsen, Julius O, Jamuar, Saumya S, Janes, Elizabeth L, Jeanson, Francis, Jené, Aina, Johns, Amber L, Joly, Yann, Jones, Steven JM, Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M, and Kekesi-Lafrance, Kristina
Subjects: Biological Sciences, Genetics, Human Genome, Clinical Research, Health Services, Generic health relevance, Good Health and Well Being
Abstract: The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
Published: 2021

7. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

Author: Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing
Subjects: Reproductive Medicine, Biomedical and Clinical Sciences, Pediatric, General Science & Technology
Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03089-4.
Published: 2021

8. The Gene Ontology resource: enriching a GOld mine

Author: Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin CC, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit HM, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, and Karra, Kalpana
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Animals, Arabidopsis, Caenorhabditis elegans, Dictyostelium, Drosophila melanogaster, Escherichia coli, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomyces cerevisiae, Schizosaccharomyces, User-Computer Interface, Zebrafish, Gene Ontology Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract: The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.
Published: 2021

9. Annotating and prioritizing human non-coding variants with RegulomeDB v.2

Author: Dong, Shengcheng, Zhao, Nanxiang, Spragins, Emma, Kagda, Meenakshi S., Li, Mingjie, Assis, Pedro, Jolanki, Otto, Luo, Yunhai, Cherry, J. Michael, Boyle, Alan P., and Hitz, Benjamin C.
Published: 2023
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10. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

Author: Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing
Subjects: Reproductive Medicine, Biomedical and Clinical Sciences, General Science & Technology
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2020

11. An atlas of dynamic chromatin landscapes in mouse fetal development

Author: Gorkin, David U, Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J Seth, Davidson, Jean M, Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan T, Harrington, Anne N, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A, Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R, Shen, Yin, Dickel, Diane E, Visel, Axel, Pennacchio, Len A, and Ren, Bing
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Biotechnology, Pediatric, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Animals, Chromatin, Chromatin Immunoprecipitation Sequencing, Datasets as Topic, Disease, Enhancer Elements, Genetic, Female, Fetal Development, Gene Expression Regulation, Developmental, Genetic Variation, Histones, Humans, Male, Mice, Mice, Inbred C57BL, Molecular Sequence Annotation, Organ Specificity, Regulatory Sequences, Nucleic Acid, Reproducibility of Results, Transposases, General Science & Technology
Abstract: The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.
Published: 2020

12. 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

13. Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author: Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Animals, Chromatin, DNA, DNA Footprinting, DNA Methylation, DNA Replication Timing, Databases, Genetic, Deoxyribonuclease I, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Mice, Transgenic, Molecular Sequence Annotation, RNA-Binding Proteins, Registries, Regulatory Sequences, Nucleic Acid, Transcription, Genetic, Transposases, ENCODE Project Consortium, General Science & Technology
Abstract: The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
Published: 2020

14. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Author: ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping
Subjects: ENCODE Project Consortium, Chromatin, Animals, Mice, Transgenic, Humans, Mice, Deoxyribonuclease I, Transposases, RNA-Binding Proteins, Histones, DNA, Registries, DNA Footprinting, Genomics, DNA Methylation, DNA Replication Timing, Transcription, Genetic, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Databases, Genetic, Molecular Sequence Annotation, Human Genome, HIV/AIDS, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract: The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
Published: 2020

15. 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

16. RNAcentral: a hub of information for non-coding RNA sequences

Author: Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley JF, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, and Williams, Kelly P
Subjects: Biological Sciences, Environmental Sciences, Chemical Sciences, The RNAcentral Consortium, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Published: 2019

17. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines

Author: Preston, Christine G., Wright, Matt W., Madhavrao, Rao, Harrison, Steven M., Goldstein, Jennifer L., Luo, Xi, Wand, Hannah, Wulf, Bryan, Cheung, Gloria, Mandell, Mark E., Tong, Howard, Cheng, Shaung, Iacocca, Michael A., Pineda, Arturo Lopez, Popejoy, Alice B., Dalton, Karen, Zhen, Jimmy, Dwight, Selina S., Babb, Lawrence, DiStefano, Marina, O’Daniel, Julianne M., Lee, Kristy, Riggs, Erin R., Zastrow, Diane B., Mester, Jessica L., Ritter, Deborah I., Patel, Ronak Y., Subramanian, Sai Lakshmi, Milosavljevic, Aleksander, Berg, Jonathan S., Rehm, Heidi L., Plon, Sharon E., Cherry, J. Michael, Bustamante, Carlos D., and Costa, Helio A.
Published: 2022
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18. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.

Author: Kramer, Michael H, Farré, Jean-Claude, Mitra, Koyel, Yu, Michael Ku, Ono, Keiichiro, Demchak, Barry, Licon, Katherine, Flagg, Mitchell, Balakrishnan, Rama, Cherry, J Michael, Subramani, Suresh, and Ideker, Trey
Subjects: Humans, Pichia, Saccharomyces cerevisiae, Glucosyltransferases, GTPase-Activating Proteins, Saccharomyces cerevisiae Proteins, Systems Biology, Genomics, Gene Expression Regulation, Fungal, Models, Genetic, Systems Integration, Databases, Genetic, Autophagy, Gene Regulatory Networks, Endosomal Sorting Complexes Required for Transport, Protein Interaction Maps, Autophagy-Related Proteins, active interaction mapping, autophagy, hierarchical modeling, human, systems biology, yeast, Gene Expression Regulation, Fungal, Models, Genetic, Databases, 1.1 Normal biological development and functioning, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract: We have developed a general progressive procedure, Active Interaction Mapping, to guide assembly of the hierarchy of functions encoding any biological system. Using this process, we assemble an ontology of functions comprising autophagy, a central recycling process implicated in numerous diseases. A first-generation model, built from existing gene networks in Saccharomyces, captures most known autophagy components in broad relation to vesicle transport, cell cycle, and stress response. Systematic analysis identifies synthetic-lethal interactions as most informative for further experiments; consequently, we saturate the model with 156,364 such measurements across autophagy-activating conditions. These targeted interactions provide more information about autophagy than all previous datasets, producing a second-generation ontology of 220 functions. Approximately half are previously unknown; we confirm roles for Gyp1 at the phagophore-assembly site, Atg24 in cargo engulfment, Atg26 in cytoplasm-to-vacuole targeting, and Ssd1, Did4, and others in selective and non-selective autophagy. The procedure and autophagy hierarchy are at http://atgo.ucsd.edu/.
Published: 2017

19. RNAcentral: a comprehensive database of non-coding RNA sequences

Author: Petrov, Anton I, Kay, Simon JE, Kalvari, Ioanna, Howe, Kevin L, Gray, Kristian A, Bruford, Elspeth A, Kersey, Paul J, Cochrane, Guy, Finn, Robert D, Bateman, Alex, Kozomara, Ana, Griffiths-Jones, Sam, Frankish, Adam, Zwieb, Christian W, Lau, Britney Y, Williams, Kelly P, Chan, Patricia P, Lowe, Todd M, Cannone, Jamie J, Gutell, Robin, Machnicka, Magdalena A, Bujnicki, Janusz M, Yoshihama, Maki, Kenmochi, Naoya, Chai, Benli, Cole, James R, Szymanski, Maciej, Karlowski, Wojciech M, Wood, Valerie, Huala, Eva, Berardini, Tanya Z, Zhao, Yi, Chen, Runsheng, Zhu, Weimin, Paraskevopoulou, Maria D, Vlachos, Ioannis S, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Puetz, Joern, Stadler, Peter F, McDonald, Daniel, Basu, Siddhartha, Fey, Petra, Engel, Stacia R, Cherry, J Michael, Volders, Pieter-Jan, Mestdagh, Pieter, Wower, Jacek, Clark, Michael B, Quek, Xiu Cheng, and Dinger, Marcel E
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Generic health relevance, Animals, Databases, Nucleic Acid, Genomics, Humans, Nucleotides, RNA, Untranslated, Sequence Analysis, RNA, Species Specificity, The RNAcentral Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract: RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.
Published: 2017

20. Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway reveals disease drivers

Author: Farahbod, Marjan, primary, Diab, Abdul Rahman, additional, Sud, Paul, additional, Kagda, Meenakshi, additional, Whaling, Ian, additional, Foroozandeh, Mehdi, additional, Goel, Ishan, additional, Daneshpajouh, Habib, additional, Hitz, Benjamin, additional, Cherry, J. Michael, additional, and Libbrecht, Maxwell, additional
Published: 2023
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21. A gene ontology inferred from molecular networks

Author: Dutkowski, Janusz, Kramer, Michael, Surma, Michal A, Balakrishnan, Rama, Cherry, J Michael, Krogan, Nevan J, and Ideker, Trey
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Fungal Proteins, Gene Regulatory Networks, Genes, Fungal, Saccharomyces cerevisiae
Abstract: Ontologies have proven very useful for capturing knowledge as a hierarchy of terms and their interrelationships. In biology a major challenge has been to construct ontologies of gene function given incomplete biological knowledge and inconsistencies in how this knowledge is manually curated. Here we show that large networks of gene and protein interactions in Saccharomyces cerevisiae can be used to infer an ontology whose coverage and power are equivalent to those of the manually curated Gene Ontology (GO). The network-extracted ontology (NeXO) contains 4,123 biological terms and 5,766 term-term relations, capturing 58% of known cellular components. We also explore robust NeXO terms and term relations that were initially not cataloged in GO, a number of which have now been added based on our analysis. Using quantitative genetic interaction profiling and chemogenomics, we find further support for many of the uncharacterized terms identified by NeXO, including multisubunit structures related to protein trafficking or mitochondrial function. This work enables a shift from using ontologies to evaluate data to using data to construct and evaluate ontologies.
Published: 2013

22. Inference of Combinatorial Regulation in Yeast Transcriptional Networks: A Case Study of Sporulation

Author: Wang, Wei, Cherry, J. Michael, Nochomovitz, Yigal, Jolly, Emmitt, Botstein, David, Li, Hao, and Fields, Stanley
Published: 2005

23. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiaegene function

Author: Tian, Weidong, Zhang, Lan V, Taşan, Murat, Gibbons, Francis D, King, Oliver D, Park, Julie, Wunderlich, Zeba, Cherry, J Michael, and Roth, Frederick P
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Algorithms, Computational Biology, Genes, Fungal, Metabolic Networks and Pathways, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Software, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract: BackgroundLearning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling', which exploits correlation between function and other gene characteristics; and 'guilt-by-association', which transfers function from one gene to another via biological relationships.ResultsWe have developed a strategy ('Funckenstein') that performs guilt-by-profiling and guilt-by-association and combines the results. Using a benchmark set of functional categories and input data for protein-coding genes in Saccharomyces cerevisiae, Funckenstein was compared with a previous combined strategy. Subsequently, we applied Funckenstein to 2,455 Gene Ontology terms. In the process, we developed 2,455 guilt-by-profiling classifiers based on 8,848 gene characteristics and 12 functional linkage graphs based on 23 biological relationships.ConclusionFunckenstein outperforms a previous combined strategy using a common benchmark dataset. The combination of 'guilt-by-profiling' and 'guilt-by-association' gave significant improvement over the component classifiers, showing the greatest synergy for the most specific functions. Performance was evaluated by cross-validation and by literature examination of the top-scoring novel predictions. These quantitative predictions should help prioritize experimental study of yeast gene functions.
Published: 2008

24. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

Author: Tian, Weidong, Zhang, Lan V, Taşan, Murat, Gibbons, Francis D, King, Oliver D, Park, Julie, Wunderlich, Zeba, Cherry, J Michael, and Roth, Frederick P
Subjects: Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Computational Biology, Genes, Fungal, Algorithms, Software, Metabolic Networks and Pathways, Bioinformatics, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract: BackgroundLearning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling', which exploits correlation between function and other gene characteristics; and 'guilt-by-association', which transfers function from one gene to another via biological relationships.ResultsWe have developed a strategy ('Funckenstein') that performs guilt-by-profiling and guilt-by-association and combines the results. Using a benchmark set of functional categories and input data for protein-coding genes in Saccharomyces cerevisiae, Funckenstein was compared with a previous combined strategy. Subsequently, we applied Funckenstein to 2,455 Gene Ontology terms. In the process, we developed 2,455 guilt-by-profiling classifiers based on 8,848 gene characteristics and 12 functional linkage graphs based on 23 biological relationships.ConclusionFunckenstein outperforms a previous combined strategy using a common benchmark dataset. The combination of 'guilt-by-profiling' and 'guilt-by-association' gave significant improvement over the component classifiers, showing the greatest synergy for the most specific functions. Performance was evaluated by cross-validation and by literature examination of the top-scoring novel predictions. These quantitative predictions should help prioritize experimental study of yeast gene functions.
Published: 2008

25. A Systematic Approach to Reconstructing Transcription Networks in Saccharomyces cerevisiae

Author: Wang, Wei, Cherry, J. Michael, Botstein, David, and Li, Hao
Published: 2002

26. Identification of Unstable Transcripts in Arabidopsis by cDNA Microarray Analysis: Rapid Decay Is Associated with a Group of Touch- and Specific Clock-Controlled Genes

Author: Gutiérrez, Rodrigo A., Ewing, Rob M., Cherry, J. Michael, and Green, Pamela J.
Published: 2002

27. CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection

Author: Oh, Dongpin, Strattan, J. Seth, Hur, Junho K., Bento, José, Urban, Alexander Eckehart, Song, Giltae, and Cherry, J. Michael
Published: 2020
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28. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Author: Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, Badger, Jonathan H, Ren, Qinghu, Amedeo, Paolo, Jones, Kristie M, Tallon, Luke J, Delcher, Arthur L, Salzberg, Steven L, Silva, Joana C, Haas, Brian J, Majoros, William H, Farzad, Maryam, Carlton, Jane M, Smith, Roger K, Garg, Jyoti, Pearlman, Ronald E, Karrer, Kathleen M, Sun, Lei, Manning, Gerard, Elde, Nels C, Turkewitz, Aaron P, Asai, David J, Wilkes, David E, Wang, Yufeng, Cai, Hong, Collins, Kathleen, Stewart, B Andrew, Lee, Suzanne R, Wilamowska, Katarzyna, Weinberg, Zasha, Ruzzo, Walter L, Wloga, Dorota, Gaertig, Jacek, Frankel, Joseph, Tsao, Che-Chia, Gorovsky, Martin A, Keeling, Patrick J, Waller, Ross F, Patron, Nicola J, Cherry, J Michael, Stover, Nicholas A, Krieger, Cynthia J, del Toro, Christina, Ryder, Hilary F, Williamson, Sondra C, Barbeau, Rebecca A, Hamilton, Eileen P, and Orias, Eduardo
Abstract: The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
Published: 2006

29. The Genome Sequence of Drosophila melanogaster

Author: Adams, Mark D., Celniker, Susan E., Holt, Robert A., Evans, Cheryl A., Gocayne, Jeannine D., Amanatides, Peter G., Scherer, Steven E., Li, Peter W., Hoskins, Roger A., Galle, Richard F., George, Reed A., Lewis, Suzanna E., Richards, Stephen, Ashburner, Michael, Henderson, Scott N., Sutton, Granger G., Wortman, Jennifer R., Yandell, Mark D., Zhang, Qing, Chen, Lin X., Brandon, Rhonda C., Rogers, Yu-Hui C., Blazej, Robert G., Champe, Mark, Pfeiffer, Barret D., Wan, Kenneth H., Doyle, Clare, Baxter, Evan G., Helt, Gregg, Nelson, Catherine R., Abril, Josep F., Agbayani, Anna, An, Hui-Jin, Andrews-Pfannkoch, Cynthia, Baldwin, Danita, Ballew, Richard M., Basu, Anand, Baxendale, James, Bayraktaroglu, Leyla, Beasley, Ellen M., Beeson, Karen Y., Benos, P. V., Berman, Benjamin P., Bhandari, Deepali, Bolshakov, Slava, Borkova, Dana, Botchan, Michael R., Bouck, John, Brokstein, Peter, Brottier, Phillipe, Burtis, Kenneth C., Busam, Dana A., Butler, Heather, Cadieu, Edouard, Chandra, Ishwar, Cherry, J. Michael, Cawley, Simon, Dahlke, Carl, Davenport, Lionel B., Davies, Peter, de Pablos, Beatriz, Delcher, Arthur, Deng, Zuoming, Mays, Anne Deslattes, Dew, Ian, Dietz, Suzanne M., Dodson, Kristina, Doup, Lisa E., Downes, Michael, Dugan-Rocha, Shannon, Dunkov, Boris C., Dunn, Patrick, Durbin, Kenneth J., Evangelista, Carlos C., Ferraz, Concepcion, Ferriera, Steven, Fleischmann, Wolfgang, Fosler, Carl, Gabrielian, Andrei E., Garg, Neha S., Gelbart, William M., Glasser, Ken, Glodek, Anna, Gong, Fangcheng, Gorrell, J. Harley, Gu, Zhiping, Guan, Ping, Harris, Michael, Harris, Nomi L., Harvey, Damon, Heiman, Thomas J., Hernandez, Judith R., Houck, Jarrett, Hostin, Damon, Houston, Kathryn A., Howland, Timothy J., Wei, Ming-Hui, Ibegwam, Chinyere, Jalali, Mena, Kalush, Francis, Karpen, Gary H., Ke, Zhaoxi, Kennison, James A., Ketchum, Karen A., Kimmel, Bruce E., Kodira, Chinnappa D., Kraft, Cheryl, Kravitz, Saul, Kulp, David, Lai, Zhongwu, Lasko, Paul, Lei, Yiding, Levitsky, Alexander A., Li, Jiayin, Li, Zhenya, Liang, Yong, Lin, Xiaoying, Liu, Xiangjun, Mattei, Bettina, McIntosh, Tina C., McLeod, Michael P., McPherson, Duncan, Merkulov, Gennady, Milshina, Natalia V., Mobarry, Clark, Morris, Joe, Moshrefi, Ali, Mount, Stephen M., Moy, Mee, Murphy, Brian, Murphy, Lee, Muzny, Donna M., Nelson, David L., Nelson, David R., Nelson, Keith A., Nixon, Katherine, Nusskern, Deborah R., Pacleb, Joanne M., Palazzolo, Michael, Pittman, Gjange S., Pan, Sue, Pollard, John, Puri, Vinita, Reese, Martin G., Reinert, Knut, Remington, Karin, Scheeler, Frederick, Shen, Hua, Shue, Bixiang Christopher, Sidén-Kiamos, Inga, Simpson, Michael, Skupski, Marian P., Smith, Tom, Spier, Eugene, Spradling, Allan C., Stapleton, Mark, Strong, Renee, Sun, Eric, Svirskas, Robert, Tector, Cyndee, Turner, Russell, Venter, Eli, Wang, Aihui H., Wang, Xin, Wang, Zhen-Yuan, Wassarman, David A., Weinstock, George M., Weissenbach, Jean, Williams, Sherita M., Woodage, Trevor, Worley, Kim C., Wu, David, Yang, Song, Yao, Q. Alison, Ye, Jane, Yeh, Ru-Fang, Zaveri, Jayshree S., Zhan, Ming, Zhang, Guangren, Zhao, Qi, Zheng, Liansheng, Zheng, Xiangqun H., Zhong, Fei N., Zhong, Wenyan, Zhou, Xiaojun, Zhu, Shiaoping, Zhu, Xiaohong, Smith, Hamilton O., Gibbs, Richard A., Myers, Eugene W., Rubin, Gerald M., and Venter, J. Craig
Published: 2000

30. Comparative Genomics of the Eukaryotes

Author: Rubin, Gerald M., Yandell, Mark D., Wortman, Jennifer R., Nelson, Catherine R., Hariharan, Iswar K., Fortini, Mark E., Li, Peter W., Apweiler, Rolf, Fleischmann, Wolfgang, Cherry, J. Michael, Henikoff, Steven, Skupski, Marian P., Misra, Sima, Ashburner, Michael, Birney, Ewan, Boguski, Mark S., Brody, Thomas, Brokstein, Peter, Celniker, Susan E., Chervitz, Stephen A., Coates, David, Cravchik, Anibal, Gabrielian, Andrei, Galle, Richard F., Gelbart, William M., George, Reed A., Gong, Fangcheng, Guan, Ping, Harris, Nomi L., Hay, Bruce A., Hoskins, Roger A., Li, Jiayin, Li, Zhenya, Hynes, Richard O., Jones, S. J. M., Kuehl, Peter M., Lemaitre, Bruno, Littleton, J. Troy, Morrison, Deborah K., Mungall, Chris, O'Farrell, Patrick H., Pickeral, Oxana K., Shue, Chris, Vosshall, Leslie B., Zhang, Jiong, Zhao, Qi, Zheng, Xiangqun H., Zhong, Fei, Zhong, Wenyan, Gibbs, Richard, Venter, J. Craig, Adams, Mark D., and Lewis, Suzanna
Published: 2000

31. Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence

Author: Chervitz, Stephen A., Aravind, L., Sherlock, Gavin, Ball, Catherine A., Koonin, Eugene V., Dwight, Selina S., Harris, Midori A., Dolinski, Kara, Mohr, Scott, Smith, Temple, Weng, Shuai, Cherry, J. Michael, and Botstein, David
Published: 1998

32. Genome Maps 9. Arabidopsis thaliana

Author: Rhee, Seung Yon, Weng, Shuai, Flanders, David, Cherry, J. Michael, Dean, Caroline, Lister, Clare, Anderson, Mary, Koornneef, Maarten, Meinke, David W., Nickle, Todd, Smith, Kelsey, and Rounsley, Steven D.
Published: 1998

33. Arabidopsis thaliana: A Model Plant for Genome Analysis

Author: Meinke, David W., Cherry, J. Michael, Dean, Caroline, Rounsley, Steven D., and Koornneef, Maarten
Published: 1998

34. 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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35. 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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36. Plant Biology in the Post-Gutenberg Era: Everything You Wanted to Know and More on the World Wide Web

Author: Somerville, Chris, Flanders, David, and Cherry, J. Michael
Published: 1997

37. The Gene Ontology knowledgebase in 2023.

Author: Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, 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, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, 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, Gene Ontology Consortium, Baryshnikova, A1, Gene Ontology Consortium, 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, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, 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, and Bakker, Erika
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

38. 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

39. Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources

Author: Wong, Edith D, primary, Miyasato, Stuart R, additional, Aleksander, Suzi, additional, Karra, Kalpana, additional, Nash, Robert S, additional, Skrzypek, Marek S, additional, Weng, Shuai, additional, Engel, Stacia R, additional, and Cherry, J Michael, additional
Published: 2023
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40. The Gene Ontology knowledgebase in 2023

Author: Consortium, Gene Ontology, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte
Subjects: Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Cell Biology
Abstract: The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
Published: 2023
Full Text: View/download PDF

41. 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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42. Objective: The Complete Sequence of a Plant Genome

Author: Bevan, Mike, Ecker, Joe, McCombia, Dick, Rounsley, Steve, Tabata, Satoshi, Salanoubat, Marcel, Cherry, J. Michael, and Meinke, David
Published: 1997
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43. Microarray data quality analysis: lessons from the AFGC project

Author: Finkelstein, David, Ewing, Rob, Gollub, Jeremy, Sterky, Fredrik, Cherry, J. Michael, Somerville, Shauna, and Town, Chris, editor
Published: 2002
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44. Iterative Linear Regresssion by Sector : Renormalization of cDNA Microarray Data and Cluster Analysis Weighted by Cross Homology

Author: Finkelstein, David B., Ewing, Rob, Gollub, Jeremy, Sterky, Fredrik, Somerville, Shauna, Cherry, J. Michael, Lin, Simon M., editor, and Johnson, Kimberly F., editor
Published: 2002
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45. An integrated RFLP map of Arabidopsis thaliana

Author: Goodman, Howard M., Hanley, Susan, Cartinhour, Sam, Cherry, J. Michael, Hauge, Brian, Meyerowitz, Elliot, Medrano, Leonard, Kempin, Sherry, Stamm, Piet, Koornneef, Maarten, Vasil, Indra K., editor, and Phillips, Ronald L., editor
Published: 2001
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46. 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

47. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author: ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping
Subjects: ENCODE Project Consortium, General Science & Technology
Abstract: In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. 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) are now included in the author list. These errors have been corrected in the online version of the article.
Published: 2022

48. eP349: Describing the Impact of Genomic Variation on Function (IGVF) Consortium submitted on behalf of the IGVF Consortium members

Author: Fulton, Lucinda, primary, Wang, Ting, additional, Yue, Feng, additional, Hitz, Benjamin, additional, and Cherry, J. Michael, additional
Published: 2022
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49. Harmonizing model organism data in the Alliance of Genome Resources

Author: 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

50. New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

Author: Engel, Stacia R, primary, Wong, Edith D, additional, Nash, Robert S, additional, Aleksander, Suzi, additional, Alexander, Micheal, additional, Douglass, Eric, additional, Karra, Kalpana, additional, Miyasato, Stuart R, additional, Simison, Matt, additional, Skrzypek, Marek S, additional, Weng, Shuai, additional, and Cherry, J Michael, additional
Published: 2021
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