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51. Ontology application and use at the ENCODE DCC.

Author

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

Published
2015
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53. The Stanford Microarray Database.

Author

Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, and J. Michael Cherry

Published
2001
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56. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

Author

Giltae Song, Benjamin J A Dickins, Janos Demeter, Stacia Engel, Jennifer Gallagher, Kisurb Choe, Barbara Dunn, Michael Snyder, and J Michael Cherry

Subjects
Medicine, Science
Abstract

The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

Published
2015
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57. Transcriptome visualization and data availability at the Saccharomyces Genome Database

Author

Stuart R. Miyasato, Sagar Jha, Suzi Aleksander, Kalpana Karra, Barbara Dunn, Patrick Ng, Stacia R. Engel, Marek S. Skrzypek, Matt Simison, Robert S. Nash, Joanna Argasinska, Felix Gondwe, Edith D. Wong, Kevin A. MacPherson, J. Michael Cherry, and Shuai Weng

Subjects
Saccharomyces cerevisiae Proteins, RNA-Seq, Genomics, Genome browser, Computational biology, Saccharomyces cerevisiae, Biology, Web Browser, Genome, Genome engineering, 03 medical and health sciences, Open Reading Frames, User-Computer Interface, Reference Values, Databases, Genetic, Genetics, Database Issue, Protein Isoforms, Gene, 030304 developmental biology, 0303 health sciences, 030302 biochemistry & molecular biology, Computational Biology, Molecular Sequence Annotation, Genome, Fungal, Transcriptome, Reference genome
Abstract

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.

Published
2019

62. SGD: Saccharomyces Genome Database.

Author

J. Michael Cherry, Caroline Adler, Catherine A. Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, Yankai Jia, Gail Juvik, TaiYun Roe, Mark Schroeder, Shuai Weng, and David Botstein

Published
1998
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66. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Author

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

Subjects
Genetic variants, Genomics, Preprint, Computational biology, Biology, Personal genomics
Abstract

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of personal epigenomes, for ∼25 tissues and >10 assays in four donors (>1500 open-access functional genomic and proteomic datasets, in total). Each dataset is mapped to a matched, diploid personal genome, which has long-read phasing and structural variants. The mappings enable us to identify >1 million loci with allele-specific behavior. These loci exhibit coordinated epigenetic activity along haplotypes and less conservation than matched, non-allele-specific loci, in a fashion broadly paralleling tissue-specificity. Surprisingly, they can be accurately modelled just based on local nucleotide-sequence context. Combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci and enables models for transferring known eQTLs to difficult-to-profile tissues. Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

Published
2021
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67. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines

Author

Dalton K, Preston Cg, Steven M. Harrison, Lawrence J. Babb, Bryan Wulf, Heidi L. Rehm, Selina S. Dwight, Jimmy Zhen, J. M. Cherry, Deborah I. Ritter, Kristy Lee, Erin Rooney Riggs, Madhavrao R, Cheng S, Jessica L. Mester, Ronak Y. Patel, Matthew Wright, Tong H, Jennifer L. Goldstein, Carlos Bustamante, Julianne M. O’Daniel, Xi Luo, Hannah Wand, Cheung G, Helio A. Costa, Zastrow Db, Jonathan S. Berg, Mandell Me, Sai Lakshmi Subramanian, Sharon E. Plon, Alice B. Popejoy, Arturo Lopez Pineda, Michael A. Iacocca, Marina T. DiStefano, and Aleksandar Milosavljevic

Subjects
Process (engineering), Computer science, Interface (Java), Genomics, QH426-470, Variant curation, Resource (project management), Genetics, Humans, Genetic Testing, Clinical genetics, Molecular Biology, Genetics (clinical), Genome, Human, Suite, Precision medicine, Genetic Variation, Pathogenicity, Data science, Identification (information), Workflow, Clinical Genome Resource Consortium, Medicine, Molecular Medicine, Software
Abstract

Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. Results Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. Conclusions The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org

Published
2021

73. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.

Author

Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, and Raja Mazumder

Published
2012
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79. Bird rookery nutrient over-enrichment as a potential accelerant of mangrove cay decline in Belize

Author

L T, Simpson, S W J, Canty, J R, Cissell, M K, Steinberg, J A, Cherry, and I C, Feller

Subjects
Birds, Wetlands, Animals, Nutrients, Belize, Ecosystem
Abstract

Coastal eutrophication is an issue of serious global concern and although nutrient subsidies can enhance primary productivity of coastal wetlands, they can be detrimental to their long-term maintenance. By supplying nutrients to coastal ecosystems at levels comparable to intensive agriculture practices, roosting colonial waterbirds provide a natural experimental design to examine the impacts of anthropogenic nutrient enrichment in these systems. We tested the hypothesis that long-term nutrient enrichment from bird guano deposition is linked to declines in island size, which may subsequently decrease the stability and resilience of mangrove cays in Belize. We combined remote sensing analysis with field- and lab-based measurements of forest structure, sediment nutrients, and porewater nutrients on three pairs of rookery and control cays in northern, central, and southern Belize. Our results indicate that rookery cays are disappearing approximately 13 times faster than cays without seasonal or resident seabird populations. Rookery cays were associated with a significantly higher concentration of nitrogen (N) in mangrove leaves and greater aboveground biomass, suggesting that eutrophication from bird guano contributes to increased aboveground productivity. Sediments of rookery cays also had lower percentages of soil organic matter and total N and carbon (C) than control islands, which suggests that eutrophication accelerates organic matter decomposition resulting in lower total C stocks on rookery cays. Our results indicate that coastal eutrophication can reduce ecosystem stability by contributing to accelerated cay loss, with potential consequences for mangrove resilience to environmental variability under contemporary and future climatic scenarios.

Published
2021

80. Prevalence of diabetic and impact on cardiovascular events and mortality in patients with chronic coronary syndromes, across multiple geographical regions and ethnicities

Author

H Appeltants, C Boesch, I Cromarty, D Carretta, S Romanov, U Windstetter, F Mibach, Jens Refsgaard, S Lebedev, F Proietti, M Y Tamimi, M C Gamboa, M Novikova, E Prada, K H Sim, E Messas, E Zherlitsyna, A Kalampalikis, N Nevolina, N Trocan, J Cohen, G Szto, R Gilabert Gómez, M Omelchenko, A Pinzani, D Goodwin, J Umaran Sánchez, Kim Fox, S H Dong, K Kronberg, E Castillo Lueña, T Ignatieva, S Joubert, C Macchi, S Lee, S Eidelman, F Alizon, S Chandra, M Akbar, D M Colquhoun, G Yanes Bowden, J de Juan Baguda, M Sebastian, C Wernham, K Miedema, R La Greca, C Morton, B S Jheeta, A C Tran, T Q Do, O Rodrigues, J Yan, S H Kim, R Jurgaitienė, Jean-Claude Tardif, R Baleón, D Hay, V Hennebelle, F Fazekas, R Davies, P Gratia, L Sorodoc, S Y Wu, C Martínez Sánchez, L Lopes Antunes, T H T Pham, I Suliman, M J Gómez Martinez, A Pernat, S H Hur, M Alanazy, L Zhabina, M Stanley, J Rogers, Y J Kim, S Geffroy, L K Andersen, S Coman, V Pedrosa del Moral, Y Garaud, J Krupicka, O Dzhkha, C Paul, M Jeżewska, B Mahler Mioto, V Abduvalieva, P Morra, L Kucheryava, C La Rosa, B Chan, M Wrębiak-Trznadel, A Kozlowski, M Sharif, L López Barreiro, V Kolesnikov, M Lawrence, A Tucker, C Okawabata, B La Hay, E Sadauskienė, B K Nguyen, L Bui, A Said, M E Ruíz Esparza, R K Saran, M S C Ho, E Homs Espinach, J R Romo Santana, J Forte De Carvalho, I Pattison, H H Phan, L Baleeva, L Kisiel, A López Granados, C Raters, F Paganelli, R Haberl, A P T Wong, D Xu, R Jagathesan, L Grekhova, H Stursova, Q B Truong, P Raymond, Y Sosnova, N H Khong, J Zarauza Navarro, C Florescu, L Gorshkova, N Saaidin, E Gordillo Higuero, L Davin, I Budanova, C Lavicka, L Gruznykh, P Bogdański, A Dufka, I Arroja, H A R Tahir, G Wilson, G Kolios, S J Yoon, Simon Cattan, K Berdnik, A Serrano, B Sievers, A Rodríguez Almodóvar, L A Holden, F O'Reilly, D Verleyen, H Hafez, K Nehrig, S M Kang, S Berrisch-Rahmel, E Meyer-Michael, P Samama, L Soares, A K Nguyen, F Tuktarova, C Weytjens, E Sandoval Rodriguez, J Cheng, F M Villasenor, João Morais, B Sullivan, R Zimoląg, Albert V. Smith, S F Ding, J C Louchart, G Guardigli, R Furtak, P Azzolini, S Chushak, J L Delgado Prieto, S Kornienko, K K Sia, J H Shin, F Baylac Domengetroy, P Błaszczak, M Saade, N Černič-Šuligoj, K Coetzee, A Kadleckova, V Scollo, O Larina, R Pal, M M Singh, N Nosova, R Burns, B S Yoo, O Gukov, F Massari, V Antia, A Brattström, G Holt, M Scherbak, V Firastrau, Y J Li, E Mikhailova, L Machado Cesar, C García García, J Pjontek, C Everton Biglow, G Pes, C Brown, A Bumbu, S Felis, R Bosch, M Lazaro, Luigi Tavazzi, R Engel, I Romeo Castillejo, Y S Byun, F Matias, I Grushetskaya, C Mestre-Fernandes, T Kheliya, S Schlesingerova, G Theodorakis, I Tsamopoulos, R Pedretti, A Puente Barragán, M P Vo, B Lammens, T Carruthers, J S Bhatt, A Khodanov, N Pasechnaya, I Petrova, G Boutros, I A Khan, E Le Moal, D Garofalo, H R Malaterre, A Bahal, J F Martínez González, H N Dinh, N V Pham, C Barjhoux, I Gilmour, C Soriano Navarro, O D Chioncel, K Tóth, N Borodina, P Khanoyan, B Sevilla Toral, H H Kim, C M A Bui, C Dernedde, N Eliseeva, M Galinier, E Kosachek, M M Doohan, L Potapska, M Tennekoon, R Nourallah, L Perez De Isla, K H Chee, E Panova, D M Walker, G Glanowska, G Hua, A Silvestre, W Wang, Matthew A. Brown, B Luke, G Jarosiński, R Davis, S Cleron, C Liatas, I Orestis, M Dereń, J Sudnik, S X Zhou, J Fuertes Alonso, O Baranova, S Mingalaeva, T N Vo, K A Ngo, J A Rodríguez Fernández, R Ishmael, G Bode, K K Chan, G Al Radaideh, S Ramphall, H D Theron, V Montagud Saavedra, A Yusuf, G F Mazzanti Mignaqui, L Evtukhova, J Lorenc, D Beacock, O B Šlapikienė, F Alitto, J N Poujois, B Berzal Martín, M Felbermayer, V Mallamaci, T Spitsina, R Ramachandran, A Jánosi, V Dženkevičiūtė, S Gillam, V Joulie, G Esna Ashari, R Henry, E Durand, A Alam, V Fourchard, H Dreycopp, R Fressonnet, C Camossa, O Jerzykowska, M Castrucci, G Sinicropi, B K Goyal, V Vasylenko, R Grogono, M Partington, B Vaquette, R Blindt, Mª T Moreno Casquete, V Kukaleva, W Streb, P F Clavette, M Pérez Paredes, V Hadjiivanov, C Bundy, D E Manyari, A Wassef, J Kuchar, W Nisker, P S Bath, S Panpunnung, G H Choo, Datshana P Naidoo, Y Pavlova, R McManus, N Brand, E Davies, L Prunier, A Schenowitz, P Sternthal, T Sinotova, J Martínez Florez, R Sykulski, J Pinar Sopena, M Balbi, Y Pesant, D A Playford, C Villar Mariscal, F Redding Escalante, W Wongcharoen, O Grechishkina, A Girão, M Speth-Nitschke, K A Mahendran, A Bianco, A Vadavi, G Singh, L Petoin Peuch, L Sukhanova, A Y Y Fong, J L Vega Barbado, A Dzien, S Honorat, G Ansalone, G Kamensky, G McLaren, T B Kim, I Bratu, R Fillet, V Rogozhyna, L Nagy, M Malgina, M A Sheikh Abdul Kader, Z C Li, L Rotaru H Rus, D Adamczyk-Kot, J Estrella, S Serrano García, P Farto E Abreu, D Mescharekova, Su Thillai Vallal, P Seal, S Möller, A Cziráki, T T H Ta, S Davies, H Ge, M Arafah, M Ovize, A Olszewski, V Aboyans, C Roche, F Al Tamimi, L Popova, V Kazachkova, R Rennert, J Aubry, G Bourgeois, J Mackrell, F Al Kandari, N Reifart, J Bérubé, W H J Hutse, O Lysunets, I Butkuvienė, J Cotroneo, J Gdalia, J Dalle Mule, R Santos, B Singh, H Mohammed, A Birkenhagen, T Chiscaneanu, H Sullivan, Jacob A. Udell, N Bolotova, A Jankowska, M Skonieczny, B S K Ch'ng, O Aiyegbayo, S Ciaroni, N Lago, S R Coimbra, R Ellis, B K Koo, S Rostik, P Jacquier, A Conradie, N Biryukova, M Ayche, A Khripun, B Peperstraete, E Velasco Espejo-Saavedra, G Cunliffe, G Grollier, C Ceraulo, T L To, Q H Tran, M Anscombe, R Jordan, I Czuriga, P Haimes, R Ancín Viguiristi, H Q Zhang, C A Chételat, A Rafter, E Rinkūnienė, K Yang, W Gao, J Pearce, L C Fernández Léoz, L Gareeva, R Fernández Alvarez, G Verret, P Astrakhantseva, C M Chu, L Murphy, P A Do, J L Liu, A Clifford, K Woollard, N Dmitrieva, N Lousada, R Díaz Juárez, N Semenova, T Fesenko, F Henschel, R Amini, G Matuszewska, R Christodorescu, J Varaldi, S Varughese, V Lafarenko, A Ashford, J L Colomer Martín, S Assouline, H Noor Hasni, A Weatherup, T Forster, R Kaserbacher, I Caldwell, N Arabadzhi, Emmanuel Sorbets, A Rink, E C Rueda Calle, J M Stordeur, P West, V C Do, Béla Merkely, J Antunes, U Altmann, S Magheru, B Bachmann, W Parkar, M de los Reyes López, M Wazana, A Frattola, M Mospan, V Koval, E Giusti Rossi, J Vasconcelos, K B Do, A Ogorodnichuk, D Lighezan, G Mentz, J M Cherry, P Pouderou, M Moretti, C M Spinu, Emmanuelle Vidal-Petiot, N Kupstytė, P Jourdain, V Voronina, O Varezhnikova, S Williams, H AlFaleh, R Lew, P Hildebrant, J Drozd, G Muscio, T H Ashton, A Achilli, J Harinasuta, T Ghose, G Walawski, Y Arkhipova, M Alves Costa, B Day, A Suntinger, A Singh, P Sheringham, A Vázquez García, J Taggeselle, J T Dong, T H Goh, G Rojas, R Schultz, A Ballet, O Likhobabina, Z M Qian, S Sandoval Navarrete, D Manzi, S Langridge, W Haerer, C K Abdullah, L Hay, Á Herdade, A Gałuszka-Bilińska, F Biausque, V M Lai, D S Eccleston, L Nikolaeva, P Kalaras, J Martínez Redding, N P H Tran, B Wauer, Philippe Gabriel Steg, B Etcheverry, J Navarro Manchón, R Augarde, C Dixon, M Y Chen, J L Gleizes, S Pustovit, J L Farges, S Cox, G Manchet, K Shein, L Parker, C C Ang, O Sinyukova, V Veth, A Kurekhyan, N Cindea Nica, N Wittlich, J Al Yazeedi, A Pucheu, V Elliott, J Bories, K Alford, M F Ferrão E Vasconcelos, A Adamkiewicz-Piejko, R Cervenak, J F Beltrame, A Castro, L Safonova, G Koutsimpanis, C de Brito Vianna, R Wysocki, V Ginzburg, J Hernández Afonso, A Ihonor, O Golubeva, M Karachaliou, S Kleta, D d'Este, Gustavs Latkovskis, F Jäger, E Gamzatov, Y Kozhelenko, J Lippai, T T L Ong, S J Ge, A Hersi, K Kyd, S Mingam, V Yordanova, L Bardachenko, E Mozerova, S W Liu, J Zdrojewska, E Chung, M Leclair, M Nazir, S Zarechnova, A Rahman, M Sołtysiak, B Maguire, F Moreira Pinto, R Fathi, E Prieto Moriche, C Priftis, P Heno, N Sytilina, A Pladys, S Shimonenko, P Keller, J F Junior, G Amiel Oster Sauvinet, J P Kanner, L Tkachenko, J Dalal, A Liston, D Herrera Fernández, J L Bonnet, A Chirivella González, R P Shah, F A Reyes Cisneros, C Avgerinos, P Ravoala, V Albero Martínez, G Suarez, V Jouve, A Frankiewicz, A Lindsay, A De Meester, H Dau, M Pornin, J Álvarez Gil, J Murin, T Hodac, J J Gómez Barrado, Y J Wu, S Jean, P Hilti, A Dayani, R Steponėnienė, G A Somsen, H Zhang, J Moore, P Tarenidis, T H Nguyen, M Maliszewski, L Voloshyna, S Novo, A Phrommintikul, I Shanina, Roberto Ferrari, P Franklin, C Turner, W Boonyapisit, F Sepulcri, P Vandergoten, J Carvalho, J Halcox, V Rotenberger, J F Baril, M Turiel, P Shiels, P Painsipp, S Reis Monteiro, T Honsig, V Vivekaphirat, J Ardill, P Brodzicki, A Khalifa, H Audibert, T Wettstein, F Auhser, D Ezekiel, D Pella, E Simarro Martín-Ambrioso, H S Seo, J A Núñez Gamero, Gabriel Steg, M Orbán, S Bykovskaya, W Gadziński, N Rozkova, G H M Vawda, R A Motyer, B Limeres González, E Fernandez Valadez, Riyaz S. Patel, I Shaikh, E Ziak, A Estriga, P Dodemant, Dragos Vinereanu, W Miao, L Marullo, F MacNamara, S K Tan, N Giacomantonio, A Leherissier, H W Li, Arpana Agrawal, Y Moreau, F David, S K Ma, A N Jamaluddin, E Alegría Ezquerra, Scalzo, M C Ta, T T Nguyen, A Sudre, R Gupta, H Lagioia, M Haiba, P Kohan, M Szentivanyi, T Dmitrieva, N Vechtomova, C Vuille, R G Schena, P Navratil, O Tsygankov, L Saaby, P Lefebvre, S King Wong, S Maheas Morlet, N H Pham, P Bonnet, S Modi, L Gaspar, M Karlicek, S Pallie, H T Pham, S Abele, N Bizyaeva, L Facila Rubio, N Meneveau, G Poluyanova, J Calaça, S Orazi, M Emonts, A Yusufali, V Sprott, Z Vazhdaeva, M R Conte, E Bulakhova, K Giokoglu, E Page, E Kotova, G Maragoni, C Jerjes Sánchez, T Kiver, M Brunehaut Petaut, A Nagy, P Singer, Zs Sziegl, B Fontanet, S Strange, A Watson, J Föchterle, Janet A. Dunn, R Šlapikas, M Stikhurova, S Salimova, J Volmar, E Otero Chulian, S Hutchinson, R Koller, X Bonnaud, E Peris Domingo, F Marín Ortuño, E Galve Basilio, S Bongo, L Payot, C Miller, A Samothrakitis, L Silva Melchor, K Orzechowski, W Hofer, L V Nguyen, R Oliver, K T Jung, J Robb, D Sobczyk, J Muller, A Tomatti, M Gruchała, C Bradshaw, D Richmond, E Mineeva, E Smirnova, A Idrissi-Sbai, H Vial, R Balai, I Kiseleva, H Jones, M Gibbs, D Ohlmeyer, Y Al Wahshi, V d’Alessandro, S Pérez Ibiricu, V Zachos, A Chernozemova, D R Spink, J Schneider, A M Peset Cubero, M Irurita Latasa, M Migliore, G Perna, E Daniels, M H Tay, N Z Khiew, I Soin, F Bernasconi, T Garban, F Omardeen, O Rodina, L Kanagaratnam, I Blum-Decary, A Jaussi, D Romero Alvira, D Vermander, N Kanumilli, M A Romero Maldonado, M Fernández-Valls Gómez, H Tran, T P Nguyen, H Omar, R S Collette, B Kisjós, H Krause-Allmendinger, J Silva E Sá, H Topf, F Panetta, T C Do, G Roul, J Leso, A Lacroix, M Fic, C Hart, R Chan, L Lema, Y Polyanskaya, R Howlett, Lesley J. Burgess, X P Chen, Hywel C Williams, V T Le, N Gurianova, R Duchowska, V P Nair, D Mitropoulos, A Allcock, T T H Bui, M Golub, E Yakovenko, M Perry, F Belcastro, K Svolis, B H R Forge, F Fernández de la Cigoña, N Murga Eizagaechevarría, G Mariano Pêgo, V Mincheva, T N Nguyen, J Moyal, M Wei, H Vinhas, A Batalla Celorio, C Romero Menor, S Rahman, N Hassler jun, F Duclos, K Ladha, A Ordóñez España, B C Chang, R Cortés Sánchez, G Lafrance, I Mihailova, Y Riou, I Pashentseva, S Tantillo, U Casas Juarezy, Ian B. 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M Baar, P Lafontaine, C O'Dong, I Petropoulos, B-M Altevogt, D Warden, T De Backer, G Miñana Escrivá, T L Mai, U Schlesinger-Irsch, M M Gomaa, E Moksyuta, M Drexler, P Monteiro, P Grooterhorst, J Moolman, P McAlavey, J O'Shea, L P Quinn, F Crespo, K Srinivasa Reddy, T Shokina, Ellen M. Schmidt, M H Jeong, K Denef, A Pleskof, I Takács, Y Tikhonov, O Ushakov, L Stevens, J Ezcurdia Sasieta, L Nkombua, O Henne Otero, J Y Fraboulet, D S Kim, G Hoh, A Tamm, M Sardon, G Chatzioakim, M A Ulecia Martínez, S Reymond, M Myint, G Proença, R Massabie, E Foster, H Dougall, Anjan Kumar Roy, C Franco Aranda, M Getman, E Filippova, C Aguiar, X D Pu, N Voronina, L L Chen, M Szulc, L Bayakhchan, M J Pinto Vaz, C Niederberger, N Vites, I Sen, Paul R. Kalra, J A Castillo Moreno, W K Ng, C Brunschwig, D Morgan, A Concepción Clemente, N Yakimova, J M Guy, A H Jaafar, J Badarienė, N Taylor, L Compson, R Amor, A Maximovitch, J L Bardají Mayor, E Marín Araez, N H Chau, N Srtumilenko, K Kelly, A Papathanasioy, S Erofeev, B Mamez, A Ribeiro, M Micko, N Alvarenga Recalde, K Atueva, Z Sebõk, P Kycina, A K Gupta, A Laucevičius, R Ahuja, A Prokop, P Stadler, S De Ridder, L Zhang, F B Ramadan, L Kapustina, V Fedoskin, A Bateman, C A Nacht, R Musetescu, M Aparici Feal, A Büttl, S Ross, M Rau, P Federico Zaragoza, G Brisson, M Zagreanu, T T H Pham, F Dominé, N Davydova, N Petrochenko, N Paul, P H Truong, S Frickel, W Bryl, G Brouillette, A Stumpp, M Barrera Bustillos, C Ziccarelli, O Zalyzniak, M eatherhead, N Watkins, G Riccioni, l Kudryavtsev, R Carvalho, J P S Sawhney, V González Toda, P Matos Dias, M Giorgadze, I Rodriguez Marrero, W Gritsch, K Lee, G W Kellam, I Parker, V Ecina, Mª I Soto Ruiz, C Delhomme, T Ivaschenko, Y W Cheah, I Grudtsina, R Chehayeb, T Dookie, O Krasnoslobodskaya, P Jarmużek, F Van den Branden, A M F Vandeplas, A Rocha De Almeida, M Espiga De Macedo, E Łotocka, K Nagy, R Paliulionienė, J L Leyva Pons, N Fedorova, Y Yanina, O Stasuk, Z Vlasuk, P Lim, P Egloff, T Berezhna, A Faria, J Cerda Rojas, E Moser, H G Jin, S J Oh, G Arquero García, K H Karner, I Leontaridis, A Banikova, J Fridrich, H Lesseliers, I Pokrovskaya, P Astridge, H Abdul Manap, R Daniel, C A Almeida Fernández, A Nowowiejska-Wiewióra, B Carvalho De Moura, M Malden, H Rosenstein, S Dixon, G Balogh, M Adam-Blanpain, A Sandalian, H Gervas Pavón, G A Antoniadis, N Naberezhnova, A Amlaiky, P Terrosu, K K H Lau, B Chartier, X Su, O Kovyrshyna, G Beale, P Primot, M H Chen, S S Ramesh, R Chyrek, E Gómez Álvarez, J Rodríguez Collado, G Sibilio, R Jeremiasz, R Colin, C Lalla, G M Fullerton, M P Samal, H Thümmel, R P Patel, J Takhar, H M Kwon, T A Cieza Lara, F Magliari, J Morrell, M Rayo Gutiérrez, T L Orenstein-Lyall, H Choi, S Kulinich, A Aftab, A Wallace, B B Abdul Kareem, S Kwok, A Królak, A Grover, Laurent Fauchier, Mª J Pinilla Lozano, G Sengupta, D Paris, M Al Dhanki, J Milewski, F Petersen Aranguren, H Brufau Redondo, H Mayr, A Arias Mendoza, M Ducoudre, A Correia, J S Awtar Singh, P Aylward, E Brscic, J Du Plooy, J L Arenas León, G Silva Alves, L Sreenivasa Murthy, P Dendale, F La Varra, S Minkin, T Eggeling, A Jamiel, G Lebischak, E Andreev, T V A Tuong, V Chaithiraphan, O Duprez, S Higgins, F Chometon, Y Cottin, A Bonny, C Guyetand, J Matos, F Henpin Yue Cesena, L Polyaeva, M Drijfhout, J Toplak, G E Vertes, N F Wang, J Doucet, A K Trivedi, P Turek, G Chouinard, A Al Lawati, W Filip, F Kovar, T J Cha, A Belanger, H L Cong, J F Robert, D López Gómez, J L Sanz Rodríguez, H Simper, P Shetty, A Chukwu, E Bukanina, C Amoros Galito, H MacCowan, T T T Tran, A Singal, K C Vu, O Ismail, A Ardiaca Capell, P Bousquet, F Goss, Z Galeeva, Maxime Guenoun, B Rijavec, Z Lazerevic, A McCracken, A C Motoc, Y Sharapova, S Wright, A J Paule Sánchez, L Mainar Latorre, I Sirazov, X L Yang, S E Paget, G Berkenboom, J Markenvard, I Surovtseva, S K George, Matthias Simon, M L Fuantos Delgado, C Christoforidis, M Lagares Carballo, P Alvarez García, J Könemann, L Crawford, I Gonos, D Saulnier, E Szabó, L Ardouin, J Bhayat, F J Abardía Oliva, X Bernard, O Sirbu, P Boutsikos, N Khmelevskikh, E Tavlueva, P LeBouthillier, I Bourazanis, A Sequeira, M López Martínez, C P Paulus, R K M Bhaskaran, F Pellerin, B Brown, B Saleh, A Lacchè, R Sola Casado, E Kaźmierczak, M Weingrod, and G Vijayaraghavan

Subjects
medicine.medical_specialty, Cardiac & Cardiovascular Systems, Epidemiology, LONG-TERM, medicine.medical_treatment, Chronic coronary syndromes, Coronary Artery Disease, Revascularization, Ventricular Function, Left, GLUCOSE, MELLITUS, Risk Factors, Internal medicine, Diabetes mellitus, Diabetes Mellitus, Ethnicity, Prevalence, medicine, Humans, ARTERY-DISEASE, Myocardial infarction, Stroke, RISK, OUTCOMES, Ejection fraction, Science & Technology, business.industry, Proportional hazards model, CLARIFY Investigators, Hazard ratio, Diabetes, Stroke Volume, Geographical disparities, Syndrome, medicine.disease, MIDDLE-EAST, EUROPEAN-SOCIETY, Treatment Outcome, MYOCARDIAL-INFARCTION, Heart failure, CLARIFY registry, Cardiovascular System & Cardiology, HEART-FAILURE, Cardiology and Cardiovascular Medicine, business, Life Sciences & Biomedicine
Abstract

BackgroundIn contrast with the setting of acute myocardial infarction, there are limited data regarding the impact of diabetes mellitus on clinical outcomes in contemporary cohorts of patients with chronic coronary syndromes. We aimed to investigate the prevalence and prognostic impact of diabetes according to geographical regions and ethnicity.Methods and resultsCLARIFY is an observational registry of patients with chronic coronary syndromes, enrolled across 45 countries in Europe, Asia, America, Middle East, Australia, and Africa in 2009–2010, and followed up yearly for 5 years. Chronic coronary syndromes were defined by ≥1 of the following criteria: prior myocardial infarction, evidence of coronary stenosis >50%, proven symptomatic myocardial ischaemia, or prior revascularization procedure.Among 32 694 patients, 9502 (29%) had diabetes, with a regional prevalence ranging from below 20% in Northern Europe to ∼60% in the Gulf countries. In a multivariable-adjusted Cox proportional hazards model, diabetes was associated with increased risks for the primary outcome (cardiovascular death, myocardial infarction, or stroke) with an adjusted hazard ratio of 1.28 (95% confidence interval 1.18, 1.39) and for all secondary outcomes (all-cause and cardiovascular mortality, myocardial infarction, stroke, heart failure, and coronary revascularization). Differences on outcomes according to geography and ethnicity were modest.ConclusionIn patients with chronic coronary syndromes, diabetes is independently associated with mortality and cardiovascular events, including heart failure, which is not accounted by demographics, prior medical history, left ventricular ejection fraction, or use of secondary prevention medication. This is observed across multiple geographic regions and ethnicities, despite marked disparities in the prevalence of diabetes.ClinicalTrials identifierISRCTN43070564

Published
2021

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

Author

Amber L. Johns, Ian Fore, Juha Törnroos, Melissa Haendel, Bimal Chaudhari, J. Patrick Woolley, Brian Walsh, Susan Fairley, Jonathan A. Tedds, Jessica Vamathevan, Martin Kuba, Clara L. Gaff, Ksenia Zaytseva, Sabine Oesterle, David Bujold, Sarion R. Bowers, Alexander Kanitz, Jordi Rambla, Anthony J. Brookes, Alice L. Mann, Gregory A. Rushton, Paul Flicek, Seik-Soon Khor, Khalid A. Fakhro, Aina Jene, Miro Cupak, Moran N. Cabili, Emilio Palumbo, Nathan C. Sheffield, Vivian Ota Wang, James K. Bonfield, Julius O.B. Jacobsen, Michael M. Hoffman, Neerjah Skantharajah, Ewan Birney, Rasko Leinonen, Anna Middleton, Anneke M. Lucassen, Ania Niewielska, Angela Page, Jeffrey Niu, Alastair A. Thomson, Elena M. Ghanaim, Albert V. Smith, Megan Doerr, Lena I. Dolman, Arcadi Navarro, Ada Hamosh, Sean Upchurch, Michael Baudis, Jerome Kelleher, Marc Fiume, Mikael Linden, Roderic Guigó, Orion J. Buske, Tristan H. Nelson, Kyle Ellrott, Lauren A. Fromont, Alex H. Wagner, Alexander Senf, Tommi Nyrönen, Michele Mattioni, David Haussler, Alejandro Metke-Jimenez, Francis Jeanson, Mélanie Courtot, David Hansen, Matthew H. Brush, Helen Parkinson, Peter Goodhand, Lindsay Smith, Jonathan Fuerth, Stephanie Li, Tim Beck, Debyani Chakravarty, Kristina Kekesi-Lafrance, Giselle Kerry, James A. Eddy, Torsten Schwede, Jaime M. Guidry Auvil, Xianglin Liu, Soichi Ogishima, Fiona Cunningham, Oliver Hofmann, Dean Hartley, Amy Nisselle, Katsushi Tokunaga, Alfonso Valencia, Hidewaki Nakagawa, Kurt W. Rodarmer, Lawrence J. Babb, Heidi J. Sofia, David Glazer, Angel Pizarro, Ammar Husami, Gil Alterovitz, Serena Scollen, J. Michael Cherry, Helen V. Firth, Zornitza Stark, Monica C. Munoz-Torres, Daniel L Cameron, Robert R. Freimuth, Manuel Rueda, Stephanie O.M. Dyke, Makoto Suematsu, Christina K. Yung, Rosalyn S. Ryan, Chisato Yamasaki, Michael S. Fitzsimons, Amanda B. Spurdle, Renee A. Rider, Karen Eilbeck, Ashley E. Hobb, Roman Valls Guimera, Calvin W. L. Ho, Robert L. Davies, Maxmillian P. Barkley, Malachi Griffith, Rishi Nag, Javier Lopez, Jacob Shujui Hsu, Isuru Udara Liyanage, Petr Holub, Dylan Spalding, Reece K. Hart, Barbara J. Wold, Fruzsina Molnár-Gábor, Sarah E. Hunt, Augusto Rendon, Danielle Denisko, Dipayan Gupta, Obi L. Griffith, Robert J. Carroll, Patrick Tan, Craig Voisin, Saumya Shekhar Jamuar, Mallory A. Freeberg, Michael Brudno, Andreas Prlic, Kenjiro Kosaki, Shu Hui Chen, Edward S. Dove, Tony Burdett, Anthony A. Philippakis, Richard Milne, Bartha Maria Knoppers, Kathryn North, David Torrents, Eva C. Winkler, Marc S. Williams, Melissa A. Konopko, Rachele M. Hendricks-Sturrup, Brian O'Connor, Grant M. Wood, Robert L. Grossman, Timothy L. Tickle, Michael F. Lin, Laura Lyman Rodriguez, Weiniu Gan, Laura A.D. Paglione, Justina Chung, Thomas M. Keane, Susan E. Wallace, Lyndon J. Zass, Heidi L. Rehm, Kazuto Kato, Alexander Bernier, Nicola Mulder, Jamal Nasir, Yann Joly, Junjun Zhang, Adrian Thorogood, Lincoln Stein, Guillaume Bourque, L. Jonathan Dursi, Tudor Groza, Jean-Pierre Hubaux, Coby Viner, Helen Schuilenburg, Sergi Beltran, Michael J.S. Beauvais, Hayley L. Clissold, Elizabeth L. Janes, Jacques S. Beckmann, Michael Lukowski, Melissa S. Cline, John F. Marshall, Alan F. Rubin, Tiffany Boughtwood, Peter N. Robinson, Robert C. Green, Robert Cook-Deegan, Esmeralda Casas-Silva, Jeremy Adams, Steven J.M. Jones, Gary I. Saunders, Danya F. Vears, Jonathan Lawson, Andrew D. Yates, David Bernick, Susheel Varma, Middleton, Anna [0000-0003-3103-8098], Milne, Richard [0000-0002-8770-2384], Apollo - University of Cambridge Repository, Abigail Wexner Research Institute, Academy of Finland, Medical Research Future Fund, BioBank Japan, Canada Foundation for Innovation, Canadian Institutes of Health Research, European Commission, German Research Foundation, Genome Canada, Google, Howard Hughes Medical Institute, Instituto de Salud Carlos III, Japan Agency for Medical Research and Development, Mayo Clinic, Fundación 'la Caixa', Ministère de l'Économie et de l'Innovation (Québec), Monarch Initiative, National Human Genome Research Institute (US), National University of Singapore, Agency for Science, Technology and Research A*STAR (Singapore), National Health and Medical Research Council (Australia), National Institutes of Health (US), National Institute of General Medical Sciences (US), Swiss Institute of Bioinformatics, State Secretariat for Education, Research and Innovation (Switzerland), Terry Fox Research Institute, Canada Research Chairs, European Molecular Biology Laboratory, Ministry of Research, Innovation and Science (Ontario), Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada, Wellcome Trust, and National Taiwan University

Subjects
Standards, Knowledge management, data sharing, precision medicine, Interoperability, Technical standard, data federation, Article, 3105 Genetics, 03 medical and health sciences, 0302 clinical medicine, data access, learning health system, Clinical Research, Health care, genomics, Genetics, Data federation, Data access, 030304 developmental biology, 0303 health sciences, business.industry, Precision medicine, Human Genome, Learning health system, 3 Good Health and Well Being, Bioethics, Genomics, Health Services, 3. Good health, Data sharing, Data aggregator, Policy, 030220 oncology & carcinogenesis, FOS: Biological sciences, standards, Business, Generic health relevance, bioethics, policy, 31 Biological Sciences
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., B.P.C. acknowledges funding from Abigail Wexner Research Institute at Nationwide Children’s Hospital; T.H. Nyrönen acknowledges funding from Academy of Finland grant #31996; A.M.-J., K.N., T.F.B., O.M.H., and Z.S. acknowledge funding from Australian Medical Research Future Fund; M.S. acknowledges funding from Biobank Japan; D. Bujold and S.J.M.J. acknowledge funding from Canada Foundation for Innovation; L.J.D. acknowledges funding from Canada Foundation for Innovation Cyber Infrastructure grant #34860; D. Bujold and G.B. acknowledge funding from CANARIE; L.J.D. acknowledges funding from CANARIE Research Data Management contract #RDM-090 (CHORD) and #RDM2-053 (ClinDIG); K.K.-L. acknowledges funding from CanSHARE; T.L.T. acknowledges funding from Chan Zuckerberg Initiative; T. Burdett acknowledges funding from Chan Zuckerberg Initiative grant #2017-171671; D. Bujold, G.B., and L.D.S. acknowledge funding from CIHR; L.J.D. acknowledges funding from CIHR grant #404896; M.J.S.B. acknowledges funding from CIHR grant #SBD-163124; M. Courtot and M. Linden acknowledge funding from CINECA project EU Horizon 2020 grant #825775; D. Bujold and G.B. acknowledge funding from Compute Canada; F.M.-G. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – NFDI 1/1 “GHGA – German Human Genome-Phenome Archive; R.M.H.-S. acknowledges funding from Duke-Margolis Center for Health Policy; S.B. and A.J.B. acknowledge funding from EJP-RD EU Horizon 2020 grant #825575; A. Niewielska, A.K., D.S., G.I.S., J.A.T., J.R., M.A.K., M. Baudis, M. Linden, S.B., S.S., T.H. Nyrönen, and T.M.K. acknowledge funding from ELIXIR; A. Niewielska acknowledges funding from EOSC-Life EU Horizon 2020 grant #824087; J.-P.H. acknowledges funding from ETH Domain Strategic Focal Area “Personalized Health and Related Technologies (PHRT)” grant #2017-201; F.M.-G. acknowledges funding from EUCANCan EU Horizon 2020 grant #825835; B.M.K., D. Bujold, G.B., L.D.S., M.J.S.B., N.S., S.E.W., and Y.J. acknowledge funding from Genome Canada; B.M.K., M.J.S.B., S.E.W., and Y.J. acknowledge funding from Genome Quebec; F.M.-G. acknowledges funding from German Human Genome-Phenome Archive; C. Voisin acknowledges funding from Google; A.J.B. acknowledges funding from Health Data Research UK Substantive Site Award; D.H. acknowledges funding from Howard Hughes Medical Institute; S.B. acknowledges funding from Instituto de Salud Carlos III; S.-S.K. and K.T. acknowledge funding from Japan Agency for Medical Research and Development (AMED); S. Ogishima acknowledges funding from Japan Agency for Medical Research and Development (AMED) grant #20kk0205014h0005; C.Y. and K. Kosaki acknowledge funding from Japan Agency for Medical Research and Development (AMED) grant #JP18kk0205012; GEM Japan acknowledges funding from Japan Agency for Medical Research and Development (AMED) grants #19kk0205014h0004, #20kk0205014h0005, #20kk0205013h0005, #20kk0205012h0005, #20km0405401h0003, and #19km0405001h0104; J.R. acknowledges funding from La Caixa Foundation under project #LCF/PR/GN13/50260009; R.R.F. acknowledges funding from Mayo Clinic Center for Individualized Medicine; Y.J. and S.E.W. acknowledge funding from Ministère de l’Économie et de l’Innovation du Québec for the Can-SHARE Connect Project; S.E.W. and S.O.M.D. acknowledge funding from Ministère de l’Économie et de l’Innovation du Québec for the Can-SHARE grant #141210; M.A.H., M.C.M.-T., J.O.J., H.E.P., and P.N.R. acknowledge funding from Monarch Initiative grant #R24OD011883 and Phenomics First NHGRI grant #1RM1HG010860; A.L.M. and E.B. acknowledge funding from MRC grant #MC_PC_19024; P.T. acknowledges funding from National University of Singapore and Agency for Science, Technology and Research; J.M.C. acknowledges funding from NHGRI; A.H.W. acknowledges funding from NHGRI awards K99HG010157, R00HG010157, and R35HG011949; A.M.-J., K.N., D.P.H., O.M.H., T.F.B., and Z.S. acknowledge funding from NHMRC grants #GNT1113531 and #GNT2000001; D.L.C. acknowledges funding from NHMRC Ideas grant #1188098; A.B.S. acknowledges funding from NHMRC Investigator Fellowship grant #APP177524; J.M.C. and L.D.S. acknowledge funding from NIH; A.A.P. acknowledges funding from NIH Anvil; A.V.S. acknowledges funding from NIH contract #HHSN268201800002I (TOPMed Informatics Research Center); S.U. acknowledges funding from NIH ENCODE grant #UM1HG009443; M.C.M.-T. and M.A.H. acknowledge funding from NIH grant #1U13CA221044; R.J.C. acknowledges funding from NIH grants #1U24HG010262 and #1U2COD023196; M.G. acknowledges funding from NIH grant #R00HG007940; J.B.A., S.L., P.G., E.B., H.L.R., and L.S. acknowledge funding from NIH grant #U24HG011025; K.P.E. acknowledges funding from NIH grant #U2C-RM-160010; J.A.E. acknowledges funding from NIH NCATS grant #U24TR002306; M.M. acknowledges funding from NIH NCI contract #HHSN261201400008c and ID/IQ Agreement #17X146 under contract #HHSN2612015000031 and #75N91019D00024; R.M.C.-D. acknowledges funding from NIH NCI grant #R01CA237118; M. Cline acknowledges funding from NIH NCI grant #U01CA242954; K.P.E. acknowledges funding from NIH NCI ITCR grant #1U24CA231877-01; O.L.G. acknowledges funding from NIH NCI ITCR grant #U24CA237719; R.L.G. acknowledges funding from NIH NCI task order #17X147F10 under contract #HHSN261200800001E; A.F.R. acknowledges funding from NIH NHGRI grant #RM1HG010461; N.M. and L.J.Z. acknowledge funding from NIH NHGRI grant #U24HG006941; R.R.F., T.H. Nelson, L.J.B., and H.L.R. acknowledge funding from NIH NHGRI grant #U41HG006834; B.J.W. acknowledges funding from NIH NHGRI grant #UM1HG009443A; M. Cline acknowledges funding from NIH NHLBI BioData Catalyst Fellowship grant #5118777; M.M. acknowledges funding from NIH NHLBI BioData Catalyst Program grant #1OT3HL142478-01; N.C.S. acknowledges funding from NIH NIGMS grant #R35-GM128636; M.C.M.-T., M.A.H., P.N.R., and R.R.F. acknowledge funding from NIH NLM contract #75N97019P00280; E.B. and A.L.M. acknowledge funding from NIHR; R.G. acknowledges funding from Project Ris3CAT VEIS; S.B. acknowledges funding from RD-Connect, Seventh Framework Program grant #305444; J.K. acknowledges funding from Robertson Foundation; S.B. and A.J.B. acknowledge funding from Solve-RD, EU Horizon 2020 grant #779257; T.S. and S. Oesterle acknowledge funding from Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN), supported by the Swiss State Secretariat for Education, Research and Innovation SERI; S.J.M.J. acknowledges funding from Terry Fox Research Institute; A.E.H., M.P.B., M. Cupak, M.F., and J.F. acknowledge funding from the Digital Technology Supercluster; D.F.V. acknowledges funding from the Australian Medical Research Future Fund, as part of the Genomics Health Futures Mission grant #76749; M. Baudis acknowledges funding from the BioMedIT Network project of Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN); B.M.K. acknowledges funding from the Canada Research Chair in Law and Medicine and CIHR grant #SBD-163124; D.S., G.I.S., M.A.K., S.B., S.S., and T.H. Nyrönen acknowledge funding from the EU Horizon 2020 Beyond 1 Million Genomes (B1MG) Project grant #951724; P.F., A.D.Y., F.C., H.S., I.U.L., D. Gupta, M. Courtot, S.E.H., T. Burdett, T.M.K., and S.F. acknowledge funding from the European Molecular Biology Laboratory; Y.J. and S.E.W. acknowledge funding from the Government of Canada; P.G. acknowledges funding from the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-206); J.Z. acknowledges funding from the Government of Ontario; C.K.Y. acknowledges funding from the Government of Ontario, Canada Foundation for Innovation; C. Viner and M.M.H. acknowledge funding from the Natural Sciences and Engineering Research Council of Canada (grant #RGPIN-2015-03948 to M.M.H. and Alexander Graham Bell Canada Graduate Scholarship to C.V.); K.K.-L. acknowledges funding from the Program for Integrated Database of Clinical and Genomic Information; J.K. acknowledges funding from the Robertson Foundation; D.F.V. acknowledges funding from the Victorian State Government through the Operational Infrastructure Support (OIS) Program; A.M.L., R.N., and H.V.F. acknowledge funding from Wellcome (collaborative award); F.C., H.S., P.F., and S.E.H. acknowledge funding from Wellcome Trust grant #108749/Z/15/Z; A.D.Y., H.S., I.U.L., M. Courtot, H.E.P., P.F., and T.M.K. acknowledge funding from Wellcome Trust grant #201535/Z/16/Z; A.M., J.K.B., R.J.M., R.M.D., and T.M.K. acknowledge funding from Wellcome Trust grant #206194; E.B., P.F., P.G., and S.F. acknowledge funding from Wellcome Trust grant #220544/Z/20/Z; A. Hamosh acknowledges funding from NIH NHGRI grant U41HG006627 and U54HG006542; J.S.H. acknowledges funding from National Taiwan University #91F701-45C and #109T098-02; the work of K.W.R. was supported by the Intramural Research Program of the National Library of Medicine, NIH. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. H.V.F. acknowledges funding from Wellcome Grant 200990/A/16/Z ‘Designing, developing and delivering integrated foundations for genomic medicine'.

Published
2021
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83. An atlas of dynamic chromatin landscapes in mouse fetal development

Author

Axel Visel, Catherine S. Novak, Tyler H. Garvin, Hongbo Yang, Anne N. Harrington, Diane E. Dickel, Yin Shen, Kyle J. Gaulton, J. Michael Cherry, Bin Li, Quan T. Pham, Yunjiang Qiu, Mengchi Wang, Jean M. Davidson, Bo Ding, Elizabeth Lee, Ingrid Plajzer-Frick, Sora Chee, Sebastian Preissl, Jee Yun Han, Diane Trout, Henry Amrhein, Yupeng He, Jennifer A. Akiyama, Momoe Kato, Joseph R. Ecker, Veena Afzal, J. Seth Strattan, Yuan Zhao, Bo Zhang, Wei Wang, Len A. Pennacchio, David U. Gorkin, Brian A. Williams, Iros Barozzi, Ah Young Lee, Hui Huang, Yoko Fukuda-Yuzawa, Yanxiao Zhang, Brandon J. Mannion, Bing Ren, Andre Wildberg, and Joshua Chiou

Subjects
Epigenomics, Male, Transposases, Datasets as Topic, Regulatory Sequences, Nucleic Acid, Inbred C57BL, ACCESSIBLE CHROMATIN, Histones, Fetal Development, Mice, Disease, Developmental, TRANSCRIPTION FACTOR, ENCODE, Regulation of gene expression, Multidisciplinary, biology, Gene Expression Regulation, Developmental, CELL IDENTITY, STATE, Chromatin, Multidisciplinary Sciences, Enhancer Elements, Genetic, Histone, Organ Specificity, Differentiation, Science & Technology - Other Topics, Chromatin Immunoprecipitation Sequencing, Female, Biotechnology, EXPRESSION, DOMAINS, Enhancer Elements, General Science & Technology, 1.1 Normal biological development and functioning, Computational biology, Article, Vaccine Related, Genetic, Genetics, Animals, Humans, Enhancer, Vaccine Related (AIDS), Gene, Science & Technology, Nucleic Acid, Prevention, Human Genome, GENOME-WIDE, Reproducibility of Results, Genetic Variation, Molecular Sequence Annotation, SUPER-ENHANCERS, GENE, Mice, Inbred C57BL, Gene Expression Regulation, biology.protein, Immunization, Generic health relevance, Chromatin immunoprecipitation, Regulatory Sequences
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., Analysis of chromatin state and accessibility in mouse tissues from twelve sites and eight developmental stages provides a comprehensive view of chromatin dynamics.

Published
2020

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

Author

Carrie A. Davis, Charles B. Epstein, Eric L. Van Nostrand, Valentina Snetkova, Michael J. Purcaro, Manolis Kellis, Yupeng He, Henry Pratt, John A. Stamatoyannopoulos, Ali Mortazavi, Xintao Wei, Michael Snyder, Jialing Zhang, Job Dekker, Anshul Kundaje, Shaimae I. Elhajjajy, Gene W. Yeo, Jessica Halow, Peggy J. Farnham, Kevin P. White, Xiaofeng Wang, Eric M. Mendenhall, Diane E. Dickel, John L. Rinn, Thomas R. Gingeras, Yin Shen, Juan Carlos Rivera-Mulia, David U. Gorkin, William Stafford Noble, Rajinder Kaul, David M. Gilbert, Jill Moore, Xiao-Ou Zhang, Peter Freese, Bing Ren, Joseph R. Ecker, Eric Lécuyer, Christopher B. Burge, Ross C. Hardison, Jing Zhang, Zhiping Weng, Richard M. Myers, Robert J. Klein, Brian A. Williams, Alexander Dobin, Alec Victorsen, Noam Shoresh, Joel Rozowsky, Jack Huey, Bradley E. Bernstein, Mark Mackiewicz, Roderic Guigó, Axel Visel, Brenton R. Graveley, J. Michael Cherry, Trupti Kawli, Mark Gerstein, Cheryl A. Keller, Barbara J. Wold, Jessika Adrian, Len A. Pennacchio, Florencia Pauli-Behn, and Surya B. Chhetri

Subjects
Epigenomics, Transcription, Genetic, DNA Replication Timing, General Science & Technology, DNA Footprinting, Transposases, Mice, Transgenic, Genomics, Context (language use), 610 Medicine & health, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, ENCODE, Genome, Article, Histones, Mice, Databases, Genetic, Animals, Deoxyribonuclease I, Humans, Registries, data integration, Multidisciplinary, Genome, Human, RNA-Binding Proteins, Molecular Sequence Annotation, Functional genomics, DNA, DNA Methylation, Chromatin, epigenomics, DNA methylation, Data integration, functional genomics
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., The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

Published
2020
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85. Incorporation of a unified protein abundance dataset into the Saccharomyces genome database

Author

Sgd, Edith D. Wong, Stacia R. Engel, Robert S. Nash, J. Michael Cherry, Shuai Weng, and Kalpana Karra

Subjects
Proteomics, Saccharomyces cerevisiae Proteins, Proteome, Locus (genetics), Computational biology, Saccharomyces cerevisiae, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, User-Computer Interface, 0302 clinical medicine, Databases, Genetic, Median absolute deviation, 030304 developmental biology, 0303 health sciences, Protein function, Internet, Saccharomyces genome database, Genomics, Data warehouse, Metadata, Database Update, Protein abundance, Genome, Fungal, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Information Systems
Abstract

The identification and accurate quantitation of protein abundance has been a major objective of proteomics research. Abundance studies have the potential to provide users with data that can be used to gain a deeper understanding of protein function and regulation and can also help identify cellular pathways and modules that operate under various environmental stress conditions. One of the central missions of the Saccharomyces Genome Database (SGD; https://www.yeastgenome.org) is to work with researchers to identify and incorporate datasets of interest to the wider scientific community, thereby enabling hypothesis-driven research. A large number of studies have detailed efforts to generate proteome-wide abundance data, but deeper analyses of these data have been hampered by the inability to compare results between studies. Recently, a unified protein abundance dataset was generated through the evaluation of more than 20 abundance datasets, which were normalized and converted to common measurement units, in this case molecules per cell. We have incorporated these normalized protein abundance data and associated metadata into the SGD database, as well as the SGD YeastMine data warehouse, resulting in the addition of 56 487 values for untreated cells grown in either rich or defined media and 28 335 values for cells treated with environmental stressors. Abundance data for protein-coding genes are displayed in a sortable, filterable table on Protein pages, available through Locus Summary pages. A median abundance value was incorporated, and a median absolute deviation was calculated for each protein-coding gene and incorporated into SGD. These values are displayed in the Protein section of the Locus Summary page. The inclusion of these data has enhanced the quality and quantity of protein experimental information presented at SGD and provides opportunities for researchers to access and utilize the data to further their research.

Published
2020

86. Author Correction: Perspectives on ENCODE

Author

Jane Loveland, Axel Visel, Michael Snyder, Adam Frankish, Giovanni Quinones-Valdez, J. Michael Cherry, Eugene Yeo, Daniel Barrell, Jonathan Mudge, and Anshul Kundaje

Subjects
Multidisciplinary
Published
2022
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88. Gene Function, Metabolic Pathways and Comparative Genomics in Yeast.

Author

Qing Dong, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Shuai Weng, David Botstein, and J. Michael Cherry

Published
2003
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89. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Author

Jonathan A Eisen, Robert S Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R Wortman, Jonathan H Badger, Qinghu Ren, Paolo Amedeo, Kristie M Jones, Luke J Tallon, Arthur L Delcher, Steven L Salzberg, Joana C Silva, Brian J Haas, William H Majoros, Maryam Farzad, Jane M Carlton, Roger K Smith, Jyoti Garg, Ronald E Pearlman, Kathleen M Karrer, Lei Sun, Gerard Manning, Nels C Elde, Aaron P Turkewitz, David J Asai, David E Wilkes, Yufeng Wang, Hong Cai, Kathleen Collins, B Andrew Stewart, Suzanne R Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L Ruzzo, Dorota Wloga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A Gorovsky, Patrick J Keeling, Ross F Waller, Nicola J Patron, J Michael Cherry, Nicholas A Stover, Cynthia J Krieger, Christina del Toro, Hilary F Ryder, Sondra C Williamson, Rebecca A Barbeau, Eileen P Hamilton, and Eduardo Orias

Subjects
Biology (General), QH301-705.5
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
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90. Saccharomyces genome database informs human biology

Author

Sage T. Hellerstedt, J. Michael Cherry, Kevin A. MacPherson, Shuai Weng, Marek S. Skrzypek, Kalpana Karra, Stacia R. Engel, Robert S. Nash, Gail Binkley, Travis K. Sheppard, Stuart R. Miyasato, Matt Simison, and Edith D. Wong

Subjects
0301 basic medicine, ved/biology.organism_classification_rank.species, Saccharomyces cerevisiae, Genes, Fungal, Computational biology, Biology, ENCODE, Saccharomyces, 03 medical and health sciences, Information resource, Species Specificity, Human biology, Databases, Genetic, Genetics, Database Issue, Humans, Model organism, Saccharomyces genome database, ved/biology, Genome, Human, biology.organism_classification, Budding yeast, 030104 developmental biology, Gene Ontology, Mutation, Genome, Fungal, Forecasting
Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.

Published
2017

91. The Encyclopedia of DNA elements (ENCODE): data portal update

Author

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

Subjects
0301 basic medicine, Download, Interface (Java), Datasets as Topic, Genomics, Biology, Bioinformatics, ENCODE, World Wide Web, 03 medical and health sciences, Mice, User-Computer Interface, Databases, Genetic, Genetics, Database Issue, Animals, Humans, Caenorhabditis elegans, Metadata, Genome, Human, High-Throughput Nucleotide Sequencing, DNA, Visualization, 030104 developmental biology, Drosophila melanogaster, Gene Components, Encyclopedia, Data Display, Forecasting
Abstract

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

Published
2017

92. SGD and the Alliance of Genome Resources

Author

Wong, Edith D., Nash, Robert S., Gondwe, Felix, Aleksander, Suzi, and J. Michael Cherry

Abstract

SGD has recently joined forces with five other model organism databases (MODs) - WormBase, FlyBase, ZFIN, RGD, and MGI - plus the Gene Ontology Consortium (GOC) to form the Alliance of Genome Resources (the Alliance; alliancegenome.org). The Alliance website integrates expertly-curated information on model organisms and the functioning of cellular systems, and enables unified access to comparative genomics and genetics data, facilitating cross-species analyses. The site is undergoing rapid development as we work to harmonize various datatypes across the various organisms. Explore your favorite genes in the Alliance to find information regarding orthology sets, gene expression, gene function, mutant phenotypes, alleles, disease associations and more!

Published
2020
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93. Integration of macromolecular complex data into the Saccharomyces Genome Database

Author

Shuai Weng, Stacia R. Engel, Marek S. Skrzypek, Gail Binkley, Sgd, Edith D. Wong, Sandra Orchard, J. Michael Cherry, Livia Perfetto, and Birgit H M Meldal

Subjects
Computer science, information science, Genomics, Computational biology, yeast, Genome, General Biochemistry, Genetics and Molecular Biology, Fungal Proteins, Saccharomyces, 03 medical and health sciences, Physical structure, marcomoleculal complexes, Databases, Genetic, Web page, protein interaction, DNA, Fungal, 030304 developmental biology, Complex data type, 0303 health sciences, Saccharomyces genome database, Data curation, 030302 biochemistry & molecular biology, Fungal genetics, Data warehouse, ComplexPortal, Original Article, Genome, Fungal, General Agricultural and Biological Sciences, Information Systems
Abstract

Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals of Saccharomyces Genome Database (SGD; www.yeastgenome.org) is to provide a complete picture of budding yeast biological processes. To this end, we have collaborated with the Molecular Interactions team that provides the Complex Portal database at EMBL-EBI to manually curate the complete yeast complexome. These data, from a total of 589 complexes, were previously available only in SGD’s YeastMine data warehouse (yeastmine.yeastgenome.org) and the Complex Portal (www.ebi.ac.uk/complexportal). We have now incorporated these macromolecular complex data into the SGD core database and designed complex-specific reports to make these data easily available to researchers. These web pages contain referenced summaries focused on the composition and function of individual complexes. In addition, detailed information about how subunits interact within the complex, their stoichiometry and the physical structure are displayed when such information is available. Finally, we generate network diagrams displaying subunits and Gene Ontology annotations that are shared between complexes. Information on macromolecular complexes will continue to be updated in collaboration with the Complex Portal team and curated as more data become available.

Published
2020
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94. Data Sanitization to Reduce Private Information Leakage from Functional Genomics

Author

Prashant Emani, Gamze Gürsoy, Charlotte M. Brannon, Andrew D. Miranker, Mark Gerstein, Arif Harmanci, J. Michael Cherry, J. Seth Strattan, and Otto Jolanki

Subjects
Genotype, RNA-Seq, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Data sanitization, Humans, Leakage (economics), Protocol (object-oriented programming), Private information retrieval, Computer Security, Phylogeny, 030304 developmental biology, 0303 health sciences, Genome, Human, Sequence Analysis, RNA, Genetic variants, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Genomics, Data science, ComputingMethodologies_PATTERNRECOGNITION, Phenotype, Privacy, Single-Cell Analysis, Functional genomics, 030217 neurology & neurosurgery
Abstract

The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). The intent behind functional genomics experiments is not necessarily to study genetic variants, yet they pose privacy concerns due to their use of next-generation sequencing. Moreover, there is a great incentive to broadly share raw reads for better statistical power and general research reproducibility. Thus, we need new modes of sharing beyond traditional controlled-access models. Here, we develop a data-sanitization procedure allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs. Our protocol works with traditional Illumina-based assays and newer technologies such as 10x single-cell RNA sequencing. It involves quantifying the privacy leakage in reads by statistically linking study participants to known individuals. We carried out these linkages using data from highly accurate reference genomes and more realistic environmental samples.

Published
2019

95. The ENCODE Portal as an Epigenomics Resource

Author

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

Subjects
Epigenomics, Computer science, Genomics, ENCODE, Article, 03 medical and health sciences, Mice, Data file, Databases, Genetic, Animals, Humans, Protocol (object-oriented programming), 030304 developmental biology, 0303 health sciences, Internet, Metadata, Information retrieval, Genome, Human, 030305 genetics & heredity, General Medicine, DNA, DNA Methylation, Metadata modeling, Chromatin, ComputingMethodologies_PATTERNRECOGNITION, Human genome, Software
Abstract

The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations. The ENCODE portal provides unrestricted access to the aforementioned data and relevant metadata as a service to the scientific community. The metadata model captures the details of the experiments, raw and processed data files, and processing pipelines in human and machine-readable form and enables the user to search for specific data either using a web browser or programmatically via REST API. Furthermore, ENCODE data can be freely visualized or downloaded for additional analyses. © 2019 The Authors. Basic Protocol: Query the portal Support Protocol 1: Batch downloading Support Protocol 2: Using the cart to download files Support Protocol 3: Visualize data Alternate Protocol: Query building and programmatic access.

Published
2019

96. The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

Author

Mary Shimoyama, Judith A. Blake, Thom Kaufman, Christopher J. Mungall, Valentina DiFrancesco, Carol J. Bult, Norbert Perrimon, Paul W. Sternberg, Monte Westerfield, Brian R. Calvi, Kevin L. Howe, J. Michael Cherry, Robert Fullem, and Paul Thomas

Subjects
ved/biology.organism_classification_rank.species, Access method, Scientific literature, Biology, computer.software_genre, Genome, Models, Biological, Knowledge commons, 03 medical and health sciences, 0302 clinical medicine, Web page, Databases, Genetic, Genetics, data stewardship, model organism databases, Model organism, Ecosystem, 030304 developmental biology, 0303 health sciences, Database, ved/biology, database sustainability, bioinformatics, Alliance, Gene Ontology, Commentary, Human genome, computer, 030217 neurology & neurosurgery
Abstract

Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp. (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified “look and feel,” the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient “knowledge commons” for model organisms using shared, modular infrastructure.

Published
2019

97. Rehabilitation across the lifespan for individuals with arthrogryposis

Author

Caroline Elfassy, Alicja Fąfara, J Suzanne Cherry, Kathleen Montpetit, Tricia Bucci, Maureen Donohoe, Marie Eriksson, Bonita Sawatzky, and Lisa V. Wagner

Subjects
musculoskeletal diseases, 0301 basic medicine, medicine.medical_specialty, Activities of daily living, medicine.medical_treatment, Longevity, Orthotics, 030105 genetics & heredity, 03 medical and health sciences, Physical medicine and rehabilitation, Multidisciplinary approach, Activities of Daily Living, Genetics, medicine, Humans, Toddler, Range of Motion, Articular, Genetics (clinical), Arthrogryposis, Arthrogryposis multiplex congenita, Rehabilitation, 030104 developmental biology, medicine.symptom, Range of motion, Psychology
Abstract

Arthrogryposis multiplex congenita (AMC) can be a perplexing diagnosis that consists of limited range of motion (ROM) and decreased muscle strength in multiple joints. The person with AMC often possesses a certain tenacity and "spunk" that assists them with adjusting and adapting to the realities of daily life. The rehabilitation process assists the individual with AMC in achieving and maintaining the maximal active and passive range of motion and strength in order to participate in activities of daily living (ADL) throughout the developmental stages. The result of this life-long process is greatly impacted by collaboration among the multidisciplinary teams. Ultimately, rehabilitation should focus on three levels of treatment: (a) body structure, (b) activity, and (c) participation. This article describes rehabilitation across the lifespan-focusing on the therapeutic needs in the infant, toddler, school age and teenage/adult years-while also highlighting opportunities for improvement.

Published
2019

98. Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

Author

Kim D. Pruitt, Lynette Hirschman, Cathy H. Wu, B. F. Francis Ouellette, Frederic B. Bastian, Granger G. Sutton, Susanna-Assunta Sansone, Paul N. Schofield, William Klimke, Claire O'Donovan, Peter D'Eustachio, Alex Bateman, Jasmine Young, J. Michael Cherry, Raja Mazumder, Michelle G. Giglio, Judith A. Blake, Renate Kania, Maria Jesus Martin, Kimberly Van Auken, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Cecilia N. Arighi, Robert D. Finn, Pascale Gaudet, Darren A. Natale, Marc Robinson-Rechavi, Sona Vasudevan, Schofield, Paul [0000-0002-5111-7263], and Apollo - University of Cambridge Repository

Subjects
media_common.quotation_subject, Library science, General Biochemistry, Genetics and Molecular Biology, World Wide Web, 03 medical and health sciences, Promotion (rank), Political science, Databases, Genetic, Animals, Data Mining, Humans, Databases, Protein, Reference standards, 030304 developmental biology, media_common, 0303 health sciences, Career Choice, 030302 biochemistry & molecular biology, Proteins, Molecular Sequence Annotation, Original Articles, Reference Standards, Disease Models, Animal, Metagenomics, Periodicals as Topic, General Agricultural and Biological Sciences, Career choice, Information Systems
Abstract

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration’s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB's goal to support exchanges among members of the biocuration community. Next year's conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society's activities (http://biocurator.org), as well as related events of interest.

Published
2019
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100. Expansion of the Gene Ontology knowledgebase and resources

Author

Ray Stefancsik, James Balhoff, Marc Feuermann, Rex Chisholm, Kim Rutherford, Nicholas Brown, Rachael Huntley, Sabrina Toro, Ivo Pedruzzi, Valerie Wood, Barbara Kramarz, Nancy Campbell, Alexander Deng, Sandip Patel, Paul Thomas, Ruth Lovering, James Hu, Cathy Wu, Kevin Howe, Jurg Bahler, Midori Harris, Michele Magrane, Giulia Antonazzo, Matthew Berriman, Paola Roncaglia, Petra Fey, J. Michael Cherry, Susan Tweedie, Jane Lomax, Marcus Chibucos, and Peter McQuilton

Subjects
0301 basic medicine, media_common.quotation_subject, Biology, Ontology (information science), Web Browser, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Resource (project management), Research community, Databases, Genetic, Genetics, Database Issue, Quality (business), Phylogeny, Causal model, media_common, Gene ontology, Computational Biology, Molecular Sequence Annotation, Genomics, Data science, 030104 developmental biology, Gene Ontology, 030217 neurology & neurosurgery, Biological network
Abstract

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.

Published
2016

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