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Rahman N, O'Cathail C, Zyoud A, Sokolov A, Oude Munnink B, Grüning B, Cummins C, Amid C, Nieuwenhuijse DF, Visontai D, Yuan DY, Gupta D, Prasad DK, Gulyás GM, Rinck G, McKinnon J, Rajan J, Knaggs J, Skiby JE, Stéger J, Szarvas J, Gueye K, Papp K, Hoek M, Kumar M, Ventouratou MA, Bouquieaux MC, Koliba M, Mansurova M, Haseeb M, Worp N, Harrison PW, Leinonen R, Thorne R, Selvakumar S, Hunt S, Venkataraman S, Jayathilaka S, Cezard T, Maier W, Waheed Z, Iqbal Z, Aarestrup FM, Csabai I, Koopmans M, Burdett T, Cochrane G. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microb Genom 2024; 10:001188. [PMID: 38358325 PMCID: PMC10926692 DOI: 10.1099/mgen.0.001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/14/2024] [Indexed: 02/16/2024] Open
Abstract
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
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Affiliation(s)
- Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Bas Oude Munnink
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Björn Grüning
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Clara Amid
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | | | - Dávid Visontai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - David Yu Yuan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Divyae K. Prasad
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Gábor Máté Gulyás
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jasmine McKinnon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeff Knaggs
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeffrey Edward Skiby
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - József Stéger
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Judit Szarvas
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Khadim Gueye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Krisztián Papp
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Maarten Hoek
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marianna A. Ventouratou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Martin Koliba
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Milena Mansurova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nathalie Worp
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Peter W. Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sundar Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Timothée Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Maier
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Istvan Csabai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Marion Koopmans
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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Shaw F, Minotto A, McTaggart S, Providence A, Harrison P, Paupério J, Rajan J, Burgin J, Cochrane G, Kilias E, Lawniczak M, Davey R. Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.18499.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.
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Lawniczak MK, Davey RP, Rajan J, Pereira-da-Conceicoa LL, Kilias E, Hollingsworth PM, Barnes I, Allen H, Blaxter M, Burgin J, Broad GR, Crowley LM, Gaya E, Holroyd N, Lewis OT, McTaggart S, Mieszkowska N, Minotto A, Shaw F, Richards TA, Sivess LA. Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17605.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vision of the Earth BioGenome Project1 is to complete reference genomes for all of the planet’s ~2M described eukaryotic species in the coming decade. To contribute to this global endeavour, the Darwin Tree of Life Project (DToL2) was launched in 2019 with the aim of generating complete genomes for the ~70k described eukaryotic species that can be found in Britain and Ireland. One of the early tasks of the DToL project was to determine, define, and standardise the important metadata that must accompany every sample contributing to this ambitious project. This ensures high-quality contextual information is available for the associated data, enabling a richer set of information upon which to search and filter datasets as well as enabling interoperability between datasets used for downstream analysis. Here we describe some of the key factors we considered in the process of determining, defining, and documenting the metadata required for DToL project samples. The manifest and Standard Operating Procedure that are referred to throughout this paper are likely to be useful for other projects, and we encourage re-use while maintaining the standards and rules set out here.
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Rajan J, Sadananda V, Hegde MN. Endodontics: Dental Undergraduate Students’ Perception of the Speciality. JPRI 2021. [DOI: 10.9734/jpri/2021/v33i53a33654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aim: The aim of this study was to evaluate the dental undergraduate students’ perception of the dental speciality Endodontics
Material and Methods: Multiple-choice questionnaire was distributed to 82 final year dental undergraduate students and 88 interns. The analysis of data was performed using methods of descriptive analysis.
Results: 79.27% of the final year students and 79.55% of interns preferred to pursue Endodontics as a future speciality course. An increase in the understanding of the speciality overall was observed among the interns.
Conclusion: The undergraduate dental students were reasonably informed the speciality Endodontics.
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Cummins C, Ahamed A, Aslam R, Burgin J, Devraj R, Edbali O, Gupta D, Harrison PW, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu V, Kay S, Kumar M, Lathi A, Leinonen R, Madeira F, Madhusoodanan N, Mansurova M, O'Cathail C, Pearce M, Pesant S, Rahman N, Rajan J, Rinck G, Selvakumar S, Sokolov A, Suman S, Thorne R, Totoo P, Vijayaraja S, Waheed Z, Zyoud A, Lopez R, Burdett T, Cochrane G. The European Nucleotide Archive in 2021. Nucleic Acids Res 2021; 50:D106-D110. [PMID: 34850158 PMCID: PMC8728206 DOI: 10.1093/nar/gkab1051] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/02/2022] Open
Abstract
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA’s services and infrastructure that have been delivered over the past year.
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Affiliation(s)
- Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alisha Ahamed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Raheela Aslam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rajkumar Devraj
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ossama Edbali
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Talal Ibrahim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eugene Ivanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vishnukumar Kadhirvelu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ankur Lathi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fabio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nandana Madhusoodanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Milena Mansurova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matt Pearce
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Swati Suman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Prabhat Totoo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Senthilnathan Vijayaraja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ, Lopez JV, Martín-Durán JM, Petersen JM, Sigwart JD, Simakov O, Sutherland KR, Sweet M, Talbot N, Thompson AW, Bender S, Harrison PW, Rajan J, Cochrane G, Berriman M, Lawniczak M, Blaxter M. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17222.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.
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Mariani N, Borsini A, Cecil CAM, Felix JF, Sebert S, Cattaneo A, Walton E, Milaneschi Y, Cochrane G, Amid C, Rajan J, Giacobbe J, Sanz Y, Agustí A, Sorg T, Herault Y, Miettunen J, Parmar P, Cattane N, Jaddoe V, Lötjönen J, Buisan C, González Ballester MA, Piella G, Gelpi JL, Lamers F, Penninx BWJH, Tiemeier H, von Tottleben M, Thiel R, Heil KF, Järvelin MR, Pariante C, Mansuy IM, Lekadir K. Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project. PLoS One 2021; 16:e0245475. [PMID: 33476328 PMCID: PMC7819604 DOI: 10.1371/journal.pone.0245475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/27/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction Depression, cardiovascular diseases and diabetes are among the major non-communicable diseases, leading to significant disability and mortality worldwide. These diseases may share environmental and genetic determinants associated with multimorbid patterns. Stressful early-life events are among the primary factors associated with the development of mental and physical diseases. However, possible causative mechanisms linking early life stress (ELS) with psycho-cardio-metabolic (PCM) multi-morbidity are not well understood. This prevents a full understanding of causal pathways towards the shared risk of these diseases and the development of coordinated preventive and therapeutic interventions. Methods and analysis This paper describes the study protocol for EarlyCause, a large-scale and inter-disciplinary research project funded by the European Union’s Horizon 2020 research and innovation programme. The project takes advantage of human longitudinal birth cohort data, animal studies and cellular models to test the hypothesis of shared mechanisms and molecular pathways by which ELS shapes an individual’s physical and mental health in adulthood. The study will research in detail how ELS converts into biological signals embedded simultaneously or sequentially in the brain, the cardiovascular and metabolic systems. The research will mainly focus on four biological processes including possible alterations of the epigenome, neuroendocrine system, inflammatome, and the gut microbiome. Life-course models will integrate the role of modifying factors as sex, socioeconomics, and lifestyle with the goal to better identify groups at risk as well as inform promising strategies to reverse the possible mechanisms and/or reduce the impact of ELS on multi-morbidity development in high-risk individuals. These strategies will help better manage the impact of multi-morbidity on human health and the associated risk.
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Affiliation(s)
- Nicole Mariani
- Department of Psychological Medicine, Stress, Psychiatry and Immunology Laboratory, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
- * E-mail:
| | - Alessandra Borsini
- Department of Psychological Medicine, Stress, Psychiatry and Immunology Laboratory, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Charlotte A. M. Cecil
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F. Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Genomic Medicine, Imperial College London, London, United Kingdom
| | - Annamaria Cattaneo
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Biological Psychiatry Laboratory, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, United Kingdom
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam UMC/Vrije Universiteit & GGZinGeest, Amsterdam Public Health and Amsterdam Neuroscience Research Institutes, Amsterdam, The Netherlands
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Juliette Giacobbe
- Department of Psychological Medicine, Stress, Psychiatry and Immunology Laboratory, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Group, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | - Ana Agustí
- Microbial Ecology, Nutrition and Health Research Group, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | - Tania Sorg
- Centre Européen de Recherche en Biologie et Médicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire, PHENOMIN-ICS, Université de Strasbourg, CNRS, INSERM, Strasbourg, France
| | - Yann Herault
- Centre Européen de Recherche en Biologie et Médicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire, PHENOMIN-ICS, Université de Strasbourg, CNRS, INSERM, Strasbourg, France
| | - Jouko Miettunen
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Priyanka Parmar
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Nadia Cattane
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Biological Psychiatry Laboratory, Brescia, Italy
| | - Vincent Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jyrki Lötjönen
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carme Buisan
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Miguel A. González Ballester
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Gemma Piella
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Josep L. Gelpi
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Femke Lamers
- Department of Psychology, University of Bath, Bath, United Kingdom
| | | | - Henning Tiemeier
- Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | | | - Rainer Thiel
- Empirica Communication and Technology Research, Bonn, Germany
| | - Katharina F. Heil
- Departament de Matemàtiques i Informàtica, Universitat de Barcelona, Barcelona, Spain
| | - Marjo-Riitta Järvelin
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - Carmine Pariante
- Department of Psychological Medicine, Stress, Psychiatry and Immunology Laboratory, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Isabelle M. Mansuy
- Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Laboratory of Neuroepigenetics, Brain Research Institute, Zürich Neuroscience Center, Zürich, Switzerland
| | - Karim Lekadir
- Departament de Matemàtiques i Informàtica, Universitat de Barcelona, Barcelona, Spain
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8
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Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Balavenkataraman Kadhirvelu V, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Res 2021; 49:D82-D85. [PMID: 33175160 PMCID: PMC7778925 DOI: 10.1093/nar/gkaa1028] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/20/2020] [Indexed: 11/12/2022] Open
Abstract
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scientific community and for the acceleration of the global research effort. Here we highlight the major developments to ENA services and content in 2020, focussing in particular on the recently released updated ENA browser, modernisation of our release process and our data coordination collaborations with specific research communities.
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Affiliation(s)
- Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alisha Ahamed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Raheela Aslam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicola Buso
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jun Fan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Talal Ibrahim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eugene Ivanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amir Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Youngmi Park
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Senthilnathan Vijayaraja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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9
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Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G. The European Nucleotide Archive in 2019. Nucleic Acids Res 2020; 48:D70-D76. [PMID: 31722421 PMCID: PMC7145635 DOI: 10.1093/nar/gkz1063] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world's public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.
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Affiliation(s)
- Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jun Fan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abdulrahman Hussein
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eugene Ivanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josue Martinez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amir Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Richards
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Senthilnathan Vijayaraja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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10
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Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G. The European Nucleotide Archive in 2018. Nucleic Acids Res 2020; 47:D84-D88. [PMID: 30395270 PMCID: PMC6323982 DOI: 10.1093/nar/gky1078] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/22/2018] [Indexed: 11/25/2022] Open
Abstract
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we outline ENA services and content in 2018 and provide an overview of a selection of focus areas of development work: extending data coordination services around ENA, sequence submissions through template expansion, early pre-submission validation tools and our move towards a new browser and retrieval infrastructure.
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Affiliation(s)
- Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cerdeño-Tárraga
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abdulrahman Hussein
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josué Martínez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Richards
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana-Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Senthilnathan Vijayaraja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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11
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Rajan J, Gaur G, Karthik S, Adinarayanan S. Theta dominance in the power spectra of eeg in chronic neurogenic pain. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. The European Nucleotide Archive in 2017. Nucleic Acids Res 2019; 46:D36-D40. [PMID: 29140475 PMCID: PMC5753375 DOI: 10.1093/nar/gkx1125] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/25/2017] [Indexed: 12/03/2022] Open
Abstract
For 35 years the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) has been responsible for making the world’s public sequencing data available to the scientific community. Advances in sequencing technology have driven exponential growth in the volume of data to be processed and stored and a substantial broadening of the user community. Here, we outline ENA services and content in 2017 and provide insight into a selection of current key areas of development in ENA driven by challenges arising from the above growth.
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Affiliation(s)
- Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana Cerdeño-Tarrága
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Josué Martínez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Manuela Menchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Rossello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana L Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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13
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Chincholkar M, Ireland K, Rajan J. Comment on 'Association between intraoperative opioid administration and 30-day readmission: a pre-specified analysis of registry data from a healthcare network in New England' (Br J Anaesth 2018;120:1090-1102). Br J Anaesth 2018; 121:986-987. [PMID: 30236273 DOI: 10.1016/j.bja.2018.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 11/25/2022] Open
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14
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Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. UniEuk: Time to Speak a Common Language in Protistology! J Eukaryot Microbiol 2017; 64:407-411. [PMID: 28337822 PMCID: PMC5435949 DOI: 10.1111/jeu.12414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
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Affiliation(s)
- Cédric Berney
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Andreea Ciuprina
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany
| | - Sara Bender
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA
| | - Jeena Rajan
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Laura Wegener Parfrey
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada
| | - Stéphane Audic
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Lucas Czech
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Frank Oliver Glöckner
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | | | - Christian Quast
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Jonathan Z Kaye
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.,Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany
| | - Javier Del Campo
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Colomban de Vargas
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
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15
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Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. European Nucleotide Archive in 2016. Nucleic Acids Res 2016; 45:D32-D36. [PMID: 27899630 PMCID: PMC5210577 DOI: 10.1093/nar/gkw1106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.
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Affiliation(s)
- Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cerdeño-Tarrága
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josué Martínez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Gibson R, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Pallreddy S, Pakseresht N, Rajan J, Rosselló M, Silvester N, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Biocuration of functional annotation at the European nucleotide archive. Nucleic Acids Res 2016; 44:D58-66. [PMID: 26615190 PMCID: PMC4702917 DOI: 10.1093/nar/gkv1311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 01/03/2023] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed.
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Affiliation(s)
- Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana Cerdeño-Tárraga
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Swapna Pallreddy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Rosselló
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Thiyagarajan P, Thandra PK, Rajan J, Satyamurthy SAV, Aghila G. Shamir Secret Sharing Scheme with Dynamic Access Structure (SSSDAS): case study on nuclear power plant. KERNTECHNIK 2015. [DOI: 10.3139/124.110489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
In recent years, due to the sophistication offered by the Internet, strategic organizations like nuclear power plants are linked to the outside world communication through the Internet. The entry of outside world communication into strategic organization (nuclear power plant) increases the hacker's attempts to crack its security and to trace any information which is being sent among the top level officials. Information security system in nuclear power plant is very crucial as even small loophole in the security system will lead to a major disaster. Recent cyber attacks in nuclear power plant provoked information security professionals to look deeply into the information security aspects of strategic organizations (nuclear power plant). In these lines, Shamir secret sharing scheme with dynamic access structure (SSSDAS) is proposed in the paper which provides enhanced security by providing dynamic access structure for each node in different hierarchies. The SSSDAS algorithm can be applied to any strategic organizations with hierarchical structures. In this paper the possible scenarios where SSSDAS algorithm can be applied to nuclear power plant is explained as a case study. The proposed SSSDAS scheme identifies the wrong shares, if any, used for reconstruction of the secret. The SSSDAS scheme also address the three major security parameters namely confidentiality, authentication and integrity.
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Affiliation(s)
- P. Thiyagarajan
- Computer Division , Indira Gandhi Centre for Atomic Research (IGCAR), Department of Atomic Energy, Kalpakkam – 603102 , India. E-mail:
| | - Prasanth Kumar Thandra
- Professor & Head , Department of Computer Science & Engineering, National Institute of Technology – Puducherry, Karaikal – 609605 , India. E-mail:
| | - J. Rajan
- Computer Division , Indira Gandhi Centre for Atomic Research (IGCAR), Department of Atomic Energy, Kalpakkam – 603102 , India. E-mail:
| | - S. A. V. Satyamurthy
- Computer Division , Indira Gandhi Centre for Atomic Research (IGCAR), Department of Atomic Energy, Kalpakkam – 603102 , India. E-mail:
| | - G. Aghila
- Professor & Head , Department of Computer Science & Engineering, National Institute of Technology – Puducherry, Karaikal – 609605 , India. E-mail:
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Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SMJ, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JGR, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 2013; 42:D865-72. [PMID: 24217909 PMCID: PMC3965069 DOI: 10.1093/nar/gkt1059] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
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Affiliation(s)
- Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2013; 22:1760-74. [PMID: 22955987 PMCID: PMC3431492 DOI: 10.1101/gr.135350.111] [Citation(s) in RCA: 3491] [Impact Index Per Article: 317.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
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Affiliation(s)
- Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
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Hafeez R, Greenhalgh R, Rajan J, Bloom S, McCartney S, Halligan S, Taylor SA. Use of small bowel imaging for the diagnosis and staging of Crohn's disease--a survey of current UK practice. Br J Radiol 2010; 84:508-17. [PMID: 21081570 DOI: 10.1259/bjr/65972479] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES This study used a postal survey to assess the current use of small bowel imaging investigations for Crohn's disease within National Health Service (NHS) radiological practice and to gauge gastroenterological referral patterns. METHODS Similar questionnaires were posted to departments of radiology (n = 240) and gastroenterology (n = 254) identified, by the databases of the Royal College of Radiologists and British Society of Gastroenterologists. Questionnaires enquired about the use of small bowel imaging in the assessment of Crohn's disease. In particular, questionnaires described clinical scenarios including first diagnosis, disease staging and assessment of suspected extraluminal complications, obstruction and disease flare. The data were stratified according to patient age. RESULTS 63 (27%) departments of radiology (20 in teaching hospitals and 43 in district general hospitals (DGHs)) and 73 (29%) departments of gastroenterology replied. These departments were in 119 institutions. Of the 63 departments of radiology, 55 (90%) routinely performed barium follow-though (BaFT), 50 (80%) CT, 29 (46%) small bowel ultrasound (SbUS) and 24 (38%) small bowel MRI. BaFT was the most commonly used investigation across all age groups and indications. SbUS was used mostly for patients younger than 40 years of age with low index of clinical suspicion for Crohn's disease (in 44% of radiology departments (28/63)). MRI was most frequently used in patients under 20 years of age for staging new disease (in 27% of radiology departments (17/63)) or in whom obstruction was suspected (in 29% of radiology departments (18/63)). CT was preferred for suspected extraluminal complications or obstruction (in 73% (46/63) and 46% (29/63) of radiology departments, respectively). Gastroenterological referrals largely concurred with the imaging modalities chosen by radiologists, although gastroenterologists were less likely to request SbUS and MRI. CONCLUSION BaFT remains the mainstay investigation for luminal small bowel Crohn's disease, with CT dominating for suspected extraluminal complications. There has been only moderate dissemination of the use of MRI and SbUS.
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Affiliation(s)
- R Hafeez
- Department of Surgery, University College London, 74 Huntley Street, London, UK
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Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genes Dev 2009; 19:1316-23. [PMID: 19498102 PMCID: PMC2704439 DOI: 10.1101/gr.080531.108] [Citation(s) in RCA: 401] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Abstract
Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.
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Affiliation(s)
- Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA.
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Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CCA, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RIS, Aubin K, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Bryant SP, Buckley D, Burford DC, Burrill WDH, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Clegg SM, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dhami P, Dovey O, Dunn M, Earthrowl M, Ellington AG, Errington H, Faulkner LM, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MRJ, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Gribble SM, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ESI, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Langford CF, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NSW, McLaren S, Milne S, Mistry S, oore MJFM, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Pandian RD, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Porter KM, Prigmore E, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall J. M. Wallis M, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR. Erratum: The DNA sequence and biological annotation of human chromosome 1. Nature 2006. [DOI: 10.1038/nature05152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Deepak VD, Rajan J, Asha SK. Hydrogen bonding and rate enhancement in the photoinduced polymerization of telechelic urethane methacrylates based on a cycloaliphatic system: Tricyclodecane dimethanol. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pola.21533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CCA, Jones MC, Gillson C, Searle S, Zhou Y, Kokocinski F, McDonald L, Evans R, Phillips K, Atkinson A, Cooper R, Jones C, Hall RE, Andrews TD, Lloyd C, Ainscough R, Almeida JP, Ambrose KD, Anderson F, Andrew RW, Ashwell RIS, Aubin K, Babbage AK, Bagguley CL, Bailey J, Beasley H, Bethel G, Bird CP, Bray-Allen S, Brown JY, Brown AJ, Buckley D, Burton J, Bye J, Carder C, Chapman JC, Clark SY, Clarke G, Clee C, Cobley V, Collier RE, Corby N, Coville GJ, Davies J, Deadman R, Dunn M, Earthrowl M, Ellington AG, Errington H, Frankish A, Frankland J, French L, Garner P, Garnett J, Gay L, Ghori MRJ, Gibson R, Gilby LM, Gillett W, Glithero RJ, Grafham DV, Griffiths C, Griffiths-Jones S, Grocock R, Hammond S, Harrison ESI, Hart E, Haugen E, Heath PD, Holmes S, Holt K, Howden PJ, Hunt AR, Hunt SE, Hunter G, Isherwood J, James R, Johnson C, Johnson D, Joy A, Kay M, Kershaw JK, Kibukawa M, Kimberley AM, King A, Knights AJ, Lad H, Laird G, Lawlor S, Leongamornlert DA, Lloyd DM, Loveland J, Lovell J, Lush MJ, Lyne R, Martin S, Mashreghi-Mohammadi M, Matthews L, Matthews NSW, McLaren S, Milne S, Mistry S, Moore MJF, Nickerson T, O'Dell CN, Oliver K, Palmeiri A, Palmer SA, Parker A, Patel D, Pearce AV, Peck AI, Pelan S, Phelps K, Phillimore BJ, Plumb R, Rajan J, Raymond C, Rouse G, Saenphimmachak C, Sehra HK, Sheridan E, Shownkeen R, Sims S, Skuce CD, Smith M, Steward C, Subramanian S, Sycamore N, Tracey A, Tromans A, Van Helmond Z, Wall M, Wallis JM, White S, Whitehead SL, Wilkinson JE, Willey DL, Williams H, Wilming L, Wray PW, Wu Z, Coulson A, Vaudin M, Sulston JE, Durbin R, Hubbard T, Wooster R, Dunham I, Carter NP, McVean G, Ross MT, Harrow J, Olson MV, Beck S, Rogers J, Bentley DR, Banerjee R, Bryant SP, Burford DC, Burrill WDH, Clegg SM, Dhami P, Dovey O, Faulkner LM, Gribble SM, Langford CF, Pandian RD, Porter KM, Prigmore E. The DNA sequence and biological annotation of human chromosome 1. Nature 2006; 441:315-21. [PMID: 16710414 DOI: 10.1038/nature04727] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2005] [Accepted: 03/13/2006] [Indexed: 11/08/2022]
Abstract
The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
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Affiliation(s)
- S G Gregory
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Abstract
The Hedgehog (Hh) signaling pathway promotes pattern formation and cell proliferation in Drosophila and vertebrates. Hh is a ligand that binds and represses the Patched (Ptc) receptor and thereby releases the latent activity of the multipass membrane protein Smoothened (Smo), which is essential for transducing the Hh signal. In Caenorhabditis elegans, the Hh signaling pathway has undergone considerable divergence. Surprisingly, obvious Smo and Hh homologs are absent whereas PTC, PTC-related (PTR), and a large family of nematode Hh-related (Hh-r) proteins are present. We find that the number of PTC-related and Hh-r proteins has expanded in C. elegans, and that this expansion occurred early in Nematoda. Moreover, the function of these proteins appears to be conserved in Caenorhabditis briggsae. Given our present understanding of the Hh signaling pathway, the absence of Hh and Smo raises many questions about the evolution and the function of the PTC, PTR, and Hh-r proteins in C. elegans. To gain insights into their roles, we performed a global survey of the phenotypes produced by RNA-mediated interference (RNAi). Our study reveals that these genes do not require Smo for activity and that they function in multiple aspects of C. elegans development, including molting, cytokinesis, growth, and pattern formation. Moreover, a subset of the PTC, PTR, and Hh-r proteins have the same RNAi phenotypes, indicating that they have the potential to participate in the same processes.
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Affiliation(s)
- Olivier Zugasti
- University of Bristol, Department of Biochemistry, School of Medical Sciences, Bristol BS8 1TD, United Kingdom
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Astin J, Merry A, Rajan J, Kuwabara PE. Caenorhabditis elegans functional genomics: omic resonance. Brief Funct Genomic Proteomic 2004; 3:26-34. [PMID: 15163357 DOI: 10.1093/bfgp/3.1.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The nematode Caenorhabditis elegans is widely used as a model organism for studying many fundamental aspects of development and cell biology, including processes underlying human disease. The genome of C. elegans encodes over 19,000 protein-coding genes and hundreds of non-coding RNAs. The availability of whole genome sequence has facilitated the development of high throughput techniques for elucidating the function of individual genes and gene products. Furthermore, attempts can now be made to integrate these substantial functional genomics data collections and to understand at a global level how the flow of genomic information that is at the core of the central dogma leads to the development of a multicellular organism.
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Affiliation(s)
- Jonathan Astin
- Department of Biochemistry, University of Bristol, The School of Medical Sciences, University Walk, Bristol BS8 1TD, UK
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Cottingham B, Borst I, Campbell PO, Gallagher K, Ho TP, Kowalski V, Lin S, MacLean DB, Mookherjae S, Polywacz J, Rajan J, Smittle R, Williams A, Wolf WR, Wong WK. Laboratory Quality Assurance Committee. J AOAC Int 1997. [DOI: 10.1093/jaoac/80.1.236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Rajan J, Valli K, Perkins RE, Sariaslani FS, Barns SM, Reysenbach AL, Rehm S, Ehringer M, Pace NR. Mineralization of 2,4,6-trinitrophenol (picric acid): characterization and phylogenetic identification of microbial strains. J Ind Microbiol 1996; 16:319-24. [PMID: 8757942 DOI: 10.1007/bf01570041] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Four bacterial strains that use picric acid as their sole carbon and energy source were isolated. Mineralization of 14C-UL-picric acid showed that up to 65% of the radioactivity was released as 14CO2. HPLC and UV/Vis spectral analyses indicated complete degradation of picric acid by these organisms. HPLC and LC/MS analyses showed transient formation of 2,4-dinitrophenol during picric acid degradation. Degradation of picric acid was concomitant with stoichiometric release of three moles of nitrite per mole of picric acid. The four picric acid degraders were identified as close relatives of Nocardioides simplex (ATCC 6946) based on their small subunit (16S) rRNA gene sequences.
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Affiliation(s)
- J Rajan
- BioProcess Development Center, Dupont Co, Wilmington, DE 19880-0173, USA
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Cottingham B, Borst I, Campbell PO, DeVries J, Gallagher K, Ho IP, Jensen TL, Koenig E, MacLean DB, McCully KA, Mookherjae S, Polywacz J, Rajan J, Williams A, Wolf WR, Wong WK. Laboratory Quality Assurance Committee. J AOAC Int 1996. [DOI: 10.1093/jaoac/79.1.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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