Graphical Pangenomics
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Ensembl Genomes: Extending Ensembl Across the Taxonomic Space P
Published online 1 November 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D563–D569 doi:10.1093/nar/gkp871 Ensembl Genomes: Extending Ensembl across the taxonomic space P. J. Kersey*, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Ka¨ ha¨ ri, R. J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A. J. Vilella and A. Yates EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK Received August 14, 2009; Revised September 28, 2009; Accepted September 29, 2009 ABSTRACT nucleotide archives; numerous other genomes exist in states of partial assembly and annotation; thousands of Ensembl Genomes (http://www.ensemblgenomes viral genomes sequences have also been generated. .org) is a new portal offering integrated access to Moreover, the increasing use of high-throughput genome-scale data from non-vertebrate species sequencing technologies is rapidly reducing the cost of of scientific interest, developed using the Ensembl genome sequencing, leading to an accelerating rate of genome annotation and visualisation platform. data production. This not only makes it likely that in Ensembl Genomes consists of five sub-portals (for the near future, the genomes of all species of scientific bacteria, protists, fungi, plants and invertebrate interest will be sequenced; but also the genomes of many metazoa) designed to complement the availability individuals, with the possibility of providing accurate and of vertebrate genomes in Ensembl. Many of the sophisticated annotation through the similarly low-cost databases supporting the portal have been built in application of functional assays. -
Abstracts Genome 10K & Genome Science 29 Aug - 1 Sept 2017 Norwich Research Park, Norwich, Uk
Genome 10K c ABSTRACTS GENOME 10K & GENOME SCIENCE 29 AUG - 1 SEPT 2017 NORWICH RESEARCH PARK, NORWICH, UK Genome 10K c 48 KEYNOTE SPEAKERS ............................................................................................................................... 1 Dr Adam Phillippy: Towards the gapless assembly of complete vertebrate genomes .................... 1 Prof Kathy Belov: Saving the Tasmanian devil from extinction ......................................................... 1 Prof Peter Holland: Homeobox genes and animal evolution: from duplication to divergence ........ 2 Dr Hilary Burton: Genomics in healthcare: the challenges of complexity .......................................... 2 INVITED SPEAKERS ................................................................................................................................. 3 Vertebrate Genomics ........................................................................................................................... 3 Alex Cagan: Comparative genomics of animal domestication .......................................................... 3 Plant Genomics .................................................................................................................................... 4 Ksenia Krasileva: Evolution of plant Immune receptors ..................................................................... 4 Andrea Harper: Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees ............................................................................................................ -
The ELIXIR Core Data Resources: Fundamental Infrastructure for The
Supplementary Data: The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences The “Supporting Material” referred to within this Supplementary Data can be found in the Supporting.Material.CDR.infrastructure file, DOI: 10.5281/zenodo.2625247 (https://zenodo.org/record/2625247). Figure 1. Scale of the Core Data Resources Table S1. Data from which Figure 1 is derived: Year 2013 2014 2015 2016 2017 Data entries 765881651 997794559 1726529931 1853429002 2715599247 Monthly user/IP addresses 1700660 2109586 2413724 2502617 2867265 FTEs 270 292.65 295.65 289.7 311.2 Figure 1 includes data from the following Core Data Resources: ArrayExpress, BRENDA, CATH, ChEBI, ChEMBL, EGA, ENA, Ensembl, Ensembl Genomes, EuropePMC, HPA, IntAct /MINT , InterPro, PDBe, PRIDE, SILVA, STRING, UniProt ● Note that Ensembl’s compute infrastructure physically relocated in 2016, so “Users/IP address” data are not available for that year. In this case, the 2015 numbers were rolled forward to 2016. ● Note that STRING makes only minor releases in 2014 and 2016, in that the interactions are re-computed, but the number of “Data entries” remains unchanged. The major releases that change the number of “Data entries” happened in 2013 and 2015. So, for “Data entries” , the number for 2013 was rolled forward to 2014, and the number for 2015 was rolled forward to 2016. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences 1 Figure 2: Usage of Core Data Resources in research The following steps were taken: 1. API calls were run on open access full text articles in Europe PMC to identify articles that mention Core Data Resource by name or include specific data record accession numbers. -
Algorithms for Computational Biology 8Th International Conference, Alcob 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings
Lecture Notes in Bioinformatics 12715 Subseries of Lecture Notes in Computer Science Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA Editorial Board Members Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this subseries at http://www.springer.com/series/5381 Carlos Martín-Vide • Miguel A. Vega-Rodríguez • Travis Wheeler (Eds.) Algorithms for Computational Biology 8th International Conference, AlCoB 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings 123 Editors Carlos Martín-Vide Miguel A. Vega-Rodríguez Rovira i Virgili University University of Extremadura Tarragona, Spain Cáceres, Spain Travis Wheeler University of Montana Missoula, MT, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Bioinformatics ISBN 978-3-030-74431-1 ISBN 978-3-030-74432-8 (eBook) https://doi.org/10.1007/978-3-030-74432-8 LNCS Sublibrary: SL8 – Bioinformatics © Springer Nature Switzerland AG 2021 This work is subject to copyright. -
Microblogging the ISMB: a New Approach to Conference Reporting
Message from ISCB Microblogging the ISMB: A New Approach to Conference Reporting Neil Saunders1*, Pedro Beltra˜o2, Lars Jensen3, Daniel Jurczak4, Roland Krause5, Michael Kuhn6, Shirley Wu7 1 School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Brisbane, Queensland, Australia, 2 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America, 3 Novo Nordisk Foundation Center for Protein Research, Panum Institute, Copenhagen, Denmark, 4 Department of Bioinformatics, University of Applied Sciences, Hagenberg, Freistadt, Austria, 5 Max-Planck-Institute for Molecular Genetics, Berlin, Germany, 6 European Molecular Biology Laboratory, Heidelberg, Germany, 7 Stanford Medical Informatics, Stanford University, Stanford, California, United States of America Cameron Neylon entitled FriendFeed for Claire Fraser-Liggett opened the meeting Scientists: What, Why, and How? (http:// with a review of metagenomics and an blog.openwetware.org/scienceintheopen/ introduction to the human microbiome 2008/06/12/friendfeed-for-scientists-what- project (http://friendfeed.com/search?q = why-and-how/) for an introduction. room%3Aismb-2008+microbiome+OR+ We—a group of science bloggers, most fraser). The subsequent Q&A session of whom met in person for the first time at covered many of the exciting challenges The International Conference on Intel- ISMB 2008—found FriendFeed a remark- for those working in this field. Clearly, ligent Systems for Molecular Biology -
Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I
EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR. -
Strategic Plan 2011-2016
Strategic Plan 2011-2016 Wellcome Trust Sanger Institute Strategic Plan 2011-2016 Mission The Wellcome Trust Sanger Institute uses genome sequences to advance understanding of the biology of humans and pathogens in order to improve human health. -i- Wellcome Trust Sanger Institute Strategic Plan 2011-2016 - ii - Wellcome Trust Sanger Institute Strategic Plan 2011-2016 CONTENTS Foreword ....................................................................................................................................1 Overview .....................................................................................................................................2 1. History and philosophy ............................................................................................................ 5 2. Organisation of the science ..................................................................................................... 5 3. Developments in the scientific portfolio ................................................................................... 7 4. Summary of the Scientific Programmes 2011 – 2016 .............................................................. 8 4.1 Cancer Genetics and Genomics ................................................................................ 8 4.2 Human Genetics ...................................................................................................... 10 4.3 Pathogen Variation .................................................................................................. 13 4.4 Malaria -
Complete Vertebrate Mitogenomes Reveal Widespread Gene Duplications and Repeats
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.177956; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats Giulio Formenti+*1,2,3, Arang Rhie4, Jennifer Balacco1, Bettina Haase1, Jacquelyn Mountcastle1, Olivier Fedrigo1, Samara Brown2,3, Marco Capodiferro5, Farooq O. Al-Ajli6,7,8, Roberto Ambrosini9, Peter Houde10, Sergey Koren4, Karen Oliver11, Michelle Smith11, Jason Skelton11, Emma Betteridge11, Jale Dolucan11, Craig Corton11, Iliana Bista11, James Torrance11, Alan Tracey11, Jonathan Wood11, Marcela Uliano-Silva11, Kerstin Howe11, Shane McCarthy12, Sylke Winkler13, Woori Kwak14, Jonas Korlach15, Arkarachai Fungtammasan16, Daniel Fordham17, Vania Costa17, Simon Mayes17, Matteo Chiara18, David S. Horner18, Eugene Myers13, Richard Durbin12, Alessandro Achilli5, Edward L. Braun19, Adam M. Phillippy4, Erich D. Jarvis*1,2,3, and The Vertebrate Genomes Project Consortium +First author *Corresponding authors; [email protected]; [email protected] Author affiliations 1. The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA 2. Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA 3. The Howards Hughes Medical Institute, Chevy Chase, MD, USA 4. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA 5. Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy 6. Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia 7. -
PROGRAM CHAIR: Eben Rosenthal, MD PROFFERED PAPERS CHAIR: Ellie Maghami, MD POSTER CHAIR: Maie St
AHNS 10TH INTERNATIONAL CONFERENCE ON HEAD & NECK CANCER “Survivorship through Quality & Innovation” JULY 22-25, 2021 • VIRTUAL CONFERENCE AHNS PRESIDENT: Cherie-Ann Nathan, MD, FACS CONFERENCE/DEVELOPMENT CHAIR: Robert Ferris, MD, PhD PROGRAM CHAIR: Eben Rosenthal, MD PROFFERED PAPERS CHAIR: Ellie Maghami, MD POSTER CHAIR: Maie St. John, MD Visit www.ahns2021.org for more information. WELCOME LETTER Dear Colleagues, The American Head and Neck Society (AHNS) is pleased to invite you to the virtual AHNS 10th International Conference on Head and Neck Cancer, which will be held July 22-25, 2021. The theme is Survivorship through Quality & Innovation and the scientific program has been thoughtfully designed to bring together all disciplines related to the treatment of head and neck cancer. Our assembled group of renowned head and neck surgeons, radiologists and oncologists have identified key areas of interest and major topics for us to explore. The entire conference will be presented LIVE online July 22-25, 2021. We encourage you to attend the live sessions in order to engage with the faculty and your colleagues. After the live meeting, all of the meeting content will be posted on the conference site and remain open for on-demand viewing through October 1, 2021. Attendees may earn up to 42.25 AMA PRA Category 1 Credit(s)TM as well as earn re- quired annual part II self-assessment credit in the American Board of Otolaryngology – Head and Neck Surgery’s Continu- ing Certification program (formerly known as MOC). At the conclusion of the activity, -
Browsing Genomes with Ensembl Annotation
Browsing genomes with EnsEMBL Annotation • During recent years release of large amounts of sequence data • Raw sequence data are not so useful on its own. They are most valuable when provided with comprehensive good quality annotation CCCAACAAGAATGTAAAATCTTTAAGTGCCTGTTTTCATACTTATTTGACCACCCTATCTCTAGAATCTTGCATGATG TCTAGCCCTAGTAGGATCAAAAAATACTTACAAAGCAACTGAATAGCTACATGAATAGATGGATGAATAAATGCATG GGTGGATGGATGGATTAATGAAATCATTTATATGACTTAAAGTTTGCAGAGGAGTATCATATTTGGAAGGCAGTAAG GAAGTCTGTGTAGTCGATGGTAAAGGCAATTGGGAAGTTTGTTAGGCACAATAGGTCAAAATTTGTTTTTGAAGTCC TGTTACTTCACGTTTCTTTGTTTCACTTTCTTAAAACAGGAAACTCTTTTCTATGATCATTCTTCCAGGGCCTGGCTCT TCATCTGCAACCCAGTAATATCCCTAATGTCAAAAAGCTACTGGTTTAATTCGTGCCATTTTCAAAGAGGACTACTGA ATTCTGATGTGGCTTCAAACATTTAGGTTAGGCATATCTAATGGAGAACTTGCAGCCACACTGACTTGTAGTGAAAT ATCTATTTTGAGCCTGCCCAGTGTTGCTTAAATTGTAGTTTTCCTTGCCAGCTATTCATACAAGAGATGTGAGAAGCA CCATAAAAGGCGTTGTGAGGAGTTGTGGGGGAGTGAGGGAGAGAAGAGGTTGAAAAGCTTATTAGCTGCTGTACGG TAAAAGTGAGCTCTTACGGGAATGGGAATGTAGTTTTAGCCCTCCAGGGATTCTATTTAGCCCGCCAGGAATTAACC TTGACTATAAATAGGCCATCAATGACCTTTCCAGAGAATGTTCAGAGACCTCAACTTTGTTTAGAGATCTTGTGTGGG TGGAACTTCCTGTTTGCACACAGAGCAGCATAAAGCCCAGTTGCTTTGGGAAGTGTTTGGGACCAGATGGATTGTAG GGAGTAGGGTACAATACAGTCTGTTCTCCTCCAGCTCCTTCTTTCTGCAACATGGGGAAGAACAAACTCCTTCATCC AAGTCTGGTTCTTCTCCTCTTGGTCCTCCTGCCCACAGACGCCTCAGTCTCTGGAAAACCGTGAGTTCCACACAGAG AGCGTGAAGCATGAACCTAGAGTCCTTCATTTATTGCAGATTTTTCTTTATATCATTCCTTTTTCTTTCCTATGATACT GTCATCTTCTTATCTCTAAGATTCCTTCCAGATTTTACAAATCTAGTTTACTCATTACTTGCTTACTTTTAATCATTCT TCCCCAACTCTCTGAAGCTCTAATATGCAAAGCCTTCCTAAGGGGTGTCAGAAATTTTTAGCTTTTTAAAAGAATAAA -
The Genomic Basis of Circadian and Circalunar Timing Adaptations in a Midge Tobias S
OPEN ARTICLE doi:10.1038/nature20151 The genomic basis of circadian and circalunar timing adaptations in a midge Tobias S. Kaiser1,2,3†, Birgit Poehn1,3, David Szkiba2, Marco Preussner4, Fritz J. Sedlazeck2†, Alexander Zrim2, Tobias Neumann1,2, Lam-Tung Nguyen2,5, Andrea J. Betancourt6, Thomas Hummel3,7, Heiko Vogel8, Silke Dorner1, Florian Heyd4, Arndt von Haeseler2,3,5 & Kristin Tessmar-Raible1,3 Organisms use endogenous clocks to anticipate regular environmental cycles, such as days and tides. Natural variants resulting in differently timed behaviour or physiology, known as chronotypes in humans, have not been well characterized at the molecular level. We sequenced the genome of Clunio marinus, a marine midge whose reproduction is timed by circadian and circalunar clocks. Midges from different locations show strain-specific genetic timing adaptations. We examined genetic variation in five C. marinus strains from different locations and mapped quantitative trait loci for circalunar and circadian chronotypes. The region most strongly associated with circadian chronotypes generates strain-specific differences in the abundance of calcium/calmodulin-dependent kinase II.1 (CaMKII.1) splice variants. As equivalent variants were shown to alter CaMKII activity in Drosophila melanogaster, and C. marinus (Cma)-CaMKII.1 increases the transcriptional activity of the dimer of the circadian proteins Cma-CLOCK and Cma-CYCLE, we suggest that modulation of alternative splicing is a mechanism for natural adaptation in circadian timing. Around the new or full moon, during a few specific hours surround- Our study aimed to identify the genetic basis of C. marinus adaptation ing low tide, millions of non-biting midges of the species C. -
ALEXA: a Microarray Design Platform for Alternative Expression Analysis
CORRESPONDENCE expression of alternative mRNA isoforms in 5-fluorouracil (5-FU)- ALEXA: a microarray design platform for sensitive and resistant colorectal cancer cell lines5 and compared alternative expression analysis the results to those from the Affymetrix ‘GeneChip Human Exon 1.0 ST’ array (see Supplementary Results, Supplementary Fig. 2 To the editor: Eukaryotic genomes are predicted to contain about and Supplementary Table 2 online). Genes and exons differentially 7,000–29,000 genes1. Each of these genes may be alternatively expressed between 5-FU–sensitive and resistant cells were identi- processed to produce multiple distinct mRNAs by alternative fied by both platforms (with significant overlap), but ALEXA arrays transcript initiation, splicing and polyadenylation (collectively provided additional information on the connectivity and boundar- referred to as alternative expression). Although analysis of avail- ies of exons (Table 1). Furthermore, alternative expression events able transcript resources indicates that up to ~75% of genes are identified by ALEXA were significantly enriched for known alterna- alternatively processed, most microarray expression platforms tive expression events represented in publicly available mRNA and cannot detect alternative transcripts2. expressed sequence tag (EST) databases (Supplementary Results methods Proof-of-principle experiments have described the use of oli- and Supplementary Data 1 online). Finally, we demonstrated the gonucleotide microarrays to profile transcript isoforms gener- advantage of the ALEXA approach by identifying several differen- ated by alternative expression, but resources to create such arrays tially expressed known and predicted isoforms with potential rele- are lacking3,4. To address this limitation we created a microarray vance to 5-FU resistance (Supplementary Fig. 3 and Supplementary .com/nature e design platform for alternative expression analysis (ALEXA), Tables 3 and 4 online).