PAG XXVI - Plant & Animal Genome Conference 2018
PAG XXVI - Plant & Animal Genome Conference 2018
If you are going to the Plant and Animal Genome conference (PAG XXVI) in January 2018, come say hello to everyone attending from EMBL-EBI! You'll find us at the at booth 405 and at the 'Genome annotation resources at EMBL-EBI' workshop. This session will introduce a number of key bioinformatics resources (either hosted at, or contributed to by, EMBL-EBI) that are freely available.
What can you use EMBL-EBI services for?
- Access our freely-available datasets
- Analyse your data with open-source tools
- Hone your skills in our training programme
- Share your data to inspire future research
|Friday, 12 January|
|14:38 - 14:53||The Functional Annotation of Animal Genomes (FAANG): Establishing Metadata Standards, Validation and the FAANG Data Portal (W442)||Peter Harrison||Sunrise Meeting - House|
|Saturday, 13 January|
|10:15 - 10:30||Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Livestock? (W168)||Adam Frankish||San Diego|
|13:35 - 13:50||Ensembl Sscrofa11.1 Genome Annotation (W974)||Thibaut Hourlier||Royal Palm Salon 1-2|
|14:40 - 14:55||Update: HGNC - nomenclature of the horse genome (W344)||Beth Yates||Royal Palm Salon 5-|
|Sunday, 14 January|
|8:00 - 9:00||Ensembl and Ensembl Genomes (W495)||Ben Moore||California|
|9:00 - 9:30||Manual Genome Annotation in Ensembl (W496)||Jane Loveland||California|
|9:30 - 9:50||The Transition of Non-Human Genetic Variation Data from dbSNP to EVA (W498)||Gary Saunders||California|
|10:20 - 10:40||The Vertebrate Gene Nomenclature Committee (VGNC) – Standardising Gene Names in Vertebrates(W499)||Susan Tweedie||California|
|10:40 - 11:10||Expert Curation of Proteins in UniProtKB/Swiss-Prot (W500)||Damien Lieberherr||California|
|11:10 - 11:30||Accessing the Gene Ontology, a Resource for Whole Genome Analysis (W501)||Sandra Orchard||California|
|11:30 - 12:00||Adding Information to Plant and Animal Proteomes in UniProt through Automatic Annotation (W502)||Kate Warner||California|
|12:00 - 12:40||ArrayExpress and Expression Atlas: Tools for Archiving, Searching and Visualising Functional Genomics Data at EMBL-EBI (W503)||Suhaib Mohammed||California|
|14:50 - 15:10||RNAcentral: A Comprehensive Collection of Non-Coding RNA Sequences||Blake Sweeney||Royal Palm Salon 3-4|
|16:30 - 17:00||Demo: RNAcentral: A Comprehensive Collection of Non-Coding RNA Sequences||Blake Sweeney||Booth 405|
|Monday, 15 January|
|10:00 - 10:30||Demo: Accessing the Gene Ontology||Sandra Orchard||Booth 405|
|10:30 - 11:00||Demo: Complete Proteomes in UniProtKB||Kate Warner||Booth 405|
|12:55 - 13:15||Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Sheep? (W621)||Jane Loveland||Towne - Meeting House|
|18:25 - 18:40||Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Goat? (W607)||Adam Frankish||Sunrise - Meeting House|
|15:00 - 16:00||Q&A: The European Variation Archive at EMBL-EBI||Gary Saunders||Booth 405|
|Tuesday, 16 January|
|9:30 - 10:30||Demo: Ensembl and Ensembl Genomes||
Ben Moore, Thibaut Hourlier
and Guy Naamati
|13:30 - 13:50||
Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Wheat? (W647)
|Jane Loveland||Pacific Salon 3|
|14:30 - 14:50||Integrating and Displaying Plant Gene Expression in Expression Atlas (W561)||Laura Huerta||California|
|14:50 - 15:10||Scaling Comparative Analysis across the Taxonomic Space (W562)||Paul Kersey||California|
Global Internet & Intranet Services Manager.
Dominic holds a PhD in Medical Informatics/AI from the University of Wales Institute of Science and Technology and a postgraduate diploma in IT Project management (OU). He is a founding director of the International Society for Computational Biology.
Peter leads the Genome Analysis team that utilises whole genome analyses to reveal genomic function. The team includes scientists and software developers that focus on the regulatory components, core infrastructure and web applications for the Ensembl project (https://www.ensembl.org/), a world renowned browser for vertebrate genomes. He has a particular focus on developing data resources to support animal agriculture and biodiversity genomics, looking to engage more extensively with external academic and industrial collaborators. He also leads the development of the data portal for the Darwin Tree of Life project that aims to sequence the genomes of all 70,000 species of eukaryotic organisms in Britain and Ireland.
Peter joined EMBL-EBI in 2015, having previously worked as a postdoc at University College London and University of Oxford on the transcriptomics and evolution of sexual selection in birds. Peter obtained his PhD from the University of York, where he investigated bacterial secondary replicons through comparative genomics. He previously obtained an MRes in Bioinformatics from University of York and an MA in Biological Sciences from University of Oxford.
Thibaut is the Principal GeneBuild Developer in EMBL-EBI’s Vertebrate Genomics team. He graduated from the Université Louis Pasteur, Strasbourg in 2007 with a Master in Bioinformatics. He started working with sunflowers at the Laboratoire des Interactions Plantes Microorganismes (LIPM) in Toulouse, then moved to vertebrate annotation when he joined the Ensembl project in 2010. He was deeply involved in the annotation of the sheep genome published in 2014, the annotation of the tilapia genome published in 2014, and in the annotation of the draft genome sequence of the ferret.
Laura Huerta Martinez
Laura works as a Senior Scientific Curator to improve the content of functional genomics data in Expression Atlas. She is involved in developing and implementing metadata standards with a particular interest on data integration through ontology annotation. She manages training activities, delivering courses on functional genomics resources at EMBL-EBI and worldwide. She also interacts with software developers to improve user experience of Expression Atlas website. Laura joined EMBL-EBI in 2015 after receiving her PhD in Molecular Biology from the Polytechnic University of Valencia, focused on studying plant development regulated by hormones through the generation and analysis of transcriptomics data.
Paul Kersey leads the Non-vertebrate Genomics team, which provides services related to the genomes of bacteria, protists, fungi, plants and animals, mainly utilising the Ensembl software platform. The team maintains the Ensembl Genomes resource, which operates as a series of collaborations with community-focused groups in individual domains. Major collaborative efforts include VectorBase (for invertebrate vectors of human pathogens), WormBase (for nematodse), Gramene (for plants) and PhytoPath (for plant pathogens). We also contribute to major European infrastructure projects including ELIXIR and INFRAVEC. Previously we have coordinated the Microme and transPLANT projects.
Paul received his PhD from the University of Edinburgh in 1995 and has been at EMBL since 1999, working on a variety of resources for completely sequenced genomes (and their corresponding proteins) including UniProt, GOA, Integr8, and IPI, prior to the launch of Ensembl Genomes in 2009.
PhD University of Edinburgh 1992. Postdoctoral work at University of Edinburgh and MRC Human Genetics Unit, Edinburgh. At EMBL-EBI since 1999.
Suhaib oversees development and manages data production pipelines, and works on various projects in Expression Atlas. Before joining EMBL-EBI in 2017, Suhaib worked at the University of Glasgow as a Bioinformatician closely with pharma industry on a research collaboration for two years in Acute Kidney Injury projects. Previously, Suhaib worked in biopharmaceutical industry as biomodelling scientist before he received his PhD from the University of Exeter in 2016, and MRes from the University of Leeds in 2010 in Bioinformatics arena.
Ben joined Ensembl as an Outreach Officer in September 2015. As a member of the Outreach Team he delivers workshops, answers helpdesk queries, creates training materials and help pages, and manages social media. Before starting at EMBL-EBI, Ben obtained his PhD in Biological Sciences from the MRC Laboratory of Molecular Biology at the University of Cambridge. He has previously hosted the BlueSci science radio show and now organises the annual Cambridge Pint of Science festival.
Guy works as a Senior Bioinformatician on Ensembl Plants, an integrative platform for accessing and comparing plant data for over 50 species. His main focus is on wheat as part of the Designing Future Wheat research program, working on developing the next generation of wheat germplasm.
Guy has been at EMBL-EBI since October 2015, and before that he worked in Evogene Ltd, a crop genomics company focused on improving crop traits such as yield and stress resistance. He holds a BSc and MSc from the Hebrew University of Jerusalem in Computer Science and Computational Biology.
Sandra Orchard is Team Leader for Protein Function Content, with a strong background in protein annotation. Her team is primarily responsible for the curation of UniProt at EMBL-EBI, and annotation of the Gene Ontology. Sandra and her team support professional training in data resources for exploring protein function, sequence analysis, interactions and pathways. She is a member and Treasurer of the Executive Committee of the International Society for Biocuration.
Sandra's team applies advanced methods for ensuring the accuracy and quality of the universal protein resource, UniProt, carrying out manual annotation and producing the rules for automated annotation. They also create and maintain value-added interfaces for exploring protein data, for example the Enzyme Portal and Complex Portal.
Gary Saunders is a Curator of the European Variation Archive and related resources: the Database of Genomics Variants archive and the European Genome-phenome Archive. It is Gary’s responsibility to manage the data within these resource(s) to ensure accuracy, clarity and discoverability. Prior to holding this position, Gary was a curator of the GENCODE project, which provides the gene set for the Ensembl genome browser. Gary moved into curation following the completion of his PhD at the University of Glasgow, where he employed a variety of phylogenomic and bioinformatic methods to investigate drug resistance in nematode parasites of human and livestock importance.
Blake Sweeney is the Project Leader for RNA resources: RNAcentral – a comprehensive database of non-coding RNA sequences, and Rfam – a database of non-coding RNA families. He joined EMBL-EBI in 2017 to work on RNAcentral and prior to that he completed his PhD at Bowling Green State University under Dr. Neocles Leontis. There he managed the data pipeline and explored quality metrics of RNA 3D structures.
Susan joined the HUGO Gene Nomenclature Committee (HGNC) at EMBL-EBI in 2014 as a Nomenclature Advisor. She is part of the curation team responsible for approving unique symbols and names for vertebrate loci, including protein coding genes, ncRNA genes and pseudogenes. Before joining EMBL-EBI, Susan was a curator at FlyBase, the Drosophila model organism database, where she was responsible for annotating gene function using the Gene Ontology. She obtained her PhD in molecular biology from University College London (1990) and her MRes in Bioinformatics from the University of York (2001).
Bethan is a Scientific Programmer for the HUGO Gene Nomenclature Committee (HGNC) at EMBL-EBI. She is responsible for developing and maintaining data production pipelines, databases and web portals for vertebrate nomenclature data. Prior to joining EMBL-EBI in 2013, she worked at the Wellcome Sanger Institute as a web developer on the Ensembl project. Bethan obtained an MSc in Bioinformatics at the University of Manchester and a BSc in Biochemistry from the University of Leeds.