Plant and Animal Genomes 2017

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Plant and Animal Genomes 2017

Saturday 14 Wednesday 18 January 2017

If you are going to the Plant and Animal Genomes conference (PAG XXV) in January 2017, 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 the 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. The featured resources have been selected as being key to genome annotation and analysis.

Please visit us if you are interested in:

  • finding out how EMBL-EBI's data resources can help you make the most of your biological data
  • bioinformatics training (both hands-on training courses and online learning)
  • careers, PhDs and postdoc positions
  • joining our industry programme

Programme

The full programme for PAG XXV is on the conference website. Here, we highlight contributions from EMBL-EBI staff.

Workshops 

Saturday, 14 November 

Connecting Crop Phenotype Data
10:30 AM - 12:40 PM; Golden Ballroom
transPLANT integrated search usingApache SolrPaul Kersey

Interoperability and Federation Across Bioinformatic Platforms and Resources
10:30 AM - 12:40 PM; California Room
Guiding users through diverse, dispersed data ecosystemsPaul Kersey

Sunday, 15 January 

Genome annotation resources at the EBI
8:00 AM - 12:30 PM; California Room

  • Ensembl and Ensembl Genomes - Helen Sparrow
  • VEGA - Jane Loveland
  • HGNC (HUGO Gene Nomenclature Committee) - Elspeth Bruford
  • The European Variation Archive at EMBL-EBI: a home for genetic variation data - Gary Saunders
  • Submitting data to EMBL-EBI resources - Laura Clarke 
  • Expression Atlas - a curated resource for ‘omics data - Amy Tang
  • Omics-DI – searing the Omics space - Sandra Orchard
  • Towards comprehensive coverage and annotation of proteome space - Ramona Britto
  • The EMBL-EBI Industry programme and ontologies for agriculture - Dominic Clark

Monday, 16 January 

Functional Annotations of Animal Genomes (FAANG)
6:10 PM - 8:20 PM; Golden West
Updates on the FAANG M&DS Committee and the FAANG DCC at EMBL-EBI Laura Clarke

Tuesday, 17 January 

Gramene Project
1:30 PM - 3:40 PM; California room
Plant gene expression in EMBL-EBIExpression Atlas - Maria Keays

Posters 

Monday, 16 January

Plant gene expression in EMBL-EBI Expression Atlas - Maria Keays and Amy Tang

The Functional Annotation of Animal Genomes (FAANG) Project: Metadata, data sharing and the FAANG data portal - Peter Harrison

Towards comprehensive coverage and annotation of proteome space - Ramona Britto 

Speakers


Paul Kersey

Paul Kersey

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.


Helen Sparrow

Helen Sparrow

Helen joined Ensembl as an Outreach Officer in September 2015. As a member of the Outreach Team she delivers workshops, answers helpdesk queries, creates training materials and help pages, and manages social media. Before starting at EMBL-EBI, Helen did her PhD in environmental biotechnology at the University of York, then worked as the community manager at academia.edu and as a museum educator at the California Academy of Sciences.

Jane Loveland

Jane Loveland

Jane is part of the HAVANA management team at the  Wellcome Trust Sanger Institute and works on the manual annotation of human, mouse and zebrafish genomes, and latterly the swine and rat genomes.

Jane has a background in virus research, plant biochemisty and molecular biology.  Whilst working in the photosynthesis group at IACR Rothamsted she completed her PhD (Lancaster University), investigating the biochemistry and molecular biological aspects of inhibitors of Rubisco (CA1Pase). After leaving bench science Jane moved into bioinformatics, working as a computational molecular biology specialist for the BBSRC, providing teaching and support for molecular biology software packages for 8 BBSRC Institutes. Jane joined the Sanger Institute in 2002 as part of the HAVANA group. As part of the HAVANA management team she has been involved in a number of major international collaborations, including generating the GENCODE annotation for the ENCODE project, collaborating with NCBI/UCSC/Ensembl/HGNC and MGI to produce the CCDS annotation and as a co-ordinator for the Immune Response Annotation Group for the swine community. Recently she has been leading a community annotation initiative with the rat genome database (RGD). She has been the co-ordinator of the Open Door Workshops since 2002, and presents human, mouse and zebrafish workshops around the world.


Elspeth Bruford

Gary Saunders

Gary Saunders

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.


Laura Clarke

Laura Clarke

Laura Clarke leads EMBL-EBI's efforts to build the Data Coordination Platform for the Human Cell Atlas (HCA). The HCA team at EMBL-EBI is primarily responsible for developing the ingest infrastructure and supporting its use. The ingest infrastructure writes data and metadata into the HCA Data Coordination Platform enabling its analysis and accessibility by the community.

Laura studied bioinformatics at Leeds University before joining the Ensembl project in 2001 at the height of the Human Genome Project. She created the primary gene sets associated with the rat, macaque and platypus genomes before moving to EMBL-EBI to establish data coordination for the 1000 Genomes Project. Since then Laura has led data coordinaton efforts for many large consortia such as Blueprint, HipSci and FAANG and continues in these efforts for the Human Cell Atlas.


Amy Tang

Amy Tang

Originally trained as a geneticist, Amy joined the functional genomics team in 2011 as a curator and Perl developer for ArrayExpress. She now manages and delivers training for the team, curates content for ArrayExpress and Expression Atlas, and collaborates with software developers on the design of ArrayExpress and Expression Atlas user interfaces. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for organisms including mouse, rat, gorilla, cow and horse. She holds a PhD in mouse epigenetics (2006) and a MSc in Bioinformatics and Systems Biology (2008), both from Imperial College London.


Sandra Orchard

Sandra Orchard

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.


Ramona Britto

Ramona Britto

Ramona Britto joined the Protein Function Content team at EMBL-EBI in 2012 as a biocurator. In her current role, she works closely with the Protein Function Development team, her biocurator colleagues and international collaborators to define and enhance the content and representation of proteomes in UniProt. Prior to this, she worked on the genomics of reproduction in Rennes, France where she obtained a PhD.


Dominic Clark

Dominic Clark

PhD in Medical Informatics, University of Wales, 1988. Imperial Cancer Research Fund, 1987–1995. UK Bioinformatics Manager, GlaxoWellcome R&D Ltd., 1995–1999. Vice President, Informatics, Pharmagene, 1999–2001. Managing Consultant, Sagentia Ltd., 2001-2009. At EMBL-EBI since 2006 (secondment 2006-2009).


Maria Keays

Maria Keays

 

Maria Keays joined the Functional Genomics group at EMBL-EBI in 2011. She works on various aspects of Expression Atlas and ArrayExpress, including data analysis, data production, and visual content. She has an MSc in Bioinformatics from the University of Leicester, and gained a PhD in evolutionary biology from the University of St. Andrews in 2011.

Exhibitors


Frank O’Donnell

Frank O’Donnell

Before joining EMBL-EBI in 2010, Frank worked for Manchester University and Astra Zeneca as in organising events and conferences in the UK and abroad. Frank joined the Training Team to help organise courses, off-site workshops and conference exhibitions. He also handles logostics for conference exhibitions.


Sandra Orchard

Sandra Orchard

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.


Helen Sparrow

Helen Sparrow

Helen joined Ensembl as an Outreach Officer in September 2015. As a member of the Outreach Team she delivers workshops, answers helpdesk queries, creates training materials and help pages, and manages social media. Before starting at EMBL-EBI, Helen did her PhD in environmental biotechnology at the University of York, then worked as the community manager at academia.edu and as a museum educator at the California Academy of Sciences.

Gary Saunders

Gary Saunders

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.


Amy Tang

Amy Tang

Originally trained as a geneticist, Amy joined the functional genomics team in 2011 as a curator and Perl developer for ArrayExpress. She now manages and delivers training for the team, curates content for ArrayExpress and Expression Atlas, and collaborates with software developers on the design of ArrayExpress and Expression Atlas user interfaces. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for organisms including mouse, rat, gorilla, cow and horse. She holds a PhD in mouse epigenetics (2006) and a MSc in Bioinformatics and Systems Biology (2008), both from Imperial College London.


Laura Clarke

Laura Clarke

Laura Clarke leads EMBL-EBI's efforts to build the Data Coordination Platform for the Human Cell Atlas (HCA). The HCA team at EMBL-EBI is primarily responsible for developing the ingest infrastructure and supporting its use. The ingest infrastructure writes data and metadata into the HCA Data Coordination Platform enabling its analysis and accessibility by the community.

Laura studied bioinformatics at Leeds University before joining the Ensembl project in 2001 at the height of the Human Genome Project. She created the primary gene sets associated with the rat, macaque and platypus genomes before moving to EMBL-EBI to establish data coordination for the 1000 Genomes Project. Since then Laura has led data coordinaton efforts for many large consortia such as Blueprint, HipSci and FAANG and continues in these efforts for the Human Cell Atlas.

Town and Country Hotel
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Twitter: #PAGXXV