Summary- Interesting insight from Birney; next step is reports from session to Scientific Committee where they will outline a white paper
Date: Saturday, January 11, 2014 Time: 8:00 AM-6:10 PM Room: Royal Palm Salons 3-4 Organizer: Steven Roberts 8:00 AM Welcoming Remarks
8:15 AM W036 A Genome Map for a Species with Male Tetrasomic Inheritance, Coho Salmon, and Location of Quantitative Trait Loci Miyako Kodama, University of Washington; Marine Brieuc, University of Washington; Robert Devlin, Fisheries and Oceans Canada; Jeff Hard, Northwest Fisheries Science Center; Kerry Naish, University of Washington
8:30 AM W037 Genomic Regions Potentially Under Selection in a Hybridized Population of Westslope Cutthroat Trout (Oncorhynchus clarkii Lewisi) Daniel P. Drinan, University of Washington
8:45 AM W038 Transcriptome Assembly and Digital Gene Expression Atlas of the Rainbow Trout Bam D Paneru, Middle Tennessee State University
9:00 AM W039 Genomic Selection Applied to Pisciricketsia salmonis Resistance in Chilean Atlantic Salmon Victor Martinez, FAVET-INBIOGEN. University of Chile
9:15 AM W040 Bulk Segregant RNA-Seq Reveals Expression and Positional Candidate Genes and Allele-Specific Expression for Disease Resistance Against Enteric Septicemia of Catfish Ruijia Wang, The Fish Molecular Genetics and Biotechnology Laboratory; Luyang Sun, The Fish Molecular Genetics and Biotechnology Laboratory; Lisui Bao, The Fish Molecular Genetics and Biotechnology Laboratory; Jiaren Zhang, The Fish Molecular Genetics and Biotechnology Laboratory; Yanliang Jiang, The Fish Molecular Genetics and Biotechnology Laboratory; Jun Yao, The Fish Molecular Genetics and Biotechnology Laboratory; Lin Song, The Fish Molecular Genetics and Biotechnology Laboratory; Jianbin Feng, The Fish Molecular Genetics and Biotechnology Laboratory; Shikai Liu, The Fish Molecular Genetics and Biotechnology Laboratory; John Liu, The Fish Molecular Genetics and Biotechnology Laboratory
9:30 AM W041 Dietary Conditioning in Poultry By Limiting Specific Nutrients Early in Life Involves Altered DNA Methylation
10:20 AM Break
10:35 AM W042 How Aquaculture Research and Development Could Contribute to Food Security in Developing Countries: Finding Solutions to Agricultural Problems That Affect People Everyday, from Field to Table
10:50 AM W043 Genome Dynamism in a Basal Vertebrate: Challenges and Biological Implications Chris Amemiya, Benaroya Research Institute; Jeramiah J. Smith, University of Kentucky
11:40 AM Lunch
1:10 PM W044 Developing Molecular Markers for Population and Quantitative Genetic Analysis of Seriola lalandi Using Transcriptome Sequencing Victor Martinez, FAVET-INBIOGEN. University of Chile; Alok Patel, FAVET-INBIOGEN. UNIVERSIDAD DE CHILE
1:25 PM W045 A Comprehensive Methylome for Crassostrea gigas Provides Insight into the Role of DNA Methylation in Bivalves Mackenzie Gavery, University of Washington; Steven Roberts, University of Washington
1:40 PM W046 Evaluating the Effectiveness of Managed Gene Flow to Reduce Adaptation to Captivity in Supportive Breeding Programs Charles D. Waters, University of Washington; Marine S. O. Brieuc, University of Washington; Curtis M. Knudsen, Oncorh Consulting; David E. Fast, Yakama Nation Fisheries; Jeff Hard, Northwest Fisheries Science Center; Kenneth I. Warheit, Washington Department of Fish and Wildlife; Kerry Naish, University of Washington
1:55 PM W047 A Dense Linkage Map for Chinook Salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence Following an Ancestral Whole Genome Duplication Event Marine S.O. Brieuc, University of Washington; Charles D. Waters, University of Washington; James E. Seeb, University of Washington; Kerry A. Naish, University of Washington
2:10 PM W048 Microbial and Tissue-Specific Regulation of Gene Transcription in the Zebrafish Intestine John F. Rawls, Duke University
3:00 PM Intermission
3:15 PM W049 Tissue‐Specific Alternative Splicing in Rainbow Trout Rafet Al-Tobasei, Middle Tennessee State University
3:30 PM W050 Atlantic Salmon Liver Transcriptome Response to Diets Containing Camelina Products Xi Xue, Memorial University of Newfoundland; Tiago S. Hori, Memorial University of Newfoundland; Marije Booman, Memorial University of Newfoundland; Stefanie M. Hixson, Memorial University of Newfoundland; Christopher C. Parrish, Memorial University of Newfoundland; Kim Johnstone, Genome Atlantic; Derek M. Anderson, Dalhousie Agricultural Campus; Matthew L. Rise, Memorial University of Newfoundland
3:45 PM W051 SNP Discovery in Blue Catfish (Ictalurus furcatus) Populations via Genotyping–by-Sequencing Eric Peatman, Auburn University; Chao Li, Auburn University; Wilawan Thongda, Auburn University; Benjamin Beck, USDA-ARS Stuttgart National Aquaculture Research Center; Brian Bosworth, USDA-ARS Warmwater Aquaculture Research Unit; Geoff Waldbieser, USDA-ARS Warmwater Aquaculture Research Unit
4:00 PM W052 Characterization of Rainbow Trout (Oncorhynchus mykiss) Spleen Transcriptome and Identification of Immune-Related Genes Ali R. Ali, Middle Tennessee State University
4:15 PM W053 Influence of Camelina Oil-Containing Diets on the Atlantic Cod Antiviral Immune Transcriptome and Elovl Family Transcript Expression Matthew L. Rise, Memorial University of Newfoundland; Marije Booman, Memorial University of Newfoundland; Xi Xue, Memorial University of Newfoundland; Qingheng Xu, Memorial University of Newfoundland; Stefanie M. Hixson, Memorial University of Newfoundland; Christopher C. Parrish, Memorial University of Newfoundland; Kim Johnstone, Genome Atlantic; Charles Y. Feng, Memorial University of Newfoundland; Derek M. Anderson, Dalhousie Agricultural Campus
4:30 PM NRSP-8 Bioinformatics coordinator - Reecy
4:45 PM AgEncode
This session will introduce a number of key bioinformatic resources either hosted at, or contributed to by, the European Bioinformatics Institute and made freely available to the user community. The featured resources have been selected as being key to genome annotation and analysis. Date: Sunday, January 12, 2014
Time: 8:00 AM-12:40 PM Room: California Organizer: Sandra Orchard 8:00 AM W357 Introduction to Public Domain Resources at the EBI Sandra Orchard, EMBL-EBI
8:15 AM W358 Genome Resources at the EBI - Ensembl and Ensembl Genomes Bert Overduin, European Bioinformatics Institute (EMBL-EBI); Ensembl Team, N/A; Ensembl Genomes Team, N/A
9:15 AM W359 The Vertebrate Genome Annotation Database (VEGA) and the Use of Otterlace As a Community Annotation Tool Jane Loveland, Wellcome Trust Sanger Institute
9:45 AM W360 Expert Curation in UniProtKB Michel Schneider, Swiss Institute of Bioinformatics; UniProt Consortium, n/a
10:15 AM W361 The UniProt-Gene Ontology Annotation (UniProt-GOA) Project: Central Resource for Multi-Species GO Annotation Rachael Huntley, EMBL-EBI
10:45 AM W362 Automatic Annotation of New Genomes Sandra Orchard, EMBL-EBI
11:15 AM W363 Functional Genomics Data and Expression look-up tools: ArrayExpress and new Expression Atlas Amy Tang, EMBL-European Bioinformatics Institute
11:45 AM W364 Train Online: Web-Based Learning for Life Scientists Katrina Costa, EMBL-EBI
Genome annotations Stand 303
Bert overduin Genome resources Ensembl AND ensembl Genome
Oyster genome browser http://metazoa.ensembl.org/Crassostrea_gigas/Info/Index
Rest api There is one for ensembl gen Consul Gets url Awesome Try
Train online !!!
Goa annotations
Extended go annotation new
amigo blast Blast2go
Interproscan
Neurolex . org
Quick go should have slim
interpro and interproscan Hyak
Array express
Co- expression Epistatic network
Programattic access at Array express Rest
Networks. Toni Reverter Pcit algorithm Seems like tf is important
Animal tf DATABASE http://www.bioguo.org/AnimalTFDB/
Gorilla
For above poster https://github.com/jguhlin/UTR-import
from IPython.display import YouTubeVideo
#An overview of the EmbryoGENE platforms for those visiting my PAG XXII poster in my absence.
YouTubeVideo('lZnnq1APceI')
High resolution figures http://www.flickr.com/photos/112046442@N02/
from IPython.display import YouTubeVideo
# A presentation of the EmbryoGENE transcriptomic platform by Dr Claude Robert.
YouTubeVideo('ble2V8d5WdQ')
from IPython.display import YouTubeVideo
# A presentation of the EmbryioGENE epigenetic platform by Dr Claude Robert.
YouTubeVideo('MVMQAMiihpw')