2022 Workshop

Held on Wednesday, February 16, 2022

Co-Chairs:	Huaijun Zhou, University of California, Davis, USA. Elisabetta Giuffra, INRA Laboratory of Animal Genetics and Integrative Biology Genetics Immunity and Health, France Chris Tuggle, Iowa State University, USA. Peter Harrison, European Bioinformatics Institute EMBL EBI, United Kingdom
Time:	7:00 AM – 1:30 PM PST (3:00 pm – 9:30 pm GMT)
Location:	Virtual.

Program

Zoom
Recordings

7:00 AM

Welcoming Remarks and Introduction

7:10 AM

EuroFAANG: empowering the future of FAANG to Fork research and infrastructure in Europe and beyond. Emily Clark, University of Edinburgh, UK, Elisabetta Giuffra, INRAE, France, Peter Harrison, EMBL-EBI, UK

7:30 AM

Midterm progress of H2020 GENE-SWitCH: Annotation of pig and chicken genomes during development. Elisabetta Giuffra, Ole Madsen, and GENE-SWitCH Consortium

7:50 AM

Towards an integrated functional annotation of the bovine genome for the BovReg project. Gabriel Costa, Christ Kuhn, Carole Charlier, Mazdak Salvati and Emily Clark

8:10 AM

Genome functional annotation in the major European farmed fish species: Progress and insights made by the H2020 AQUA-FAANG project. Matthew Kent, Dan Macqueen, Sigbjørn Lien, on behalf of the AQUA-FAANG consortium

8:30 PM

USDA Pig FAANG Resources: Progress and Insight toward Understanding Transcriptional Regulation in Tissues and Cells. Christopher K. Tuggle, Iowa State University, USA

8:50 PM

USDA Bovine FAANG Resources: Progress on the Functional Annotation of the Bovine Genome. Huaijun Zhou, University of California, Davis, USA

9:10 PM

USDA Chicken FAANG effort. David Hawkins, University of Washington School of Medicine, USA

9:30 AM

Poster session (See below for a List of Abstracts)

10:15 AM

Lightening talks

Eleonora Cappelletti, Italy, Epigenetic characterization of horse centromeric domains in different tissues and individuals from the FAANG equine consortium
Alex Caulton, New Zealand, Systematic evaluation of methylation profiling assays
Jingjin Li, China, Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome
Loan Nguyen, Australia, An epigenetic aging clock for cattle using portable long read sequencing technology
Andreas Pfenning, USA, Applying machine learning prediction of regulatory elements to identify trait-associated loci within the human population and across species

10:45 AM

Ovine FAANG Update. Brenda M. Murdoch, University of Idaho, USA

11:05 AM

Equine FAANG: Off to the Races. Jessica Petersen, University of Nebraska, Theodore Kalbfleisch, University of Kentucky, USA

11:25 AM

An update on the rainbow trout genome annotation. Rafet Al-Tobasei, Middle Tennessee State University, Mohamed Salem, University of Maryland, USA

11:35 AM

A new perspective on the immune cell atlas of the chicken. Wesley Warren, University of Missouri, USA

11:45 PM

FarmGTEx-Pig: a comprehensive catalogue of regulatory variants in the pig transcriptome. Lingzhao Fang, University of Edinburgh, UK

12:05 PM

Using variants with functional significance to improve genome-wide mapping and prediction of complex traits. Ruidong Xiang, Ed. Breen, C. Prowse-Wilkins, A.J. Chamberlain, M.E. Goddard, University of Melbourne, Australia

12:25 PM

Implementing the next phase of FAANG. (Round Table Discussion).

1:30 PM

Adjourn

List of posters for poster session (9:30 - 10:15AM)
		Abstract	Poster
1	Jingjin Li, Yue Xiang, Lu Zhang, Xiaolong Qi, et al. Enhancer-promoter interaction maps provide ...
2	Dailu Guan, on the behalf of FarmGTEx et al. The Chicken Genotype-Tissue Expression ...
3	Jinghui Li, Dailu Guan, Michelle M. Halstead, et al. Transcriptome Annotation of 17 Porcine Tissues ...
4	Loan T. Nguyen, Ben J. Hayes, Mehrnush Forutan, et al. An epigenetic aging clock for cattle using ...
5	Mehrnush Forutan, Christy J Vander Jagt, et al. Genome wide analysis of bovine enhancers and ...
6	Mazdak Salavati, Richard Clark, Doreen Becker, et al. Transcriptome analysis of crossbred and purebred ...
7	Liqi An, Ying Wang, Zhangyuan Pan, Dailu Guan, et al. Functionally Validate Enhancers in the Chicken ...
8	Ying Wang, Zhangyuan Pan, Liqi An, Ganrea et al. Systematic characterization of chromatin dynamics ...
9	Daoyuan Wang, Renzhuo Kuang, Honghong Zhou, et al. Multi-omics data reveal transcriptomes and ...
10	Li Rong, Jinping Cai, Jiuhong Nan, Sendong Yang, et al. Genome functional annotation of organs related to ...
11	Zhangyuan Pan, Joana Damas, Dailu Guan, Xiaoqin et al. Comparative Epigenomic Annotation of Regulatory ...
12	Laura Morel, Peter W. Harrison, Guillaume et al. VizFaDa: Visualisations of FAANG ...
13	Akshatha Nayak, Alexey Sokolov, Yogmatee Roochun, et al. The FAANG Data Portal: Infrastructure to Enable ...
14	S. Chalabi, L. Loonen, W. Lakhal, J. Lluch, H. et al. Influence of maternal diet on the liver and ...
15	Ryan J. Corbett, Haibo Liu, Timothy P.L Smith, et al. Allele-biased DNA methylation is widespread in ...
16	Irene M. Kaplow,, Daniel E. Schaffer, BaDoi N. et al. Applying machine learning prediction of ...
17	Pengxin Yang, Lance Daharsh, Juber Herrera Uribe, et al. Porcine PBMC chromatin accessibility at single ...
18	Eleonora Cappelletti, Francesca M. Piras, Lorenzo et al. Epigenetic characterization of horse centromeric ...
19	Alex Caulton, Rudiger Brauning, Ken G. Dodds, et al. Systematic evaluation of DNA methylation ...
20	Alexa M. Barber, Nicole B. Kingsley, Sichong et al. Identifying Tissue-Specific Regulatory Regions in ...
21	Jose EspinosaCarrasco, Bjrn Langer, Andreia et al. nf-core as the standard for BovReg reference ...