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Functional Annotation of ANimal Genomes (FAANG) Project — A coordinated international action to accelerate Genome to Phenome

Publications

•   Landmark Papers:
  2015
  • Andersson Leif, Archibald Alan L, Bottema Cynthia D, Brauning Rudiger, Burgess Shane C, Burt Dave W, Casas Eduardo, Cheng Hans H, Clarke Laura, Couldrey Christine, Dalrymple Brian P, Elsik Christine G, Foissac Sylvain, Giuffra Elisabetta, Groenen Martien A, Hayes Ben J, Huang LuSheng S, Khatib Hassan, Kijas James W, Kim Heebal, Lunney Joan K, McCarthy Fiona M, McEwan John C, Moore Stephen, Nanduri Bindu, Notredame Cedric, Palti Yniv, Plastow Graham S, Reecy James M, Rohrer Gary A, Sarropoulou Elena, Schmidt Carl J, Silverstein Jeffrey, Tellam Ross L, Tixier-Boichard Michele, Tosser-Klopp Gwenola, Tuggle Christopher K, Vilkki Johanna, White Stephen N, Zhao Shuhong, Zhou Huaijun (2015) Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome biology, 16 : 57
  2016
  • Tuggle Christopher K, Giuffra Elisabetta, White Stephen N, Clarke Laura, Zhou Huaijun, Ross Pablo J, Acloque Hervé, Reecy James M, Archibald Alan, Bellone Rebecca R, Boichard Michèle, Chamberlain Amanda, Cheng Hans, Crooijmans Richard P M A, Delany Mary E, Finno Carrie J, Groenen Martien A M, Hayes Ben, Lunney Joan K, Petersen Jessica L, Plastow Graham S, Schmidt Carl J, Song Jiuzhou, Watson Mick (2016) GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes. Animal genetics, 47 (5): 528-33
  2019
  • Giuffra Elisabetta, Tuggle Christopher K, Archibald Alan L., Acloque Herve, Chamberlain Amanda J., Cochrane Guy, Daetwyler Hans D., Djebali Sarah, Eory Lel, Foissac Sylvain, Goddard Michael E., Groenen Martien A.M., Halstead Michelle, Harrison Peter W., Hayes Benjamin J., Kern Colin, Khatib Hasan, Kuo Richard I., MacHugh David E., Macleod Iona M., Madsen Ole, Reecy James M., Ross Pablo J., Watson Mick, Wells Jerry M., Zhou Huaijun (2019) Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annual review of animal biosciences, 7 : 65-88
  2020
  • Clark Emily L, Archibald Alan L, Daetwyler Hans D, Groenen Martien A M, Harrison Peter W, Houston Ross D, Kühn Christa, Lien Sigbjørn, Macqueen Daniel J, Reecy James M, Robledo Diego, Watson Mick, Tuggle Christopher K, Giuffra Elisabetta (2020) From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome biology, 21 (1): 285
•   Scientific publications:
  2015
  • Choi Minkyeung, Lee Jongin, Le Min Thong, Nguyen Dinh Truong, Park Suhyun, Soundrarajan Nagasundarapandian, Schachtschneider Kyle M, Kim Jaebum, Park Jin-Ki, Kim Jin-Hoi, Park Chankyu (2015) Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA research , 22 (5): 343-55
  2017
  • Bush Stephen J, McCulloch Mary E B, Summers Kim M, Hume David A, Clark Emily L (2017) Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. BMC bioinformatics, 18 (1): 301
  2018
  • Bush Stephen J, Muriuki Charity, McCulloch Mary E B, Farquhar Iseabail L, Clark Emily L, Hume David A (2018) Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. Genetics, selection, evolution , 50 (1): 20
  • Palasca Oana, Santos Alberto, Stolte Christian, Gorodkin Jan, Jensen Lars Juhl (2018) TISSUES 2.0: an integrative web resource on mammalian tissue expression. Database , 2018
  • Waddell Lindsey A, Lefevre Lucas, Bush Stephen J, Raper Anna, Young Rachel, Lisowski Zofia M, McCulloch Mary E B, Muriuki Charity, Sauter Kristin A, Clark Emily L, Irvine Katharine M, Pridans Clare, Hope Jayne C, Hume David A (2018) ADGRE1 (EMR1, F4/80) Is a Rapidly-Evolving Gene Expressed in Mammalian Monocyte-Macrophages. Frontiers in immunology, 9 : 2246
  2019
  • Alexandre Pâmela A, Naval-Sanchez Marina, Porto-Neto Laercio R, Ferraz José Bento S, Reverter Antonio, Fukumasu Heidge (2019) Systems Biology Reveals as Key Regulators of Feed Efficiency in Beef Cattle. Frontiers in genetics, 10 : 230
  • Foissac Sylvain, Djebali Sarah, Munyard Kylie, Vialaneix Nathalie, Rau Andrea, Muret Kevin, Esquerré Diane, Zytnicki Matthias, Derrien Thomas, Bardou Philippe, Blanc Fany, Cabau Cédric, Crisci Elisa, Dhorne-Pollet Sophie, Drouet Françoise, Faraut Thomas, Gonzalez Ignacio, Goubil Adeline, Lacroix-Lamandé Sonia, Laurent Fabrice, Marthey Sylvain, Marti-Marimon Maria, Momal-Leisenring Raphaelle, Mompart Florence, Quéré Pascale, Robelin David, Cristobal Magali San, Tosser-Klopp Gwenola, Vincent-Naulleau Silvia, Fabre Stéphane, Pinard-Van der Laan Marie-Hélène, Klopp Christophe, Tixier-Boichard Michèle, Acloque Hervé, Lagarrigue Sandrine, Giuffra Elisabetta (2019) Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC biology, 17 (1): 108
  • Kingsley N B, Kern Colin, Creppe Catherine, Hales Erin N, Zhou Huaijun, Kalbfleisch T S, MacLeod James N, Petersen Jessica L, Finno Carrie J, Bellone Rebecca R (2019) Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq. Genes, 11 (1)
  • Low Wai Yee, Tearle Rick, Bickhart Derek M, Rosen Benjamin D, Kingan Sarah B, Swale Thomas, Thibaud-Nissen Françoise, Murphy Terence D, Young Rachel, Lefevre Lucas, Hume David A, Collins Andrew, Ajmone-Marsan Paolo, Smith Timothy P L, Williams John L (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature communications, 10 (1): 260
  • Muriuki Charity, Bush Stephen J, Salavati Mazdak, McCulloch Mary E B, Lisowski Zofia M, Agaba Morris, Djikeng Appolinaire, Hume David A, Clark Emily L (2019) A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus). Frontiers in genetics, 10 : 1080
  • Nolte Wietje, Weikard Rosemarie, Brunner Ronald M, Albrecht Elke, Hammon Harald M, Reverter Antonio, Kühn Christa (2019) Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle. Frontiers in genetics, 10 : 1130
  • Salavati Mazdak, Bush Stephen J, Palma-Vera Sergio, McCulloch Mary E B, Hume David A, Clark Emily L (2019) Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep. Frontiers in genetics, 10 : 863
  • Schwartz John C, Sanderson Nicholas D, Bickhart Derek M, Smith Timothy P L, Hammond John A (2019) The Structure, Evolution, and Gene Expression Within the Caprine Leukocyte Receptor Complex. Frontiers in immunology, 10 : 2302
  • Young Rachel, Lefevre Lucas, Bush Stephen J, Joshi Akshay, Singh Salam Herojeet, Jadhav Santosh Kumar, Dhanikachalam Velu, Lisowski Zofia M, Iamartino Daniela, Summers Kim M, Williams John L, Archibald Alan L, Gokhale Suresh, Kumar Satish, Hume David A (2019) A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis). Frontiers in genetics, 10 : 668
  2020
  • Alexandre Pâmela A, Reverter Antonio, Berezin Roberta B, Porto-Neto Laercio R, Ribeiro Gabriela, Santana Miguel H A, Ferraz José Bento S, Fukumasu Heidge (2020) Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. Genes, 11 (9)
  • Dorji Jigme, Vander Jagt Christy J, Garner Josie B, Marett Leah C, Mason Brett A, Reich Coralie M, Xiang Ruidong, Clark Emily L, Cocks Benjamin G, Chamberlain Amanda J, MacLeod Iona M, Daetwyler Hans D (2020) Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle. BMC genomics, 21 (1): 720
  • Halstead Michelle M, Kern Colin, Saelao Perot, Wang Ying, Chanthavixay Ganrea, Medrano Juan F, Van Eenennaam Alison L, Korf Ian, Tuggle Christopher K, Ernst Catherine W, Zhou Huaijun, Ross Pablo J (2020) A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC genomics, 21 (1): 698
  • Herrera-Uribe Juber, Liu Haibo, Byrne Kristen A, Bond Zahra F, Loving Crystal L, Tuggle Christopher K (2020) Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure. Frontiers in genetics, 11 : 817
  • Nolte Wietje, Weikard Rosemarie, Brunner Ronald M, Albrecht Elke, Hammon Harald M, Reverter Antonio, Küehn Christa (2020) Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bulls. International journal of molecular sciences, 21 (9)
  • Tsang Hiu-Gwen, Clark Emily L, Markby Greg R, Bush Stephen J, Hume David A, Corcoran Brendan M, MacRae Vicky E, Summers Kim M (2020) Expression of Calcification and Extracellular Matrix Genes in the Cardiovascular System of the Healthy Domestic Sheep (Ovis aries). Frontiers in genetics, 11 : 919
  2021
  • Goszczynski Daniel E, Halstead Michelle M, Islas-Trejo Alma D, Zhou Huaijun, Ross Pablo J (2021) Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Genome research, 31 (4): 732-744
  • Halstead Michelle M, Islas-Trejo Alma, Goszczynski Daniel E, Medrano Juan F, Zhou Huaijun, Ross Pablo J (2021) Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell. Frontiers in genetics, 12 : 664260
  • Kern Colin, Wang Ying, Xu Xiaoqin, Pan Zhangyuan, Halstead Michelle, Chanthavixay Ganrea, Saelao Perot, Waters Susan, Xiang Ruidong, Chamberlain Amanda, Korf Ian, Delany Mary E, Cheng Hans H, Medrano Juan F, Van Eenennaam Alison L, Tuggle Chris K, Ernst Catherine, Flicek Paul, Quon Gerald, Ross Pablo, Zhou Huaijun (2021) Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature communications, 12 (1): 1821
  • Pan Zhangyuan, Yao Yuelin, Yin Hongwei, Cai Zexi, Wang Ying, Bai Lijing, Kern Colin, Halstead Michelle, Chanthavixay Ganrea, Trakooljul Nares, Wimmers Klaus, Sahana Goutam, Su Guosheng, Lund Mogens Sandø, Fredholm Merete, Karlskov-Mortensen Peter, Ernst Catherine W, Ross Pablo, Tuggle Christopher K, Fang Lingzhao, Zhou Huaijun (2021) Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nature communications, 12 (1): 5848
  • Tixier-Boichard Michèle, Fabre Stéphane, Dhorne-Pollet Sophie, Goubil Adeline, Acloque Hervé, Vincent-Naulleau Silvia, Ross Pablo, Wang Ying, Chanthavixay Ganrea, Cheng Hans, Ernst Catherine, Leesburg Vicki, Giuffra Elisabetta, Zhou Huaijun, Taragnat Catherine, Berri Cecile, Jardet Déborah, Godet Estelle, Laurent Fabrice, Gomot Gilles, Dardente Hughes, Grasseau Isabelle, Dubois Jean-Philippe, Gautron Joel, Gérard Nadine, Quéré Pascale, Lavocat Roger-Paul, Dalbies-Tran Rozenn, Métayer Sonia, Marthey Sylvain, Coustham Vincent, Druart Xavier (2021) Tissue Resources for the Functional Annotation of Animal Genomes. Frontiers in genetics, 12 : 666265
•   Presentations and posters
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Last updated: Apr 07, 2025, 10:31am CDT