Publications

1. D. Guan, Z. Bai, X. Zhu, C. Zhong, Y. Hou, D. Zhu, H. Li, F. Lan, S. Diao, Y. Yao, B. Zhao, X. Li, Z. Pan, Y. Gao, Y. Wang, D. Zou, R. Wang, T. Xu, C. Sun, H. Yin, J. Teng, Z. Xu, Q. Lin, S. Shi, D. Shao, F. Degalez, S. Lagarrigue, Y. Wang, M. Wang, M. Peng, D. Rocha, M. Charles, J. Smith, K. Watson, A.J. Buitenhuis, G. Sahana, M.S. Lund, W. Warren, L. Frantz, G. Larson, S.J. Lamont, W. Si, X. Zhao, B. Li, H. Zhang, C. Luo, D. Shu, H. Qu, W. Luo, Z. Li, Q. Nie, X. Zhang, R. Xiang, S. Liu, Z. Zhang, Z. Zhang, G.E. Liu, H. Cheng, N. Yang, X. Hu, H. Zhou, L. Fang, Genetic regulation of gene expression across multiple tissues in chickens, Nat Genet (2025) 1–11. https://doi.org/10.1038/s41588-025-02155-9.

2. D. Guan, J. Bruscadin, W. Yang, C. Prowse-Wilkins, J. Wang, B. Petry, H. Li, H. Zhang, X. Xu, Y. Wang, Z. Pan, Y. Utsunomiya, G. Rincon, S. Corum, H. Jiang, B.M. Murdoch, S.D. McKay, M. Rijnkels, C. Gill, T.P.L. Smith, Z. Jiang, W. Liu, J. Reecy, J.F. Mendrano, J. Deeb, Z. Weng, J.E. Koltes, J. Jiang, L. Fang, P. Ross, H. Zhou, An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in cattle, bioRxiv (2025).

3. D. Guan, V. Landi, M.G. Luigi-Sierra, J.V. Delgado, X. Such, A. Castelló, B. Cabrera, E. Mármol-Sánchez, J. Fernández-Alvarez, J.L.R. de la Torre Casañas, A. Martínez, J. Jordana, M. Amills, Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats, Journal of Animal Science and Biotechnology 11 (2020) 35. https://doi.org/10.1186/s40104-020-00435-4.

4. D. Guan, M.M. Halstead, A.D. Islas-Trejo, D.E. Goszczynski, H.H. Cheng, P.J. Ross, H. Zhou, Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing, Front. Genet. 13 (2022). https://doi.org/10.3389/fgene.2022.997460.

5. D. Guan, A. Castelló, M.G. Luigi-Sierra, V. Landi, J.V. Delgado, A. Martínez, M. Amills, Estimating the copy number of the agouti signaling protein (ASIP) gene in goat breeds with different color patterns, Livestock Science 246 (2021) 104440. https://doi.org/10.1016/j.livsci.2021.104440.

6. D. Guan, A. Martínez, M.G. Luigi-Sierra, J.V. Delgado, V. Landi, A. Castelló, J. Fernández Álvarez, X. Such, J. Jordana, M. Amills, Detecting the footprint of selection on the genomes of Murciano-Granadina goats, Animal Genetics 52 (2021) 683–693. https://doi.org/10.1111/age.13113.

7. D. Guan, E. Mármol-Sánchez, T.F. Cardoso, X. Such, V. Landi, N.R. Tawari, M. Amills, Genomic analysis of the origins of extant casein variation in goats, Journal of Dairy Science 102 (2019) 5230–5241. https://doi.org/10.3168/jds.2018-15281.

8. D. Guan, N. Luo, X. Tan, Z. Zhao, Y. Huang, R. Na, J. Zhang, Y. Zhao, Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus), Sci Rep 6 (2016) 36372. https://doi.org/10.1038/srep36372.

9. J. Li, D. Guan^#, M.M. Halstead, A.D. Islas-Trejo, D.E. Goszczynski, C.W. Ernst, H. Cheng, P. Ross, H. Zhou, Transcriptome annotation of 17 porcine tissues using nanopore sequencing technology, Animal Genetics 54 (2023) 35–44. https://doi.org/10.1111/age.13274.

10. H. Yin, L. Yang, Q. Zhao, W. Yao, J. Teng, Y. Gao, Z. Xu, Q. Lin, S. Diao, X. Liu, F. Zhao, Z. Zhou, Q. Wang, J. Li, Z. Zhang, H. Zhou, M.A.M. Groenen, O. Madsen, L. Bai, D. Guan^*, L. Fang, K. Li, Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs, BMC Biol 23 (2025) 188. https://doi.org/10.1186/s12915-025-02279-8.

11. B. Zhao, K. Dai, S. Li, G. Zhang, W. Lv, W. Liu, Y. Cai, F. Wang, H. Zhou, D. Guan^*, Y. Zhang, Integrative single-cell transcriptomics of sheep ovarian development reveals dynamic transcriptional programs relevant to reproductive traits, iScience 28 (2025). https://doi.org/10.1016/j.isci.2025.112422.

12. C. Zhong, X. Li, D. Guan, B. Zhang, X. Wang, L. Qu, H. Zhou, L. Fang, C. Sun, N. Yang, Age-dependent genetic architectures of chicken body weight explored by multidimensional GWAS and molQTL analyses, Journal of Genetics and Genomics 51 (2024) 1423–1434. https://doi.org/10.1016/j.jgg.2024.09.003.

13. H. Zhou, E. Clark, D. Guan, S. Lagarrigue, L. Fang, H. Cheng, C.K. Tuggle, M. Kapoor, Y. Wang, E. Giuffra, G. Egidy, Comparative Genomics and Epigenomics of Transcriptional Regulation, Annual Review of Animal Biosciences 13 (2025) 73–98. https://doi.org/10.1146/annurev-animal-111523-102217.

14. J. Li, T. Zhao, D. Guan, Z. Pan, Z. Bai, J. Teng, Z. Zhang, Z. Zheng, J. Zeng, H. Zhou, L. Fang, H. Cheng, Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits, Cell Genomics 3 (2023) 100390. https://doi.org/10.1016/j.xgen.2023.100390.

15. D. Guan, A. Martínez, A. Castelló, V. Landi, M.G. Luigi-Sierra, J. Fernández-Álvarez, B. Cabrera, J.V. Delgado, X. Such, J. Jordana, M. Amills, A genome-wide analysis of copy number variation in Murciano-Granadina goats, Genetics Selection Evolution 52 (2020) 44. https://doi.org/10.1186/s12711-020-00564-4.

16. J. Teng, Y. Gao, H. Yin, Z. Bai, S. Liu, H. Zeng, L. Bai, Z. Cai, B. Zhao, X. Li, Z. Xu, Q. Lin, Z. Pan, W. Yang, X. Yu, D. Guan, Y. Hou, B.N. Keel, G.A. Rohrer, A.K. Lindholm-Perry, W.T. Oliver, M. Ballester, D. Crespo-Piazuelo, R. Quintanilla, O. Canela-Xandri, K. Rawlik, C. Xia, Y. Yao, Q. Zhao, W. Yao, L. Yang, H. Li, H. Zhang, W. Liao, T. Chen, P. Karlskov-Mortensen, M. Fredholm, M. Amills, A. Clop, E. Giuffra, J. Wu, X. Cai, S. Diao, X. Pan, C. Wei, J. Li, H. Cheng, S. Wang, G. Su, G. Sahana, M.S. Lund, J.C.M. Dekkers, L. Kramer, C.K. Tuggle, R. Corbett, M.A.M. Groenen, O. Madsen, M. Gòdia, D. Rocha, M. Charles, C. Li, H. Pausch, X. Hu, L. Frantz, Y. Luo, L. Lin, Z. Zhou, Z. Zhang, Z. Chen, L. Cui, R. Xiang, X. Shen, P. Li, R. Huang, G. Tang, M. Li, Y. Zhao, G. Yi, Z. Tang, J. Jiang, F. Zhao, X. Yuan, X. Liu, Y. Chen, X. Xu, S. Zhao, P. Zhao, C. Haley, H. Zhou, Q. Wang, Y. Pan, X. Ding, L. Ma, J. Li, P. Navarro, Q. Zhang, B. Li, A. Tenesa, K. Li, G.E. Liu, Z. Zhang, L. Fang, A compendium of genetic regulatory effects across pig tissues, Nat Genet 56 (2024) 112–123. https://doi.org/10.1038/s41588-023-01585-7.

17. S. Liu, Y. Gao, O. Canela-Xandri, S. Wang, Y. Yu, W. Cai, B. Li, R. Xiang, A.J. Chamberlain, E. Pairo-Castineira, K. D’Mellow, K. Rawlik, C. Xia, Y. Yao, P. Navarro, D. Rocha, X. Li, Z. Yan, C. Li, B.D. Rosen, C.P. Van Tassell, P.M. Vanraden, S. Zhang, L. Ma, J.B. Cole, G.E. Liu, A. Tenesa, L. Fang, A multi-tissue atlas of regulatory variants in cattle, Nat Genet 54 (2022) 1438–1447. https://doi.org/10.1038/s41588-022-01153-5.

18. L. Fang, J. Teng, Q. Lin, Z. Bai, S. Liu, D. Guan, B. Li, Y. Gao, Y. Hou, M. Gong, Z. Pan, Y. Yu, E.L. Clark, J. Smith, K. Rawlik, R. Xiang, A.J. Chamberlain, M.E. Goddard, M. Littlejohn, G. Larson, D.E. MacHugh, J.F. O’Grady, P. Sørensen, G. Sahana, M.S. Lund, Z. Jiang, X. Pan, W. Gong, H. Zhang, X. He, Y. Zhang, N. Gao, J. He, G. Yi, Y. Liu, Z. Tang, P. Zhao, Y. Zhou, L. Fu, X. Wang, D. Hao, L. Liu, S. Chen, R.S. Young, X. Shen, C. Xia, H. Cheng, L. Ma, J.B. Cole, R.L. Baldwin, C. Li, C.P. Van Tassell, B.D. Rosen, N. Bhowmik, J. Lunney, W. Liu, L. Guan, X. Zhao, E.M. Ibeagha-Awemu, Y. Luo, L. Lin, O. Canela-Xandri, M.F.L. Derks, R.P.M.A. Crooijmans, M. Gòdia, O. Madsen, M.A.M. Groenen, J.E. Koltes, C.K. Tuggle, F.M. McCarthy, D. Rocha, E. Giuffra, M. Amills, A. Clop, M. Ballester, G. Tosser-Klopp, J. Li, C. Fang, M. Fang, Q. Wang, Z. Hou, Q. Wang, F. Zhao, L. Jiang, G. Zhao, Z. Zhou, R. Zhou, H. Liu, J. Deng, L. Jin, M. Li, D. Mo, X. Liu, Y. Chen, X. Yuan, J. Li, S. Zhao, Y. Zhang, X. Ding, D. Sun, H.-Z. Sun, C. Li, Y. Wang, Y. Jiang, D. Wu, W. Wang, X. Fan, Q. Zhang, K. Li, H. Zhang, N. Yang, X. Hu, W. Huang, J. Song, Y. Wu, J. Yang, W. Wu, C. Kasper, X. Liu, X. Yu, L. Cui, X. Zhou, S. Kim, W. Li, H.K. Im, E.S. Buckler, B. Ren, M.C. Schatz, J.J. Li, A.A. Palmer, L. Frantz, H. Zhou, Z. Zhang, G.E. Liu, The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, Nat Genet (2025) 1–11. https://doi.org/10.1038/s41588-025-02121-5.

19. W. Wang, C. Shen, X. Wen, A. Li, Q. Gao, Z. Xu, Y. Wei, Y. Li, D. Guan, B. Liu, Prediction of transcript isoforms and identification of tissue-specific genes in cucumber, BMC Genomics 26 (2025) 25. https://doi.org/10.1186/s12864-025-11212-w.

20. H. Li, H. Zhang, P. Zhao, Q. Zhang, S. Zhu, T. Shi, Y.-N. Wang, J.-S. Lu, L. Yang, J.F. O’Grady, D.E. MacHugh, Y. Wang, Z. Wei, X. Lu, M.-S. Wang, B. Han, W. Zheng, A. Chen, S. Akter, N. Bhowmik, Y. Ma, R.L. Baldwin, C. Li, J. Jiang, L. Ma, C. Maltecca, J. Wang, M. Gong, X. Zhu, Q. Lin, Y. Xi, D. Zhu, J. Teng, D. Guan, B. An, J. Ren, Y. Hou, F. Wang, B. Li, L.A.F. Frantz, G. Larson, Z. Cai, G. Sahana, Y. Jiang, H. Sun, D. Sun, G.E. Liu, L. Fang, An atlas of cell type specific regulatory effects in cattle, BioRxiv (under review in Nature Genetics) (2025) 2025.06.23.661035. https://doi.org/10.1101/2025.06.23.661035.

21. T.S. Kalbfleisch, S.D. McKay, B.M. Murdoch, D.L. Adelson, D. Almansa-Villa, G. Becker, L.M. Beckett, M.J. Benítez-Galeano, F. Biase, T. Casey, E. Chuong, E. Clark, S. Clarke, N. Cockett, C. Couldrey, B.W. Davis, C.G. Elsik, T. Faraut, Y. Gao, C. Genet, P. Grady, J. Green, R. Green, D. Guan, D. Hagen, G.A. Hartley, M. Heaton, S.J. Hoyt, W. Huang, E. Jarvis, J. Kalleberg, H. Khatib, K.-P. Koepfi, J. Koltes, S. Koren, C. Kuehn, T. Leeb, A. Leonard, G.E. Liu, W.Y. Low, H. McConnell, K. McRae, K. Miga, M. Mousel, H. Neibergs, T. Olagunju, M. Pennell, B. Petry, M. Pewsner, A.M. Phillippy, B.D. Pickett, P. Pineda, T. Potapova, S. Rachagani, A. Rhie, M. Rijnkels, A. Robic, N. Rodriguez Osorio, Y. Safonova, G. Schettini, R.D. Schnabel, N. Sirpu Natesh, M. Stegemiller, J. Storer, P. Stothard, C. Stull, G. Tosser-Klopp, G.M. Traglia, C.K. Tuggle, C.P. Van Tassell, C. Watson, R. Weikard, K. Wimmers, S. Xie, L. Yang, T.P.L. Smith, R.J. O’Neill, B.D. Rosen, The Ruminant Telomere-to-Telomere (RT2T) Consortium, Nat Genet (2024) 1–8. https://doi.org/10.1038/s41588-024-01835-2.

22. M.G. Luigi-Sierra, Y. Ramayo-Caldas, D. Guan, M. Amills, Short communication: Comparing the microbiota diversity from the core, middle part and rind of six Spanish commercial goat cheeses, Livestock Science 285 (2024) 105496. https://doi.org/10.1016/j.livsci.2024.105496.

23. B. Liu, C.-C. Shen, S.-W. Xia, S.-S. Song, L.-H. Su, Y. Li, Q. Hao, Y.-J. Liu, D.-L. Guan, N. Wang, W.-J. Wang, X. Zhao, H.-X. Li, X.-X. Li, Y.-S. Lai, A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation, Plant Physiology 195 (2024) 970–985. https://doi.org/10.1093/plphys/kiae153.

24. E. Varela-Martínez, M.G. Luigi-Sierra, D. Guan, M. López-Béjar, E. Casas, S. Olvera-Maneu, J. Gardela, M.J. Palomo, U.I. Osuagwuh, U.L. Ohaneje, E. Mármol-Sánchez, M. Amills, The landscape of long noncoding RNA expression in the goat brain, Journal of Dairy Science 107 (2024) 4075–4091. https://doi.org/10.3168/jds.2023-23966.

25. W. Wang, Y. Wei, Z. Xu, C. Shen, A. Li, D. Guan, X. Zhang, B. Liu, Evidence Supporting a Role of Alternative Splicing Participates in Melon (Cucumis melo L.) Fruit Ripening, International Journal of Molecular Sciences 25 (2024) 5886. https://doi.org/10.3390/ijms25115886.

26. L. Yang, H. Yin, L. Bai, W. Yao, T. Tao, Q. Zhao, Y. Gao, J. Teng, Z. Xu, Q. Lin, S. Diao, Z. Pan, D. Guan, B. Li, H. Zhou, Z. Zhou, F. Zhao, Q. Wang, Y. Pan, Z. Zhang, K. Li, L. Fang, G.E. Liu, Mapping and functional characterization of structural variation in 1060 pig genomes, Genome Biology 25 (2024) 116. https://doi.org/10.1186/s13059-024-03253-3.

27. D. Colombi, G. Rovelli, M.G. Luigi-Sierra, S. Ceccobelli, D. Guan, F. Perini, F. Sbarra, A. Quaglia, F.M. Sarti, M. Pasquini, M. Amills, E. Lasagna, Population structure and identification of genomic regions associated with productive traits in five Italian beef cattle breeds, Sci Rep 14 (2024) 8529. https://doi.org/10.1038/s41598-024-59269-z.

28. F. Degalez, M. Charles, S. Foissac, H. Zhou, D. Guan, L. Fang, C. Klopp, C. Allain, L. Lagoutte, F. Lecerf, H. Acloque, E. Giuffra, F. Pitel, S. Lagarrigue, Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues, Sci Rep 14 (2024) 6588. https://doi.org/10.1038/s41598-024-56705-y.

29. M. Macri, M.G. Luigi-Sierra, D. Guan, J.V. Delgado, J.F. Alvarez, M. Amills, A.M. Martínez, Univariate and multivariate genome-wide association studies for hematological traits in Murciano-Granadina goats, Animal Genetics 54 (2023) 491–499. https://doi.org/10.1111/age.13328.

30. M.G. Luigi-Sierra, D. Guan, M. López-Béjar, E. Casas, S. Olvera-Maneu, J. Gardela, M.J. Palomo, U.I. Osuagwuh, U.L. Ohaneje, E. Mármol-Sánchez, M. Amills, A protein-coding gene expression atlas from the brain of pregnant and non-pregnant goats, Front. Genet. 14 (2023). https://doi.org/10.3389/fgene.2023.1114749.

31. Z. Pan, Y. Wang, M. Wang, Y. Wang, X. Zhu, S. Gu, C. Zhong, L. An, M. Shan, J. Damas, M.M. Halstead, D. Guan, N. Trakooljul, K. Wimmers, Y. Bi, S. Wu, M.E. Delany, X. Bai, H.H. Cheng, C. Sun, N. Yang, X. Hu, H.A. Lewin, L. Fang, H. Zhou, An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics, Science Advances 9 (2023) eade1204. https://doi.org/10.1126/sciadv.ade1204.

32. J.C. Lin, T.F. Bishop, J.R. Owen, S.L. Hennig, D.S. Fitzpatrick, M.L. Mueller, D. Guan, M.L. Angove, A. Hua, E.G. Balogh, R.J. Swift, P.J. Ross, A.L. Van Eenennaam, Optimization of Electroporation and Adeno-Associated Virus-Mediated Generation of 2.7 kb Knock-In Livestock Blastocysts, GEN Biotechnology 2 (2023) 120–132. https://doi.org/10.1089/genbio.2022.0037.

33. M.G. Luigi-Sierra, A. Fernández, A. Martínez, D. Guan, J.V. Delgado, J.F. Álvarez, V. Landi, F.X. Such, J. Jordana, M. Saura, M. Amills, Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats, Journal of Animal Science and Biotechnology 13 (2022) 35. https://doi.org/10.1186/s40104-022-00684-5.

34. B. Liu, J. Weng, D. Guan, Y. Zhang, Q. Niu, E. López-Juez, Y. Lai, J. Garcia-Mas, D. Huang, A domestication-associated gene, CsLH, encodes a phytochrome B protein that regulates hypocotyl elongation in cucumber, Mol Horticulture 1 (2021) 3. https://doi.org/10.1186/s43897-021-00005-w.

35. E. Mármol-Sánchez, M.G. Luigi-Sierra, A. Castelló, D. Guan, R. Quintanilla, R. Tonda, M. Amills, Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes, Genet Sel Evol 53 (2021) 43. https://doi.org/10.1186/s12711-021-00632-3.

36. L. Yang, D. Guan, M. Valls, W. Ding, Sustainable natural bioresources in crop protection: antimicrobial hydroxycoumarins induce membrane depolarization-associated changes in the transcriptome of, Pest Management Science 77 (2021) 5170–5185. https://doi.org/10.1002/ps.6557.

37. G. Rovelli, M.G. Luigi-Sierra, D. Guan, F. Sbarra, A. Quaglia, F.M. Sarti, M. Amills, E. Lasagna, Evolution of inbreeding: a gaze into five Italian beef cattle breeds history, PeerJ 9 (2021) e12049. https://doi.org/10.7717/peerj.12049.

38. M.G. Luigi-Sierra, V. Landi, D. Guan, J.V. Delgado, A. Castelló, B. Cabrera, E. Mármol-Sánchez, J.F. Alvarez, M. Gómez-Carpio, A. Martínez, X. Such, J. Jordana, M. Amills, A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats, Journal of Dairy Science 103 (2020) 11605–11617. https://doi.org/10.3168/jds.2020-18461.

39. B. Liu, D. Guan, X. Zhai, S. Yang, S. Xue, S. Chen, J. Huang, H. Ren, X. Liu, Selection footprints reflect genomic changes associated with breeding efforts in 56 cucumber inbred lines, Horticulture Research 6 (2019) 127. https://doi.org/10.1038/s41438-019-0209-4.

40. Y. Zhao, H. Xu, Z. Zhao, Narisu, J. Mao, D. Guan, C. Xie, Polymorphisms of osteopontin gene and their association with placental efficiency and prolificacy in goats, Journal of Applied Animal Research 43 (2015) 272–278. https://doi.org/10.1080/09712119.2014.963098.