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2025 | 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,Nature Genetics (2025) 1–11. https://doi.org/10.1038/s41588-025-02155-9.
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| 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. IF = 4.1
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| 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.
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| 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.
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| 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,Nature Genetics (2024) 1–8. https://doi.org/10.1038/s41588-024-01835-2. IF = 29
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| D. Zhu, K. Shi, C. Li, Y. Yan, H. Li, Z. Bai, L. Tan,D. Guan, Y. Zhao, Y. Wang, B. Fan, Z. Jiang, Z. Xu, C. Feng, L. Fang, X. Hu, Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits.Nature Communications 17, 553 (2025).
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2024 | 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 Genomics51 (2024) 1423–1434. https://doi.org/10.1016/j.jgg.2024.09.003.
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| 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,Nature Genetics 56 (2024) 112–123. https://doi.org/10.1038/s41588-023-01585-7.
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| 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.
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| 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.
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| 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.
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| 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.
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| 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.
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| 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,Scientific Reports 14 (2024) 8529. https://doi.org/10.1038/s41598-024-59269-z.
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| 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,Scientific Reports 14 (2024) 6588. https://doi.org/10.1038/s41598-024-56705-y.
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2023 | 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.
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| 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.
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| 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.
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| 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,Frontiers in Genetics. 14 (2023). https://doi.org/10.3389/fgene.2023.1114749.
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| 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.
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| 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.
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2022 | 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,Frontiers in Genetics. 13 (2022). https://doi.org/10.3389/fgene.2022.997460.
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| 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,Nature Genetics 54 (2022) 1438–1447. https://doi.org/10.1038/s41588-022-01153-5.
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| 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.
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2021 | 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.
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| 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.
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| 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,Molecular Horticulture1 (2021) 3. https://doi.org/10.1186/s43897-021-00005-w.
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| 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,Genetics Selection Evolution 53 (2021) 43. https://doi.org/10.1186/s12711-021-00632-3.
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| 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.
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| 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.
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2020 | 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.
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| 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.
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| 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 Science103 (2020) 11605–11617. https://doi.org/10.3168/jds.2020-18461.
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2019 and before | 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.
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| 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),Scientific Reports 6 (2016) 36372. https://doi.org/10.1038/srep36372.
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| 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.
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