Publications, code and resources.

Publications_

• 01 / 14

  Pangenome-based structural variant imputation enables large-scale genotype–phenotype studies in dairy cattle

  Yang L, Wang J, Kuhn K, et al., Jiang J, Fang L, Ma L, Liu GE

  Nature Communications · 2026First author

  Genotyped 93,059 structural variants in 1,571 cattle from the H20D pangenome, built the HolPIP imputation panel, imputed 86.7% of them into 50,299 bulls at Beagle R² ≥ 0.8, and ran GWAS on 43 complex traits — 1,225 SV–trait associations and 32 fine-mapped candidates, including a 75 bp ANKRD11 deletion linked to stature.

• 02 / 14

  Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle

  Yang L, Gao Y, Kuhn KL, et al., Ma L, Smith TPL, Liu GE

  Nature Communications · 2026First author

  H20D — a Holstein breed-specific pangenome graph from 40 phased haploid assemblies of 20 cows. It outperforms assembly- and read-based long-read callers, finds over 10,000 additional SVs per sample versus short-read approaches, and beats graphs built across breeds or from fewer or unphased assemblies, particularly in complex regions.

• 03 / 14

  Mapping and functional characterization of structural variation in 1060 pig genomes

  Yang L, Yin H, Bai L, et al.

  Genome Biology · 2024First author

  An SV catalogue across 1,060 pigs from 101 breeds covering 9.6% of the genome — 42,487 deletions, 37,913 mobile element insertions, 3,308 duplications and 1,664 inversions — with functional characterisation against expression and complex traits.

• 04 / 14

  Long-read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle

  Gao Y, Yang L, Kuhn K, et al., Smith TPL, Liu GE

  Journal of Advanced Research · 2025Second author

  28 HiFi assemblies at 20×, five read-based plus one assembly-based SV caller, and breed-specific catalogues spanning 7.4% of the Holstein and 5.0% of the Jersey genome. SV discovery saturates at twenty Holsteins but not when Jerseys are added — the practical argument for breed-specific graphs.

• 05 / 14

  Pangenome variation analysis uncovers the impacts of SNP-independent structural variations in modern European cattle breeding

  Dai S, Xu L, Yang L, et al., Liu GE, Zhou Y

  iMetaOmics · 2026Co-first author
• 06 / 14

  Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs

  Yin H, Yang L, Zhao Q, et al., Fang L, Li K

  BMC Biology · 2025Second author
• 07 / 14

  A compendium of genetic regulatory effects across pig tissues

  Teng J, Gao Y, Yin H, et al. (incl. Yang L), Zhang Z, Fang L

  Nature Genetics · 2024PigGTEx Consortium

  The PigGTEx resource — regulatory effects across 34 pig tissues, and the reference map that most downstream porcine functional work now builds on.

• 08 / 14

  Pangenome graph reveals the structural variation landscape in 2,929 cattle samples and its impact on gene regulation

  Zhao P, Peng C, Gao Y, Dai S, Yang L, et al.

  Genomics, Proteomics & Bioinformatics · 2026

  80,328 high-quality SVs across 2,929 samples, and 637 SV-eQTL from paired WGS and blood RNA-seq in 170 Simmental cattle — 10.8% of the expression heritability of their target genes.

• 09 / 14

  Global pangenome analysis highlights the critical role of structural variants in cattle improvement and identifies a unique event as a novel enhancer in IGFBP7+ cells

  Dai S, Zhao P, Li W, et al., Yang L, et al.

  Molecular Biology and Evolution · 2025
• 10 / 14

  Gene variants in the pheromone vomeronasal receptors and QTLs around behavioral and fat metabolism genes associated with altered feed efficiency in cattle

  Shirak A, Yang L, Bhowmik N, et al.

  Scientific Reports · 2026
• 11 / 14

  Selection signature analysis of whole-genome sequences to identify genome differences between selected and unselected Holstein cattle

  Cai J, Yang L, Gao Y, Liu GE, Da Y, Ma L

  Animals · 2025
• 12 / 14

  Exploring tissue- and sex-specific DNA methylation in cattle using a pan-mammalian Infinium array

  Hu Z, Boschiero C, Neupane M, Bhowmik N, Yang L, et al.

  Int. J. Molecular Sciences · 2025
• 13 / 14

  A pilot detection and association study of gene presence–absence variation in Holstein cattle

  Boschiero C, Neupane M, Yang L, et al., Liu GE

  Animals · 2024
• 14 / 14

  The Ruminant Telomere-to-Telomere (RT2T) Consortium

  Kalbfleisch TS, McKay SD, Murdoch BM, et al. (incl. Yang L)

  Nature Genetics · 2024Consortium author

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