Algorithms for transcript isoforms, structural variation, and regulatory disruption from PacBio and ONT long reads.
We develop computational methods for long-read RNA-seq and DNA-seq that resolve complex transcript isoforms, fusion transcripts, structural variation, and regulatory disruption that are difficult to capture with short-read assays. Our methods span bulk and single-cell modalities and target both reference-based and assembly-based representations of the genome.
Lab-led contributions include CTAT-LR-Fusion for accurate fusion transcript identification at bulk or single-cell resolution (Qin et al., 2025), somatic structural variant calling that combines pangenome and de novo personal genome assembly (Qin et al., 2025), and diploid donor-specific assemblies (DSAs) as cancer reference genomes that recover over 20% additional somatic SVs missed on GRCh38 or CHM13 (Zhang et al., 2025). Related publications in this space include colorSV, a long-range somatic SV caller that uses matched tumor-normal co-assembly graphs to recover translocations and other complex events (Le et al., 2025); LongcallD, a local-haplotagging variant caller that jointly calls and phases small, structural, and low-fraction mosaic variants from PacBio HiFi and ONT reads (Gao et al., 2026); and FuFiHLA, a tool for full-field HLA allele typing directly from PacBio HiFi and ONT long reads (Hu et al., 2026). Together these tools improve sensitivity and precision for clinically relevant variation that short-read pipelines routinely miss.
References
2026
bioRxiv
LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads
Yan Gao, Wen-Wei Liao, Qian Qin, and 2 more authors
@article{Gao2026LongcallD,title={{LongcallD}: joint calling and phasing of small, structural and mosaic variants from long reads},author={Gao, Yan and Liao, Wen-Wei and Qin, Qian and Hall, Ira M and Li, Heng},journal={bioRxiv},pages={2026.03.20.713111},month=mar,year={2026},doi={10.64898/2026.03.20.713111},}
Bioinformatics
FuFiHLA: A tool for full-field HLA typing from long-read data
@article{Hu2026FuFiHLA,title={{FuFiHLA}: A tool for full-field {HLA} typing from long-read data},author={Hu, Jingqing and Qin, Qian and Li, Heng and Zhou, Ying},journal={Bioinformatics},pages={btag231},month=may,year={2026},doi={10.1093/bioinformatics/btag231},}
2025
Genome Res
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
Qian Qin, Victoria Popic, Kirsty Wienand, and 11 more authors
@article{Qin2025CTATLRFusion,title={Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution},author={Qin, Qian and Popic, Victoria and Wienand, Kirsty and Yu, Houlin and White, Emily and Khorgade, Akanksha and Shin, Asa and Georgescu, Christophe and Campbell, Catarina D and Dondi, Arthur and Beerenwinkel, Niko and Vazquez, Francisca and Al'Khafaji, Aziz M and Haas, Brian J},journal={Genome Research},volume={35},number={4},pages={967--986},month=apr,year={2025},doi={10.1101/gr.279200.124},}
bioRxiv
Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly
@article{Qin2025LongReadSV,title={Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly},author={Qin, Qian and Heinz, Jakob and Li, Heng},journal={bioRxiv},pages={2025.10.28.685154},month=oct,year={2025},doi={10.1101/2025.10.28.685154},}
bioRxiv
Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes
@article{Zhang2025DSASV,title={Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes},author={Zhang, Yuwei and Qu, Han and Qin, Qian and Li, Heng and Park, Peter J},journal={bioRxiv},pages={2025.10.28.685155},month=oct,year={2025},doi={10.1101/2025.10.28.685155},}
@article{Le2025colorSV,title={{colorSV}: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs},author={Le, M K and Qin, Qian and Li, Heng},journal={Genomics, Proteomics \& Bioinformatics},pages={qzaf082},month=sep,year={2025},doi={10.1093/gpbjnl/qzaf082},}