about | Qin AIM Lab

Principal Investigator

Professor, School of AI

Welcome to the Qin AIM Lab, the AI and Multi-Omics Research for Precision Medicine Lab at the School of AI, Wuhan University. We develop AI-driven computational biology methods and multi-omics platforms to understand gene regulation, cancer evolution, immune-mediated disease mechanisms, and clinically relevant genomic variation.

The lab combines expertise in epigenomics, clinical genomics, cancer genomics, long-read sequencing, single-cell analysis, spatial transcriptomics, and biomedical software translation. A major focus is long-read RNA-seq and DNA-seq methodology development for resolving complex transcript isoforms, structural variation, regulatory disruption, and multi-omics signals that are difficult to capture with short-read assays.

We also emphasize Xenium spatial transcriptomics methodology development, including scalable cell segmentation, tissue architecture analysis, cell-state mapping, and cell-cell interaction workflows for immune-mediated disease research. Across these areas, our goal is to build robust algorithms, reproducible pipelines, and widely usable data resources that connect large-scale omics data with biological discovery and precision medicine.

Join the lab

We welcome motivated students, postdocs, engineers, and clinicians interested in computational biology, biomedical AI, spatial and single-cell multi-omics, long-read sequencing, and translational genomics. For inquiries, contact Qian Qin at qinqian [at] whu [dot] edu [dot] cn.

See the people page for current members and publications for recent work.

news

May 01, 2026	The Qin AIM Lab website is live.

selected publications

GigaScience

Challenges in structural variant calling in low-complexity regions

Qian Qin and Heng Li

GigaScience, 2025

DOI Bib HTML

@article{Qin2025LCRSV,
  title = {Challenges in structural variant calling in low-complexity regions},
  author = {Qin, Qian and Li, Heng},
  journal = {GigaScience},
  volume = {14},
  pages = {giaf154},
  year = {2025},
  doi = {10.1093/gigascience/giaf154},
}

J Mol Diagn

Survival Motor Neuron Gene Copy Number Analysis by Exome Sequencing: Assisting Spinal Muscular Atrophy Diagnosis and Carrier Screening

B Liu, Y Lu, B Wu, and 7 more authors

The Journal of Molecular Diagnostics*Co-senior authors , 2020

Bib HTML

@article{Liu2020SMN,
  title = {Survival Motor Neuron Gene Copy Number Analysis by Exome Sequencing: Assisting Spinal Muscular Atrophy Diagnosis and Carrier Screening},
  author = {Liu, B and Lu, Y and Wu, B and Yang, L and Liu, R and Wang, H and Dong, X and Li, G and Qin, Qian and Zhou, W},
  journal = {The Journal of Molecular Diagnostics},
  volume = {22},
  number = {5},
  pages = {619--628},
  year = {2020},
}

NAR

Cistrome Data Browser: a data portal for ChIP-seq and chromatin accessibility data in human and mouse

S Mei, Qian Qin, Q Wu, and 11 more authors

Nucleic Acids Research*Co-first authors , 2017

Bib HTML

@article{Mei2017CistromeDataBrowser,
  title = {{Cistrome Data Browser}: a data portal for {ChIP-seq} and chromatin accessibility data in human and mouse},
  author = {Mei, S and Qin, Qian and Wu, Q and Sun, H and Zheng, R and Zang, C and Zhu, M and Wu, J and Shi, X and Taing, L and Liu, T and Brown, M and Meyer, C A and Liu, X S},
  journal = {Nucleic Acids Research},
  volume = {45},
  number = {D1},
  pages = {D658--D662},
  year = {2017},
}

BMC Bioinformatics

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

Qian Qin, S Mei, Q Wu, and 14 more authors

BMC Bioinformatics*Co-first authors , 2016

Bib HTML

@article{Qin2016ChiLin,
  title = {{ChiLin}: a comprehensive {ChIP-seq} and {DNase-seq} quality control and analysis pipeline},
  author = {Qin, Qian and Mei, S and Wu, Q and Sun, H and Li, L and Taing, L and Chen, S and Li, F and Liu, T and Zang, C and Xu, H and Chen, Y and Meyer, C A and Zhang, Y and Brown, M and Long, H W and Liu, X S},
  journal = {BMC Bioinformatics},
  volume = {17},
  number = {1},
  pages = {404},
  year = {2016},
}

PLoS Comput Biol

Imputation for transcription factor binding predictions based on deep learning

Qian Qin and Jianfeng Feng

PLoS Computational Biology, 2017

DOI Bib

@article{Qin2017DeepLearningTF,
  title = {Imputation for transcription factor binding predictions based on deep learning},
  author = {Qin, Qian and Feng, Jianfeng},
  journal = {PLoS Computational Biology},
  volume = {13},
  number = {2},
  pages = {e1005403},
  year = {2017},
  doi = {10.1371/journal.pcbi.1005403},
}

Genome Biol

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Qian Qin, J Fan, R Zheng, and 8 more authors

Genome Biology*Co-first authors , 2020

Bib HTML

@article{Qin2020Lisa,
  title = {{Lisa}: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and {ChIP-seq} data},
  author = {Qin, Qian and Fan, J and Zheng, R and Wan, C and Mei, S and Wu, Q and Sun, H and Brown, M and Zhang, J and Meyer, C A and Liu, X S},
  journal = {Genome Biology},
  volume = {21},
  number = {1},
  pages = {32},
  year = {2020},
}

bioRxiv

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

Qian Qin, Jakob Heinz, and Heng Li

bioRxiv, Oct 2025

DOI Bib HTML

@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},
}

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

Genome Research, Apr 2025

DOI Bib HTML

@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

Spatial Transcriptomics Identify T Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis

Qian Qin, Lennard Ostendorf, Sophia L Wells, and 24 more authors

bioRxiv, Oct 2025

DOI Bib HTML

@article{Qin2025ICIAIN,
  title = {Spatial Transcriptomics Identify {T} Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis},
  author = {Qin, Qian and Ostendorf, Lennard and Wells, Sophia L and Gao, Ce and Tran, Miles and Alikhan, Firasat M and Zhang, Xiwen and Chewcharat, Api and Rider, Robert S and Prell, Sean A and Chowdhury, Raad B and Weins, Astrid and Shah, Sujal I and Mistry, Kavita and Bowman, Teresa and Villani, Alexandra-Chloe and LeBoeuf, Nicole R and Selamet, Umut and Ravi, Katherine Scovner and Sharon, Elad and Leaf, David E and Moledina, Dennis G and Sise, Meghan E and De Vlaminck, Iwijn and Rao, Deepak A and Wei, Kevin and Gupta, Shruti},
  journal = {bioRxiv},
  pages = {2025.10.31.685702},
  month = oct,
  year = {2025},
  doi = {10.1101/2025.10.31.685702},
}

Nat Cancer

Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma

Y Wei, Qian Qin, C Yan, and 1 more author

Nature Cancer*Co-first authors , 2022

DOI Bib

@article{Wei2022Rhabdomyosarcoma,
  title = {Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma},
  author = {Wei, Y and Qin, Qian and Yan, C and others},
  journal = {Nature Cancer},
  year = {2022},
  doi = {10.1038/s43018-022-00414-w},
}