关于 | Qin AIM Lab

课题组负责人

人工智能学院教授

欢迎来到 Qin AIM Lab。我们是武汉大学人工智能学院面向精准医学的 AI 与多组学研究实验室，致力于发展 AI 驱动的计算生物学方法和多组学平台，用于理解基因调控、癌症演化、免疫相关疾病机制以及具有临床意义的基因组变异。

课题组结合表观基因组学、临床基因组学、癌症基因组学、长读长测序、单细胞分析、空间转录组学和生物医学软件转化等方向的经验。当前重点之一是发展 long-read RNA-seq 和 DNA-seq 方法，解析短读长技术难以捕获的复杂转录本异构体、结构变异、调控扰动和多组学信号。

我们也重点发展 Xenium 空间转录组学方法，包括可扩展的细胞分割、组织结构分析、细胞状态图谱构建以及细胞间相互作用分析流程，并将其应用于免疫相关疾病研究。围绕这些方向，我们希望构建稳健的算法、可复现的分析流程和易于推广的数据资源，将大规模组学数据与生物学发现和精准医学连接起来。

加入我们

我们欢迎对计算生物学、生物医学 AI、空间与单细胞多组学、长读长测序和转化基因组学感兴趣的学生、博士后、工程师和临床合作者加入或交流。请联系秦谦：qinqian [at] whu [dot] edu [dot] cn。

当前成员请见成员页面，近期研究请见发表论文页面。

新闻

2026-05-01	Qin AIM Lab 网站已上线。

代表性论文

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},
}