publications | Qin AIM Lab

For the most up-to-date citation record, see Qian Qin’s Google Scholar profile.

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

bioRxiv, Mar 2026

@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

Jingqing Hu, Qian Qin, Heng Li, and 1 more author

Bioinformatics, May 2026

DOI Bib HTML Code

@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},
}

bioRxiv

Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis

Vikram Khedgikar, Qian Qin, Miles Tran, and 12 more authors

bioRxivCo-corresponding authors: Vikram Khedgikar and Kevin Wei , Mar 2026

DOI Bib HTML

@article{Khedgikar2026RAneurotrophin,
  title = {Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis},
  author = {Khedgikar, Vikram and Qin, Qian and Tran, Miles and Kazerounian, Shideh and Ce, Gao and Prell, Sean A and McIntyre, Alexa B R and Bhamidipati, Kartik and Presti, Sonia and Blazar, Philip E and Lange, Jeffrey K and Jones, Morgan H and Gravallese, Ellen M and Wechalekar, Mihir D and Wei, Kevin},
  journal = {bioRxiv},
  pages = {2026.03.12.711120},
  month = mar,
  year = {2026},
  doi = {10.64898/2026.03.12.711120},
}

2025

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},
}

GPB

colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs

M K Le, Qian Qin, and Heng Li

Genomics, Proteomics & Bioinformatics, Sep 2025

DOI Bib HTML Code

@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},
}

Nat Biotechnol

Defining and benchmarking open problems in single-cell analysis

Malte D Luecken, Scott Gigante, Daniel B Burkhardt, and 14 more authors

Nature Biotechnology, Jul 2025

DOI Bib HTML

@article{Luecken2025OpenProblems,
  title = {Defining and benchmarking open problems in single-cell analysis},
  author = {Luecken, Malte D and Gigante, Scott and Burkhardt, Daniel B and Cannoodt, Robrecht and Strobl, Daniel C and Markov, Nikolay S and Zappia, Luke and Palla, Giovanni and Lewis, Wesley and Dimitrov, Daniel and Vinyard, Michael E and Magruder, D S and Mueller, Michaela F and Andersson, Alma and Dann, Emma and Qin, Qian and others},
  journal = {Nature Biotechnology},
  volume = {43},
  number = {7},
  pages = {1035--1040},
  month = jul,
  year = {2025},
  doi = {10.1038/s41587-025-02694-w},
}

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},
}

Nature

The Somatic Mosaicism across Human Tissues Network

Tim H H Coorens, Ji Won Oh, Yujin Angelina Choi, and 5 more authors

Nature, Jul 2025

DOI Bib HTML

@article{SMaHT2025Network,
  title = {The Somatic Mosaicism across Human Tissues Network},
  author = {Coorens, Tim H H and Oh, Ji Won and Choi, Yujin Angelina and Lim, Nam Seop and Zhao, Boxun and Voshall, Adam and Abyzov, Alexej and others},
  journal = {Nature},
  volume = {643},
  number = {8070},
  pages = {47--59},
  month = jul,
  year = {2025},
  doi = {10.1038/s41586-025-09096-7},
}

Nat Commun

The PIK3CA/AKT pathway drives therapy resistance in rhabdomyosarcoma

Q Yang, Y Wang, L A Corchete Sanchez, and 13 more authors

Nature Communications, Dec 2025

DOI Bib HTML

@article{Yang2025RMSResistance,
  title = {The {PIK3CA/AKT} pathway drives therapy resistance in rhabdomyosarcoma},
  author = {Yang, Q and Wang, Y and Corchete Sanchez, L A and Mathavarajah, S and Qin, Qian and Wei, Y and Alpert, E and Whelton, L and Sharma, P and Strom, S and Oultache, I and Iafrate, A J and Pinello, L and Rheinbay, E and Yan, C and Langenau, D M},
  journal = {Nature Communications},
  volume = {17},
  number = {1},
  pages = {65},
  month = dec,
  year = {2025},
  doi = {10.1038/s41467-025-66632-9},
}

bioRxiv

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

Yuwei Zhang, Han Qu, Qian Qin, and 2 more authors

bioRxiv, Oct 2025

DOI Bib HTML

@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},
}

2022

bioRxiv

Pyro-Velocity: Probabilistic RNA Velocity inference from single-cell data

Qian Qin, E Bingham, G La Manno, and 2 more authors

bioRxiv, 2022

DOI Bib

@article{Qin2022PyroVelocity,
  title = {{Pyro-Velocity}: Probabilistic {RNA} Velocity inference from single-cell data},
  author = {Qin, Qian and Bingham, E and La Manno, G and Langenau, D M and Pinello, L},
  journal = {bioRxiv},
  year = {2022},
  doi = {10.1101/2022.09.12.507691},
}

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},
}

2021

Curr Opin Syst Biol

Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate

L Wang, Q Zhang, Qian Qin, and 1 more author

Current Opinion in Systems Biology, 2021

DOI Bib

@article{Wang2021TrajectoryReview,
  title = {Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate},
  author = {Wang, L and Zhang, Q and Qin, Qian and others},
  journal = {Current Opinion in Systems Biology},
  volume = {26},
  year = {2021},
  doi = {10.1016/j.coisb.2021.03.006}
}

2020

Nature

Expanded encyclopaedias of DNA elements in the human and mouse genomes

ENCODE Project Consortium

Nature, 2020

Bib HTML

@article{ENCODE2020Expanded,
  title = {Expanded encyclopaedias of {DNA} elements in the human and mouse genomes},
  author = {{ENCODE Project Consortium}},
  journal = {Nature},
  volume = {583},
  number = {7818},
  pages = {699--710},
  year = {2020},
}

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},
}

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},
}

Genome Biol

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

C Wang, D Sun, X Huang, and 13 more authors

Genome Biology, 2020

Bib HTML

@article{Wang2020MAESTRO,
  title = {Integrative analyses of single-cell transcriptome and regulome using {MAESTRO}},
  author = {Wang, C and Sun, D and Huang, X and Wan, C and Li, Z and Han, Y and Qin, Qian and Fan, J and Qiu, X and Xie, Y and Meyer, C A and Brown, M and Tang, M and Long, H and Liu, T and Liu, X S},
  journal = {Genome Biology},
  volume = {21},
  number = {1},
  pages = {198},
  year = {2020},
}

NPJ Genom Med

Clinical utility of 24-h rapid trio-exome sequencing for critically ill infants

H Wang, Y Qian, Y Lu, and 7 more authors

NPJ Genomic Medicine, 2020

Bib HTML

@article{Wang2020RapidTrioExome,
  title = {Clinical utility of 24-h rapid trio-exome sequencing for critically ill infants},
  author = {Wang, H and Qian, Y and Lu, Y and Qin, Qian and Lu, G and Cheng, G and Zhang, P and Yang, L and Wu, B and Zhou, W},
  journal = {NPJ Genomic Medicine},
  volume = {5},
  pages = {20},
  year = {2020},
}

2019

BMC Med Genet

Feeding difficulty is the dominant feature in 12 Chinese newborns with CHD7 pathogenic variants

X Chen, K Yan, Y Gao, and 6 more authors

BMC Medical Genetics*Co-senior authors , 2019

Bib HTML

@article{Chen2019CHD7,
  title = {Feeding difficulty is the dominant feature in 12 {Chinese} newborns with {CHD7} pathogenic variants},
  author = {Chen, X and Yan, K and Gao, Y and Wang, H and Chen, G and Wu, B and Qin, Qian and Yang, L and Zhou, W},
  journal = {BMC Medical Genetics},
  volume = {20},
  number = {1},
  pages = {93},
  year = {2019},
}

Mol Biol Rep

Relationship between phenotype and genotype of 102 Chinese newborns with Prader-Willi syndrome

M M Ge, Y Y Gao, B B Wu, and 5 more authors

Molecular Biology Reports, 2019

Bib HTML

@article{Ge2019PraderWilli,
  title = {Relationship between phenotype and genotype of 102 {Chinese} newborns with {Prader-Willi} syndrome},
  author = {Ge, M M and Gao, Y Y and Wu, B B and Yan, K and Qin, Qian and Wang, H and Zhou, W and Yang, L},
  journal = {Molecular Biology Reports},
  volume = {46},
  number = {5},
  pages = {4717--4724},
  year = {2019},
}

NAR

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

R Zheng, C Wan, S Mei, and 8 more authors

Nucleic Acids Research, 2019

Bib HTML

@article{Zheng2019CistromeDataBrowser,
  title = {{Cistrome Data Browser}: expanded datasets and new tools for gene regulatory analysis},
  author = {Zheng, R and Wan, C and Mei, S and Qin, Qian and Wu, Q and Sun, H and Chen, C H and Brown, M and Zhang, X and Meyer, C A and Liu, X S},
  journal = {Nucleic Acids Research},
  volume = {47},
  number = {D1},
  pages = {D729--D735},
  year = {2019},
}

2018

CSH Mol Case Stud

Early-onset infant epileptic encephalopathy associated with a de novo PPP3CA gene mutation

Y Qian, B Wu, Y Lu, and 4 more authors

Cold Spring Harbor Molecular Case Studies, 2018

Bib HTML

@article{Qian2018PPP3CA,
  title = {Early-onset infant epileptic encephalopathy associated with a de novo {PPP3CA} gene mutation},
  author = {Qian, Y and Wu, B and Lu, Y and Dong, X and Qin, Qian and Zhou, W and Wang, H},
  journal = {Cold Spring Harbor Molecular Case Studies},
  volume = {4},
  number = {6},
  year = {2018},
}

2017

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},
}

Cancer Res

Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer

S Mei, C A Meyer, R Zheng, and 11 more authors

Cancer Research, 2017

Bib HTML

@article{Mei2017CistromeCancer,
  title = {{Cistrome Cancer}: A Web Resource for Integrative Gene Regulation Modeling in Cancer},
  author = {Mei, S and Meyer, C A and Zheng, R and Qin, Qian and Wu, Q and Jiang, P and Li, B and Shi, X and Wang, B and Fan, J and Shih, C and Brown, M and Zang, C and Liu, X S},
  journal = {Cancer Research},
  volume = {77},
  number = {21},
  pages = {e19--e22},
  year = {2017},
}

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},
}

2016

Bioinformatics

CRISPR-DO for genome-wide CRISPR design and optimization

J Ma, J Koster, Qian Qin, and 9 more authors

Bioinformatics, 2016

Bib HTML

@article{Ma2016CRISPRDO,
  title = {{CRISPR-DO} for genome-wide {CRISPR} design and optimization},
  author = {Ma, J and Koster, J and Qin, Qian and Hu, S and Li, W and Chen, C and Cao, Q and Wang, J and Mei, S and Liu, Q and Xu, H and Liu, X S},
  journal = {Bioinformatics},
  volume = {32},
  number = {21},
  pages = {3336--3338},
  year = {2016},
}

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},
}

Genome Res

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles

S Wang, C Zang, T Xiao, and 10 more authors

Genome Research, 2016

Bib HTML

@article{Wang2016H3K27ac,
  title = {Modeling cis-regulation with a compendium of genome-wide histone {H3K27ac} profiles},
  author = {Wang, S and Zang, C and Xiao, T and Fan, J and Mei, S and Qin, Qian and Wu, Q and Li, X and Xu, K and He, H H and Brown, M and Meyer, C A and Liu, X S},
  journal = {Genome Research},
  volume = {26},
  number = {10},
  pages = {1417--1429},
  year = {2016},
}

Mol Cancer Res

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

H Xu, K Xu, H H He, and 11 more authors

Molecular Cancer Research, 2016

Bib HTML

@article{Xu2016EZH2E2F1,
  title = {Integrative Analysis Reveals the Transcriptional Collaboration between {EZH2} and {E2F1} in the Regulation of Cancer-Related Gene Expression},
  author = {Xu, H and Xu, K and He, H H and Zang, C and Chen, C H and Chen, Y and Qin, Qian and Wang, S and Wang, C and Hu, S and Li, F and Long, H and Brown, M and Liu, X S},
  journal = {Molecular Cancer Research},
  volume = {14},
  number = {2},
  pages = {163--172},
  year = {2016},
}

Nat Commun

High-dimensional genomic data bias correction and data integration using MANCIE

C Zang, T Wang, K Deng, and 11 more authors

Nature Communications, 2016

Bib HTML

@article{Zang2016MANCIE,
  title = {High-dimensional genomic data bias correction and data integration using {MANCIE}},
  author = {Zang, C and Wang, T and Deng, K and Li, B and Hu, S and Qin, Qian and Xiao, T and Zhang, S and Meyer, C A and He, H H and Brown, M and Liu, J S and Xie, Y and Liu, X S},
  journal = {Nature Communications},
  volume = {7},
  pages = {11305},
  year = {2016},
}

2014

NAR

CR Cistrome: a ChIP-seq database for chromatin regulators and histone modification linkages in human and mouse

Q Wang, J Huang, H Sun, and 9 more authors

Nucleic Acids Research, 2014

Bib HTML

@article{Wang2014CRCistrome,
  title = {{CR Cistrome}: a {ChIP-seq} database for chromatin regulators and histone modification linkages in human and mouse},
  author = {Wang, Q and Huang, J and Sun, H and Liu, J and Wang, J and Wang, Q and Qin, Qian and Mei, S and Zhao, C and Yang, X and Liu, X S and Zhang, Y},
  journal = {Nucleic Acids Research},
  volume = {42},
  number = {Database issue},
  pages = {D450--D458},
  year = {2014},
}

Genome Biol

MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes

X Zheng, Q Zhao, H J Wu, and 15 more authors

Genome Biology, 2014

Bib HTML

@article{Zheng2014MethylPurify,
  title = {{MethylPurify}: tumor purity deconvolution and differential methylation detection from single tumor {DNA} methylomes},
  author = {Zheng, X and Zhao, Q and Wu, H J and Li, W and Wang, H and Meyer, C A and Qin, Qian and Xu, H and Zang, C and Jiang, P and Li, F and Hou, Y and He, J and Wang, J and Wang, J and Zhang, P and Zhang, Y and Liu, X S},
  journal = {Genome Biology},
  volume = {15},
  number = {8},
  pages = {419},
  year = {2014},
}