@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},}
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
@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
@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},}
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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
@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},}