Year

No

Articles

2025

6

Ting Qi, Lakshmanan Lakshmi Narayanan, Yuwei Yang, Ying Zhou, Min Pan, Anders Jacobsen Skanderup*, Qinyu Ge*. Read-level DNA methylation deconvolution enhances circulating tumor DNA detection. Briefings In Bioinformatics, 2025, https://doi.org/ 10.1093/bib/bbaf551.

5

Qinyu Ge, Erteng Jia, Tian Wen, Ruibin Zhao, Xiangwei Zhao. Enhanced RNA Preservation in Mouse Brain Tissue: A Strategy Combining Cardiac Perfusion with Hypersaline Immersion. ACS Omega. 2025, https://doi.org/10.1021/acsomega.5c05379. 

4

Ying Zhou, Qinyu Ge,* Moxin Li, Ting Q, Zhihui Li, Yuqi Sheng, Min Pan, Quanjun Liu, Xiangwei Zhao, Zuhong Lu*.   Full-length spatial transcriptome strategy based on robust and low-cost target tissue capture. Biosensors and   Bioelectronics.2025, https://doi.org/ 10.1016/j.bios.2025.118018.

3

Ziyi Zhao, Dehui Zhu, Zuoran Hou, Ying   Zhou, Min Pan* and Qinyu Ge*. Breaking the double-stranded limitation:single-stranded cfDNA sequencing technology opens a new era in precision medicine. Analyst.   https://doi.org/10.1039/d5an00632e

2

Ying Zhou,† Kun Bi,† Qi Xu, Quanjun   Liu, Xiangwei Zhao, Qinyu Ge,* and Zuhong Lu. The Ultrafast and Accurate DNA   Storage and Reading Integrated System Via Microfluidic Magnetic Beads   Polymerase Chain Reaction. ACS Nano, 2025,   https://doi.org/10.1021/acsnano.4c17817.

1

Qinyu Ge, Yanyan Piao, Zhihui Li, Yuwei Yang, Min Pan, Yunfei Bai. Environmental DNA integrity index is sensitive for   species biomass estimation in freshwater. Sci Total Environ. 2025, 966:178734. https://doi:10.1016/j.scitotenv.2025.178734.

Year

No

Articles

2024

9

Zhiyu Liu, Yuwei Yang, Yunfei Bai,   Qinyu Ge. Determination of Cell-Free DNA (cfDNA) Methylation by   Methylation-Sensitive High-Resolution Melting (MS-HRM) in Human Plasma for   the Diagnosis of Gestational Diabetes Mellitus (GDM). Analytical   Letters. 2024. https://doi.org/10.1080/00032719.2024.2399182.

8

Ying Zhou, Kun Bi, Qinyu Ge*, Zuhong   Lu. Advances and Challenges in Random Access Techniques for In VitroDNA Data   Storage. ACS Appl. Mater. Interfaces. 2024, https://doi.org/10.1021/acsami.4c07235.

7

Yanting Shen, Xiawei Fei, Junyan Xu,   Rui Yang*, Qinyu Ge*, Zhong Wang*. Performance analysis of markers for prostate   cell typing in single-cell data. Gene & Disease,   2024,11,101157. https://doi.org/10.1016/j.gendis.2023.101157.

6

Min Pan, Huajuan Shi, Ting Qi, Lingbo   Cai*, Qinyu Ge*. The biological characteristics of long cell-free DNA in   spent embryos culture medium as noninvasive biomarker in in-vitro embryo   selection. Gene. 2024. 927 (2024) 148667. https://doi.org/10.1016/j.gene.2024.148667.

5

Ying Zhou, Yuwei Yang, Ting Qi, Zhuoran   Hou, Qinyu Ge*, and Zuhong Lu. Transcriptome Study of rd1Mouse Brain and   Association with Parkinson’s Disease. ACS Omega. 2024, 9, 24,   25756-25765.. https://doi.org/10.1021/acsomega.3c09938.

4

Ying Zhou, Ting Qi, Yuwei Yang, Zhiyu   Liu, Zhuoran Hou, Xiangwei Zhao, Qinyu Ge*, Zuhong Lu. Effect of Different   Staining Methods on Brain Cryosections. ACS Chem. Neurosci. 2024,   15, 2243−2252. https://doi.org/10.1021/acschemneuro.4c00069.

3

Ting Qi, Ying Zhou, Yuqing Sheng, Zhiyu   Liu, Yuwei Yang, Qunajun Liu, Qinyu Ge*. Prediction of Transcription Factor   Binding Sites on Cell-Free DNA Based on Deep Learning. J.Chem. Inf. Model.   2024, 64, 4002−4008. https://doi.org/10.1021/acs.jcim.4c00047.

2

Zhiyu Liu, Tinglan Ouyang, Yuwei Yang,   Yuqi Sheng, Huajuan Shi, Quanjun Liu, Yunfei Bai, Qinyu Ge*. The Impact of   Blood Sample Processing on Ribonucleic Acid (RNA) Sequencing. Genes.   2024, 15, 502. https://doi.org/10.3390/genes15040502.

1

Huajuan Shi, Qinyu Ge*, Min Pan, Yuqi   Sheng, Ting Qi, Ying Zhou, Yuqing Sun, Yunfei Bai, Lingbo Cai*. Agarose   amplification based sequencing characterization cell-free RNA in   preimplantation spent embryo medium. Analytica Chimica Acta.   2024, 342331 https://doi.org//10.1016/j.aca.2024.342331.

Year

No

Articles

2023

9

Zhou Y, Sheng YQ, Pan M, Tu J, Zhao XW, Ge QY*.   Spatial Transcriptomic Analysis Reveals Regional Transcript Changes in Early   and Late Stages of rd1 Model Mice with Retinitis Pigmentosa. Int. J. Mol. Sci.   2023, 24, 14869. https://doi.org/10.3390/ijms241914869.

8

Zhou Y, Qi T, Pan M, Tu J, Zhao XW, Ge QY*. Deep-Cloud:   A Deep Neural Network-Based Approach for Analyzing Differentially Expressed   Genes of RNA-seq Data. J. Chem. Inf. Model. 2023. https://pubs.acs.org/doi/10.1021/acs.jcim.3c00766.

7

Sun YQ, Liu ZY, Fu Y, Yang YW, Lu JR, Pan M, Wen T, Xie   XY, Bai YF, Ge QY*. Single-cell multi-omics sequencing and its application in tumor heterogeneity. Briefings in Functional Genomics,2023   elad009, https://doi.org/10.1093/bfgp/elad009.

6

Sheng YQ, Wu JS, Li XM, Qiu JY, Li J, Ge QY*,   Cheng L*, Han JW*. iATMEcell: identification of abnormal tumor   microenvironment cells to predict the clinical outcomes in cancer based on   cell–cell crosstalk network. Briefings in Bioinformatics, 2023,   1–13. https://doi.org/10.1093/bib/bbad074.

5

Lu Junru, Sheng Yuqi, Qian Weiheng, Pan Min,   Zhao Xiangwei, Ge Qinyu*, scRNA‐seqdataanalysismethodto improve   analysisperformance. IET Nanobiotechnol. 1–11(2023). https://doi.org/10.1049/nbt2.12115

4

Erteng Jia, Yuqi Sheng, Huajuan Shi, Ying Wang, Ying Zhou, Zhiyu   Liu, Ting Qi, Min Pan,Yunfei Bai, Xiangwei Zhao,* and Qinyu Ge*,Spatial   Transcriptome Profiling of Mouse Hippocampal Single Cell Microzone in   Parkinson’s Disease. Int. J. Mol. Sci. 2023, 24,   1810. https://doi.org/10.3390/ijms2403181.

3

Huajuan Shi, Min Pan, Erteng Jia, Wenxiang Lu,   Ying Zhou, Yuqi Sheng, Xiangwei Zhao, Lingbo Cai* and Qinyu Ge*. A comprehensive characterization of cell-free   RNA in spent blastocyst medium and quality prediction for blastocyst. Clinical Science. 2023, 00 1-14.   https://doi.org/10.1042/CS20220495

2

Ting Qi, Min Pan, Huajuan Shi, Liangying Wang,   Yunfei Bai and Qinyu Ge*. Cell-Free DNA Fragmentomics: The Novel Promising   Biomarker. Int. J. Mol. Sci. 2023, 24, 1503. https://doi.org/10.3390/ijms24021503

1

Yuwei Yang, Zhiyu Liu, Junru Lu, Yuqing Sun,   Yue Fu, Min Pan, Xueying Xie & Qinyu Ge*. Analysis approaches for the   identification and prediction of N6-methyladenosine sites. Epigenetics. 2023,   https://doi.org/10.1080/15592294.2022.2158284.

Year

No

Articles

2022

3

Shi Huajuan, Pan   Min,   Sheng Yuqi Jia Erteng Wang Ying, Dong Juan Tu Jing Bai   Yunfei, Cai Lingbo*  & Ge Qinyu*.   Extracellular cell-free RNA profile in human large follicles and   small   follicles. Front. Cell Dev. Biol. 10:940336. doi:     10.3389/fcell.2022.940336

2

Ying Zhou,   Erteng   Jia , Huajuan Shi, Zhiyu Liu, Yuqi Sheng, Min Pan, Jing   Tu, Qinyu Ge,*   and Zuhong Lu. Prediction of Time-Series   Transcriptomic Gene Expression Based   on Long Short-Term Memory with   Empirical Mode Decomposition. Int. J. Mol. Sci. 2022, 23, 7532.   https://doi.org/10.3390/ijms23147532

1

Ying Zhou,   Erteng   Jia, ……Xiangwei Zhao*, Qinyu Ge*, Zuhong Lu.   Sensitive and Low-Bias Transcriptome Sequencing Using Agarose PCR. ACS   Applied Materials & Interfaces. 2022, 14, 19154-19167.   https://doi.org/10.1021/acsami.2c02133.

Year

No

Articles

2021

7

Shi HJ; Zhou Y; Jia ET;……Ge QY*. Comparative analysis of circular RNA enrichment methods. RNA Biology, 2021,   https://doi.org/10.1080/15476286.2021.2012632

6

Pan M; Shi HJ; LiuZY;……Cai LB*; Ge QY*.   The integrity of cfDNA in follicular fuid and spent medium from embryo culture is associated with embryo grade in patients undergoing in vitro fertilization. Journal of Assisted Reproduction and Genetics,   2021, https://doi.org/10.1007/s10815-021-02357-0

5

Jia ET; Shi HJ; Wang Y; Zhou Y; …Ge QY*.   Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues.  BMC Genomics, 2021, 22: 809.  doi:   10.1186/s12864-021-08132-w.

4

Pan, M; Lu, JF; Liu, ZY;…Ge QY*. Integrity of cfDNA in maternal plasma extracellular vesicles as a potential biomarker for  NIPT. Int J Gynaecol Obstet. 2021. doi: 10.1002/ijgo.13976

3

Zhou, Y; Jia, ET; Qiao, Y; Shi, HJ; Liu, ZY; Pan, M;   Zhao, XW; Bai, YF; Ge, QY*.   Low bias multiple displacement amplification with confinement effect based on agarose gel. ANALYTICAL   AND BIOANALYTICAL CHEMISTRY. 2021, 413: 4397_4405.   10.1007/s00216-021-03415-3

2

Shi, HJ; Zhou, Y; Jia, ET; Pan, M; Bai, YF; Ge,   QY*. Bias in   RNA-seq Library Preparation: Current Challenges and Solutions. BIOMED RESEARCH INTERNATIONAL.2021,   2021: 6647597. 10.1155/2021/6647597

1

Jia, ET; Zhou, Y; Shi, HJ; Pan, M; Zhao, XW; Ge,   QY*. Effects of brain tissue section processing and storage time on gene expression.  ANALYTICA  CHIMICA ACTA. 2021, 1142:  38_47. 10.1016/j.aca.2020.10.046