| Exaggerated false positives by popular differential expression methods when analyzing human population samples Y Li, X Ge, F Peng, W Li, JJ Li Genome biology 23 (1), 79, 2022 | 197 | 2022 |
| DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features J Lyu, JJ Li, J Su, F Peng, YE Chen, X Ge, W Li Science advances 6 (46), eaba6784, 2020 | 51 | 2020 |
| Clipper: p-value-free FDR control on high-throughput data from two conditions X Ge, YE Chen, D Song, ML McDermott, K Woyshner, A Manousopoulou, ... Genome biology 22, 1-29, 2021 | 48 | 2021 |
| DreamAI: algorithm for the imputation of proteomics data W Ma, S Kim, S Chowdhury, Z Li, M Yang, S Yoo, F Petralia, J Jacobsen, ... Biorxiv, 2020.07. 21.214205, 2020 | 32 | 2020 |
| Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms A Patowary, P Zhang, C Jops, CK Vuong, X Ge, K Hou, M Kim, N Gong, ... Science 384 (6698), eadh7688, 2024 | 26* | 2024 |
| A remark on copy number variation detection methods S Li, X Dou, R Gao, X Ge, M Qian, L Wan PLoS One 13 (4), e0196226, 2018 | 20 | 2018 |
| ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping D Song, K Li, X Ge, JJ Li Research Square, 2023 | 17 | 2023 |
| METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL Y Wu, M Jin, M Fernandez, KL Hart, A Liao, X Ge, SM Fernandes, ... Blood Cancer Discovery 4 (3), 228-245, 2023 | 17 | 2023 |
| EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences X Ge, H Zhang, L Xie, WV Li, SB Kwon, JJ Li Nucleic acids research 47 (13), e77-e77, 2019 | 8 | 2019 |
| A large-sample crisis? exaggerated false positives by popular differential expression methods Y Li, X Ge, F Peng, W Li, JJ Li bioRxiv, 2021.08. 25.457733, 2021 | 6 | 2021 |
| APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control YE Chen, X Ge, K Woyshner, ML McDermott, A Manousopoulou, ... Genomics, Proteomics & Bioinformatics, qzae042, 2024 | 2 | 2024 |
| Fasting mimicking diet cycles versus a Mediterranean diet and cardiometabolic risk in overweight and obese hypertensive subjects: a randomized clinical trial A Mishra, M Fanti, X Ge, D Vaughn, S Brandhorst, M Wei, KM Hong, ... npj Metabolic Health and Disease 1 (1), 1, 2023 | 2 | 2023 |
| ClipperQTL: ultrafast and powerful eGene identification method HJ Zhou, X Ge, JJ Li bioRxiv, 2023 | 2 | 2023 |
| Wilcoxon rank-sum test still outperforms dearseq after accounting for the normalization impact in semi-synthetic RNA-seq data simulation Y Li, X Ge, F Peng, W Li, JJ Li bioRxiv, 2022.06. 07.494963, 2022 | 2 | 2022 |
| Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA T Sun, J Yuan, Y Zhu, J Li, S Yang, J Zhou, X Ge, S Qu, W Li, JJ Li, Y Li Genome Biology 25 (1), 318, 2024 | | 2024 |
| Response to" Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and" Winsorization greatly reduces false positives … X Ge, Y Li, W Li, JJ Li Genome Biology 25 (1), 283, 2024 | | 2024 |
| Computation Methods in the Era of Big Biology Data: Opportunities and Obstacles M Wang, X Ge XRDS: Crossroads, The ACM Magazine for Students 30 (2), 7-8, 2024 | | 2024 |
| Enhancing Rigor in Computational Methods for Biological Data Analysis X Ge XRDS: Crossroads, The ACM Magazine for Students 30 (2), 34-37, 2024 | | 2024 |
| Systematic Evaluation of Cell Type Deconvolution Methods for Plasma Cell-free DNA T Sun, J Yuan, Y Zhu, S Yang, J Zhou, X Ge, S Qu, W Li, JJ Li, Y Li bioRxiv, 2024.03. 25.586507, 2024 | | 2024 |
| Proteogenomic Features Define Novel Subtypes of Mantle Cell Lymphoma Y Yan, X Ge, J Sun, L Yu, Q Zhang, Y Yu, Z Jia, D Zou, J Li, L Qiu, L Wang, ... Blood 142, 4368, 2023 | | 2023 |
