An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57-74, 2012 | 16761 | 2012 |
An accurate and robust imputation method scImpute for single-cell RNA-seq data WV Li, JJ Li Nature Communications 9 (1), 997, 2018 | 671 | 2018 |
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions S MacArthur, XY Li, J Li, JB Brown, HC Chu, L Zeng, BP Grondona, ... Genome biology 10 (7), 1-26, 2009 | 397 | 2009 |
Comparative analysis of the transcriptome across distant species MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ... Nature 512 (7515), 445-448, 2014 | 333 | 2014 |
System wide analyses have underestimated protein abundances and the importance of transcription in mammals JJ Li, PJ Bickel, MD Biggin PeerJ 2, e270, 2014 | 331 | 2014 |
Comparative analysis of regulatory information and circuits across distant species AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, ... Nature 512 (7515), 453-456, 2014 | 224 | 2014 |
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation JJ Li, CR Jiang, JB Brown, H Huang, PJ Bickel Proceedings of the National Academy of Sciences 108 (50), 19867-19872, 2011 | 191 | 2011 |
Statistics or biology: the zero-inflation controversy about scRNA-seq data R Jiang, T Sun, D Song, JJ Li Genome biology 23 (1), 1-24, 2022 | 168 | 2022 |
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila WW Fisher, JJ Li, AS Hammonds, JB Brown, BD Pfeiffer, R Weiszmann, ... Proceedings of the National Academy of Sciences 109 (52), 21330-21335, 2012 | 161 | 2012 |
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 | 141 | 2022 |
Benchmarking computational doublet-detection methods for single-cell RNA sequencing data NM Xi, JJ Li Cell systems 12 (2), 176-194. e6, 2021 | 140 | 2021 |
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data JJ Li, H Huang, PJ Bickel, SE Brenner Genome research 24 (7), 1086-1101, 2014 | 109 | 2014 |
Neyman-Pearson classification algorithms and NP receiver operating characteristics X Tong, Y Feng, JJ Li Science advances 4 (2), eaao1659, 2018 | 80 | 2018 |
scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured T Sun, D Song, WV Li, JJ Li Genome biology 22 (1), 1-37, 2021 | 79* | 2021 |
Oct4 was a novel target of Wnt signaling pathway J Li, J Li, B Chen Molecular and cellular biochemistry 362 (1-2), 233-240, 2012 | 77 | 2012 |
Modeling and analysis of RNA-seq data: a review from a statistical perspective WV Li, JJ Li Quantitative Biology 6 (3), 195-209, 2018 | 71 | 2018 |
Statistics requantitates the central dogma JJ Li, MD Biggin Science 347 (6226), 1066-1067, 2015 | 65 | 2015 |
A statistical simulator scDesign for rational scRNA-seq experimental design WV Li, JJ Li Bioinformatics 35 (14), i41–i50, 2019 | 61 | 2019 |
Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis Y Zhang, CJ Harris, Q Liu, W Liu, I Ausin, Y Long, L Xiao, L Feng, X Chen, ... Proceedings of the National Academy of Sciences 115 (5), E1069-E1074, 2018 | 58 | 2018 |
PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data D Song, JJ Li Genome biology 22 (1), 124, 2021 | 53 | 2021 |