Hongkai’s Research Group


(* corresponding author, § equal contribution, bold: lab members and advisees)


New Papers

1. Ji ZC, Zhou WQ, Hou WP, Ji HK* (2020) Single-cell ATAC-seq signal extraction and enhancement with SCATE. Genome Biology, 21:161 [Link] [Link to SCATE]

2. Hou WP, Ji ZC, Ji HK*, Hicks SC* (2020) A systematic evaluation of single-cell RNA-sequencing imputation methods. Genome Biology, 21:218 [Link]


All Publications in Chronological Order

             Peer-reviewed Journal Publications

             Others (Book chapters, Thesis, Technical reports, Editorials)


Selected Publications


Methods and Software


1. Ji HK, Jiang H, Ma W, Johnson DS, Myers RM and Wong WH (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology. 26: 1293-1300. [Link] [Link to CisGenome]

               Keywords: ChIP-seq, ChIP-chip, Peak calling, Motif Discovery, Sequence analysis, Genome annotation

                              Software, Graphical user interface, Statistical modeling, Gibbs sampling, Matching control


2. Zhou WQ, Sherwood B, Ji ZC, Xue Y, Du F, Bai JW, Ying MY, Ji HK*. (2017) Genome-wide prediction of DNase I hypersensitivity using gene expression. Nature Communications. 8: 1038.  [Link] [Link to BIRD] [Link to PDDB] [bioRxiv Preprint].

               Keywords: DNase-seq, Exon array, RNA-seq, Chromatin, Gene expression, Publicly available data

                              Big data, Prediction, High-dimensional regression, Machine learning, Software, Database


3. Zhou WQ, Ji ZC, Fang WX, Ji HK* (2019) Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq. Nucleic Acids Research. 47: e121 [Link] [Link to BIRD]

               Keywords: Single-cell RNA-seq, Single-cell ATAC-seq, Chromatin

                              Prediction, Machine learning, Software


4. Ji ZC, Ji HK* (2016) TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Research. 44(13): e117 [Link] [Link to TSCAN]

               Keywords: Single-cell genomics, Single-cell RNA-seq

                              Pseudotime analysis, Cluster-based minimum spanning tree, Unsupervised learning, Software


5. Ji ZC, Zhou WQ, Hou WP, Ji HK* (2020) Single-cell ATAC-seq signal extraction and enhancement with SCATE. Genome Biology, 21:161 [Link] [Link to SCATE]

               Keywords: Single-cell genomics, Single-cell ATAC-seq, Epigenome, Chromatin

                              Sparse data, Signal detection, Statistical modeling, Machine learning, Data integration, Software


6. Ji HK*, Li X, Wang QF, Ning Y (2013) Differential principal component analysis of ChIP-seq. Proc. Natl. Acad. Sci. USA. 110: 6789-6794. [Link] [Link to dPCA]

               Keywords: ChIP-seq, Epigenome, Histone modification, Chromatin

                              Scalable data integration, Differential signal detection, Differential principal component analysis


7. Wei YY, Tenzen T, Ji HK* (2015) Joint analysis of differential gene expression in multiple studies using correlation motifs. Biostatistics. 16:31-46. [Link] [arXiv Preprint] [Link to CorMotif]

               Keywords: Gene expression, microarray, multiple datasets

                              Scalable data integration, Latent mixture model, Differential signal detection, Software


8. Ji HK and Wong WH (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21: 3629-3636. [Link] [Supporting Website: TileMap]

               Keywords: Tiling array, ChIP-chip, Transcription factor binding site, Histone modification

                              Hidden Markov Model, Hierarchical model, Variance shrinkage, Software


9. Chen L, Wu G, Ji HK* (2011) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. Bioinformatics. 27: 1447-1448. [Link] [Link to hmChIP]

               Keywords: ChIP-seq, ChIP-chip

                              Database, Interactive Web Server


10. Ji ZC, Vokes SA, Dang CV, Ji HK* (2016) Turning publicly available gene expression data into discoveries using gene set context analysis. Nucleic Acids Research. 44(1): e8 [Link] [Link to GSCA]

               Keywords: Publicly available gene expression data, Gene Set Context Analysis

                              Big data, Data mining, Software, Interactive user interface



Biology and Collaboration


11. Chen ZY§, Ji ZC§, Ngiow SF, Manne S, Cai ZY, Huang AC, Johnson J, Staupe RP, Bengsch B, Xu CY, Yu SX, Kurachi M, Herati RS, Vella LA, Baxter AE, Wu JE, Khan O, Beltra JC, Giles JR, Stelekati E, McLane LM, Lau CW, Yang XL, Berger SL, Vahedi G, Ji HK, Wherry EJ (2019)   TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision. Immunity. 51(5):840-855.e5. [Link]

               Keywords: Immune, Single-cell RNA-seq, Gene regulation


12. Kuang Z, Pinglay S, Ji HK*, Boeke JD*. (2017) Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth. eLife. 6:e29938 [Link]

               Keywords: Yeast, Metabolic cell cycle, Gene regulation, Dynamic process, Time course, Chromatin


13. Vokes SA, Ji HK, Wong WH and McMahon AP (2008) A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog mediated patterning of the mammalian limb. Genes & Development. 22: 2651-2663. [Link]

               Keywords: Mouse, Sonic hedgehog pathway, Gene regulation, Embryonic development


14. Niakan KK, Ji HK§, Maehr R§, Vokes SA§, Rodolfa KT, Sherwood RI, Yamaki M, Dimos JT, Chen AE, Melton DA, McMahon AP and Eggan K (2010) Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes & Development. 24: 312-326. [Link]

               Keywords: Mouse, Stem cell, Differentiation, Gene regulation, Transcription factor binding


15. Ji HK*, Wu G, Zhan X, Nolan A, Koh C, De Marzo A, Doan, HM, Fan JS, Cheadle C, Fallahi M, Cleveland JL, Dang CV*, Zeller K*. (2011) Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation. PLoS ONE. 6:e26057. Doi:10.1371/journal.pone.0026057 [Link]

               Keywords: Human, Mouse, Embryonic stem cell, Cancer, Gene regulation, MYC


16. Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ,  Ji HK, Boeke JD, Burns KH (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell. 141: 1171-1182. [Link]

               Keywords: Human, Retrotransposon, TIP-chip


17. The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437: 69-87. [Link]

               Keywords: Chimpanzee, Human, Genome, Comparative genomics, Evolution