Hongkai’s Research Group


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


New Papers

1. Zhang JJ§, Ji ZC§, Caushi JX§, Asmar ME§, Anagnostou V, Cottrell TR, Chan HY, Suri P, Guo HD, Merghoub T, Chaft JE, Reuss JE, Tam A, Blosser R, Abu-Akeel M, Sidhom JW, Zhao N, Ha JS, Jones DR, Marrone KA, Naidoo J, Gabrielson E, Taube JM, Velculescu VE, Brahmer JR,  Housseau F, Hellmann MD, Forde PM, Pardoll DM, Ji HK*, Smith KN* (2019) Compartmental analysis of T cell clonal dynamics as a function of pathologic response to neoadjuvant PD-1 blockade. Clinical Cancer Research. To appear

2. 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. DOI:https://doi.org/10.1016/j.immuni.2019.09.013 [Link]

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. gkz716 [Link] [Link to BIRD]

4. Azuine RE, Ji YL, Chang HY, Kim Y, Ji HK, DiBari J, Hong XM, Wang GY, Singh GK, Pearson C, Zuckerman B, Surkan PJ, Wang XB (2019) Prenatal Risk Factors, Peri- and Post-natal Outcomes associated with Maternal Opioids Exposure in a U.S. Urban Low-Income Multi-Ethnic Population. JAMA Network Open. 2(6):e196405 [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. gkz716 [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 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


6. Ji ZC§, Zhou WQ§, Ji HK*. (2017) Single cell regulome data analysis by SCRAT.  Bioinformatics. 33(18):2930-2932. [Link] [Link to SCRAT at github] [Link to SCRAT web server]

                 Keywords: Single-cell genomics, Single-cell ATAC-seq, Single-cell DNase-seq, Single-cell ChIP-seq

                                  Software, Database, Sparse data, Data integration


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. 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


12. 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


13. 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


14. 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


15. 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


16. 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