Selected Publications

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

Methods, Software & Database

Single cell genomics

  • Fang WX, Bell CM, Sapirstein A, Asami S, Leeper K, Zack DJ, Ji HK*, Kalhor R* (2022) Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Cell. 185:4604–4620 [Link]
  • 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]
  • Hou WP, Ji ZC, Ji HK*, Hicks SC* (2020) A systematic evaluation of single-cell RNA-sequencing imputation methods. Genome Biology. 21:218 [Link]
  • 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]
  • 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]
  • 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]

High-throughput regulome, epigenome & transcriptome analysis

  • 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]
  • Wu G§, Yustein JT§, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji HK* (2013) ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.  Bioinformatics. 29: 1182-1189. [Link] [Link to ChIP-PED]
  • 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]
  • Wu H and Ji HK* (2010) JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics. 26:1864-1870. [Link] [Link to JAMIE]
  • 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]
  • Ji HK, Vokes SA and Wong WH (2006) A comparative analysis of genome-wide ChIP-chip data for mammalian transcription factors. Nucleic Acids Research. 34: e146. [Link] [Supporting Website]
  •  Ji HK and Wong WH (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21: 3629-3636. [Link] [Supporting Website: TileMap]

Big data and scalable data integration

  • 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]
  • 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]
  • 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]

Applications to biology, medicine and public health

Gene regulation, development & stem cells

  • 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]
  • 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]
  • Lee EY, Ji HK, Ouyang ZQ, Zhou BY, Ma WX, Vokes SA, McMahon AP, Wong WH, Scott MP (2010) Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis. Proc. Natl. Acad. Sci. USA. 107: 9736-9741. [Link]
  • 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]
  • Vokes SA, Ji HK, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh WJ, Davidson EH, Wong WH and McMahon AP (2007) Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development, 134: 1977-1989. [Link]

Cancer & cancer immunology

  • Caushi J§, Zhang JJ§, Ji ZC, Vaghasia A, Zhang BY, Hsiue EHC, Mog BJ, Hou WP, Justesen S, Blosser R, Tam A, Anagnostou V, Cottrell TR, Guo HD, Chan HY, Singh D, Thapa S, Dykema AG, Burman P, Choudhury B, Aparicio L, Cheung LS, Lanis M, Belcaid Z, El Asmar M, Illei PB, Wang RL, Meyers J, Schuebel K, Gupta A, Skaist A, Wheelan S, Naidoo J, Marrone KA, Brock M, Ha J, Bush EL, Park BJ, Bott M, Jones DR, Reuss JE, Velculescu VE, Chaft JE, Kinzler KW, Zhou SB, Vogelstein B, Taube JM, Hellmann MD, Brahmer JR, Merghoub T, Forde PM, Yegnasubramanian S*, Ji HK*, Pardoll DM*, Smith KN* (2021) Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. Nature. [Link]
  • 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. DOI: 10.1158/1078-0432.CCR-19-2931 [Link]
  • 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]
  • Wang QF, Wu G, Mi SL, He FH, Wu J, Dong JF, Luo R, Mattison R, Kaberlein J, Prabhakar S, Ji HK, Thirman MJ. (2011) MLL fusion proteins preferentially regulate a subset of wild type MLL target genes in the leukemic genome. Blood. 117: 6895-6905[Link].
  • Paik JH, Kollipara R, Chu G, Ji HK, Xiao Y, Ding Z, Miao L, Tothova Z, Horner JW, Carrasco DR, Jiang S, Gilliland DG, Chin L, Wong WH, Castrillon DH and DePinho RA (2007) FoxOs are lineage-restricted redundant tumor suppressors and critical regulators of endothelial cell homeostasis. Cell. 128 (2): 309-323. [Link]

Immune & infectious disease

  • Karaba AH§, Zhou WQ§, Hsieh LL, Figueroa A, Massaccesi G, Rothman RE, Fenstermacher KZJ, Sauer L, Shaw-Saliba K, Blair PW, Robinson ML, Leung S, Wesson R, Alachkar N, El-Diwany R, Ji HK, Cox AL (2021) Differential cytokine signatures of SARS-CoV-2 and influenza infection highlight key differences in pathobiology. Clinical Infectious Diseases. In press. [Link]
  • Dykema AG§, Zhang BY§, Woldemeskel BA, Garliss CC, Cheung LS, Choudhury D, Zhang JJ, Aparicio L, Bom S, Rashid R, Caushi JX, Hsiue EHC, Cascino K, Thompson EA, Kwaa AK, Singh D, Thapa S, Ordonez AA, Pekosz A, D’Alessio FR, Powell JD, Yegnasubramanian S, Zhou SB, Pardoll DM, Ji HK, Cox AL, Blankson JN, Smith KN (2021) Functional characterization of CD4+ T-cell receptors cross-reactive for SARS-CoV-2 and endemic coronaviruses. Journal of Clinical Investigation. 131(10):e146922 [Link]
  • 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]

Genome analysis (comparative genomics, retrotransposons)

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