Hongkai’s Research Group

Publications

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

 

Representative Publications

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]

2. 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]

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

4. 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]

5. 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]

6. 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]

7. 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]

8. 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]             

 

Peer Reviewed Journal Articles

2017

1. Hong XM, Hao K, Ji HK, Peng SN, Sherwood B, Narzo AD, Tsai HJ, Liu X, Burd I, Wang GY, Ji YL, Caruso D, Mao GY, Bartell TR, Zhang ZY, Pearson C, Hefferner L, Cerda S, Beaty T, Fallin MD, Lee-Parritz A, Zuckerman B, Weeks DE, Wang XB (2017) Genome-wide approach identified a novel gene-maternal pre-pregnancy BMI interaction on preterm birth. Nature Communications. To appear

2. White DT, Sengupta S, Saxena MT, Xu Q, Hanes J, Ding D, Ji HK, Mumm JS (2017) Innate immune system regulation of retinal regeneration – immunomodulatory enhancement of photoreceptor replacement kinetics in zebrafish. Proc. Natl. Acad. Sci. USA. To appear [Link]

3. Hong XM, Sherwood B, Ladd-Acosta C, Peng S, Ji HK, Hao K, Burd I, Bartell TR, Wang G, Tsai HJ, Liu X, Ji Y, Wahl A, Caruso D, Lee-Parritz A, Zuckerman B, Wang X (2017) Genome-wide DNA methylation associations with spontaneous preterm birth in US blacks: findings in maternal and cord blood samples. Epigenetics. To appear [Link]

 

2016

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]

5. Wang J, Xia SL, Arand B, Zhu H, Machiraju R, Huang K, Ji HK, Qian J (2016) Single-cell co-expression analysis reveals distinct functional modules, co-regulation mechanisms and clinical outcomes. PLoS Computational Biology. 12(4): e1004892. [Link]

6. Li Q, Lex RK, Chung HW, Giovanetti SM, Ji ZC, Ji HK, Person MD, Kim J, Vokes SA (2016) NANOG binds to GLI proteins and represses hedgehog-mediated transcription. Journal of Biological Chemistry 291:7171-7182 [Link]

7. Hong XM, Ladd-Acosta C, Hao K, Sherwood B, Ji HK, Keete CA, Kumarf R, Carusoa D, Liu X, Wang GY, Chen Z, Ji YL, Mao GY, Walker SO,  Bartell TR, Ji ZC, Sun YF, Tsai HJ, Pongracic JA, Weeks DE, Wang XB (2016) Epigenome-wide association study links site-specific DNA methylation changes with cow’s milk allergy. Journal of Allergy and Clinical Immunology. 138 (3): 908 - 911.e9 [Link]

8. Wang GY, Hu FB, Mistry KB, Zhang CL, Ren FZ, Huo Y, Paige D, Bartell T, Hong XM, Caruso D, Ji ZC, Chen Z, Ji YL, Pearson C, Ji HK, Zuckerman B, Cheng TL, Wang XB. (2016) Associations of maternal prepregnancy BMI and plasma folate concentrations with child metabolic health. JAMA Pediatrics. 170(8):e160845. [Link]

9. Mao G, Nachman RM, Sun Q, Zhang X, Koehler K, Chen Z, Hong XM, Wang GY, Caruso D, Zong G, Pearson C, Ji HK, Biswal S, Zuckerman B, Wills-Karp M, Wang XB (2016) Individual and Joint Effects of Early-Life Ambient PM2.5 Exposure and Maternal Pre-Pregnancy Obesity on Childhood Overweight or Obesity. Environmental Health Perspectives. DOI:10.1289/EHP261 [Link]

10. Zhou WQ, Sherwood B, Ji HK* (2016) Global prediction of the functional genomic landscape: applications, methods and challenges. Human Heredity. 81:88-105. [Link]

11. Norrie JL, Li Q, Co S, Huang BL, Ding D, Uy JC, Ji ZC, Mackem S, Bedford MT, Galli A, Ji HK, Vokes SA (2016) PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud. Development. 143:4608-4619. [Link]

12. White DT, Eroglu AU, Wang G, Zhang L, Sengupta S, Ding D, Rajpurohit SK, Walker SL, Ji HK, Qian J, Mumm JS (2016) ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates. Nature Protocols 11:2432–2453 [Link]

 

2015

13. 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]

14. Lewandowski JP, Du F, Zhang SL, Powell MB, Falkenstein KN, Ji HK, Vokes SA (2015) Spatiotemporal regulation of GLI target genes in the mammalian limb bud. Developmental Biology. 406(1): 92-103. [Link]

15. Jin K, Park S, Teo WW, Korangath P, Cho S, Yoshida T, Gyorffy B, Goswami CP, Nakshatri H, Cruz LA, Zhou WQ, Ji HK, Su Y, Ekram M, Wu Z, Zhu T, Polyak K, Sukumar S (2015) HOXB7 is an ERα cofactor in the activation of HER2 and multiple ER target genes leading to endocrine resistance. Cancer Discovery. 5: 944-959. DOI: 10.1158/2159-8290.CD-15-0090 [Link]

16. Wamaitha SE, del Valle I, Cho LTY, Wei YY, Fogarty NME, Blakeley P, Sherwood RI, Ji HK, Niakan KK (2015) Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells. Genes & Development. 29: 1239-1255 [Link]

17. Zhang SL, Du F, Ji HK* (2015) A novel DNA sequence motif in human and mouse genomes. Scientific Reports. 5: 10444 doi:10.1038/srep10444. [Link]

 

2014

18. Wei YY, Tenzen T, Ji HK* (2014) Joint analysis of differential gene expression in multiple studies using correlation motifs. Biostatistics. 16:31-46. [Link] [arXiv Preprint] [Link to CorMotif]

19. Ying MY, Tilghman J, Wei YY, Guerrero-Cazares H, Quinones-Hinojosa A, Ji HK, Laterra J (2014) Kruppel-like factor-9 (KLF9) inhibits glioblastoma stemness through global transcription repression and integrin alpha6 inhibition. Journal of Biological Chemistry. 289: 32742-32756. doi: 10.1074/jbc.M114.588988 [Link]

20. Kuang Z, Cai L, Zhang XK, Ji HK, Tu B, Boeke JD (2014) A high temporal resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nature Structural & Molecular Biology. 21: 854-863. doi:10.1038/nsmb.2881 [Link]

21. Wu H*, Ji HK* (2014) PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information. PLoS ONE. 9: e89694. [Link] [Link to PolyaPeak]

 

2013

22. 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]

23. 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]

24. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji HK, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. (2013) Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 9:655. [Link]

25. Wang JY, Park JS, Wei YY, Rajurkar M, Cotton JL, Fan Q, Lewis BC, Ji HK, Mao JH (2013) TRIB2 acts downstream of Wnt/TCF in liver cancer cells to regulate YAP and C/EBPalpha function. Molecular Cell. 51: 211-225 [Link]

26. Wu G, Ji HK* (2013) ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking. BMC Bioinformatics. 14:188. [Link] [Link to ChIPXpress]

27. Jaffe AE, Storey JD, Ji HK, Leek JT (2013) Gene set bagging for estimating the probability a statistically significant result will replicate. BMC Bioinformatics. 14:360 [Link]

 

2012

28. Wei YY§, Li X§, Wang QF, Ji HK* (2012) iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets. BMC Genomics 13:681. [Link] [Link to iASeq]

29. Hwang W, Hackler L Jr, Wu G, Ji HK, Zack DJ, Qian J (2012) Dynamics of Regulatory Networks in the Developing Mouse Retina. PLoS ONE 7(10): e46521. doi:10.1371/journal.pone.0046521. [Link]

30. Kano S, Colantuoni C, Han F, Zhou ZF, Yuan QP, Wilson A, Takayanagi Y, Lee Y, Rapoport J, Eaton W, Cascella N, Ji HK, Goldman D, Sawa A (2012) Genome-wide profiling of multiple histone methylations in olfactory cells: further implications for cellular susceptibility to oxidative stress in schizophrenia. Molecular Psychiatry. doi: 10.1038/mp.2012.120. In press [Link]

31. Wei YY, Wu G, Ji HK* (2012) Global mapping of transcription factor binding sites by sequencing chromatin surrogates: a perspective on experimental design, data analysis, and open problems. Statistics in Biosciences. In press [Link]

 

2011

32. 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]

33. 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]

34. 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].

 

2010

35. 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]

36. Ji HK* and Liu XS* (2010) Analyzing ’omics data using hierarchical models. Nature Biotechnology. 28: 337-340. [Link]

37. 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]

38. 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]

39. Sun Y, Fan XY, Cao DM, Tang W, He K, Zhu JY, He JX, Bai MY, Zhu S, Oh E, Patil S, Kim TW, Ji HK, Wong WH, Rhee SY, Wang ZY. (2010) Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental Cell. 19: 765-777. [Link]

40. Wu H and Ji HK* (2010) JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics. 26:1864-1870. [Link] [Link to JAMIE]

 

2009

41. Judy JT and Ji HK* (2009) TileProbe: modeling tiling array probe effects using publicly available data. Bioinformatics. 25: 2369-2375. doi: 10.1093/bioinformatics/btp425. [Link] [Link to TileProbe]

42. Nishi Y, Ji HK, Wong WH, McMahon AP and Vokes SA (2009) Modeling the spatio-temporal network that drives patterning in the vertebrate central nervous system. BBA - Gene Regulatory Mechanisms. 1789: 299-305. [Link]

 

2008

43. 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]

44. 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]             

 

2007 and before

45. 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]

46. 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]

47. 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. doi:10.1093/nar/gkl803. [Link] [Supporting Website]

48. Ji HK and Wong WH (2006) Computational biology: towards deciphering gene regulatory information in mammalian genomes. Biometrics, 62: 645-663. [Link] [Preprint]

49. Kim RS, Ji HK and Wong WH (2006) An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. BMC Bioinformatics, 7:44. doi:10.1186/1471-2105-7-44. [Link]

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

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

52. Hellmann I, Prüfer K, Ji HK, Zody MC, Pääbo S and Ptak SE (2005) Why do human diversity levels vary at a megabase scale? Genome Research, 15: 1222-1231. [Link]

53. Chinese Schizophrenia Consortium (2004) Association study of an SNP combination pattern in the dopaminergic pathway in paranoid schizophrenia: a novel strategy for complex disorders. Molecular Psychiatry, 9: 510-521. (Joint First Authors: Xu Q§, Ji HK§, Yuan YB§ and Yu YQ§) [Link]

54. Ji HK§, Zhou Q§, Wen F, Xia HY, Lu X and Li YD (2001) AsMamDB: an alternative splice database of mammals. Nucleic Acids Research, 29: 260-263. [Link]

55. Ji HK, Zhou Q, Wen F and Ji L (2001) Research on multiple alignments for alternative splicing. Journal of Tsinghua University (Science and Technology), 41(9): 111-114. (In Chinese)

 

Book Chapters

56. Wei YY, Tenzen T and Ji HK (2016) Cormotif: An R package for jointly detecting differential gene expression in multiple studies. Computational Biology and Bioinformatics, pp 28-47. Edited by Ka-Chun Wong, CRC Press

57. Ji HK* and Wei YY (2015) Integrative Analysis of Multiple ChIP-X Data Sets Using  Correlation Motifs. Integrating Omics Data, edited by George C. Tseng, Debashis Ghosh, Xianghong Jasmine Zhou, pp 110-133. Cambridge University Press [Link]

58. Wu H and Ji HK* (2012) JAMIE: A Software Tool for Jointly Analyzing Multiple ChIP-chip Experiments. Methods Mol Biol. (Next Generation Microarray Bioinformatics edited by Junbai Wang, Aik C Tang, Tianhai Tian)  802: 363-375 [Link]

59. Ji HK, Jiang H, Ma WX and Wong WH (2011) Using CisGenome to Analyze ChIP-chip and ChIP-seq Data. Current Protocols in Bioinformatics, 2011 Mar, Chapter 2: Unit2.13. Wiley. [Link]

60. Ji HK (2011) Computational Analysis of ChIP-chip Data. In the Handbook of Computational Statistics, Part 2, 257-282, DOI: 10.1007/978-3-642-16345-6_12 (edited by Henry Horng-Shing Lu, Bernhard Schölkopf and Hongyu Zhao) [Link]

61. Ji HK (2010) Computational Analysis of ChIP-seq Data. Methods Mol Biol. (Computational Biology of Transcription Factor Binding edited by Istvan Ladunga) 674: 143-159 [Link]

62. Cullen P et al. including Ji HK (2004) Computational methods and bioinformatic tools. In Analysing Gene Expression, edited by Lorkowski S and Cullen P, pp 769-904, Wiley-VCH Verlag GmbH & Co. KGaA

 

Dissertations

63. Ji HK (PhD Thesis): Towards Deciphering Gene Regulatory Networks in Mammalian Genomes: Statistical Models and a Case Study. Harvard University, 2007

64. Ji HK (Master’s Thesis): Analysis of Alternative Splicing and Complex Disease based on Population Comparisons. Tsinghua University, 2002

 

Technical Reports

65. Ji HK and Wong WH. (2005) Increasing power of microarray gene selection: an empirical Bayes approach (Harvard Qualifying Paper) [Link] [Supplementary Notes] [Supporting Website: PowerExpress]