All Publications

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

Preprints

  • [Lamian] A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples [Link] [Software]
  • [TreeCorTreat] Tree-based correlation screen and visualization for exploring phenotype-cell type association in multiple sample single-cell RNA-sequencing experiments [Link] [Software]

Peer reviewed journal articles

2023

  1. Fang YQ, Ji ZC§, Zhou WQ§, Abante J§, Koldobskiy MA, Ji HK*, Feinberg AP* (2023) DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence. Nucleic Acids Research. 51(5):2046–2065 [Link]
  2. Liu W, Liao X, Luo ZY, Yang Y, Lau MC, Jiao YL, Shi XJ, Zhai WW, Ji HK, Yeong J, Liu J (2023) Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST. Nature Communications. 14(1):296 [Link] [Link to PRECAST]

2022

  1. 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] [Link to QFM]
  2. Ramachandran J, Zhou WQ, Bardenhagen AE, Nasr T, Yates ER, Zorn AM, Ji HK, Vokes SA (2022) Hedgehog regulation of epithelial cell state and morphogenesis in the larynx. eLife. 11:e77055 [Link]
  3. Hou WP, Zhang MY, Ji YL, Hong XM, Wang GY, Xu R, Liang LM, Saria S, Ji HK (2022) In utero exposure to cigarette smoking on child long-term risk of obesity: concordance of self-report, maternal and cord blood biomarkers. Precision Nutrition. 1(3):e00017 [Link]
  4. Liu QB, Miao HY, Li S, Zhang P, Gerber GF, Follmann D, Ji HK, Zeger SL, Chertowa DS, Quinna TC, Robinson ML, Kickler TS, Rothman RE, Fenstermacher KZJ, Braunstein EM, Cox AL, Farci P, Fauci AS, Lusso P (2022) Anti-PF4 Antibodies Associated with Disease Severity in Covid-19. Proc. Natl. Acad. Sci. USA. 119 (47): e2213361119 [Link]
  5. Frumento N, Figueroa A, Wang TC, Zahid MN, Wang SY, Massaccesi G, Stavrakis G, Crowe Jr. JE, Flyak AI, Ji HK, Ray SC, Shaw GM, Cox AL, Bailey JR (2022) Repeated exposure to heterologous hepatitis C viruses associates with enhanced neutralizing antibody breadth and potency. Journal of Clinical Investigation. 132(15):e160058 [Link]
  6. Dykema AG, Zhang BY, Woldemeskel BA, Garliss CC, Rashid R, Westlake T, Zhang L, Zhang JJ, Cheung LS, Caushi JX, Pardoll DM, Cox AL, Ji HK, Smith KN, Blankson JN (2022) SARS-CoV-2 vaccination diversifies the CD4+ spike-reactive T cell repertoire in patients with prior SARS-CoV-2 infection. eBioMedicine. 80:104048 [Link]
  7. Shu C, Jaffe AE, Sabunciyan S, Ji HK, Astemborski J, Sun J, Bakulski KM, Sosnowski DW, Mehta SH, Kirk GD, Maher BS (2022) Epigenome-wide association analyses of active injection drug use. Drug and Alcohol Dependence. 235(1): 109431 [Link]
  8. Wei X, Li ZY, Ji HK, Wu H (2022) EDClust: An EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. Bioinformatics. 38(10):2692-2699 [Link]
  9. Lex RK, Zhou WQ, Ji ZC, Falkenstein KN, Schuler KE, Windsor KE, Kim JD, Ji HK, Vokes SA (2022) GLI transcriptional repression is inert prior to Hedgehog pathway activation. Nature Communications. 13:808 [Link]
  10. Sharrock AV, Mulligan TS, Hall KR, Williams EM, White DT, Zhang L, Emmerich K, Matthews F, Nimmagadda S, Washington S, Le KD, Meir-Levi D, Cox OL, Saxena MT, Calof AL, Lopez-Burks ME, Lander AD, Ding D, Ji HK, Ackerley DF, Mumm JS (2022) NTR 2.0: a rationally-engineered prodrug converting enzyme with substantially enhanced efficacy for targeted cell ablation. Nature Methods. 19:205–215 [Link]
  11. Hong XM, Liang LM, Ji HK, Guerrerio P, Wang GY, Pearson C, Stampfer MJ, Hu F, Wang XB (2022) Fetal lipidome and incident risk of food allergy: a prospective birth cohort study. Pediatric Allergy and Immunology. 33(2):e13722 [Link]

2021

  1. 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. 596: 126–132 [Link]
  2. Stephens KE, Zhou WQ, Renfro Z, Ji ZC, Ji HK, Guan Y, Taverna SD (2021) Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain. Journal of Neuroinflammation. 18:185 [Link]
  3. Wang GY, Foney D, DiBari J, Hong XM, Showell N, Kim KS, Ji HK, Pearson C, Mirolli G, Rusk S, Sharfstein J, Cheng T, Zuckerman B, Wang XB (2021) A prospective cohort study on the intersectionality of obesity, chronic disease, social factors, and incident risk of COVID-19 in US low-income minority middle-age mothers. International Journal of Obesity. 45:2577–2584 [Link]
  4. Turnbull AE, Ji HK, Dinglas VD, Mendez-Tellez PA, Dennison Himmelfarb C, Shanholtz CB, Hosey MM, Hopkins RO, Needham DM. (2022) Understanding patients’ perceived health after critical illness: analysis of two prospective, longitudinal studies of ARDS survivors. Chest. 161(2):407-41 [Link]
  5. Zhang LY, Chen C, Fu J, Lilley B, Berlinicke C, Hansen B, Ding D, Wang G, Wang T, Shou D, Ye Y, Mulligan T, Emmerich K, Saxena MT, Hall KR, Sharrock AV, Brandon C, Park H, Kam TI, Dawson VL, Dawson TM, Shim JS, Hanes J, Ji HK, Liu JO, Qian J, Ackerley DF, Rohrer B, Zack DJ, Mumm JS (2021) Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa. eLife. 10:e57245 [Link]
  6. Cottrell TR, Zhang J, Zhang BY, Kaunitz GJ, Chan HY, Verde F, Bell JM, Hooper JE, Hammers HJ, Allaf ME, Ji HK, Taube JM, Smith KN (2021) Evaluating T cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance. Journal for ImmunoTherapy of Cancer. 9(7):e002642 [Link]
  7. Akindele NP, Kouo T, Gordon O, Karaba AH, Fenstermacher KZJ, Rubens JH, Beaudry J, Atik CC, Zhou WQ, Ji HK, Tao XT, Vaidya D, Mostafa H, Caturegli P, Blair P, Sauer L, Cox AL, Persaud D (2021) Distinct cytokine and chemokine dysregulation in hospitalized children with acute COVID-19 and multisystem inflammatory syndrome with similar levels of aasopharyngeal SARS-CoV-2. The Journal of Infectious Diseases. 224(4):606-615 [Link]
  8. 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 (2022) Differential cytokine signatures of SARS-CoV-2 and influenza infection highlight key differences in pathobiology. Clinical Infectious Diseases. 74(2):254-262. [Link]
  9. Gao ML, Fu Y, Zhou WQ, Gui GG, Lal B, Li YQ, Xia SL, Ji HK, Eberhart CG, Laterra J, Ying MY (2021) EGFR activates a TAZ-driven oncogenic program in glioblastoma. Cancer Research. 81(13):3580-3592 [Link]
  10. 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]
  11. Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou WQ, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji HK, Goutsias J, Feinberg AP (2021) Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nature Biomedical Engineering. 5: 360–376 [Link]
  12. Thompson EA, Cascino K, Ordonez AA, Zhou WQ, Vaghasia A, Hamacher-Brady A, Brady NR, Sun IH, Wang R, Rosenberg AZ, Delannoy M, Rothman R, Fenstermacher K, Sauer L, Shaw-Saliba K, Bloch EM, Redd AD, Tobian AAR, Horton M, Smith K, Pekosz A, D’Alessio FR, Yegnasubramanian S, Ji HK, Cox AL, Powell JD (2021) Metabolic programs define dysfunctional immune responses in severe COVID-19 patients. Cell Reports. 34(11): 108863 [Link]
  13. Chamling X, Kallman A, Fang WX, Berlinicke C, Mertz J, Devkota P, Pantoja IM, Smith M, Ji ZC, Chang C, Kaushik A, Chen L, Whartenby K, Calabresi P, Mao HQ, Ji HK, Wang TH, Zack DJ (2021) Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells. Nature Communications. 12:652 [Link]
  14. Ji ZC, Ji HK* (2021) Discussion of “Exponential-family Embedding with Application to Cell Developmental Trajectories for Single-cell RNA-seq Data”. Journal of the American Statistical Association. 116(534): 471-474 [Link]
  15. Xu R, Hong XM, Zhang BY, Huang WY, Hou WP, Wang GY, Wang XB, Igusa T, Liang LM, Ji HK (2021) DNA methylation mediates the effect of maternal smoking on offspring birthweight: A birth cohort study of multi-ethnic US mother-newborn pairs. Clinical Epigenetics. 13:47 [Link]

2020

  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]
  3. Qiu X, Ma F, Zhao MM, Cao Y, Shipp L, Liu A, Dutta A, Singh A, Braikia FZ, De S, Wood III WH, Becker KG, Zhou WQ, Ji HK, Zhao KJ, Atchison ML, Sen R  (2020) Altered 3D chromatin structure permits inversional recombination at the IgH locus. Science Advances. 6(33):eaaz8850 [Link]
  4. Lex RL§, Ji ZC§, Falkenstein KN§, Zhou WQ, Henry JL, Ji HK, Vokes SA (2020) GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. eLife. 9:e50670 [Link]
  5. Surkan PJ, Hong XM, Zhang BY, Nawa N, Ji HK, Tang WY, Ji YL, Kimmel MC, Wang GY, Pearson C, Wang XB (2020) Can social support during pregnancy affect maternal DNA methylation? Findings from a cohort of African-Americans. Pediatric Research. 88:131-138 [Link]
  6. Hong XM, Surkan P, Zhang BY, Keiser A, Ji YL, Ji HK, Burd I, Bustamante-Helfrich B, Ogunwole SM, Tang WY, Liu L, Pearson C, Cerda S, Zuckerman B, Hao LX, Wang XB (2020) Genome-wide association study identifies a novel maternal gene × stress interaction associated with spontaneous preterm birth. Pediatric Research. 89(6):1549-1556 [Link]
  7. Hong XM, Zhang BY, Liang LM, Zhang Y, Ji YL, Wang GY, Ji HK, Clish C, Burd I, Pearson C, Zuckerman B, Hu FB, Wang XB (2020) Postpartum plasma metabolomic profile among women with preeclampsia and preterm delivery: implications for long-term health. BMC Medicine. 18(1):277 [Link]
  8. Sinha S, Satpathy AT, Zhou WQ, Ji HK, Stratton JA, Jaffer A, Bahlis N, Morrissy S, Biernaskie JA (2021) Profiling chromatin accessibility at single-cell resolution.  Genomics, Proteomics & Bioinformatics. 19(2):172-190 [Link]
  9. Shu C, Jaffe AE, Sabunciyan S, Ji HK, Astemborski J, Sun J, Bakulski KM, Mehta SH, Kirk GD, Maher BS (2020) Epigenome-wide association scan identifies methylation sites associated with HIV infection. Epigenomics. 12(21):1917-1927 [Link]
  10. Wang GY, Tang WY, Wills-Karp M, Ji HK, Bartell TR, Ji YL, Hong XM, Pearson C, Cheng TL, Wang XB (2020) A nonlinear relationship between maternal red blood cell manganese concentrations and child’s blood pressure at age 6-12 y: A prospective birth cohort study. The Journal of Nutrition. 151(3): 570–578 [Link]
  11. Wang GY, Tang WY, Ji HK, Wang XB (2020) Prenatal exposure to mercury and precocious puberty: a prospective birth cohort study. Human Reproduction. 36(3): 712–720 [Link]
  12. Zhou WQ, Ji HK (2020) Genome-wide prediction of chromatin accessibility based on gene expression. WIREs Computational Statistics. 13:e1544 [Link]

2019

  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* (2020) Compartmental analysis of T cell clonal dynamics as a function of pathologic response to neoadjuvant PD-1 blockade. Clinical Cancer Research. 26(6):1327-1337. [Link]
  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. 51(5):840-855.e5. [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. 47: e121 [Link] [Link to BIRD]
  4. Wang GY, DiBari J, Bind E, Steffens AM, Mukherjee J, Azuine RE, Singh GK, Hong XM, Ji YL, Ji HK, Pearson C, Zuckerman BS, Cheng TL, Wang XB (2019) Association Between Maternal Exposure to Lead, Maternal Folate Status, and Intergenerational Risk of Childhood Overweight and Obesity. JAMA Network Open. 2(10):e1912343 [Link]
  5. 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]
  6. Hong XM, Liang L, Sun Q, Keet CA, Tsai HJ, Ji Y, Wang G, Ji HK, Clish C, Pearson C, Wang Y, Wood RA, Hu FB, Wang X. (2019) Maternal triacylglycerol signature and risk of food allergy in offspring. Journal of Allergy and Clinical Immunology. 144(3): 729–737 [Link]
  7. Olapeju B, Ahmed S, Wang GY, Ji YL, Hong XM, Raghavan R, Summers A, Keiser A, Ji HK, Zuckerman B, Yarrington C, Hao LX, Surkan P, Cheng T, Wang XB (2019) Maternal postpartum plasma folate status and preterm birth in a high-risk US population. Public Health Nutrition. 22(7):1281-1291. [Link]
  8. Stephens KE, Zhou WQ, Ji ZC, Chen Z, He S, Ji HK, Guan Y, Taverna SD (2019) Sex differences in gene regulation in the dorsal root ganglion after nerve injury. BMC Genomics. 20(1):147 [Link]

2018

  1. Zhang BY, Hong XM, Ji HK, Tang WY, Kimmel M, Ji YL, Wang GY, Pearson C, Zuckerman B, Surkan PJ, Wang XB. (2018) Maternal smoking during pregnancy and cord blood DNA methylation: new insight on sex differences and effect modification by maternal folate. Epigenetics. 13(5):505-518 [Link]
  2. Qiu X, Kumari G, Gerasimova, T, Du H, Labaran L, Singh A, De S, Wood III WH, Becker KG, Zhou WQ, Ji HK, Sen R (2018) Sequential enhancer sequestration dysregulates recombination center formation at the IgH locus. Molecular Cell. 70:21-33 [Link]
  3. Zhao MM, Joy J, Zhou WQ, De S, Wood III WH, Becker KG, Ji HK, Sen R (2018) Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation. PLoS Biology. 16(9):e2006347 [Link]
  4. Wang J, Zibetti C, Shang P, Sripathi SR, Zhang PW, Cano M, Hoang T, Xia SL, Ji HK, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. (2018) ATAC-seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nature Communications. 9:1364 [Link]
  5. Kuang Z, Ji HK, Boeke JD. (2018) Stress response factors drive regrowth of quiescent cells. Current Genetics. 64(4):807-810 [Link]
  6. Kuang Z, Ji ZC, Boeke JD*, Ji HK*. (2018) Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. Nucleic Acids Research. 46(1): e2 [Link]
  7. Ji YL, Riley A, Lee LC, Hong XM, Wang GY, Tsai HJ, Mueller N, Pearson C, Thermitus J, Panjwani A, Ji HK, Bartell T, Burd I, Fallin MD, Wang XB (2018) Maternal biomarkers of acetaminophen use and offspring attention deficit hyperactivity disorder. Brain Sciences. 8(7). pii: E127 [Link]
  8. Tsai HJ, Wang GY, Hong XM, Yao TC, Ji YL, Radovick S, Ji HK, Cheng TL, Wang XB (2018) Early life weight gain and development of childhood asthma in a prospective birth cohort. Annals of the American Thoracic Society. 15(10):1197-1204 [Link]

2017

  1. Han F, Ji HK, Ji ZC, Wang HL. (2017) A provable smoothing approach for high dimensional generalized regression with an application in genomics. Electronic Journal of Statistics. 11(2):4347-4403 [Link] [Preprint]
  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].
  3. 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]
  4. 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]
  5. Surkan PJ, Dong LM, Ji YL, Hong XM, Ji HK, Kimmel M, Tang WY, Wang XB. (2017) Paternal involvement and support and risk of preterm birth: findings from the Boston Birth Cohort. Journal of Psychosomatic Obstetrics & Gynecology. 40(1):48-56 [Link]
  6. Martos SN§, Li T§, Ramos RB, Lou D, Dai HZ, Xu JC, Gao GL, Gao Y, Wang QL, An C, Zhang XL, Jia YK, Dawson VL, Dawson TM, Ji HK, Wang ZB. (2017) Two approaches reveal a new paradigm of ‘switchable or genetics-influenced allele-specific DNA methylation (ASM) with potential in human disease. Cell Discovery  3: 17038 [Link]
  7. 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. 8:15608 [Link]
  8. White DT, Sengupta S, Saxena MT, Xu Q, Hanes J, Ding D, Ji HK, Mumm JS (2017) Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina. Proc. Natl. Acad. Sci. USA. 114(18): E3719–E3728 [Link]
  9. 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. 13(2):163-172[Link]
  10. Ji YL, Riley AW, Lee LC, Volk H, Hong XM, Wang GY, Angomas R, Stivers T, Wahl A, Ji HK, Bartell TR, Burd I, Paige D, Fallin MD, Zuckerman B, Wang XB. (2017) A prospective birth cohort study on maternal cholesterol levels and offspring attention deficit hyperactivity disorder: new insight on sex differences. Brain Sciences. 8(1). pii: E3

2016

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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. 125(6):067005 [Link]
  7. Zhou WQ, Sherwood B, Ji HK* (2016) Global prediction of the functional genomic landscape: applications, methods and challenges. Human Heredity. 81:88-105. [Link]
  8. 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]
  9. 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]
  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]

2015

  1. 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]
  2. 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  [Link]
  3. 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]
  4. Zhang SL, Du F, Ji HK* (2015) A novel DNA sequence motif in human and mouse genomes. Scientific Reports. 5: 10444 [Link]
  5. 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]

2014

  1. 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. [Link]
  2. 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]
  3. 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]

2008-2013

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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 (2013) Genome-wide profiling of multiple histone methylations in olfactory cells: further implications for cellular susceptibility to oxidative stress in schizophrenia. Molecular Psychiatry. 18(7):740-2 [Link]
  8. 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]
  9. 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. [Link]
  10. 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. 5(1):156-178 [Link]
  11. 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]
  12. 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. [Link]
  13. 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].
  14. 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]
  15. Ji HK* and Liu XS* (2010) Analyzing ’omics data using hierarchical models. Nature Biotechnology. 28: 337-340. [Link]
  16. 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]
  17. 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]
  18. 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]
  19. Wu H and Ji HK* (2010) JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics. 26:1864-1870. [Link] [Link to JAMIE]
  20. Judy JT and Ji HK* (2009) TileProbe: modeling tiling array probe effects using publicly available data. Bioinformatics. 25: 2369-2375.  [Link] [Link to TileProbe]
  21. 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]
  22. 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]
  23. 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

  1. 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]
  2. 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]
  3. 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]
  4. Ji HK and Wong WH (2006) Computational biology: towards deciphering gene regulatory information in mammalian genomes. Biometrics, 62: 645-663. [Link] [Preprint]
  5. 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. [Link]
  6. Ji HK and Wong WH (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21: 3629-3636. [Link] [Supporting Website: TileMap]
  7. The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437: 69-87. [Link]
  8. 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]
  9. 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]
  10. 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]
  11. 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)

Editorials and others

  1. Rudin C, Dunson D, Irizarry R, Ji HK, Laber E, Leek J, McCormick T, Rose S, Schafer C, van der Laan M, Wasserman L, Xue L. (2014) Discovery with data: Leveraging statistics with computer science to transform science and society. American Statistical Association White Paper

Book chapters

  1. Ji ZC, Ji HK* (2019) Pseudotime Reconstruction Using TSCAN. Computational Methods for Single-Cell Data Analysis, pp 115-124, Edited by Guo-Cheng Yuan, Humana Press, Springer
  2. 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
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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

  1. Ji HK (PhD Thesis): Towards Deciphering Gene Regulatory Networks in Mammalian Genomes: Statistical Models and a Case Study. Harvard University, 2007
  2. Ji HK (Master’s Thesis): Analysis of Alternative Splicing and Complex Disease based on Population Comparisons. Tsinghua University, 2002

Technical reports

  1. 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]