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2020

GLI transcriptional repression regulates tissue-specific enhancer activity in response to hedgehog signaling

Lex, R. K., Ji, Z., Falkenstein, K. N., Zhou, W., Henry, J. L., Ji, H. & Vokes, S. A., Jan 2020, In : eLife. 9, e50670.

Research output: Contribution to journalArticle

Open Access
2019

Association Between Maternal Exposure to Lead, Maternal Folate Status, and Intergenerational Risk of Childhood Overweight and Obesity

Wang, G., DiBari, J., Bind, E., Steffens, A. M., Mukherjee, J., Azuine, R. E., Singh, G. K., Hong, X., Ji, Y., Ji, H., Pearson, C., Zuckerman, B. S., Cheng, T. L. & Wang, X., Oct 2 2019, In : JAMA Network Open. 2, 10, p. e1912343

Research output: Contribution to journalArticle

Open Access

Can social support during pregnancy affect maternal DNA methylation? Findings from a cohort of African-Americans

Surkan, P. J., Hong, X., Zhang, B., Nawa, N., Ji, H., Tang, W. Y., Ji, Y., Kimmel, M. C., Wang, G., Pearson, C. & Wang, X., Jan 1 2019, In : Pediatric research.

Research output: Contribution to journalArticle

Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq

Zhou, W., Ji, Z., Fang, W. & Ji, H., Nov 4 2019, In : Nucleic acids research. 47, 19, p. e121

Research output: Contribution to journalArticle

Open Access

Maternal postpartum plasma folate status and preterm birth in a high-risk US population

Olapeju, B., Saifuddin, A., Wang, G., Ji, Y., Hong, X., Raghavan, R., Summers, A., Keiser, A., Ji, H., Zuckerman, B., Yarrington, C., Hao, L., Surkan, P. J., Cheng, T. L. & Wang, X., May 1 2019, In : Public health nutrition. 22, 7, p. 1281-1291 11 p.

Research output: Contribution to journalArticle

Maternal triacylglycerol signature and risk of food allergy in offspring

Hong, X., Liang, L., Sun, Q., Keet, C. A., Tsai, H. J., Ji, Y., Wang, G., Ji, H., Clish, C., Pearson, C., Wang, Y., Wood, R. A., Hu, F. B. & Wang, X., Sep 2019, In : Journal of Allergy and Clinical Immunology. 144, 3, p. 729-737 9 p.

Research output: Contribution to journalArticle

Prenatal Risk Factors and Perinatal and Postnatal Outcomes Associated with Maternal Opioid Exposure in an Urban, Low-Income, Multiethnic US Population

Azuine, R. E., Ji, Y., Chang, H. Y., Kim, Y., Ji, H., Dibari, J., Hong, X., Wang, G., Singh, G. K., Pearson, C., Zuckerman, B., Surkan, P. J. & Wang, X., Jan 1 2019, In : JAMA Network Open.

Research output: Contribution to journalArticle

Open Access

Pseudotime Reconstruction Using TSCAN

Ji, Z. & Ji, H. K., Jan 1 2019, In : Methods in molecular biology (Clifton, N.J.). 1935, p. 115-124 10 p.

Research output: Contribution to journalArticle

Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Stephens, K. E., Zhou, W., Ji, Z., Chen, Z., He, S., Ji, H., Guan, Y. & Taverna, S. D., Feb 19 2019, In : BMC genomics. 20, 1, 147.

Research output: Contribution to journalArticle

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

Chen, Z., Ji, Z., Ngiow, S. F., Manne, S., Cai, Z., Huang, A. C., Johnson, J., Staupe, R. P., Bengsch, B., Xu, C., Yu, S., Kurachi, M., Herati, R. S., Vella, L. A., Baxter, A. E., Wu, J. E., Khan, O., Beltra, J. C., Giles, J. R., Stelekati, E. & 7 others, McLane, L. M., Lau, C. W., Yang, X., Berger, S. L., Vahedi, G., Ji, H. & Wherry, E. J., Nov 19 2019, In : Immunity. 51, 5, p. 840-855.e5

Research output: Contribution to journalArticle

2018

A prospective birth cohort study on maternal cholesterol levels and offspring attention deficit hyperactivity disorder: New insight on sex differences

Ji, Y., Riley, A. W., Lee, L-C., Volk, H., Hong, X., Wang, G., Angomas, R., Stivers, T., Wahl, A., Ji, H. K., Bartell, T. R., Burd, I., Paige, D. M., Fallin, D. D., Zuckerman, B. & Wang, X., Jan 1 2018, In : Brain Sciences. 8, 1, 3.

Research output: Contribution to journalArticle

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

Wang, J., Zibetti, C., Shang, P., Sripathi, S. R., Zhang, P., Cano, M., Hoang, T., Xia, S., Ji, H. K., Merbs, S. L., Zack, D. J., Handa, J., Sinha, D., Blackshaw, S. & Qian, J., Dec 1 2018, In : Nature Communications. 9, 1, 1364.

Research output: Contribution to journalArticle

Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

Kuang, Z., Ji, Z., Boeke, J. D. & Ji, H. K., Jan 9 2018, In : Nucleic acids research. 46, 1, p. e2

Research output: Contribution to journalArticle

Open Access

Early life weight gain and development of childhood asthma in a prospective birth cohort

Tsai, H. J., Wang, G., Hong, X., Yao, T. C., Ji, Y., Radovick, S., Ji, H. K., Cheng, T. L. & Wang, X., Oct 1 2018, In : Annals of the American Thoracic Society. 15, 10, p. 1197-1204 8 p.

Research output: Contribution to journalArticle

Genome-wide DNA methylation associations with spontaneous preterm birth in US blacks: findings in maternal and cord blood samples

Hong, X., Sherwood, B., Ladd-Acosta, C. M., Peng, S., Ji, H. K., Hao, K., Burd, I., Bartell, T. R., Wang, G., Tsai, H. J., Liu, X., Ji, Y., Wahl, A., Caruso, D., Lee-Parritz, A., Zuckerman, B. & Wang, X., Mar 1 2018, (Accepted/In press) In : Epigenetics. p. 1-10 10 p.

Research output: Contribution to journalArticle

Maternal biomarkers of acetaminophen use and offspring attention deficit hyperactivity disorder

Ji, Y., Riley, A. W., Lee, L-C., Hong, X., Wang, G., Tsai, H. J., Mueller, N., Pearson, C., Thermitus, J., Panjwani, A., Ji, H. K., Bartell, T. R., Burd, I., Fallin, D. D. & Wang, X., Jul 1 2018, In : Brain Sciences. 8, 7, 127.

Research output: Contribution to journalArticle

Maternal smoking during pregnancy and cord blood DNA methylation: new insight on sex differences and effect modification by maternal folate levels

Zhang, B., Hong, X., Ji, H. K., Tang, W-Y., Kimmel, M., Ji, Y., Pearson, C., Zuckerman, B., Surkan, P. & Wang, X., Jan 1 2018, (Accepted/In press) In : Epigenetics.

Research output: Contribution to journalArticle

Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus

Qiu, X., Kumari, G., Gerasimova, T., Du, H., Labaran, L., Singh, A., De, S., Wood, W. H., Becker, K. G., Zhou, W., Ji, H. K. & Sen, R., Apr 5 2018, In : Molecular Cell. 70, 1, p. 21-33.e6

Research output: Contribution to journalArticle

Stress response factors drive regrowth of quiescent cells

Kuang, Z., Ji, H. K. & Boeke, J. D., Feb 17 2018, (Accepted/In press) In : Current Genetics. p. 1-4 4 p.

Research output: Contribution to journalArticle

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

Zhao, M., Joy, J., Zhou, W., De, S., Wood, W. H., Becker, K. G., Ji, H. K. & Sen, R., Sep 1 2018, In : PLoS Biology. 16, 9, e2006347.

Research output: Contribution to journalArticle

2017

A provable smoothing approach for high dimensional generalized regression with applications in genomics

Han, F., Ji, H. K., Ji, Z. & Wang, H., Jan 1 2017, In : Electronic Journal of Statistics. 11, 2, p. 4347-4403 57 p.

Research output: Contribution to journalArticle

Genome-wide approach identifies a novel gene-maternal pre-pregnancy BMI interaction on preterm birth

Hong, X., Hao, K., Ji, H., Peng, S., Sherwood, B., Di Narzo, A., Tsai, H. J., Liu, X., Burd, I., Wang, G., Ji, Y., Caruso, D., Mao, G., Bartell, T. R., Zhang, Z., Pearson, C., Heffner, L., Cerda, S., Beaty, T. H., Fallin, M. D. & 4 others, Lee-Parritz, A., Zuckerman, B., Weeks, D. E. & Wang, X., Jun 9 2017, In : Nature communications. 8, 1 p.

Research output: Contribution to journalArticle

Genome-wide prediction of DNase i hypersensitivity using gene expression

Zhou, W., Sherwood, B., Ji, Z., Xue, Y., Du, F., Bai, J., Ying, M. & Ji, H. K., Dec 1 2017, In : Nature Communications. 8, 1, 1038.

Research output: Contribution to journalArticle

Immunomodulation-accelerated neuronal regeneration following selective rod photoreceptor cell ablation in the zebrafish retina

White, D. T., Sengupta, S., Saxena, M. T., Xu, Q., Hanes, J. S., Ding, D., Ji, H. K. & Mumm, J., May 2 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 18, p. E3719-E3728

Research output: Contribution to journalArticle

Individual and joint effects of early-life ambient PM2.5 exposure and maternal prepregnancy obesity on childhood overweight or obesity

Mao, G., Nachman, R. M., Sun, Q., Zhang, X., Koehler, K., Chen, Z., Hong, X., Wang, G., Caruso, D., Zong, G., Pearson, C., Ji, H., Biswal, S., Zuckerman, B., Wills-Karp, M. & Wang, X., Jun 2017, In : Environmental health perspectives. 125, 6, 067005.

Research output: Contribution to journalArticle

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth

Kuang, Z., Pinglay, S., Ji, H. K. & Boeke, J. D., Sep 26 2017, In : eLife. 6, e29938.

Research output: Contribution to journalArticle

Paternal involvement and support and risk of preterm birth: findings from the Boston birth cohort

Surkan, P., Dong, L., Ji, Y., Hong, X., Ji, H. K., Kimmel, M., Tang, W-Y. & Wang, X., Nov 14 2017, (Accepted/In press) In : Journal of Psychosomatic Obstetrics and Gynecology. p. 1-9 9 p.

Research output: Contribution to journalArticle

Single-cell regulome data analysis by SCRAT

Ji, Z., Zhou, W. & Ji, H. K., 2017, In : Bioinformatics. 33, 18, p. 2930-2932 3 p.

Research output: Contribution to journalArticle

Two approaches reveal a new paradigm of 'switchable or genetics-influenced allele-specific DNA methylation' with potential in human disease

Martos, S. N., Li, T., Ramos, R. B., Lou, D., Dai, H., Xu, J. C., Gao, G., Gao, Y., Wang, Q., An, C., Zhang, X., Jia, Y., Dawson, V. L., Dawson, T. M., Ji, H. & Wang, Z., Nov 14 2017, In : Cell Discovery. 3, 17038.

Research output: Contribution to journalArticle

2016

ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

White, D. T., Eroglu, A. U., Wang, G., Zhang, L., Sengupta, S., Ding, D., Rajpurohit, S. K., Walker, S. L., Ji, H. K., Qian, J. & Mumm, J., Dec 1 2016, In : Nature Protocols. 11, 12, p. 2432-2453 22 p.

Research output: Contribution to journalArticle

Association between maternal prepregnancy body mass index and plasma folate concentrations with child metabolic health

Wang, G., Hu, F. B., Mistry, K. B., Zhang, C., Ren, F., Huo, Y., Paige, D. M., Bartell, T., Hong, X., Caruso, D., Ji, Z., Chen, Z., Ji, Y., Pearson, C., Ji, H. K., Zuckerman, B., Cheng, T. L. & Wang, X., Aug 1 2016, In : JAMA Pediatrics. 170, 8

Research output: Contribution to journalArticle

Epigenome-wide association study links site-specific DNA methylation changes with cow's milk allergy

Hong, X., Ladd-Acosta, C., Hao, K., Sherwood, B., Ji, H., Keet, C. A., Kumar, R., Caruso, D., Liu, X., Wang, G., Chen, Z., Ji, Y., Mao, G., Walker, S. O., Bartell, T. R., Ji, Z., Sun, Y., Tsai, H. J., Pongracic, J. A., Weeks, D. E. & 1 others, Wang, X., Sep 1 2016, In : Journal of Allergy and Clinical Immunology. 138, 3, p. 908-911.e9

Research output: Contribution to journalArticle

PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud

Norrie, J. L., Li, Q., Co, S., Huang, B. L., Ding, D., Uy, J. C., Ji, Z., Mackem, S., Bedford, M. T., Galli, A., Ji, H. K. & Vokes, S. A., Dec 15 2016, In : Development (Cambridge). 143, 24, p. 4608-4619 12 p.

Research output: Contribution to journalArticle

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Wang, J., Xia, S., Arand, B., Zhu, H., Machiraju, R., Huang, K., Ji, H. K. & Qian, J., Apr 1 2016, In : PLoS Computational Biology. 12, 4, e1004892.

Research output: Contribution to journalArticle

The pluripotency factor NANOG binds to GLI proteins and represses hedgehog-mediated transcription

Li, Q., Lex, R. K., Chung, H., Giovanetti, S. M., Ji, Z., Ji, H., Person, M. D., Kim, J. & Vokes, S. A., Mar 25 2016, In : Journal of Biological Chemistry. 291, 13, p. 7171-7182 12 p.

Research output: Contribution to journalArticle

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

Ji, Z. & Ji, H. K., Jul 27 2016, In : Nucleic Acids Research. 44, 13, p. e117

Research output: Contribution to journalArticle

Turning publicly available gene expression data into discoveries using gene set context analysis

Ji, Z., Vokes, S. A., Dang, C. V. & Ji, H., Jan 8 2016, In : Nucleic acids research. 44, 1, p. e8

Research output: Contribution to journalArticle

2015

A novel DNA sequence motif in human and mouse genomes

Zhang, S., Du, F. & Ji, H., May 20 2015, In : Scientific reports. 5, 10444.

Research output: Contribution to journalArticle

Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells

Wamaitha, S. E., del Valle, I., Cho, L. T. Y., Wei, Y., Fogarty, N. M. E., Blakeley, P., Sherwood, R. I., Ji, H. & Niakan, K. K., Jun 15 2015, In : Genes and Development. 29, 12, p. 1239-1255 17 p.

Research output: Contribution to journalArticle

HOXB7 is an ERα cofactor in the activation of HER2 and multiple ER target genes leading to endocrine resistance

Jin, K., Park, S., Teo, W. W., Korangath, P., Cho, S. S., Yoshida, T., Győrffy, B., Goswami, C. P., Nakshatri, H., Cruz, L. A., Zhou, W., Ji, H., Su, Y., Ekram, M., Wu, Z., Zhu, T., Polyak, K. & Sukumar, S., Sep 1 2015, In : Cancer discovery. 5, 9, p. 944-959 16 p.

Research output: Contribution to journalArticle

Joint analysis of differential gene expression in multiple studies using correlation motifs

Wei, Y., Tenzen, T. & Ji, H., Jan 1 2015, In : Biostatistics. 16, 1, p. 31-46 16 p.

Research output: Contribution to journalArticle

Spatiotemporal regulation of GLI target genes in the mammalian limb bud

Lewandowski, J. P., Du, F., Zhang, S., Powell, M. B., Falkenstein, K. N., Ji, H. & Vokes, S. A., Oct 1 2015, In : Developmental biology. 406, 1, p. 92-103 12 p.

Research output: Contribution to journalArticle

2014

High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

Kuang, Z., Cai, L., Zhang, X., Ji, H., Tu, B. P. & Boeke, J. D., Jan 1 2014, In : Nature Structural and Molecular Biology. 21, 10, p. 854-863 10 p.

Research output: Contribution to journalArticle

Kruppel-like factor-9 (KLF9) inhibits glioblastoma stemness through global transcription repression and integrin α6 inhibition

Ying, M., Tilghman, J., Wei, Y., Guerrero-Cazares, H., Quinones-Hinojosa, A., Ji, H. & Laterra, J., Nov 21 2014, In : Journal of Biological Chemistry. 289, 47, p. 32742-32756 15 p.

Research output: Contribution to journalArticle

Polya peak: Detecting transcription factor binding sites from Ch IP-seq using peak shape information

Wu, H. & Ji, H., Mar 7 2014, In : PloS one. 9, 3, e89694.

Research output: Contribution to journalArticle

2013

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.

Wu, G., Yustein, J. T., McCall, M. N., Zilliox, M., Irizarry, R. A., Zeller, K., Dang, C. V. & Ji, H., May 1 2013, In : Unknown Journal. 29, 9, p. 1182-1189 8 p.

Research output: Contribution to journalArticle

ChIPXpress: Using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

Wu, G. & Ji, H., Jun 10 2013, In : BMC Bioinformatics. 14, 1, 188.

Research output: Contribution to journalArticle

Construction of human activity-based phosphorylation networks

Newman, R. H., Hu, J., Rho, H. S., Xie, Z., Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, H. M., Hu, S., Hwang, W., Seop Jeong, J., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, K. N. & 14 others, Birnbaum, M. J., Cole, P. A., Knapp, S., Ryazanov, A. G., Zack, D. J., Blackshaw, S., Pawson, T., Gingras, A. C., Desiderio, S., Pandey, A., Turk, B. E., Zhang, J., Zhu, H. & Qian, J., Jan 1 2013, In : Molecular systems biology. 9, 655.

Research output: Contribution to journalArticle

Differential principal component analysis of ChIP-seq

Ji, H., Li, X., Wang, Q. F. & Ning, Y., Apr 23 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 17, p. 6789-6794 6 p.

Research output: Contribution to journalArticle

Gene set bagging for estimating the probability a statistically significant result will replicate

Jaffe, A. E., Storey, J. D., Ji, H. & Leek, J. T., Dec 12 2013, In : BMC Bioinformatics. 14, 1, 360.

Research output: Contribution to journalArticle