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Research Output 2001 2019

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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
Maternal Exposure
Pediatric Obesity
Folic Acid
Mothers
Obesity

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

DNA Methylation
Social Support
African Americans
Mothers
Pregnancy

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
Chromatin
Cell Count
RNA
Technology
Transcriptome

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., Jan 1 2019, In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticle

Food Hypersensitivity
Triglycerides
Mothers
Food
Immunoglobulin E

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
Maternal Exposure
Opioid Analgesics
Mothers
Population
Neonatal Abstinence Syndrome

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

Biological Phenomena
RNA
Gene Expression
Computer Simulation
Biological Science Disciplines
Spinal Ganglia
Neurosciences
Sex Characteristics
Peripheral Nervous System

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

Eragrostis
Gene Regulatory Networks
T-Lymphocytes
Transcription Factors
T Cell Transcription Factor 1
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

Attention Deficit Disorder with Hyperactivity
Sex Characteristics
Cohort Studies
Cholesterol
Mothers

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

chromatin
degeneration
Macular Degeneration
Chromatin
epithelium

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
Biological Phenomena
Transcription Factors
Binding Sites
Chromatin
Histone Code

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

Weight Gain
Asthma
Parturition
Weights and Measures
Body Mass Index

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

Premature Birth
DNA Methylation
Fetal Blood
Mothers
Genome

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

Attention Deficit Disorder with Hyperactivity
Acetaminophen
Biomarkers
Mothers
Logistic Models

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

Olapeju, B., Ahmed, S., Wang, G., Ji, Y., Hong, X., Raghavan, R., Summers, A., Keiser, A., Ji, H. K., Zuckerman, B., Yarrington, C., Hao, L., Surkan, P., Cheng, T. L. & Wang, X., Jan 1 2018, (Accepted/In press) In : Public Health Nutrition.

Research output: Contribution to journalArticle

Premature Birth
Folic Acid
Postpartum Period
Mothers
Population

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

DNA Methylation
Fetal Blood
Folic Acid
Sex Characteristics
Smoking

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

Immunoglobulin Heavy Chains
Genetic Recombination
Intergenic DNA
Insulator Elements
Gene Rearrangement

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

Transcription Factors
Food
Acetyl Coenzyme A
Glycolysis
Regulator Genes

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

NF-kappa B
Gene expression
Chemical activation
Gene Expression
kinetics
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

Genomics
Smoothing
Regression Model
High-dimensional
Regression

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

Hong, X., Hao, K., Ji, H. K., 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. L., Fallin, D. 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
pregnancy
Premature Birth
genes
Genes

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

Deoxyribonucleases
genome
gene expression
Deoxyribonuclease I
Transcriptome

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

Retinal Rod Photoreceptor Cells
Immunomodulation
Zebrafish
Retina
Regeneration

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. A., Chen, Z., Hong, X., Wang, G., Caruso, D., Zong, G., Pearson, C., Ji, H. K., Biswal, S., Zuckerman, B., Wills-Karp, M. & Wang, X., Jun 1 2017, In : Environmental Health Perspectives. 125, 6, 067005.

Research output: Contribution to journalArticle

Maternal Exposure
Pediatric Obesity
Obesity
Confidence Intervals
Mothers

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

Acetyl Coenzyme A
Nutrients
Genes
Yeast
Enzymes

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

Premature Birth
Gestational Age
Parturition
Pregnancy
Fathers

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

Transcription factors
Data analysis
Transcription Factors
Genes
Deoxyribonucleases

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., Gao, G., Gao, Y., Wang, Q., An, C., Zhang, X., Jia, Y., Dawson, V., Dawson, T. M., Ji, H. K. & Wang, Z., Nov 14 2017, In : Cell Discovery. 3, 17038.

Research output: Contribution to journalArticle

Methylation
DNA Methylation
Alleles
Genes
Cell Line
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

Zebrafish
Drug Discovery
Screening
Throughput
Insulin

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

Folic Acid
Body Mass Index
Mothers
Obesity
Parturition

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

Hong, X., Ladd-Acosta, C. M., Hao, K., Sherwood, B., Ji, H. K., Keet, C., 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., 2016, (Accepted/In press) In : The Journal of Allergy and Clinical Immunology.

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

Limb Buds
Stem Cells
Maintenance
Cartilage
Adult Stem Cells

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

Genes
Gene
Distinct
tumor
Module

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. K., 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

Hedgehog Proteins
Transcription
Stem cells
Stem Cells
Embryonic Stem Cells

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

Single-Cell Analysis
RNA
Gene Expression
Transcriptome
Computer Simulation

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

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

Research output: Contribution to journalArticle

Genetic Association Studies
Gene Expression
Genes
Research Personnel
Software
2015

A novel DNA sequence motif in human and mouse genomes

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

Research output: Contribution to journalArticle

Nucleotide Motifs
Human Genome
Genetic Promoter Regions
Genome
Deoxyribonuclease I

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. K. & Niakan, K. K., Jun 15 2015, In : Genes & development. 29, 12, p. 1239-1255 17 p.

Research output: Contribution to journalArticle

Endoderm
Stem Cells
Transcription Factors
Genes
Chromatin Immunoprecipitation

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. K., 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

erbB-2 Genes
Estrogen Receptors
Breast Neoplasms
Tamoxifen
Genes

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

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

Research output: Contribution to journalArticle

Differential Expression
Gene Expression
Gene
Genes
Model Complexity

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. K. & Vokes, S. A., Oct 1 2015, In : Developmental Biology. 406, 1, p. 92-103 12 p.

Research output: Contribution to journalArticle

Limb Buds
Genes
Hedgehog Proteins
Nucleotide Motifs
Gene Regulatory Networks
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. K., Tu, B. P. & Boeke, J. D., Jan 1 2014, In : Nature structural & molecular biology. 21, 10, p. 854-863 10 p.

Research output: Contribution to journalArticle

Saccharomycetales
Chromatin
Acetylation
Ribosomes
Histones

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. K. & Laterra, J. J., Nov 21 2014, In : Journal of Biological Chemistry. 289, 47, p. 32742-32756 15 p.

Research output: Contribution to journalArticle

Kruppel-Like Transcription Factors
Transcription
Glioblastoma
Integrins
Cell Differentiation

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

Wu, H. & Ji, H. K., Mar 7 2014, In : PLoS One. 9, 3, e89694.

Research output: Contribution to journalArticle

binding sites
Transcription Factors
transcription factors
Binding Sites
Noise
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. K., May 1 2013, In : Bioinformatics. 29, 9, p. 1182-1189 8 p.

Research output: Contribution to journalArticle

Transcription factors
Sequencing
High Throughput
Chip
Transcription Factors

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

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

Research output: Contribution to journalArticle

Transcription factors
Transcription Factor
Gene Expression Data
Oligonucleotide Array Sequence Analysis
Gene expression

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. K., 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., 2013, In : Molecular Systems Biology. 9, 655.

Research output: Contribution to journalArticle

Phosphorylation
Human Activities
phosphorylation
phosphotransferases (kinases)
Phosphotransferases

Differential principal component analysis of ChIP-seq

Ji, H. K., 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

Principal Component Analysis
DNA
Chromatin
Proteins
Transcription Factors

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

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

Research output: Contribution to journalArticle

Bagging
Genes
Gene
Resampling
p-Value