PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information.

by Hao Wu, Hongkai Ji
Published 2014-01-01

Single-cell ATAC-seq signal extraction and enhancement with SCATE

by Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji
Published 2020-07-01

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

by Zheng Kuang, Sudarshan Pinglay, Hongkai Ji, Jef D Boeke
Published 2017-09-01

A systematic evaluation of single-cell RNA-sequencing imputation methods

by Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie C. Hicks
Published 2020-08-01

Dynamics of regulatory networks in the developing mouse retina.

by Woochang Hwang, Laszlo Hackler, George Wu, Hongkai Ji, Donald J Zack, Jiang Qian
Published 2012-01-01

Genome-wide prediction of DNase I hypersensitivity using gene expression

by Weiqiang Zhou, Ben Sherwood, Zhicheng Ji, Yingchao Xue, Fang Du, Jiawei Bai, Mingyao Ying, Hongkai Ji
Published 2017-10-01

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

by Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian
Published 2016-04-01

Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

by Kimberly E. Stephens, Weiqiang Zhou, Zachary Renfro, Zhicheng Ji, Hongkai Ji, Yun Guan, Sean D. Taverna
Published 2021-08-01

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

by Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H Wood, Kevin G Becker, Hongkai Ji, Ranjan Sen
Published 2018-09-01

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

by Rachel K Lex, Zhicheng Ji, Kristin N Falkenstein, Weiqiang Zhou, Joanna L Henry, Hongkai Ji, Steven A Vokes
Published 2020-01-01

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

by Kimberly E. Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan, Sean D. Taverna
Published 2019-02-01

Postpartum plasma metabolomic profile among women with preeclampsia and preterm delivery: implications for long-term health

by Xiumei Hong, Boyang Zhang, Liming Liang, Yan Zhang, Yuelong Ji, Guoying Wang, Hongkai Ji, Clary B. Clish, Irina Burd, Colleen Pearson, Barry Zuckerman, Frank B. Hu, Xiaobin Wang
Published 2020-10-01

Evaluating T-cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance

by Jiajia Zhang, Franco Verde, Tricia Cottrell, Hans Hammers, Kellie N Smith, Janis Taube, Boyang Zhang, Genevieve J Kaunitz, Poromendro Burman, Hok-Yee Chan, Jody E Hooper, Mohamad E Allaf, Hongkai Ji
Published 2021-07-01

Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation.

by Hongkai Ji, George Wu, Xiangcan Zhan, Alexandra Nolan, Cheryl Koh, Angelo De Marzo, Hoang Mai Doan, Jinshui Fan, Christopher Cheadle, Mohammad Fallahi, John L Cleveland, Chi V Dang, Karen I Zeller
Published 2011-01-01

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

by Jie Wang, Cristina Zibetti, Peng Shang, Srinivasa R. Sripathi, Pingwu Zhang, Marisol Cano, Thanh Hoang, Shuli Xia, Hongkai Ji, Shannath L. Merbs, Donald J. Zack, James T. Handa, Debasish Sinha, Seth Blackshaw, Jiang Qian
Published 2018-04-01

Maternal Biomarkers of Acetaminophen Use and Offspring Attention Deficit Hyperactivity Disorder

by Yuelong Ji, Anne W. Riley, Li-Ching Lee, Xiumei Hong, Guoying Wang, Hui-Ju Tsai, Noel T. Mueller, Colleen Pearson, Jessica Thermitus, Anita Panjwani, Hongkai Ji, Tami R. Bartell, Irina Burd, M. Daniele Fallin, Xiaobin Wang
Published 2018-07-01

A Prospective Birth Cohort Study on Maternal Cholesterol Levels and Offspring Attention Deficit Hyperactivity Disorder: New Insight on Sex Differences

by Yuelong Ji, Anne W. Riley, Li-Ching Lee, Heather Volk, Xiumei Hong, Guoying Wang, Rayris Angomas, Tom Stivers, Anastacia Wahl, Hongkai Ji, Tami R. Bartell, Irina Burd, David Paige, Margaret D. Fallin, Barry Zuckerman, Xiaobin Wang
Published 2017-12-01

Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

by Xitiz Chamling, Alyssa Kallman, Weixiang Fang, Cynthia A. Berlinicke, Joseph L. Mertz, Prajwal Devkota, Itzy E. Morales Pantoja, Matthew D. Smith, Zhicheng Ji, Calvin Chang, Aniruddha Kaushik, Liben Chen, Katharine A. Whartenby, Peter A. Calabresi, Hai-Quan Mao, Hongkai Ji, Tza-Huei Wang, Donald J. Zack
Published 2021-01-01

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

by Xiumei Hong, Ke Hao, Hongkai Ji, Shouneng Peng, Ben Sherwood, Antonio Di Narzo, Hui-Ju Tsai, Xin Liu, Irina Burd, Guoying Wang, Yuelong Ji, Deanna Caruso, Guangyun Mao, Tami R. Bartell, Zhongyang Zhang, Colleen Pearson, Linda Heffner, Sandra Cerda, Terri H. Beaty, M. Daniele Fallin, Aviva Lee-Parritz, Barry Zuckerman, Daniel E. Weeks, Xiaobin Wang
Published 2017-06-01

Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa

by Liyun Zhang, Conan Chen, Jie Fu, Brendan Lilley, Cynthia Berlinicke, Baranda Hansen, Ding Ding, Guohua Wang, Tao Wang, Daniel Shou, Ying Ye, Timothy Mulligan, Kevin Emmerich, Meera T Saxena, Kelsi R Hall, Abigail V Sharrock, Carlene Brandon, Hyejin Park, Tae-In Kam, Valina L Dawson, Ted M Dawson, Joong Sup Shim, Justin Hanes, Hongkai Ji, Jun O Liu, Jiang Qian, David F Ackerley, Baerbel Rohrer, Donald J Zack, Jeff S Mumm
Published 2021-06-01