| Year |
Citation |
Score |
| 2020 |
Qiu X, Ma F, Zhao M, Cao Y, Shipp L, Liu A, Dutta A, Singh A, Braikia FZ, De S, Wood WH, Becker KG, Zhou W, Ji H, Zhao K, et al. Altered 3D chromatin structure permits inversional recombination at the locus. Science Advances. 6: eaaz8850. PMID 32851160 DOI: 10.1126/Sciadv.Aaz8850 |
0.305 |
|
| 2020 |
Ji Z, Zhou W, Hou W, Ji H. Single-cell ATAC-seq signal extraction and enhancement with SCATE. Genome Biology. 21: 161. PMID 32620137 DOI: 10.1186/S13059-020-02075-3 |
0.363 |
|
| 2020 |
Lex RK, Ji Z, Falkenstein KN, Zhou W, Henry JL, Ji H, Vokes SA. GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. Elife. 9. PMID 31989924 DOI: 10.7554/Elife.50670 |
0.366 |
|
| 2019 |
Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, Huang AC, Johnson J, Staupe RP, Bengsch B, Xu C, Yu S, Kurachi M, Herati RS, Vella LA, Baxter AE, ... ... Ji H, et al. TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision. Immunity. PMID 31606264 DOI: 10.1016/J.Immuni.2019.09.013 |
0.342 |
|
| 2019 |
Zhou W, Ji Z, Fang W, Ji H. Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq. Nucleic Acids Research. PMID 31428792 DOI: 10.1093/Nar/Gkz716 |
0.343 |
|
| 2019 |
Caushi JX, Ji Z, Zhang J, Asmar ME, Anagnostou V, Cottrell TR, Chan HY, Guo H, Merghoub T, Wolchok JD, Naidoo J, Marrone KA, Chaft JE, Hellmann MD, Gabrielson E, ... ... Ji H, et al. Abstract 4041: Coupling neoantigen specific T cell clonotypes and their molecular phenotypes at the single cell level in resectable anti-PD-1 treated NSCLC Cancer Research. 79: 4041-4041. DOI: 10.1158/1538-7445.Am2019-4041 |
0.352 |
|
| 2018 |
Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nature Communications. 9: 1364. PMID 29636475 DOI: 10.1038/S41467-018-03856-Y |
0.31 |
|
| 2018 |
Kuang Z, Ji Z, Boeke JD, Ji H. Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. Nucleic Acids Research. 46: e2. PMID 29325176 DOI: 10.1093/Nar/Gkx905 |
0.33 |
|
| 2017 |
Kuang Z, Pinglay S, Ji H, Boeke JD. Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth. Elife. 6. PMID 28949295 DOI: 10.7554/Elife.29938 |
0.328 |
|
| 2017 |
Ji Z, Zhou W, Ji H. Single-cell regulome data analysis by SCRAT. Bioinformatics (Oxford, England). PMID 28505247 DOI: 10.1093/Bioinformatics/Btx315 |
0.362 |
|
| 2016 |
Wang J, Xia S, Arand B, Zhu H, Machiraju R, Huang K, Ji H, Qian J. Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. Plos Computational Biology. 12: e1004892. PMID 27100869 DOI: 10.1371/Journal.Pcbi.1004892 |
0.377 |
|
| 2015 |
Ji Z, Vokes SA, Dang CV, Ji H. Turning publicly available gene expression data into discoveries using gene set context analysis. Nucleic Acids Research. PMID 26350211 DOI: 10.1093/Nar/Gkv873 |
0.339 |
|
| 2015 |
Lewandowski JP, Du F, Zhang S, Powell MB, Falkenstein KN, Ji H, Vokes SA. Spatiotemporal regulation of GLI target genes in the mammalian limb bud. Developmental Biology. 406: 92-103. PMID 26238476 DOI: 10.1016/J.Ydbio.2015.07.022 |
0.384 |
|
| 2015 |
Jin K, Park S, Teo WW, Korangath P, Cho SS, Yoshida T, Gyorffy B, Goswami CP, Nakshatri H, Cruz LA, Zhou W, Ji H, Su Y, Ekram M, Wu Z, et al. HOXB7 is an ERα cofactor in the activation of HER2 and multiple ER target genes leading to endocrine resistance. Cancer Discovery. PMID 26180042 DOI: 10.1158/2159-8290.Cd-15-0090 |
0.308 |
|
| 2015 |
Wamaitha SE, Del Valle I, Cho LT, Wei Y, Fogarty NM, Blakeley P, Sherwood RI, Ji H, Niakan KK. Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells. Genes & Development. 29: 1239-55. PMID 26109048 DOI: 10.1101/Gad.257071.114 |
0.381 |
|
| 2014 |
Ying M, Tilghman J, Wei Y, Guerrero-Cazares H, Quinones-Hinojosa A, Ji H, Laterra J. Kruppel-like factor-9 (KLF9) inhibits glioblastoma stemness through global transcription repression and integrin α6 inhibition. The Journal of Biological Chemistry. 289: 32742-56. PMID 25288800 DOI: 10.1074/Jbc.M114.588988 |
0.381 |
|
| 2014 |
Kuang Z, Cai L, Zhang X, Ji H, Tu BP, Boeke JD. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nature Structural & Molecular Biology. 21: 854-63. PMID 25173176 DOI: 10.1038/Nsmb.2881 |
0.345 |
|
| 2014 |
Wu H, Ji H. Polya peak: Detecting transcription factor binding sites from Ch IP-seq using peak shape information Plos One. 9. PMID 24608116 DOI: 10.1371/Journal.Pone.0089694 |
0.319 |
|
| 2014 |
Fan T, Le A, Stine Z, Yang Y, Zeller K, Zhou W, Ji H, Higashi R, Dang C, Lane A. Antagonistic effects of MYC and hypoxia in channeling glucose and glutamine into de novo nucleotide biosynthesis Cancer & Metabolism. 2: O10. DOI: 10.1186/2049-3002-2-S1-O10 |
0.319 |
|
| 2013 |
Jaffe AE, Storey JD, Ji H, Leek JT. Gene set bagging for estimating the probability a statistically significant result will replicate. Bmc Bioinformatics. 14: 360. PMID 24330332 DOI: 10.1186/1471-2105-14-360 |
0.357 |
|
| 2013 |
Wang J, Park JS, Wei Y, Rajurkar M, Cotton JL, Fan Q, Lewis BC, Ji H, Mao J. TRIB2 acts downstream of Wnt/TCF in liver cancer cells to regulate YAP and C/EBPα function. Molecular Cell. 51: 211-25. PMID 23769673 DOI: 10.1016/J.Molcel.2013.05.013 |
0.315 |
|
| 2013 |
Wei Y, Wu G, Ji H. 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: 156-178. PMID 23762209 DOI: 10.1007/S12561-012-9066-5 |
0.393 |
|
| 2013 |
Ji H, Li X, Wang QF, Ning Y. Differential principal component analysis of ChIP-seq Proceedings of the National Academy of Sciences of the United States of America. 110: 6789-6794. PMID 23569280 DOI: 10.1073/Pnas.1204398110 |
0.372 |
|
| 2013 |
Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics (Oxford, England). 29: 1182-1189. PMID 23457041 DOI: 10.1093/Bioinformatics/Btt108 |
0.398 |
|
| 2012 |
Wu H, Ji H. JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments. Methods in Molecular Biology (Clifton, N.J.). 802: 363-75. PMID 22130893 DOI: 10.1007/978-1-61779-400-1_24 |
0.364 |
|
| 2012 |
Wei Y, Li X, Wang Q, Ji H. iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding Bmc Bioinformatics. 13: 1-1. DOI: 10.1186/1471-2105-13-S18-A6 |
0.322 |
|
| 2011 |
Ji H, Wu G, Zhan X, Nolan A, Koh C, de Marzo A, Doan HM, Fan J, Cheadle C, Fallahi M, Cleveland JL, Dang CV, Zeller KI. Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation Plos One. 6. PMID 22039435 DOI: 10.1371/Journal.Pone.0026057 |
0.4 |
|
| 2011 |
Chen L, Wu G, Ji H. hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data Bioinformatics. 27: 1447-1448. PMID 21450710 DOI: 10.1093/Bioinformatics/Btr156 |
0.336 |
|
| 2011 |
Ji H, Jiang H, Ma W, Wong WH. Using CisGenome to analyze ChIP-chip and ChIP-seq data. Current Protocols in Bioinformatics. Unit2.13. PMID 21400695 DOI: 10.1002/0471250953.Bi0213S33 |
0.38 |
|
| 2011 |
Ji H, Wu G, Zhan X, Nolan A, Koh C, Marzo AD, Fan J, Cheadle C, Fallahi M, Cleveland J, Dang CV, Zeller K. Abstract 928: Species and cell type independent core MYC target genes in cancer and stem cells Cancer Research. 71: 928-928. DOI: 10.1158/1538-7445.Am2011-928 |
0.391 |
|
| 2010 |
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 H, Wong WH, Rhee SY, et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental Cell. 19: 765-77. PMID 21074725 DOI: 10.1016/J.Devcel.2010.10.010 |
0.344 |
|
| 2010 |
Ji H. Computational analysis of ChIP-seq data Methods in Molecular Biology (Clifton, N.J.). 674: 143-159. PMID 20827590 DOI: 10.1007/978-1-60761-854-6_9 |
0.378 |
|
| 2010 |
Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ, Ji H, Boeke JD, Burns KH. Mobile interspersed repeats are major structural variants in the human genome. Cell. 141: 1171-82. PMID 20602999 DOI: 10.1016/J.Cell.2010.05.026 |
0.307 |
|
| 2010 |
Lee EY, Ji H, Ouyang Z, Zhou B, Ma W, Vokes SA, McMahon AP, Wong WH, Scott MP. Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America. 107: 9736-41. PMID 20460306 DOI: 10.1073/Pnas.1004602107 |
0.404 |
|
| 2010 |
Niakan KK, Ji H, Maehr R, Vokes SA, Rodolfa KT, Sherwood RI, Yamaki M, Dimos JT, Chen AE, Melton DA, McMahon AP, Eggan K. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes & Development. 24: 312-26. PMID 20123909 DOI: 10.1101/Gad.1833510 |
0.389 |
|
| 2010 |
Mi S, He F, Wu J, Zhou J, Wu G, Thirman MJ, Ji H, Wang Q. Genome Wide Location Analysis Reveals Deregulated MicroRNA Genes In MLL Rearragned Leukemic Genome Blood. 116: 2507-2507. DOI: 10.1182/Blood.V116.21.2507.2507 |
0.352 |
|
| 2009 |
Wang QJ, Wu G, Mi S, He F, Dong J, Mattison RJ, Kaberlein J, Wang Q, Prabhakar S, Ji H, Thirman MJ. MLL Fusion Proteins Directly Regulate a Small Set of Wild Type MLL Target Genes. Blood. 114: 1279-1279. DOI: 10.1182/Blood.V114.22.1279.1279 |
0.415 |
|
| 2008 |
Vokes SA, Ji H, Wong WH, McMahon AP. A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes & Development. 22: 2651-63. PMID 18832070 DOI: 10.1101/Gad.1693008 |
0.392 |
|
| 2007 |
Vokes SA, Ji H, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh WJ, Davidson EH, Wong WH, McMahon AP. Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development (Cambridge, England). 134: 1977-89. PMID 17442700 DOI: 10.1242/Dev.001966 |
0.381 |
|
| 2007 |
Paik JH, Kollipara R, Chu G, Ji H, Xiao Y, Ding Z, Miao L, Tothova Z, Horner JW, Carrasco DR, Jiang S, Gilliland DG, Chin L, Wong WH, Castrillon DH, et al. FoxOs are lineage-restricted redundant tumor suppressors and regulate endothelial cell homeostasis. Cell. 128: 309-23. PMID 17254969 DOI: 10.1016/J.Cell.2006.12.029 |
0.348 |
|
| 2006 |
Kim RS, Ji H, Wong WH. An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. Bmc Bioinformatics. 7: 44. PMID 16438730 DOI: 10.1186/1471-2105-7-44 |
0.394 |
|
| 2005 |
Ji H, Wong WH. TileMap: Create chromosomal map of tiling array hybridizations Bioinformatics. 21: 3629-3636. PMID 16046496 DOI: 10.1093/Bioinformatics/Bti593 |
0.35 |
|
| 2001 |
Ji H, Zhou Q, Wen F, Xia H, Lu X, Li Y. AsMamDB: an alternative splice database of mammals Nucleic Acids Research. 29: 260-263. PMID 11125106 DOI: 10.1093/Nar/29.1.260 |
0.354 |
|
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