Hu:Publications

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(†) Co-first authorship; (*) Corresponding/Co-corresponding authorship

2019

  1. Hu G* (2019) Evaluation of 3D Chromatin Interactions using Hi-C. Stem Cell Transcriptional Networks (in press).
  2. Monaghan K, Zheng W, Hu G*, Wan E* (2019) Monocytes and monocyte-derived antigen-presenting cells have distinct gene signatures in experimental model of multiple sclerosis. Frontiers in Immunology, 10:2779.
  3. Zhong C, Zheng M, Cui K, Martins A, Hu G, Li D, Tessarollo L, Kozlov S, Keller J, Tsang J, Zhao K, Zhu J (2019) Quantitative Expression of GATA3 Specifies Lineage Fates and Functions of Innate Lymphoid Cells. Immunity (in press).
  4. Carter B, Ku WL, Kang JY, Hu G, Perrie J, Tang Q, Zhao K (2019) Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq). Nature Communications, 10: 3747.
  5. Ku WL, Nakamura K, Gao W, Cui K, Hu G, Tang Q, Ni B, Zhao K (2019) Single cell chromatin immunocleavage sequencing (scChlC-seq) to profile histone modification. Nature Methods, 16:323-325.

2018

  1. Hu G†*, Cui K†, Fang D, Hirose S, Wang X, Wangsa D, Jin W, Ried T, Liu P, Zhu J, Rothenberg E, Zhao K (2018) Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells. Immunity, 48:227-242.
  2. Lai B†, Tang Q†, Jin W†, Hu G†, Wangsa D, Cui K, Stanton B, Ren G, Ding Y, Zhao M, Liu S, Song J, Ried T, Zhao K (2018) Trac-looping measures genome structure and chromatin accessibility. Nature Methods, 15:741-747.
  3. Fang D, Cui K, Hu G, Gurram RK, Zhong C, Oler A, Yagi R, Zhao M, Sharma S, Liu P, Sun B, Zhao K, Zhu J (2018) Bcl11b, a Novel GATA3-Interacting Protein, Suppresses Th1 while Limiting Th2 Cell Differentiation. Journal of Experimental Medicine, 215(5):1449-1462.
  4. Fang D, Cui K, Mao K, Hu G, Li R, Zheng M, Riteau N, Reiner S, Sher A, Zhao K, Zhu J (2018) Transient T-bet expression functionally specifies a distinct T follicular helper subset. Journal of Experimental Medicine, DOI: 10.1084/jem.20180927.
  5. Lai B, Gao W, Cui K, Xie W, Tang Q, Jin W, Hu G, Ni B, Zhao K (2018) Principles of nucleosome organization revealed by single-cell MNase-seq. Nature, DOI: 10.1038/s41586-018-0567-3.
  6. Yu F, Sharma S, Jankovic D, Gurram RK, Su P, Hu G, Li R, Rieder S, Zhao K, Sun B, Zhu J (2018) The transcription factor Bhlhe40 is a switch of inflammatory versus anti-inflammatory Th1 cell fate determination. Journal of Experimental Medicine, 215(7):1813-1821.

2017

  1. Placek K†, Hu G†, Cui K†, Zhang D, Ding Y, Lee JE, Jang Y, Wang C, Konkel JE, Song J, Liu C, Ge K, Chen W & Zhao K (2017) MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping. Nature Immunology, 18(9):1035-1045.
  2. Kidder BL, Hu G, Cui K, Zhao K (2017) SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics & Chromatin, 10 (1), 8.
  3. Ren G, Jin W, Cui K, Rodrigez J, Hu G, Larson D & Zhao K (2017) CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression. Molecular Cell, 67 (6), 1049-1058.

2016

  1. Hu G, Zhao K (2016) Looping around Bcl6 in Germinal Center to Sharpen B Cell Immunity. Immunity, 45 (3), 459–461.
  2. Wang R., Zhao T, Cui K, Hu G, Chen Q, Chen W, Wang X, Soto-Gutierrez A, Zhao K, Deng C (2016) Negative reciprocal regulation between Sirt1 and Per2 modulates the circadian clock and aging. Scientific Reports, 6: 28633.
  3. Zhong C, Cui K, Wilhelm C, Hu G, Mao K, Belkaid Y, Zhao K, Zhu J (2016) Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nature Immunology, 17 (2), 169-178.

2015

  1. Hu G, Zhao K (2015) Identification of intergenic long non-coding RNA by deep sequencing. Epigenetics Gene Regulation and Expression, 223-232.
  2. Hu G, Zhu H (2015) MetaTISA: Metagenomic Gene Start Prediction. Encyclopedia of Metagenomics, 464-467.
  3. Krupovic M, Zhi N, Li J, Hu G, Koonin E, Wong S, Shevchenko S, Zhao K, Young N (2015) Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biology and Evolution, 7:993-1001.
  4. He Y, Ding Y, Zhan F, Zhang H, Han B, Hu G, Zhao K, Yang N, Yu Y, Mao L, Song J (2015) The conservation and signatures of lincRNAs in Marek’s disease of chicken. Scientific Reports, 5:15184.

2014

  1. Hu G*, Zhao K (2014) Correlating Histone Modification Patterns with Gene Expression Data during Hematopoiesis. Stem Cell Transcriptional Networks: Methods and Protocols, 175-187.
  2. Kidder BL†, Hu G†, Zhao K (2014) KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. Genome Biology, 15(2): R32.
  3. Yagi R, Zhong C, Northrup D, Yu F, Bouladoux N, Spencer S, Hu G, Barron L, Sharma S, Nakayama T, Belkaid Y, Zhao K, Zhu J (2014) The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid Cells. Immunity, 40:378-388.
  4. Zhi N, Hu G, Wong S, Zhao K, Mao Q, Young NS (2014) Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method. PNAS, 111:E977.

2013

  1. Hu G†, Cui K†, Northrup D†, Liu C, Wang C, Tang Q, Ge K, Leven D, Crane-Robinson C, Zhao K (2013) H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell, 12:180-192.
  2. Hu G†, Tang Q†, Sharma S†, Yu F, Escobar T, Muljo S, Zhu J, Zhao K (2013) Expression and regulation of lincRNAs during T cell development and differentiation. Nature Immunology, 14: 1190-1198.
  3. Xu B†, Zhi N†, Hu G†, Wan Z, Zheng X, Liu X, Wong S, Kajigaya S, Zhao K, Mao Q, Young N (2013) Identification and characterization of a novel human parvovirus in seronegative hepatitis patient by next generation sequencing, PNAS, 110: 10264-10269.
  4. Liu Y, Guo J, Hu G, Zhu H (2013) Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics, 14(Suppl 5):S12.
  5. Kidder BL, Hu G, Yu ZX, Liu C, Zhao K (2013) Extended self-renewal and accelerated reprogramming in the absence of Kdm5b. Molecular and Cellular Biology, 33(24): 4793-4810.

2012

  1. Nie Z†, Hu G†, Wei G, Cui K, Yamane A, Resch W, Tessarollo L, Cassellas R, Zhao K, Levens D (2012) c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell, 151:68-79.
  2. Jia J, Zheng X, Hu G, Cui K, Zhang J, Zhang A, Du Y, Liu B, Yates J, Liu C, Zhao K, Zheng Y (2012) Regulation of pluripotency and self-renewal of ES cells through epigenetic threshold modulation and mRNA pruning. Cell, 151:576-589.
  3. Wei G, Hu G, Cui K, Zhao K (2012) Genome-wide mapping of nucleosome occupancy, histone modifications and gene expression using next generation sequencing technology. Methods in Enzymology, 513:297-313.
  4. Zhu J, Jankovic D, Oler A, Wei G, Sharma S, Hu G, Guo L, Yagi R., Yamane H., Punkosdy G., Feigenbaum L, Zhao K, Paul W (2012) T-bet is induced by multiple pathways and prevents an endogenous Th2 program during Th1 responses. Immunity, 37:660-673.

2011

  1. Hu G†, Schones D†, Cui K†, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo N, Huang S, Zhao K (2011) Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Research, 21:1650-1658.
  2. Zheng X, Hu GQ, She ZS, Zhu H (2011) Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics, 12: 361.
  3. Kidder B, Hu G, Zhao K (2011) ChIP-Seq: technical consideration for obtaining high quality data. Nature Immunology, 12: 918-922.
  4. Kang B, Pu M, Hu G, Wen W, Dong Z, Zhao K, Stillman B, Zhang Z (2011) Phosphorylation of H4 serine 47 promotes HIRA-mediated nucleosome assembly. Genes & Development, 25: 1359-1364.

2010

  1. Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, Yaghi NK, Lim H, Garcia BA, Brizuela L, Zhao K, Roberts TM, Shi Y (2010) Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature, 466(7305):503-507.

2009 and before

  1. Hu GQ, Zheng X, Zhu HQ, She ZS (2009) Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics, 25(1):123-125.
  2. Hu GQ†, Guo JT†, Liu YC†, Zhu H (2009) MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics, 25(14):1843-1845.
  3. Luo C, Hu GQ, Zhu H (2009) Genomic analysis to fully understand the virulence of uropathogenic Escherichia coli CFT073. Acta Biophysica Sinica, 25:264-268
  4. Luo C†, Hu GQ†, Zhu H (2009) Genome reannotation of Escherichia coli CFT073 with new insights into virulence. BMC Genomics, 10:552.
  5. Hu GQ†, Zheng X†, Ju LN, Zhu H, She ZS (2008) Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics, 9:160.
  6. Hu GQ, Liu YC, Zheng XB, Yang YF, She ZS, Zhu HQ (2008) New solutions of translation initiation site prediction for prokaryotic genomes. Progress in Biochemistry and Biophysics, 35(11): 1254-1262.
  7. Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H (2008) ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Research, 36:D114-D119.
  8. Zhu H, Hu GQ, Yang YF, Wang J, She ZS (2007) MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. BMC Bioinformatics, 8:97.
  9. Zhu HQ, Hu GQ, Ouyang ZQ, Wang J, She ZS (2004) Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics, 20(18): 3308-3317.