Publications

Selected Peer-Reviewed Publications

After 2013:

  1. Zang C, Wang T, Deng K , Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He H, Brown M, Liu J, Xie Y, Liu X. High-dimensional genomic data bias correction and data integration using MANCIE. Nature communications. Accepted. IF=10.74.
  2. Ma F, Ye H, He H, Gerrin SJ, Chen S, Tanenbaum BA, Cai C, Sowalsky A, He L, Wang H, Balk SP, Yuan X. SOX9 drives WNT pathway activation in Prostate Cancer. J Clin Invest. Accepted. IF=13.77.
  3. Xu H, Xu K, He H, Zang C, Chen C, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu X.S. Integrative Analysis Revealed the collaboration between EZH2 and E2F1 in transcriptional regulation of cancer-related genes. Molecular Cancer Research. 2015. PMID: 26659825. IF=4.50.
  4. Shu S*, Lin CY*, He H*, Doherty E*, Brown J, Mohammed H, D’Santos C, Mckeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Chiang C, Anders L, Young RA, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K. Response and resistance to BET bromodomain inhibitors in triple negative breast cancer. Nature, Accetpted. IF=42.35.
  5. Hsieh CL, Botta G, Gao S, Li T, Van Allen EM, Treacy DJ, Cai C, He H, Sweeney CJ, Brown M, Balk SP, Nelson PS, Garraway LA, Kantoff PW. PLZF, a Tumor Suppressor Genetically Lost in Metastatic Castration-Resistant Prostate Cancer, Is a Mediator of Resistance to Androgen Deprivation Therapy. Cancer Res. 2015. PMID: 25808865. IF=9.28.
  6. Cai C*, He H*, Chen S, Yu Z, Gao Y, Chen S, Schüle R, Liu X.S, Brown M  and Balk S.P. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. Cell Reports. 2014. PMID: 25482560. IF=7.21.
  7. He H*, Meyer CA*, Hu SS, Chen MW, Zang CZ, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods. 2014. PMID: 24317252. IF=25.95.
  8. Sun T, Wang X, He H, Sweeney C.J, Liu X.S, Brown M, Lee G.M, Kantoff P.W. MiR-221 promotes the development of androgen independence in prostate cancer cells via downregulation of HECTD2 and RAB1A. Oncogene. 2014. PMID: 23770851. IF=8.56.
  9. Yang Y, Liu R, Qiu R, Zheng Y, Huang W, Hu H, Ji Q, He H, Shang Y, Gong Y, Wang Y. CRL4B promotes tumorigenesis by coordinating with SUV39H1/HP1/DNMT3A in DNA methylation-based epigenetic silencing. Oncogene. 2013. PMID: 24292684. IF=8.56.

​Before 2013:

  1. Jeselsohn RM, Werner L, Regan MM, Fatima A, Gilmore L, Collins LC, Beck AH, Bailey ST, He H, Buchwalter G, Brown M, Iglehart JD, Richardson A, Come SE. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response. . 2013. PLoS One. PMID: 23741308. IF=3.53.
  2. May T, Yang J, Shoni M, Liu S, He H, Gali R, Ng S.K, Crum C, Berkowitz R.S and Ng S.W. BRCA1 Expression is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein-2. Neoplasia. 2013. PMID: 23730208. IF=5.40.
  3. Cai C, Wang H, He H, Chen S, Mucci L, Wang Q, Flore C, Sowalsky A, Loda M, Liu XS, Brown M, Balk S, Yuan X. ERG Activation of an Androgen Receptor Regulated Enhancer in the SOX9 Gene Mediates Tumor Development in TMPRSS2:ERG Fusion Positive Prostate Cancer. J Clin Invest. 2013. PMID: 23426182. IF=13.77.
  4. He H*, Meyer CA*, Chen MW, Jordan VC, Brown M, Liu XS.  Differential DNase I Hypersensitivity reveals Factor-dependent Chromatin Dynamics. Genome Research. 2012. PMID: 22508765. IF=13.85.
  5. Xu K, Wu Z, Groner A, He H, Cai C, Liu T, Thornton J, Gregory R, Loda M, Stack E, Kantoff P, Balk S, Liu X.S, Brown M. EZH2 Oncogenic Activity in Castration Resistant Prostate Cancer is Polycomb-Independent. Science. 2012. PMID: 23239736. IF=31.48.
  6. Xu Y, Xu C, Kato A, Tempel W, Abreu JC, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He H, Cui Q, Clark E, Ma C, Barbara A, Veenstra J, Xu G, Kaiser G, Liu XS, Sugrue S, He X, Min J, Kato Y, Shi Y. Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development. Cell. 2012. PMID: 23217707. IF=33.12.
  7. Chen Y, Negre N, Li Q, Mieczkowska J, Slattery M, Liu T, Zhang Y, Kim T, He H, Zieba J, Ruan Y, Bickel P, Myers R,Wold B, White K, Lieb J, Liu X.S. Systematic evaluation of factors influencing ChIP-seq fidelity using ultra-deep sequencing. Nature Methods. 2012. PMID: 22522655. IF=25.95.
  8. Cai C, He H, Chen S, Coleman I, Wang H, Fang Z, Nelson PS, Chen S, Brown M, Balk SP. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell. 2011. PMID: 22014572. IF=23.89.
  9. Meyer CA, He H, Brown M, Liu XS. BINOCh: Binding Inference from Nucleosome Occupancy Changes. Bioinformatics. 2011. PMID: 21551136. IF=4.62.
  10. Wang Y, Chen J, Wei G, He H, Zhu X, Xiao T, Wei G, Dong B, He S, Skogerbø G, Chen R. The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage specific expression. Nucleic acids research. 2011. PMID: 21378118. IF=8.81.
  11. Fujiki R, Hashiba W, Sekine H, Yokoyama A, Chikanishi T, Ito S, Imai Y, Kim J, He H, Igarashi K, Kanno J, Ohtake F, Kitagawa H, Roeder R, Brown M, Kato S. GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature. 2011. PMID: 22121020. IF=42.35.
  12. He H*, Meyer CA*, Shin H, Bailey S, Wei G, Wang Q, Zhang Y, Xu K, Brown M, Liu. XS. Nucleosome Dynamics Define Transcriptional Enhancers. Nature Genetics. 2010 Apr; 42(4): 343-7. PMID: 20208536. IF=29.65.
  13. Verzi M, Shin H, He H, Sulahian R, Meyer C, Montgomery R, Fleet J, Brown M, Liu XS, Shivdasani R. Differentiation-specific histone modifications reveal dynamic chromatin interactions and alternative partners for the intestinal transcription factor CDX2. Developmental Cell. November 2010. PMID: 21074721. IF=10.37.
  14. Ahmadiyeh N, Pomerantz MM, Grisanzio C, Herman P, Jia L, Almendro V, He H, Brown M, Liu XS, Davis M, Caswell JL, Beckwith CA, Hills A, Macconaill L, Coetzee GA, Regan MM, Freedman ML. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A. 2010 May 7. PMID: 20453196. IF=9.81.
  15. Li T*, He H*, Wang Y, Skogerbø G, Chen R. “In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs”. BMC Mol Biol. 2008; 9:71. PMID: 18680611. IF=2.06.
  16. He S, Su H, Liu C, Skogerbo G, He H, He D, Zhu X, Liu T, Zhao Y, Chen R. "MicroRNA-encoding long non-coding". BMC Genomics. 2008; 9:236. PMID: 18492288. IF=2.06.
  17. Aftab MN*, He H*, Li T, Skogerbø G, Chen R. “Microarrray Analysis of ncRNA expression patterns after RNAi against snoRNA associated proteins”. BMC Genomics. 2008; 9:278. PMID: 18547420. IF=4.04.
  18. Jia D*, Cai L*, He H*, Skogerbø G, Li T, Aftab MN, Chen R. “Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans”. BMC Mol Biol. 2007; 8:86. PMID: 17903271. IF=2.06.
  19. He H*, Wang J*, Liu T*, Liu XS, Li T, Wang Y, Qian Z, Zheng H, Zhu X, Wu T,  Shi B, Deng W, Zhou W, Skogerbø G, Chen R. “Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray”. Genome Res. 2007; 17:1471–1477. PMID: 17785534. IF=13.85.
  20. He H*, Cai L*, Skogerbø G, Deng W, Liu T, Zhu X, Wang Y, Jia D, Zhang Z, Tao Y, Zeng H, Aftab MN, Cui Y, Liu G, Chen R. “Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray”. Nucleic Acids Res. 2006; 34: 2976–2983. PMID: 16738136. IF=8.81.
  21. Deng W, Zhu X, Skogerbø G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res. 2006; 16(1):20-29. PMID: 16344563. IF=13.85.
  22. Wang H, He H, Bao J. Average cycle period in asymmetrical flashing ratchet, Commun. Theor. Phys. 2005. 43-229.