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    Hao Li, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentBiochemistry and Biophysics
    Address1700 4th Street
    San Francisco CA 94158
    Phone415-502-8187

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods. 2014 Apr; 11(4):443-8.
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      2. Huang V, Zheng J, Qi Z, Wang J, Place RF, Yu J, Li H, Li LC. Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet. 2013; 9(9):e1003821.
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      3. He X, Fuller CK, Song Y, Meng Q, Zhang B, Yang X, Li H. Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet. 2013 May 2; 92(5):667-80.
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      4. Nelson CS, Fuller CK, Fordyce PM, Greninger AL, Li H, DeRisi JL. Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic Acids Res. 2013 Jul; 41(12):5991-6004.
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      5. Rafelski SM, Viana MP, Zhang Y, Chan YH, Thorn KS, Yam P, Fung JC, Li H, Costa Lda F, Marshall WF. Mitochondrial network size scaling in budding yeast. Science. 2012 Nov 9; 338(6108):822-4.
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      6. Kimmig P, Diaz M, Zheng J, Williams CC, Lang A, Aragón T, Li H, Walter P. The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis. Elife. 2012; 1:e00048.
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      7. Chubukov V, Zuleta IA, Li H. Regulatory architecture determines optimal regulation of gene expression in metabolic pathways. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):5127-32.
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      8. Chen L, Zheng J, Yang N, Li H, Guo S. Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genes. J Biol Chem. 2011 May 27; 286(21):18641-9.
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      9. Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ. Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol. 2010 Oct 5; 6:420.
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      10. Li H, Johnson AD. Evolution of transcription networks--lessons from yeasts. Curr Biol. 2010 Sep 14; 20(17):R746-53.
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      11. Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep; 28(9):970-5.
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      12. Wu R, Li H. Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters. Genome Res. 2010 Apr; 20(4):473-84.
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      13. Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 Jan 15; 337(2):484-95.
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      14. Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One. 2009; 4(10):e7453.
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      15. Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H. CompMoby: comparative MobyDick for detection of cis-regulatory motifs. BMC Bioinformatics. 2008; 9:455.
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      16. Chin CS, Chubukov V, Jolly ER, DeRisi J, Li H. Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 2008 Jun 17; 6(6):e146.
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      17. Tuch BB, Li H, Johnson AD. Evolution of eukaryotic transcription circuits. Science. 2008 Mar 28; 319(5871):1797-9.
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      18. Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 2008 Feb; 6(2):e38.
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      19. Wu RZ, Chaivorapol C, Zheng J, Li H, Liang S. fREDUCE: detection of degenerate regulatory elements using correlation with expression. BMC Bioinformatics. 2007; 8:399.
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      20. Bolton EC, So AY, Chaivorapol C, Haqq CM, Li H, Yamamoto KR. Cell- and gene-specific regulation of primary target genes by the androgen receptor. Genes Dev. 2007 Aug 15; 21(16):2005-17.
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      21. Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet. 2007 Aug; 3(8):e145.
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      22. So AY, Chaivorapol C, Bolton EC, Li H, Yamamoto KR. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet. 2007 Jun; 3(6):e94.
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      23. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 2007; 4:40.
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      24. Kim Guisbert KS, Li H, Guthrie C. Alternative 3' pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivo. PLoS Biol. 2007 Jan; 5(1):e6.
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      25. Tsong AE, Tuch BB, Li H, Johnson AD. Evolution of alternative transcriptional circuits with identical logic. Nature. 2006 Sep 28; 443(7110):415-20.
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      26. Nochomovitz YD, Li H. Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output. Proc Natl Acad Sci U S A. 2006 Mar 14; 103(11):4180-5.
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      27. Jolly ER, Chin CS, Herskowitz I, Li H. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. BMC Bioinformatics. 2005; 6:275.
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      28. Klebes A, Sustar A, Kechris K, Li H, Schubiger G, Kornberg TB. Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes. Development. 2005 Aug; 132(16):3753-65.
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      29. McCarroll SA, Li H, Bargmann CI. Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation. Curr Biol. 2005 Feb 22; 15(4):347-52.
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      30. Kim Guisbert K, Duncan K, Li H, Guthrie C. Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. RNA. 2005 Apr; 11(4):383-93.
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      31. Chin CS, Chuang JH, Li H. Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Res. 2005 Feb; 15(2):205-13.
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      32. Chuang JH, Li H. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol. 2004 Feb; 2(2):E29.
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      33. McCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, Jan YN, Kenyon C, Bargmann CI, Li H. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet. 2004 Feb; 36(2):197-204.
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      34. Li H, Wang W. Dissecting the transcription networks of a cell using computational genomics. Curr Opin Genet Dev. 2003 Dec; 13(6):611-6.
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      35. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, Kenyon C. Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature. 2003 Jul 17; 424(6946):277-83.
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      36. Li H, Rhodius V, Gross C, Siggia ED. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc Natl Acad Sci U S A. 2002 Sep 3; 99(18):11772-7.
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      37. Li H. Computational approaches to identifying transcription factor binding sites in yeast genome. Methods Enzymol. 2002; 350:484-95.
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