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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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    Collapse Research 
    Collapse Research Activities and Funding
    Transcriptional Activation by Small RNA: Mechanism and Design Rules
    NIH R01GM090293Sep 25, 2009 - Aug 31, 2014
    Role: Principal Investigator
    Signals from the reproductive system that regulate aging in C. elegans
    NIH R01AG032435Jul 1, 2008 - Mar 31, 2019
    Role: Principal Investigator
    Structure function and evolution of yeast transcription networks
    NIH R01GM070808Apr 1, 2004 - Mar 31, 2014
    Role: Principal Investigator

    Collapse ORNG Applications 
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    Collapse Bibliographic 
    Collapse Publications
    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.
    List All   |   Timeline
    1. Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 2016 Mar; 26(3):320-35. PMID: 26902284.
      View in: PubMed
    2. Berglund K, Clissold K, Li HE, Wen L, Park SY, Gleixner J, Klein ME, Lu D, Barter JW, Rossi MA, Augustine GJ, Yin HH, Hochgeschwender U. Luminopsins integrate opto- and chemogenetics by using physical and biological light sources for opsin activation. Proc Natl Acad Sci U S A. 2016 Jan 19; 113(3):E358-67. PMID: 26733686.
      View in: PubMed
    3. Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H. Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry. Proc Natl Acad Sci U S A. 2015 Sep 22; 112(38):11977-82. PMID: 26351681; PMCID: PMC4586869 [Available on 03/22/16].
    4. Wang X, Zhao X, Johnston SC, Xian Y, Hu B, Wang C, Wang D, Liu L, Li H, Fang J, Meng X, Wang A, Wang Y, Wang Y. Effect of clopidogrel with aspirin on functional outcome in TIA or minor stroke: CHANCE substudy. Neurology. 2015 Aug 18; 85(7):573-9. PMID: 26283758; PMCID: PMC4548281 [Available on 08/18/16].
    5. Wang Y, Zhao X, Jiang Y, Li H, Wang L, Johnston SC, Liu L, Wong KS, Wang C, Pan Y, Jing J, Xu J, Meng X, Zhang M, Li Y, Zhou Y, Zhao W, Wang Y. Prevalence, knowledge, and treatment of transient ischemic attacks in China. Neurology. 2015 Jun 9; 84(23):2354-61. PMID: 25957333; PMCID: PMC4464739 [Available on 06/09/16].
    6. 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. PMID: 24608180; PMCID: PMC4016179.
    7. 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. PMID: 24086155; PMCID: PMC3784563.
    8. 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. PMID: 23643380; PMCID: PMC3644637.
    9. 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. PMID: 23625967; PMCID: PMC3695516.
    10. 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. PMID: 23139336; PMCID: PMC3602416.
    11. 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. PMID: 23066505; PMCID: PMC3470409.
    12. 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. PMID: 22416120; PMCID: PMC3324031.
    13. 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. PMID: 21471212; PMCID: PMC3099680.
    14. 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. PMID: 20959818; PMCID: PMC2990640.
    15. Li H, Johnson AD. Evolution of transcription networks--lessons from yeasts. Curr Biol. 2010 Sep 14; 20(17):R746-53. PMID: 20833319; PMCID: PMC3438143.
    16. 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. PMID: 20802496; PMCID: PMC2937095.
    17. 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. PMID: 20133331; PMCID: PMC2847750.
    18. 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. PMID: 19850031; PMCID: PMC3330829.
    19. 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. PMID: 19834618; PMCID: PMC2759544.
    20. 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. PMID: 18950538; PMCID: PMC2605473.
    21. 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. PMID: 18563967; PMCID: PMC2429954.
    22. Tuch BB, Li H, Johnson AD. Evolution of eukaryotic transcription circuits. Science. 2008 Mar 28; 319(5871):1797-9. PMID: 18369141.
      View in: PubMed
    23. 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. PMID: 18303948; PMCID: PMC2253631.
    24. 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. PMID: 17941998; PMCID: PMC2174516.
    25. 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. PMID: 17699749; PMCID: PMC1948856.
    26. 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. PMID: 17784790; PMCID: PMC1959362.
    27. 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. PMID: 17559307; PMCID: PMC1904358.
    28. 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. PMID: 17477878; PMCID: PMC1892812.
    29. 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. PMID: 17194212; PMCID: PMC1717019.
    30. Tsong AE, Tuch BB, Li H, Johnson AD. Evolution of alternative transcriptional circuits with identical logic. Nature. 2006 Sep 28; 443(7110):415-20. PMID: 17006507.
      View in: PubMed
    31. 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. PMID: 16537505; PMCID: PMC1449667.
    32. 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. PMID: 16297241; PMCID: PMC1326232.
    33. 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. PMID: 16077094.
      View in: PubMed
    34. 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. PMID: 15723796.
      View in: PubMed
    35. 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. PMID: 15703440; PMCID: PMC1370728.
    36. 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. PMID: 15653830; PMCID: PMC546519.
    37. 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. PMID: 14966531; PMCID: PMC340940.
    38. 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. PMID: 14730301.
      View in: PubMed
    39. Li H, Wang W. Dissecting the transcription networks of a cell using computational genomics. Curr Opin Genet Dev. 2003 Dec; 13(6):611-6. PMID: 14638323.
      View in: PubMed
    40. 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. PMID: 12845331.
      View in: PubMed
    41. 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. PMID: 12181488; PMCID: PMC129344.
    42. Li H. Computational approaches to identifying transcription factor binding sites in yeast genome. Methods Enzymol. 2002; 350:484-95. PMID: 12073331.
      View in: PubMed
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