Recent Publications

2006 - Present

• A global characterization of the translational and transcriptional programs induced by methionine restriction through ribosome profiling and RNA-seq
• Ke Zou, Qi Ouyang, Hao Li, Jiashun Zheng BMC Genomics 2017 18:189 DOI: 10.1186/s12864-017-3483-2
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• Using Microfluidic Devices to Measure Lifespan and Cellular Phenotypes in Single Budding Yeast Cells
• Zou, K., Ren, D. S., Ou-yang, Q., Li, H., Zheng, J. J. Vis. Exp. (121), e55412, doi:10.3791/55412 (2017).
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• saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription
• Cell Res. 2016 Mar; 26(3):320-35. Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC.
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• 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. doi: 10.1073/pnas.1506054112. Epub 2015 Sep 8. Jing Yang, Mark A. McCormick, Jiashun Zheng, Zhengwei Xie, Mitsuhiro Tsuchiya, Scott Tsuchiyama, Hana El-Samad, Qi Ouyang, Matt Kaeberlein, Brian K. Kennedy, and Hao Li
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• Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance
• Br J Psychiatry. 2015 Sep 3. pii: bjp.bp.114.156976. Li, M., Luo XJ, Landén M., Bergen SE, Hultman CM, Li X., Zhang W., Yao YG, Zhang C., Liu J., Mattheisen M., Cichon S., Mühleisen TW, Degenhardt FA, Nöthen MM, Schulze TG, Grigoroiu-Serbanescu M., Li H., Fuller CK, Chen C., Dong Q., Chen C., Jamain S., Leboyer M., Bellivier F., Etain B., Kahn JP, Henry C., Preisig M., Kutalik Z., Castelao E., Wright A., Mitchell PB, Fullerton JM, Schofield PR, Montgomery GW, Medland SE, Gordon SD, Martin NG, MooDS Consortium, Swedish Bipolar Study Group, Rietschel M., Liu C., Kleinman JE, Hyde TM, Weinberger DR, and Su B.
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• Early telomerase inactivation accelerates aging independently of telomere length.
• Cell. 2015 Feb 26;160(5):928-39. doi: 10.1016/j.cell.2015.02.002. Zhengwei Xie, Kyle A. Jay, Dana L. Smith, Yi Zhang, Zairan Liu, Jiashun Zheng, Ruilin Tian, Hao Li, Elizabeth H. Blackburn
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• Heterogeneously expressed fezf2 patterns gradient Notch activity in balancing the quiescence, proliferation, and differentiation of adult neural stem cells
• J.Neurosci. (2014) 34(42): 13911-23. Michael Berberoglu, Zhiqiang Dong, Guangnan Li, Jiashun Zheng, Luz del Carmen Martinez, Jisong peng, Mahendra Wagle, brian Reichholf, Claudia Petritsch, Hao Li, Samuel Pleasure,and Su Guo
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• Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry
• Nature Methods (2014) doi:10.1038/nmeth.2879. Ignacio A Zuleta, Andrés Aranda-Díaz, Hao Li & Hana El-Samad
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• Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells
• PLoS Genet 9(9): e1003821. doi:10.1371/journal.pgen.10038212013. Vera Huang, Jiashun Zheng, Zhongxia Qi, Ji Wang, Robert F. Place, Jingwei Yu, Hao Li,Long-Cheng Li. (2013)
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• Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS
• Am J Hum Genet. 2013 May 2;92(5):667-80. doi: 10.1016/j.ajhg.2013.03.022. Xin He, Chris K. Fuller, Yi Song, Qingying Meng, Bin Zhang, Xia Yang and Hao Li. (2013)
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• 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 Research. 2013. Christopher S. Nelson, Chris K. Fuller, Polly M. Fordyce, Alexander L. Greninger, Hao Li, and Joseph L. DeRisi. (2013)
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• Mitochondrial network size scaling in budding yeast.
• Science. 2012 Nov 9;338(6108):822-4. doi: 10.1126/science.1225720. Rafelski SM, Viana MP, Zhang Y, Chan YH, Thorn KS, Yam P, Fung JC, Li H, Costa Lda F, Marshall WF.(2012)
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• Single cell analysis of yeast replicative aging using a new generation of microfluidic device
• PLoS One. 2012;7(11):e48275. doi: 10.1371/journal.pone.0048275. Zhang Y, Luo C, Zou K, Xie Z, Brandman O, Ouyang Q, Li H.(2012)
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• The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis
• eLife. 2012; 1: e00048. Published online 2012 October 15. doi: 10.7554/eLife.00048. Kimmig P, Diaz M, Zheng J, Williams CC, Lang A, Aragón T, Li H, Walter P.(2012)
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• Molecular Phenotyping of Aging in Single Yeast Cells Using a Novel Microfluidic Device
• Aging Cell. 2012 Apr 12. doi: 10.1111/j.1474-9726.2012.00821.x. Xie Z, Zhang Y, Zou K, Brandman O, Luo C, Ouyang Q, Li H (2012)
• PDF file, highlighted in Nature, News & Views

• Regulatory architecture determines optimal regulation of gene expression in metabolic pathways
• Proc Natl Acad Sci U S A. 109(13):5127-32 , Chubukov V, Zuleta IA, Li H (2012)
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• Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genes
• J Biol Chem. Chen L, Zheng J, Yang N, Li H, Guo S. (2011)
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• Epistatic relationships reveal the functional organization of yeast transcription factors
• Molecular systems Biology, doi:10.1038/msb.2010.77, Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ (2010)
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• Evolution of Transcription Networks: Lessons from Yeasts
• Current Biology, 2010 20(17): R746-R753 Li H and Johnson AD
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• De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
• Nat Biotechnol. 2010 28(9):970-5 Fordyce PM, Gerber D, Tran D, Zheng J, Li H, Derisi JL, Quake SR.
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• Positioned and G/C capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters
• Genome Research. 2010 20(4): 473-84 Wu R and Li H
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• A systematic approach to identify functional motifs within vertebrate developmental enhancers
• Developmental Biology. 2010 337(2):484-95 Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S
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• An enhanced single base extension technique for the analysis of complex viral populations
• PLoS One. 2009 4(10):e7453 Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL
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• Dynamics and design principles of a basic regulatory architecture controlling metabolic pathway
• PLoS Biol. 2008 6(6):e146. C. Chin, V. Chubukov, E. Jolly, J. DeRisi, H. Li
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• Evolution of Eukaryotic Transcription Circuits
• Science 2008 319:1797. B. Tuch, H. Li, and A. D. Johnson
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• The evolution of combinatorial gene regulation in fungi
• PLoS Biol. 2008 6(2):e38. B. Tuch, D. Galgoczy, A. Hernday, H. Li, and A. D. Johnson
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• cREDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
• BMC Bioinformatics 2008 9: 506. K. Kechris and H. Li
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• CompMoby: Comparative MobyDick for detection of cis-regulatory motifs
• BMC Bioinformatics 2008 9: 455. C. Chaivorapol, C. Melton, G. Wei, R. F. Yeh, M. Ramalho-Santos, R. Bellloch, and H. Li
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• fREDUCE: Detection of Degenerate Regulatory Elements Using Correlation With Expression
• BMC Bioinformatics 2007 8:399. R. Z. Wu, C. Chaivorapol, H. Li, and S. Liang
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• Systematic Identification Of Cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
• PLoS Genet. 2007 3(8):e145. M. Grskovic, C. Chaivorapol, A. Gaspar-Maia, H. Li, and M. Ramalho-Santos
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• Cell- and gene-specific regulation of primary target genes by the androgen receptor
• Genes Dev. 2007 21(16):2005-17. E. C. Bolton, A. Y. So, C. Chaivorapol, C. M. Haqq, H. Li, K. R. Yamamoto
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• Similarity of Synonymous Substitution Rates Across Mammalian Genomes
• J Mol Evol. 2007 65(3):236-48. J. Chuang and H. Li
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• Determinants of Cell- and Gene-Specific Transcriptional Regulation by the Glucocorticoid Receptor
• PLoS Genet. 2007 3(6):e94. A. Y. So, C. Chaivorapol, E. C. Bolton, H. Li, K. R. Yamamoto
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• Genome-wide diversity and selective pressure in the human rhinovirus
• Virology Journal, 2007 4(1): 40. A. L. Kistler , D. R. Webster , S. Rouskin , V. Magrini , J. J. Credle , D. P. Schnurr , H. A. Boushey , E. R. Mardis , H. Li and J. L. DeRisi
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• Evolution of alternative transcriptional circuits with identical logic
• Nature 2006 443(7110):415-20. A. E. Tsong, B. Tuch, H. Li, A. D. Johnson
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• Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output
• Proc. Natl. Acad. Sci. 2006 103(11):4180-5. Y. Nochomovitz, H. Li
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• Alternative 3' Pre-mRNA Processing in Saccharomyces cerevisiae is Modulated by Nab4/Hrp1 in Vivo
• PLoS Biology 2006 Dec; 5(1):e6. K. S. K. Guisbert, H. Li, C. Guthrie
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2000 - 2005

• Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
• BMC Bioinformatics 2005 6:275. E. Jolly, C. S. Chin, I. Herskowitz, H. Li
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• Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes
• Development 2005, 132(16):3753-65.39. A. Klebes, A Sustar, K. Kechris, H. Li, G. Schubiger, T. B. Kornberg PDF file

• Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
• Proc. Natl. Acad. Sci. 2005 vol 102: 1998. W. Wang, J. M. Cherry, Y. Nochomovitz, E. Jolly, D. Botstein, and H. Li PDF file

• Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence
• Genome Research 2005 vol 15: 205. C. S. Chin, J. Chuang, and H. Li PDF file

• Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation
• Curr Biol. 2005 15(4):347-52 S. A. McCarroll, H. Li, and C. I. BargmannPDF file

• Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles
• RNA, February 9, 2005. K. Kim, K. Duncan, H. Li, and C. Guthrie PDF file

• Gcn4p and Novel Upstream Activating Sequences Regulate Targets of the Unfolded Protein Response
• PLoS Biology 2004 Aug 2(8): E246, With P. Walter and C. Patil, PDF file

• functional bias and spatial organization of genes in mutational hot and cold regions in the human genome
• PLoS Biology, 2004 Feb;2(2):E29, J. Chuang and H. Li PDF file

• Comparing genomic expression patterns across species identifies shared transcriptional program in aging
• Nature Genetics 36, 197 (2004), with McCarroll et al. PDF file

• Designability and Thermal Stability of Protein Structures
• Polymer 45, 699 (2004), with Wingreen and Tang PDF file

• Genes that Act Downstream of DAF-16 to Influence the Lifespan of Caenorhabditis elegans.
• Nature 424(6946), 277-283 (2003), with Murphy, Kenyon et al PDF file

• Dissecting the transcription networks of a cell using computational genomics
• Curr Opin Genet Dev. 2003, 13(6):611-6, H. Li and W. Wang PDF file

• A Systematic Approach to Reconstructing Transcription Networks in Saccharomyces cerevisiae
• Proc. Natl. Acad. Sci. vol 99, 16893 (2002), with Wang, Cherry, and Botstein PDF file

• Identification of the binding sites of Regulatory Proteins in Bacterial Genomes
• Proc. Natl. Acad. Sci. vol 99, 11772 (2002), with Rhodius, Gross, and Siggia PDF file

• The Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix
• Proteins vol 49, 403 (2002). with Tang and Wingreen PDF file

• Fast Tree Search for Enumeration of a Lattice Model of Protein Folding
• J. Chem. Phys. vol 116, 352 (2002) with Cejtin et al. PDF file

• Regulatory Element Detection Using Correlation with Expression
• Nature Genetics vol 27, 167 (2001) with Bussemaker and Siggia PDF file
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• Ising Model in Physics and Statistical Genetics
• American Journal of Human Genetics vol 69, 853 (2001), with Majewski and Ott PDF file

• The Designability of Protein Structures
• J. Mol. Graph. Model. 19, 157 (2001), with Helling et al. PDF file

• Regulatory Element Detection Using A Probabilistic Segmentation Model
• Proceedings of ISMB 2000, with Bussemaker and Siggia PDF file
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• Building A Dictionary for Genomes: Identification of Presumptive Regulatory Sites by Statistical Analysis
• Proc. Natl. Acad. Sci. vol 97, 10096 (2000), with Bussemaker and Siggia PDF file
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1996 - 1999

• Designability, Thermodynamic Stability and Dynamics in Protein Folding: A Lattice Model Study
• J. Chem. Phys. vol 110, 1252 (1999), with Melin et al.

• Dynamics and stress in gravity driven granular flow
• C. Denniston & H. Li, Phys. Rev. E 59, 3289 (1999).

• Are Protein Folds Atypical?
• Proc. Natl. Acad. Sci. 95, 4987 (1998), with Tang and Wingreen

• Nature of Driving Force for Protein Folding: A Result From Analyzing the Statistical Potential
• Phys. Rev. Lett. 79, 765 (1997), with Tang and Wingreen

• Emergence of Preferred Structures in a Simple Model of Protein Folding
• Science 273, 666 (1996), with Tang, Wingreen and Helling

Earlier Work

• Fluctuation and persistence length of charged flexible polymers
• H. Li & T. Witten, Macromolecules 28, 5921 (1995).

• Breakdown of hydrodynamics in a one-dimensional system of inelastic particles
• Y. Du, H. Li & L.P. Kadanoff, Phys. Rev. Lett. 74, 1268 (1995).

• Ridge singularities in a crumpled elastic sheet
• A. Lobkovsky, S. Gentges, H. Li, D. Morse, & T. Witten, Science 270, 1482 (1995).

• Singular shape of a fluid drop in an electric or magnetic field
• H. Li, T. Halsey, & A. Lobkovsky, Europhys. Lett. 27, 575 (1994).

• Polymers grafted to convex surfaces: A variational approach
• H. Li & T.A. Witten, Macromolecules 27, 449 (1994)

• Statistical mechanics of polyampholytes
• Y. Kantor, M. Kardar & H. Li, Phys. Rev. E 49, 1383 (1994).

• Asymptotic shape of a fullerene ball
• T.A. Witten & H. Li, Europhys. Lett. 23, 51 (1993).

• Conformations of polyampholytes
• Y. Kantor, H. Li & M. Kardar, Phys. Rev. Lett. 69, 61 (1992).

• Confinement between rough substrates: Fluctuation-induced forces, and other manifestations
• M. Kardar & H. Li, Proceedings of MRS Fall meeting, Vol. 290, Dynamics in Small Confining Systems (1992).

• Fluctuation induced forces between manifolds immersed in correlated fluids
• H. Li & M. Kardar, Phys. Rev. A 46, 6490 (1992).

• Fluctuation induced forces between rough substrates
• H. Li & M. Kardar, Phys. Rev. Lett. 63, 3761 (1991).

• Finite-size scaling with surface ordering
• H. Li, M. Paczuski, M. Kardar & K. Huang, Physica A, 177, 207 (1991).

• Surface ordering and finite-size effects in liquid-crystal films
• H. Li, M. Paczuski, M. Kardar & K. Huang, Phys. Rev.B 44, 8274 (1991).

• Wetting phenomena on rough substrates
• H. Li & M. Kardar, Phys. Rev. B 42, 6546 (1990).