Recent Publications

• Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways

PLoS Biol. 2008 6(6):e146. C. Chin, V. Chubukov, E. Jolly, J. DeRisi, H. Li PDF file

• Evolution of Eukaryotic Transcription Circuits

Science 2008 319:1797. B. Tuch, H. Li, and A. D. Johnson PDF file

• 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 PDF file

• cREDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

BMC Bioinformatics 2008 9: 506. K. Kechris and H. Li PDF file

• 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 PDF file

• 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 PDF file

• 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 PDF file

• 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 PDF file

• Similarity of Synonymous Substitution Rates Across Mammalian Genomes

J Mol Evol. 2007 65(3):236-48. J. Chuang and H. Li PDF file

• 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 PDF file

• 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 PDF file

• Evolution of alternative transcriptional circuits with identical logic

Nature 2006 443(7110):415-20. A. E.Tsong, B. Tuch, H. Li, A. D. Johnson PDF file

• 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 PDF file

• 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 PDF file

• 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 PDF file

• 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 ps file

• 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 ps file

• 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 ps file

• 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

More Publications

• 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).