Research Topics
Genomes and Genes | Hao LiSummaryAffiliation: University of California Country: USA Publications
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Publications
Functional bias and spatial organization of genes in mutational hot and cold regions in the human genomeJeffrey H Chuang
Department of Biochemistry and Biophysics, University of California, San Francisco, USA
PLoS Biol 2:E29. 2004..Overall, our results show that genes are located nonrandomly with respect to hot and cold regions, offering the possibility that selection acts at the level of gene location in the human genome...- c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expressionKaterina Kechris
Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, 4200 East Ninth Avenue, B 119, Denver, CO 80262, USA
BMC Bioinformatics 9:506. 2008..Correlation-based motif finding strategies are used to identify motifs that correlate with expression data and do not rely on promoter sequences from a pre-determined set of genes... - Evolution of transcription networks--lessons from yeastsHao Li
Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
Curr Biol 20:R746-53. 2010.... 
Dissecting the transcription networks of a cell using computational genomicsHao Li
Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
Curr Opin Genet Dev 13:611-6. 2003..Genomic approaches have profoundly changed the way biologists investigate transcriptional regulation, and global pictures of the transcription networks for several model organisms are beginning to emerge...- Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysisEmmitt R Jolly
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
BMC Bioinformatics 6:275. 2005..We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis... - fREDUCE: detection of degenerate regulatory elements using correlation with expressionRandy Z Wu
Department of Biochemistry and Biophysics, UCSF, 1700 4th Street, San Francisco, CA 94143 2542, USA
BMC Bioinformatics 8:399. 2007..A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs... - CompMoby: comparative MobyDick for detection of cis-regulatory motifsChristina Chaivorapol
Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143 2540, USA
BMC Bioinformatics 9:455. 2008..Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans... - Comparing genomic expression patterns across species identifies shared transcriptional profile in agingSteven A McCarroll
Program in Neuroscience, University of California, San Francisco, California 94143, USA
Nat Genet 36:197-204. 2004..Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation... - Cell- and gene-specific regulation of primary target genes by the androgen receptorEric C Bolton
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
Genes Dev 21:2005-17. 2007..Our results provide new insights into cell- and gene-specific mechanisms of transcriptional regulation of androgen-responsive gene networks... - Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genesLishan Chen
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
J Biol Chem 286:18641-9. 2011.... 
Evolution of eukaryotic transcription circuitsBrian B Tuch
Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
Science 319:1797-9. 2008....- Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentationSteven A McCarroll
Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143 USA
Curr Biol 15:347-52. 2005..This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system... - De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysisPolly M Fordyce
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
Nat Biotechnol 28:970-5. 2010..We expect that these data and future use of this technique will provide information essential for understanding transcription factor specificity, improving identification of regulatory sites and reconstructing regulatory interactions... - Evolution of alternative transcriptional circuits with identical logicAnnie E Tsong
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143-2200, USA
Nature 443:415-20. 2006..These changes indicate specific mechanisms by which fitness barriers were traversed during the transition... - Alternative 3' pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivoKaren S Kim Guisbert
Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
PLoS Biol 5:e6. 2007..We propose that alternative 3' pre-mRNA processing is mediated by a Nab4-based mechanism and that these alternative processing events could help control gene expression as part of a physiological response in S. cerevisiae... - The evolution of combinatorial gene regulation in fungiBrian B Tuch
Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
PLoS Biol 6:e38. 2008..The large turnover of Mcm1 binding sites and the evolution of new Mcm1-cofactor interactions illuminate in sharp detail the rapid evolution of combinatorial transcription networks... - Epistatic relationships reveal the functional organization of yeast transcription factorsJiashun Zheng
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143 2542, USA
Mol Syst Biol 6:420. 2010..Collectively, these data suggest that parallel/compensating relationships between regulators, rather than linear pathways, often characterize transcriptional circuits... - Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cellsMarica Grskovic
Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
PLoS Genet 3:e145. 2007..Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species... - Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptorAlex Yick Lun So
Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
PLoS Genet 3:e94. 2007..We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information... - An enhanced single base extension technique for the analysis of complex viral populationsDale R Webster
Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE 4:e7453. 2009.... - Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genesAnsgar Klebes
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Development 132:3753-65. 2005..Our findings are likely to be relevant to the mechanisms that lead to disease when homologs of Wingless are expressed at abnormal levels and to the manifestation of pluripotency of stem cells... - Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequenceChen-Shan Chin
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
Genome Res 15:205-13. 2005..The separation of functionally conserved sequence from the neutral background allows us to estimate the complexity of cis-regulation on a genomic scale... - A systematic approach to identify functional motifs within vertebrate developmental enhancersQiang Li
Department of Biopharmaceutical Sciences, Programs in Biological Sciences and Human Genetics, University of California, San Francisco, CA 94143 2811, USA
Dev Biol 337:484-95. 2010..Moreover, this dataset provides a useful resource for further dissection of vertebrate brain development and function... - Regulatory architecture determines optimal regulation of gene expression in metabolic pathwaysVictor Chubukov
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 109:5127-32. 2012..Our results suggest that the parameters regulating metabolic enzyme expression are optimized by evolution, under the strong constraint of the underlying regulatory architecture... - Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promotersRandy Wu
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143 2542, USA
Genome Res 20:473-84. 2010..These observations are consistent with a model in which localized and G:C-capped poly(dA:dT) tracts initiate or facilitate the formation of NFRs at their center, possibly with chromatin remodeling and transcriptional machines involved... - Identification of the binding sites of regulatory proteins in bacterial genomesHao Li
Department of Biochemistry, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 99:11772-7. 2002..The algorithm is efficient for analyzing newly sequenced bacterial genomes for which little is known about transcriptional regulation... - Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profilesKaren Kim Guisbert
Department of Biochemistry and Biophysics, 600 16th Street, Genentech Hall, University of California at San Francisco, San Francisco, CA 94143, USA
RNA 11:383-93. 2005..These specialized associations of the hnRNP proteins of Saccharomyces cerevisiae suggest the opportunity to regulate the processing of particular transcripts between transcription and translation... - Dynamics and design principles of a basic regulatory architecture controlling metabolic pathwaysChen Shan Chin
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
PLoS Biol 6:e146. 2008..It is likely that principles emerging from this work can reveal how gene regulation has evolved to optimize performance in other metabolic pathways with similar architecture... - Mitochondrial network size scaling in budding yeastSusanne M Rafelski
Department of Biochemistry and Biophysics, University of California San Francisco UCSF, San Francisco, CA, USA
Science 338:822-4. 2012..Thus, yeast populations achieve a stable scaling relation between mitochondrial content and cell size despite asymmetry in inheritance... - A human sterile alpha motif domain polymerizomeMary Jane Knight
Department of Chemistry and Biochemistry, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
Protein Sci 20:1697-706. 2011.... - Genome-wide diversity and selective pressure in the human rhinovirusAmy L Kistler
Department of Microbiology and Immunology, University of California, San Francisco, California, USA
Virol J 4:40. 2007..Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV... - Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic outputYigal D Nochomovitz
Graduate Group in Biophysics, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 103:4180-5. 2006.... - Computational approaches to identifying transcription factor binding sites in yeast genomeHao Li
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
Methods Enzymol 350:484-95. 2002 - Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegansColeen T Murphy
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143-2200, USA
Nature 424:277-83. 2003.... - Single cell analysis of yeast replicative aging using a new generation of microfluidic deviceYi Zhang
The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Center for Quantitative Biology, and School of Physics, Peking University, China
PLoS ONE 7:e48275. 2012..Utilizing the capability of the new device to trap mother-daughter pairs, we analyzed mother-daughter inheritance and found age dependent asymmetric partitioning of a general stress response reporter between mother and daughter cells... - The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasisPhilipp Kimmig
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
elife 1:e00048. 2012..Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER.DOI:http://dx.doi.org/10.7554/eLife.00048.001... - Analysis of oligonucleotide array experiments with repeated measures using mixed modelsHao Li
Department of Statistics, 815 Patterson Office Tower, University of Kentucky, Lexington, Kentucky 40506 0027, USA
BMC Bioinformatics 5:209. 2004..In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations... - Identification of gene expression patterns using planned linear contrastsHao Li
Department of Statistics, University of Kentucky, Lexington, KY 40536 0027, USA
BMC Bioinformatics 7:245. 2006..In addition, multiple testing problems are complicated in experiments with multi-level treatments when thousands of genes are involved... - Characterization of human rabies virus vaccine strain in ChinaJialiang Du
Department of Viral Encephalitis, Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Xuan Wu District, Beijing, China
Virus Res 135:260-6. 2008..In addition, some mutations and new functional regions were discovered that are presumed crucial to the function of leader region and L protein. There is an equal role for all five genes in the phylogenetics of rabies virus... - Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein responseChristopher K Patil
Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
PLoS Biol 2:E246. 2004..The discovery of a role for Gcn4p in the yeast UPR reveals an additional level of complexity and demonstrates a surprising conservation of the signaling circuit between yeast and metazoan cells... - A systematic approach to reconstructing transcription networks in SaccharomycescerevisiaeWei Wang
Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
Proc Natl Acad Sci U S A 99:16893-8. 2002..Correlating the activation of a module to a specific perturbation predicts links in the cell's regulatory networks, and examining coactivated modules suggests specific instances of crosstalk between regulatory pathways... - Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulationWei Wang
Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
Proc Natl Acad Sci U S A 102:1998-2003. 2005..We show that this model accounts for the temporal control of the "middle" sporulation genes and suggest a similar regulatory arrangement can be found in developmental programs in higher organisms... - Effect of NF-kappaB on the induction of PDGF-B transcription by angiotensin II in the ECV304 cell lineHao Li
Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
Chin Med J (Engl) 115:433-8. 2002..CONCLUSION: Ang II is effective in stimulating NF-kappaB activation through a pathway dependent on NIK, IKK(alpha) and IKK(beta), and induces PDGF-B transcription in the endothelial cell line, ECV304.v.. - Further characterization of human DNA polymerase delta interacting protein 38Bin Xie
Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
J Biol Chem 280:22375-84. 2005.... - [Human bone marrow multipotent adult progenitor cells differentiate into hepatocyte-like cells with hepatocyte growth factor plus fibroblast growth factor-4 in vitro]Li jun Tang
Department of Surgery 1, 476th Fuzhou General Hospital of PLA, Fuzhou 350002, China
Zhonghua Gan Zang Bing Za Zhi 13:652-5. 2005..To investigate the possibility of the human bone marrow multipotent adult progenitor cells (hMAPCs) to differentiate into hepatocytes with hepatocyte growth factor (HGF)/ fibroblast growth factor-4 (FGF-4) in vitro... - Similarity of synonymous substitution rates across mammalian genomesJeffrey H Chuang
Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
J Mol Evol 65:236-48. 2007..Genes with above-average substitution rates also exhibit significant, though somewhat weaker, rate correlations, suggesting that some neutral processes may have persisted in the phylogeny as well... - Protein kinase C-dependent activation of P44/42 mitogen-activated protein kinase and heat shock protein 70 in signal transduction during hepatocyte ischemic preconditioningYi Gao
Department of Hepatobiliary Surgery, Zhujiang Hospital, 253 Gongye Road, Guangzhou 510282, Guangdong Province, China
World J Gastroenterol 10:1019-27. 2004..To investigate the significance of protein kinase C(PKC), P44/42 mitogen-activated protein kinase (MAPKs) and heat shock protein (HSP)70 signal transduction during hepatocyte ischemic preconditioning... - intersex, a gene required for female sexual development in Drosophila, is expressed in both sexes and functions together with doublesex to regulate terminal differentiationCarrie M Garrett-Engele
Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
Development 129:4661-75. 2002..Taken together, the above findings strongly suggest that IX and DSX(F) function in a complex, in which IX acts as a transcriptional co-factor for the DNA-binding DSX(F)... - Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrixHao Li
NEC Research Institute, Princeton, New Jersey 08540, USA
Proteins 49:403-12. 2002..In particular, highly designable structures in the HP model are also highly designable in the MJ model-and vice versa-with the associated sequences having enhanced thermodynamic stability... - Direct interaction of p21 with p50, the small subunit of human DNA polymerase deltaHao Li
Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
Cell Cycle 5:428-36. 2006..Our results suggested that p50 might target or anchor p21 to pol delta complex upon certain DNA damage such as adriamycin treatment... - Defective dissociation of a "slow" RecA mutant protein imparts an Escherichia coli growth defectJulia M Cox
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 1544, USA
J Biol Chem 283:24909-21. 2008..RecA protein plays a sufficiently intimate role in the bacterial cell cycle that its properties can limit the growth rate of a bacterial culture... - Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivoHao Li
Center for Neuroscience, Aging, and Stem Cell Research, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 105:9397-402. 2008..Our data support a crucial role for MEF2C in programming early neuronal differentiation and proper distribution within the layers of the neocortex... - An improved algorithm for vessel centerline tracking in coronary angiogramsYan Xu
Department of Biomedical Engineering, Tsinghua University, China
Comput Methods Programs Biomed 88:131-43. 2007..Results show that the proposed algorithm outperforms the conventional methods. By adopting the proposed algorithm, centerlines are successfully extracted under these complicated situations, and with satisfactory accuracy... - Preparation, characterization and transfection efficiency of cationic PEGylated PLA nanoparticles as gene delivery systemsJiji Chen
National Key Laboratory of Nanobiological Technology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
J Biotechnol 130:107-13. 2007..These results suggested that MePEG-PLA-CS NPs have favorable properties for non-viral gene delivery... - Identification of novel modulators of mitochondrial function by a genome-wide RNAi screen in Drosophila melanogasterJian Chen
Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA
Genome Res 18:123-36. 2008.... - Multiple testing in the genomics era: findings from Genetic Analysis Workshop 15, Group 15Lisa J Martin
Department of Pediatrics, Cincinnati Children s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
Genet Epidemiol 31:S124-31. 2007..We show that while each approach may have certain advantages, adequate error control is largely dependent upon the question under consideration and often requires the use of multiple analytic strategies... - Genetic variations and treatments that affect the lifespan of the NPC1 mouseBenny Liu
Department of Internal Medicine, University of Texas Southwestern Medical School, Dallas, TX 75390 9151, USA
J Lipid Res 49:663-9. 2008..It is currently not clear which of these effects is nonspecific or which might relate directly to the molecular defect present in the NPC1 syndrome... - The phytoestrogen coumestrol is a naturally occurring antagonist of the human pregnane X receptorHongwei Wang
Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, New York 10461, USA
Mol Endocrinol 22:838-57. 2008..These studies provide the basis for development of novel small molecule inhibitors of PXR with the ultimate goal of clinical applications toward preventing drug-drug interactions... - Liver X receptor activation enhances cholesterol loss from the brain, decreases neuroinflammation, and increases survival of the NPC1 mouseJoyce J Repa
Department of Internal Medicine, University of Texas Southwestern Medical School, Dallas, Texas 75390 9151, USA
J Neurosci 27:14470-80. 2007..Thus, LXR activation resulted in increased cholesterol excretion from the brain, decreased neuroinflammation, and deactivation of microglia to slow neurodegeneration and extend the lifespan of the NPC1 mouse... - Silencing invariant chain of DCs enhances Th1 response using small interfering RNAShan Ke
Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200025, PR China
Cell Biol Int 31:663-71. 2007..Our findings indicate that silencing the Ii gene in DCs with siRNA may offer a potential approach to enhancing antitumor immunotherapy... - Potential target genes of EMX2 include Odz/Ten-M and other gene families with implications for cortical patterningHao Li
Molecular Neurobiology Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd, La Jolla, CA 92037, USA
Mol Cell Neurosci 33:136-49. 2006.... - Chiral amine-catalyzed enantioselective cascade aza-ene-type cyclization reactionsLiansuo Zu
Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
Chemistry 14:6333-5. 2008 - [Major constituent proteins in donkey hide and their interaction]Hao Li
Institute of Biotechnology, Fuzhou University, China
Zhongguo Zhong Yao Za Zhi 31:659-63. 2006..CONCLUSION: Donkey serum albumin is a main protein component in the hide, which is a clue to expose is the effect of Ejiao on blood... - Functional roles of p12, the fourth subunit of human DNA polymerase deltaHao Li
Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
J Biol Chem 281:14748-55. 2006..We propose a model in which pol delta interacts with PCNA via at least two of its subunits, and one in which p12 could play a role in stabilizing the overall pol delta-PCNA complex as well as pol delta itself... - A semi-weakly confined erbium-doped waveguide amplifier with double-layered buffer/claddingHengsheng Tang
The State Key Lab for Advanced Photonic Materials and Devices, Department of Optical Science and Engineering, School of Information Science and Engineering, Fudan University, Shanghai 200433, China
Opt Express 16:9844-9. 2008..The EDWA has a passive core and double-layered buffer/cladding. A small coupling loss of 0.4 dB/facet and an internal gain of 1.9 dB via evanescent wave amplification near 1550 nm were obtained...
Research Grants
- Genomic Reconstruction of Yeast Transcription NetworksHao Li; Fiscal Year: 2007..We will develop methods integrating information from the genome sequences for several yeast species and genome-wide functional data, and we will combine bioinformatics analysis with mechanistic models of gene regulation. ..
- Structure function and evolution of yeast transcription networksHao Li; Fiscal Year: 2010..A global understanding of the structure, function and evolution of the transcription networks in yeast will likely lead to general principles applicable to humans and have a significant impact on human health. ..