FACULTY RESEARCH

Faculty List

Huiying Li, Ph.D.

Work Email Address: huiying@mednet.ucla.edu

Lab Number: (310) 983-3212

Office Phone Number: (310) 206-5585

Department Address:
Crump Institute for Molecular Imaging

Laboratory Address:
CNSI 4338

Office Address:
CNSI 4339
570 Westwood Plaza, Building 114
Crump Institute
Los Angeles, CA 90095

Department / Division Affiliations
Assistant Professor, Molecular & Medical Pharmacology
Faculty, Crump Institute for Molecular Imaging

Research Interests
My research interest is to understand the gene regulation and protein interaction networks in organisms at a systems level. I have previously applied bioinformatics, X-ray crystallography and gene expression profiling to study protein functions and interactions in metabolism and infectious diseases. My current research focuses on understanding the human microbiome (the collective genome of trillions of microorganisms in human microflora) and its interactions with the host in relation to human health and diseases. Using a systems biology approach, including high-throughput genome sequencing, metagenomic microarrays and computational modeling, the aim of the research is to detect signature microflora patterns and to develop diagnostic markers and therapeutics for microorganism-related human diseases. By combining computational and experimental approaches, the ultimate goal of my research is to understand the human-microflora symbiotic system at both molecular level and systems level.


Publications
Kasimatis Gabriela, Fitz-Gibbon Sorel, Tomida Shuta, Wong Marthew, Li Huiying Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. BioMed research international. 2013; 2013(1): 918320.
Tomida Shuta, Nguyen Lin, Chiu Bor-Han, Liu Jared, Sodergren Erica, Weinstock George M, Li Huiying Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. mBio. 2013; 4(3): e00003-13.
Fitz-Gibbon Sorel, Tomida Shuta, Chiu Bor-Han, Nguyen Lin, Du Christine, Liu Minghsun, Elashoff David, Erfe Marie C, Loncaric Anya, Kim Jenny, Modlin Robert L, Miller Jeff F, Sodergren Erica, Craft Noah, Weinstock George M, Li Huiying Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. The Journal of investigative dermatology. 2013; 133(9): 2152-60.
McDowell Andrew, Barnard Emma, Nagy István, Gao Anna, Tomida Shuta, Li Huiying, Eady Anne, Cove Jonathan, Nord Carl E, Patrick Sheila An expanded multilocus sequence typing scheme for propionibacterium acnes: investigation of 'pathogenic', 'commensal' and antibiotic resistant strains. PloS one. 2012; 7(7): e41480.
Ahuja Umesh, Liu Minghsun, Tomida Shuta, Park Jihye, Souda Puneet, Whitelegge Julian, Li Huiying, Harvill Eric T, Parkhill Julian, Miller Jeff F Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica. BMC microbiology. 2012; 12(33): 167.
Maretti-Mira Ana Claudia, Bittner Jaime, Oliveira-Neto Manoel Paes, Liu Minghsun, Kang Dezhi, Li Huiying, Pirmez Claude, Craft Noah Transcriptome patterns from primary cutaneous Leishmania braziliensis infections associate with eventual development of mucosal disease in humans. PLoS neglected tropical diseases. 2012; 6(9): e1816.
Ochoa Maria T, Teles Rosane, Haas Blake E, Zaghi Danny, Li Huiying, Sarno Euzenir N, Rea Thomas H, Modlin Robert L, Lee Delphine J A role for interleukin-5 in promoting increased immunoglobulin M at the site of disease in leprosy. Immunology. 2010; 131(3): 405-14.
Lee Delphine J, Li Huiying, Ochoa Maria T, Tanaka Motoyuki, Carbone Ryan J, Damoiseaux Robert, Burdick Anne, Sarno Euzenir N, Rea Thomas H, Modlin Robert L Integrated pathways for neutrophil recruitment and inflammation in leprosy. The Journal of infectious diseases. 2010; 201(4): 558-69.
Grossman Arthur R, Karpowicz Steven J, Heinnickel Mark, Dewez David, Hamel Blaise, Dent Rachel, Niyogi Krishna K, Johnson Xenie, Alric Jean, Wollman Francis-André, Li Huiying, Merchant Sabeeha S Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynthesis research. 2010; 106(1-2): 3-17.
Tabita F Robert, Hanson Thomas E, Li Huiying, Satagopan Sriram, Singh Jaya, Chan Sum Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiology and molecular biology reviews : MMBR. 2007; 71(4): 576-99.
Yooseph Shibu, Sutton Granger, Rusch Douglas B, Halpern Aaron L, Williamson Shannon J, Remington Karin, Eisen Jonathan A, Heidelberg Karla B, Manning Gerard, Li Weizhong, Jaroszewski Lukasz, Cieplak Piotr, Miller Christopher S, Li Huiying, Mashiyama Susan T, Joachimiak Marcin P, van Belle Christopher, Chandonia John-Marc, Soergel David A, Zhai Yufeng, Natarajan Kannan, Lee Shaun, Raphael Benjamin J, Bafna Vineet, Friedman Robert, Brenner Steven E, Godzik Adam, Eisenberg David, Dixon Jack E, Taylor Susan S, Strausberg Robert L, Frazier Marvin, Venter J Craig The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS biology. 2007; 5(3): e16.
Liu Philip T, Stenger Steffen, Li Huiying, Wenzel Linda, Tan Belinda H, Krutzik Stephan R, Ochoa Maria Teresa, Schauber Jürgen, Wu Kent, Meinken Christoph, Kamen Diane L, Wagner Manfred, Bals Robert, Steinmeyer Andreas, Zügel Ulrich, Gallo Richard L, Eisenberg David, Hewison Martin, Hollis Bruce W, Adams John S, Bloom Barry R, Modlin Robert L Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response. Science (New York, N.Y.). 2006; 311(5768): 1770-3.
Li Huiying, Sawaya Michael R, Tabita F Robert, Eisenberg David Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure (London, England : 1993). 2005; 13(5): 779-89.
Li Huiying, Pellegrini Matteo, Eisenberg David Detection of parallel functional modules by comparative analysis of genome sequences. Nature biotechnology. 2005; 23(2): 253-60.
Krutzik Stephan R, Tan Belinda, Li Huiying, Ochoa Maria Teresa, Liu Philip T, Sharfstein Sarah E, Graeber Thomas G, Sieling Peter A, Liu Yong-Jun, Rea Thomas H, Bloom Barry R, Modlin Robert L TLR activation triggers the rapid differentiation of monocytes into macrophages and dendritic cells. Nature medicine. 2005; 11(6): 653-60.
Bleharski, J. R.* <span face="bold" font="default" size="100%">Li, H.* Meinken, C.* Graeber, T. G.* Ochoa, M. T. Yamamura, M. Burdick, A. Sarno, E. N. Wagner, M. Rollinghoff, M. Rea, T. H. Colonna, M. Stenger, S. Bloom, B. R. Eisenberg, D. Modlin, R. L. Use of genetic profiling in leprosy to discriminate clinical forms of the disease. Science. 2003; 301(5639): 1527-30. (*equal contribution).
Li, H. Guo, Z. F. Zhu, Y. X. Molecular cloning and analysis of a pea cDNA that is expressed in darkness and very rapidly induced by gibberellic acid. Mol Gen Genet. 1998; 259(4): 393-7.
Zhu, Y. Zhang, Y. <span face="bold" font="default" size="100%">Li, H. Molecular cloning of GA-suppressed G2 pea genes by cDNA RDA. Science in China, Series C. 1997; 40: 379-83.