All Faculty

Huiying Li

Associate Professor, Molecular & Medical Pharmacology
Faculty, Crump Institute for Molecular Imaging

Systems biology of human microbiome and diseases, metagenomics

Work Email Address:
Work Email Address:

Department Address:
Crump Institute for Molecular Imaging
Laboratory Address:
CNSI 4338
Office Address:
CNSI 4339

Phone Numbers:
(310) 983-3212 Lab
Phone Numbers:
(310) 206-5585 Office

Research Interest:

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.

Selected Publications:

Barnard Emma, Li Huiying Shaping of cutaneous function by encounters with commensals. The Journal of physiology. 2016; 8(18): .
JohnsonTremylla , Kang Dezhi, Barnard Emma, Li Huiying Strain-level differences in porphyrin production and regulation in Propionibacterium acnes elucidate disease associations. mSphere 2016; 1(1): e00023-15.
Kang Dezhi, Shi Baochen, Erfe Marie C, Craft Noah, Li Huiying Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Science translational medicine. 2015; 7(293): 293ra103.
Liu Jared, Yan Riceley, Zhong Qiao, Ngo Sam, Bangayan Nathanael J, Nguyen Lin, Lui Timothy, Liu Minghsun, Erfe Marie C, Craft Noah, Tomida Shuta, Li Huiying The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. The ISME journal. 2015; 9(9): 2078-93.
Shi Baochen, Chang Michaela, Martin John, Mitreva Makedonka, Lux Renate, Klokkevold Perry, Sodergren Erica, Weinstock George M, Haake Susan K, Li Huiying Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. mBio. 2015; 6(1): e01926-14.
Liu Jared, Cheng Alison, Bangayan Nathanael Joshua, Barnard Emma, Curd Emily, Craft Noah, Li Huiying Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1. Genome announcements. 2014; 2(4): .
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Bleharski Joshua R*, Li Huiying*, 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 Huiying, Guo Zhefeng, Zhu Yuxian 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 Yuxian, Zhang Yifeng, Li Huiying Molecular cloning of GA-suppressed G2 pea genes by cDNA RDA. Science in China, Series C. 1997; 40: 379-83.
Barnard Emma, Liu Jared, Yankova Eliza, Cavalcanti Silvana M, Magalhães Marcelo, Li Huiying, Patrick Sheila, McDowell Andrew Strains of the Propionibacterium acnes type III lineage are associated with the skin condition progressive macular hypomelanosis. Scientific reports. 2016; 6(4): 31968.
Shi Baochen, Bangayan Nathanael J, Curd Emily, Taylor Patricia A, Gallo Richard L, Leung Donald Y M, Li Huiying The skin microbiome is different in pediatric versus adult atopic dermatitis. The Journal of allergy and clinical immunology. 2016; 138(4): 1233-1236.
McDowell Andrew, Barnard Emma, Liu Jared, Li Huiying, Patrick Sheila Proposal to reclassify Propionibacterium acnes type I as Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov. International journal of systematic and evolutionary microbiology. 2016; 138(4): 1233-1236.
Achermann Yvonne, Liu Jared, Zbinden Reinhard, Zingg Patrick O, Anagnostopoulos Alexia, Barnard Emma, Sutter Reto, Li Huiying, McDowell Andrew, Zinkernagel Annelies S Propionibacterium avidum: A Virulent Pathogen Causing Hip Periprosthetic Joint Infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2018; 66(1): 54-63.
Shi Baochen, Leung Donald Y M, Taylor Patricia A, Li Huiying Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis. The Journal of investigative dermatology. 2018; 138(7): 1668-1671.
Shi Baochen, Wu Tingxi, McLean Jeffrey, Edlund Anna, Young Youngik, He Xuesong, Lv Hongyang, Zhou Xuedong, Shi Wenyuan, Li Huiying, Lux Renate The Denture-Associated Oral Microbiome in Health and Stomatitis. mSphere. 2017; 1(6): 145.
Curd Emily E , Martiny Jennifer B H , Li Huiying , Smith Thomas B Bacterial diversity is positively correlated with soil heterogeneity. Ecosphere. 2018; 9(1): e02079.
Barnard Emma, Shi Baochen, Kang Dezhi, Craft Noah, Li Huiying The balance of metagenomic elements shapes the skin microbiome in acne and health. Scientific reports. 2016; 6(1): 39491.