About

Dr. Huiying Li is currently Professor in the Department of Molecular and Medical Pharmacology at UCLA. She earned her Ph.D. in Biochemistry and Molecular Biology from UCLA, where her studies focused on protein structure using X-ray crystallography and gene expression analysis by bioinformatics. After completing her postdoctoral study at UCLA on microbial genomics and metagenomics, she joined the faculty at UCLA. Her research centers on studying the human microbiome through genomics, metagenomics, bioinformatics, and microbiology approaches. Dr. Li’s team has been involved in the NIH funded Human Microbiome Project and investigates the human skin, oral, and vaginal microbiomes in relation to important diseases. Her research aims to understand the molecular mechanisms of the human microbiome in health and disease, with the goal of developing new diagnostics and therapeutics. Using multidisciplinary approaches, including high-throughput sequencing, microbiology, biochemistry, and computational methods, her lab seeks to elucidate the human-microbiome symbiotic system at both molecular and systems levels, identifying molecular interactions and potential targets for intervention.

Research topics

• Biology
• Genetics
• Microbiology
• Cell biology
• Chemistry
• Endocrinology
• Chromatography
• Medicine
• Biochemistry
• Cancer research
• Internal medicine
• Immunology
• Bioinformatics
• Physiology

Selected publications

• Unbiased Single-Cell Transcriptome-Proteome Co-Profiling Reveals Malignant Dormancy and Post-Transcriptional Buffering of CTCs

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-18

  articleOpen access

  Abstract Leptomeningeal metastasis is driven by rare cerebrospinal fluid circulating tumor cells (CSF-CTCs). However, the mechanisms underlying their adaptation to chemotherapeutic stress remain elusive, primarily because transcriptomics alone poorly predicts functional protein states. Here, we present scMAPS, a single-cell multi-omics method that employs magnetic-assisted partitioning cell lysates to enable unbiased transcriptome-proteome co-profiling without loss-prone physical splitting and precision device. By coupling scMAPS with our custom CLEAP (CTC Label-free Enrichment and Accurate Picking) system, we performed the first deep multi-omics profiling of rare clinical CSF-CTCs before and after localized chemotherapy, detecting an average of 2,547 proteins and 7,821 genes per cell. The integrated CLEAP-scMAPS pipeline reveals a coordinated prioritizing survival over proliferation malignant dormancy phenotype and identified post-transcriptional buffering as the primary driver of treatment resistance. Our platform enables the comprehensive molecular phenotyping of rare clinical specimens, providing a highly versatile framework for decoding complex post-transcriptional regulatory networks.

  PublisherDOI

• A hybrid statistical sampling and iterative regularization method in sparse-view computed tomography

  arXiv (Cornell University) · 2026-03-16

  preprintOpen access1st authorCorresponding

  Sparse-view computed tomography (CT) is an effective method to reduce the radiation exposure in medical imaging. To reduce the severe streaking artifacts that occur in reconstructed images due to violation of the Nyquist/Shannon sampling criterion, regularization is widely used to minimize the cost function. However, the iterative methods may lead to the accumulation and propagation of errors, which adversely affects the restoration of image details and textures. In this paper, we propose a hybrid model that integrates statistical sampling with iterative regularization to simultaneously shorten the sampling time and enhance the reconstruction quality. The proposed method is validated using three datasets: the Shepp-Logan phantom, the actual walnut X-ray projections provided by the Finnish Inverse Problems Society, and the clinical lung CT images.

  PublisherDOI

• Study on the improvement of cough variant asthma by the Tongfu Zhike formula via the TLR4/MyD88/NF-κB signaling pathway

  Journal of Chromatography B · 2026-02-07

  article
  PublisherDOI

• New Inhibitors of Neuronal Nitric Oxide Synthase for the Treatment of Melanoma

  Journal of Medicinal Chemistry · 2026-01-30 · 1 citations

  articleOpen access

  In 2024, an estimated 100,640 new cases of invasive melanoma were diagnosed in the U.S., with 9290 deaths. Our previous studies revealed that neuronal nitric oxide synthase (nNOS) derived nitric oxide plays a critical role in melanoma progression, making nNOS inhibition a promising strategy. High structural similarity among NOS isoforms requires careful design of nNOS inhibitors to avoid off-target effects. Our previous lead, HH044, demonstrated potent antimelanoma activity but exhibited only moderate nNOS selectivity. Here, we utilized a structure-based approach to design nNOS inhibitors that promote interactions with human nNOS-specific residue His342. Compound 9 exhibited inhibition of both human (Ki = 1.7 nM) and rat nNOS (Ki = 2.3 nM), with 5654-fold selectivity over human eNOS and 250-fold selectivity over iNOS. X-ray crystallography and molecular modeling revealed a novel SAR, forming the basis for nNOS inhibition and providing a foundation for further innovative design of nNOS inhibitors for melanoma treatment.

  PublisherDOI

• MRI-based morphological and spatial characteristics of leptomeningeal metastasis: prognostic value in non-small cell lung cancer

  Frontiers in Oncology · 2026-04-10

  articleOpen access

  Background: Leptomeningeal metastasis (LM) represents a devastating complication of non-small cell lung cancer (NSCLC), with limited survival and poorly defined imaging-based prognostic markers. Purpose: This study evaluated the combined prognostic value of MRI-based morphological and spatial patterns in NSCLC patients with LM, whose prognostic relevance remains poorly defined. Methods: We retrospectively reviewed 71 NSCLC patients with LM confirmed by 3.0T black-blood MRI, selected from 109 initially screened after applying exclusion criteria. Patients were classified into linear (n=41) and mixed (n=30) morphological subtypes based on MRI, and stratified by the number of involved brain regions (>3 vs. ≤3). Clinical, imaging, and survival data were analyzed using Kaplan-Meier estimates and multivariate Cox regression to identify independent prognostic factors. Results: The mixed subtype exhibited a significantly higher lesion burden than the linear subtype (26.86 ± 26.72 vs. 7.25 ± 10.95, p<0.001). Involvement of more than three brain regions was associated with significantly shorter median overall survival (14 vs. 24 months, p=0.016). Multivariate analysis identified several independent adverse prognostic factors: increased lesion number (HR = 1.02, 95% CI: 1.01-1.03, p<0.01), temporal lobe invasion (HR = 1.96, 95% CI: 1.07-3.58, p=0.029), Regionsinvolved (HR = 0.52, p=0.020). Conclusion: MRI-based morphological subtyping and spatial distribution provide significant prognostic value in NSCLC-LM. The mixed morphology, extensive brain involvement (>3 regions), and invasions of specific location such as the tempoarl lobe is associated with poorer survival outcomes. These findings support the use of MRI phenotyping for risk-adapted clinical management in NSCLC-LM.

  PublisherOA PDFDOI

• Identification of a complex chromosomal insertion using the chromosome conformation based karyotyping technique for the implementation of PGT-SR

  BMC Genomics · 2026-01-07

  articleOpen access

  OBJECTIVE: This study completed the karyotyping of a patient with a complex chromosomal insertion and identified the location of the breakpoint for implementing preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) to differentiate between normal and carrier embryos, aiming to assess the clinical outcome of PGT-SR in couples with complex chromosome rearrangements (CCRs). METHOD: The Chromosome conformation based Karyotyping technique (C-Moka) was implemented to identify karyotypes and analyze chromosomal breakpoints, with subsequent verification of karyotype results by fluorescence in situ hybridization (FISH). Whole genome sequencing (WGS) of embryos followed by copy number variation and second-generation sequencing (NGS) based single nucleotide polymorphism (SNP) haplotyping to discriminate between normal and carrier embryos were carried out in PGT-SR cycles. RESULTS: Based on the precise breakpoint sequences identified by C-Moka, mapping allele with resolved carrier status (MaReCs) was used to distinguish a normal embryo from a carrier embryo among two balanced euploidy embryos, resulting in the birth of a healthy baby after transfer of the normal embryo. CONCLUSION: This case demonstrates the feasibility of C-Moka technique in assisting CCRs diagnosis and directly identifying breakpoints to construct haplotypes without family lineage or reference embryo pre-tests.

  PublisherDOI

• Characteristics of <i>Mycoplasma synoviae</i> Strains Isolated From Layer Eggs and Broiler Knee Joints or Foot Pads Mainly in Chongqing, China

  Transboundary and Emerging Diseases · 2026-01-01

  articleOpen access

  Mycoplasma synoviae infection causes infectious synovitis and respiratory disease in broilers and a reduction in egg production and eggshell apex abnormalities (EAA) in layers, with widespread prevalence in the Chinese mainland since 2010. However, data on this pathogen in Chongqing remain scarce. The present study aimed to investigate the prevalence, sequence types (STs), hemagglutination activity, pathogenicity, and susceptibility to antimicrobials and Chinese herbal monomers of M. synoviae isolates from broilers and layers mainly in Chongqing. Additionally, we analyzed the genotype–phenotype correlations underlying the resistance of these isolates to fluoroquinolones and macrolides. A total of 23 M. synoviae isolates were recovered from 148 Chinese indigenous broilers, and 22 isolates were obtained from 210 eggs with EAA, yielding 45 isolates totally. These isolates were classified into five novel STs, namely ST196, ST258, ST261, ST264, and ST265. Phylogenetic analysis indicated that isolates belonging to the same ST formed distinct monophyletic clusters, and all isolates shared the closest genetic affinity with strains previously isolated in China. Of the 45 isolates, 42.2% were able to agglutinate chicken erythrocytes. All isolates were susceptible to doxycycline, tylvalosin, tilmicosin, lincomycin, and tiamulin but uniformly resistant to enrofloxacin. The majority of isolates displayed minimum inhibitory concentration (MIC) values &gt;4 μg/mL for amikacin (97.8%), apramycin (93.3%), and erythromycin (91.1%). Notably, the Chinese herbal monomer berberine hydrochloride exhibited potent anti‐ M. synoviae activity, with an MIC range of 2–32 μg/mL. Genotypic analysis identified mutations in the parC gene (A56T, T85I, N89D) and ribosomal protein L4 (I174V, N215S), which were associated with the resistance of isolates to enrofloxacin and erythromycin, respectively. Both joint‐ and egg‐derived isolates induced infectious synovitis and caseous exudates in specific pathogen‐free (SPF) chickens. These findings highlight M. synoviae genetic/phenotypic diversity in Chongqing, emphasizing the need for rational antimicrobial stewardship to curb drug‐resistant M. synoviae isolates.

  PublisherDOI

• Comparison of quality differences in Gastrodia elata wines fermented with different Saccharomyces cerevisiae and potential for sleep improvement in Saccharomyces cerevisiae SY Gastrodia elata fermented wine

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Biological characterization, sequence type distribution and drug resistance profiling of Mycoplasma hyorhinis field isolates from pigs in Chongqing, China

  Frontiers in Veterinary Science · 2026-01-30

  articleOpen access1st author

  Mycoplasma hyorhinis is a ubiquitous pathogen of swine that causes polyserositis and polyarthritis and is also associated with conjunctivitis, meningitis, pneumonia, and abortions. This microorganism is a high prevalence pathogen in Chinese swine herds. However, few studies on M. hyorhinis have been reported in Chongqing, China. The overuse of antimicrobials has led to an increased risk of antimicrobial resistance, but a series of Chinese herbal monomers exhibited antibacterial activity to drug-resistant bacteria, including mycoplasmas. The aim of the study was to determine the prevalence, sequence types, growth kinetics, susceptibility to antimicrobials and Chinese herbal monomers, and relationships between the phenotypes and genotypes in terms of the resistance of M. hyorhinis to fluoroquinolones, macrolides and lincomycin. A total of 28 M. hyorhinis strains were recovered from the lungs of 404 slaughtered pigs. The isolates belonging to 11 novel STs, ST226, ST227, ST228, ST229, ST230, ST260, ST261, ST262, ST263, ST264 and ST265, were clustered separately from other reference isolates in the database. The growth kinetic of each isolate was generated, and the maximum color changing unit (CCU) values of isolates varied from 10 12 to 10 20 CCU/ml. In vitro susceptibility testing showed that the isolates were inhibited by low concentrations of tiamulin (MIC: ≤ 0.25 μg/ml), doxycycline (MIC: ≤ 0.25–1 μg/ml), ciprofloxacin (MIC: ≤ 0.25–2 μg/ml), florfenicol (MIC: 0.5–2 μg/ml), kanamycin (MIC: ≤ 0.25–4 μg/ml), enrofloxacin (MIC: 0.5–4 μg/ml) and berberine hydrochloride (MIC range: 1–8 μg/ml). However, the MICs of erythromycin were high (MIC: 32–≥128 μg/ml) for all isolates. The MICs of tylosin, tilmicosin and lincomycin for 50%, 60.7% and 46.4% of isolates were equal to or &amp;gt;16, 32 and 8 μg/ml, respectively. No correlation was detected between resistance to fluoroquinolones and QRDRs. However, the high MICs of tylosin, tilmicosin and lincomycin were most likely attributed to an A1553G mutation in domain V of the 23S rRNA . Our findings demonstrated the diversity of STs among M. hyorhinis isolates in Chongqing. The high MICs of M. hyorhinis isolates to macrolides and lincomycin suggested that the use of lincomycin for the treatment of M. hyorhinis infections should be carefully evaluated.

  PublisherOA PDFDOI

• A hybrid statistical sampling and iterative regularization method in sparse-view computed tomography

  ArXiv.org · 2026-03-16

  articleOpen access1st authorCorresponding

  Sparse-view computed tomography (CT) is an effective method to reduce the radiation exposure in medical imaging. To reduce the severe streaking artifacts that occur in reconstructed images due to violation of the Nyquist/Shannon sampling criterion, regularization is widely used to minimize the cost function. However, the iterative methods may lead to the accumulation and propagation of errors, which adversely affects the restoration of image details and textures. In this paper, we propose a hybrid model that integrates statistical sampling with iterative regularization to simultaneously shorten the sampling time and enhance the reconstruction quality. The proposed method is validated using three datasets: the Shepp-Logan phantom, the actual walnut X-ray projections provided by the Finnish Inverse Problems Society, and the clinical lung CT images.

  PublisherOA PDF

Recent grants

• NIH Grant UH2AR057503

  NIH · $1.2M · 2012

• NIH Grant R01DE021574

  NIH · $2.8M · 2016

• NIH Grant RC1DE020298

  NIH · $960k · 2013

• NIH Grant R01GM099530

  NIH · $1.4M · 2018

Frequent coauthors

• Dan Liu

  Institute of Crop Sciences

  183 shared

• Rui Liu

  Huazhong Agricultural University

  140 shared

• Rui Peng

  National Institute for Viral Disease Control and Prevention

  119 shared

• T.L. Poulos

  University of California, Irvine

  95 shared

• Jiaqi Wang

  Shanxi Normal University

  88 shared

• Nan Zheng

  Ministry of Agriculture and Rural Affairs

  83 shared

• Qianqian Yao

  Chinese Academy of Agricultural Sciences

  66 shared

• Lili Pang

  Fudan University

  61 shared