Author
S. Li
Primary ORCID profile (0000-0002-6864-5644 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints
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Biology Disciplines
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2017-2025 · peak 90/yrCo-Author Collaboration Network
10 top collaborators · 43 mutual co-author links358 papers
Recent·Most cited
- BiochemistrybioRxivPreprint
Chemical structures of cyclic ADP ribose (cADPR) isomers and the molecular basis of their production and signaling
M. K. Manik, Y. Shi, S. Li…·B. Kobe
The paper reports the chemical structures of two cADPR isomers, their production mechanism, and their roles in antiviral signaling and plant immunity suppression.
DOI 10.1101/2022.05.07.491051 - MicrobiologybioRxivPreprint
Subtyping evaluation of Salmonella Enteritidis using SNP and core genome MLST with nanopore reads
Z. Xian, S. Li, D. A. Mann…·X. Deng
This study evaluates the use of nanopore sequencing for SNP and cgMLST subtyping of Salmonella Enteritidis, showing high concordance with Illumina data despite sequencing errors.
DOI 10.1101/2022.05.03.490560 - Cancer BiologyNAR CancerPeer-reviewed
PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery
S. Koc, M. W. Lloyd, J. Grover…·J. H. Chuang
The paper introduces the PDXNet Portal, a centralized resource for PDX models and data, offering analysis workflows and facilitating cancer research collaboration.
DOI 10.1093/narcan/zcac014 - BiochemistrybioRxiv
Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes
This paper describes a scalable method for producing high-quality recombinant three-finger proteins using E. coli, enabling their use as molecular probes.
DOI 10.1186/s12934-024-02316-1 - BiochemistrybioRxivPreprint
A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-Cov-2 virus and Omicron variant through a unique binding mode
D. Zhao, L. Liu, X. Liu…·H. Huang
This paper reports a synthetic nanobody, C5G2, that neutralizes SARS-CoV-2 and Omicron variants with high potency through a unique binding mechanism.
DOI 10.1101/2022.04.11.487660 - MicrobiologybioRxiv
Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response
G. Garcia, Y. Wang, J. I. Irudayam…·V. Arumugaswami
This study identifies Hippo signaling pathway activation as an antiviral response to SARS-CoV-2 infection and shows pharmacological targeting of the pathway can reduce virus replication.
DOI 10.1371/journal.pbio.3001851 - MicrobiologybioRxiv
Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes
S. Li, D. Mosier, X. Dong…·M. Diao
This study investigates how microbial response strategies vary with environmental change frequency in sulfidic stream microbiomes, finding that rapid changes favor stochasticity and bet-hedging, while slow changes benefit codon-usage bias.
DOI 10.1038/s41396-023-01515-9 - Plant BiologybioRxivPreprint
Phase-separated TRB-PRC2 aggregates contribute to Polycomb silencing in plants
H. Xuan, Y. Liu, J. Zhao…·H. Yang
The paper shows that phase-separated TRB proteins aggregate with PRC2 to enhance Polycomb silencing in plants.
DOI 10.1101/2022.03.27.485997 - EcologybioRxiv
Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks
T. Tang, N. Zhang, F. J. Bongers…·X. Liu
This study shows that both tree species and genetic diversity increase productivity through functional diversity and trophic feedbacks, with genetic diversity effects varying between monocultures and mixtures.
DOI 10.7554/elife.78703 - MicrobiologyApplied and Environmental MicrobiologyPeer-reviewed
Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type
Y. Fu, N. M. M'ikanatha, C. A. Whitehouse…·E. G. Dudley
This study sequenced S. Typhimurium strains from wild birds in the U.S. and identified three distinct lineages associated with different bird types, improving source attribution and outbreak investigation.
DOI 10.1128/aem.01979-21 - Pharmacology & ToxicologybioRxivPreprint
High-throughput Production of Diverse Xenobiotic Metabolites with P450-transduced Huh7 Hepatoma Cell Lines
C.-m. Lee, K. H. Liu, G. Singer…·E. T. Morgan
This paper develops P450-expressing Huh7 cell lines to generate xenobiotic metabolites, enabling high-throughput analysis of drug metabolism and identification of specific enzyme-substrate interactions.
DOI 10.1101/2022.03.12.484071 - BiochemistrybioRxiv
Oligomer-to-Monomer Transition Underlies the Chaperone Function of AAGAB in AP1/AP2 Assembly
Y. Tian, I. Datta, R. Yang…·Q. Yin
This study identifies the dual role of AAGAB's tetramerization domain in stabilizing AAGAB and binding substrates during AP1/AP2 complex assembly.
DOI 10.1073/pnas.2205199120 - Animal Behavior & CognitionbioRxiv
Convergence of monosynaptic inputs from neurons in the brainstem and forebrain on parabrachial neurons that project to the paraventricular nucleus of the thalamus
The paper identifies monosynaptic inputs to parabrachial neurons projecting to the paraventricular nucleus of the thalamus, revealing their connectivity with brainstem and forebrain regions involved in arousal and homeostasis.
DOI 10.1007/s00429-022-02534-6 - ImmunologybioRxiv
Omicron booster in ancestral strain vaccinated mice augments protective immunities against both the Delta and Omicron variants
L. Jia, Y. Zhou, S. Li…·C. Qiu
This study shows that an Omicron-matched DNA vaccine booster enhances cross-reactive immunity against Delta and Omicron variants in mice compared to an ancestral strain booster.
DOI 10.3389/fimmu.2022.897879 - ImmunologybioRxivPreprint
The Transcription Factor Bach2 Negatively Regulates Natural Killer Cell Maturation and Function
S. Li, M. Bern, B. Miao…·W. M. Yokoyama
This study shows Bach2 negatively regulates NK cell maturation and function by correlating with TCF1 and opposing effector molecule and cell cycle gene expression.
DOI 10.1101/2022.02.14.480364 - MicrobiologybioRxivPreprint
Microbial dysbiosis and metabolic disorders promote rheumatoid arthritis across successive stages: a multi-omics cohort study
M. Cheng, Y. Zhao, Y. Cui…·J. Han
This study identifies stage-specific microbial and metabolic changes in RA progression using multi-omics data from a cohort of patients.
DOI 10.1101/2022.02.13.480248 - Cell BiologybioRxivPreprint
ZNF598 responds to mitochondrial stress to abort stalled translation on mitochondrial outer membrane and maintain tissue homeostasis
DOI 10.1101/2022.02.04.479092 - BiophysicsbioRxiv
Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA
T. Nguyen, S. Li, J. Chang…·S. Liu
This study shows that Sox2 forms DNA condensates that exert mechanical forces up to 7 pN, but chromatin nucleosomes reduce this force by sequestering Sox2.
DOI 10.1038/s41467-022-31738-x - BiophysicsbioRxivPreprint
Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics Simulations
D. Wang, J. Li, L. Wang…·C. Song
This study constructs multiscale models of SARS-CoV-2 using coarse-grained molecular dynamics simulations and experimental data, revealing dynamic behavior of membrane proteins and lipid interactions.
DOI 10.1101/2022.01.31.478415 - Evolutionary BiologybioRxiv
The genomic basis of the plant island syndrome in Darwin's giant daisies
J. Cerca, B. Petersen, J. M. Lazaro Guevara…·M. D. Martin
This study characterizes the genomic basis of the plant island syndrome in Darwin's giant daisies by analyzing the genome of Scalesia atractyloides, identifying subgenomes, polyploidization events, and genes under selection.
DOI 10.1038/s41467-022-31280-w - ImmunologybioRxivPreprint
Molecular basis of broad neutralization against SARS-CoV-2 variants including Omicron by a human antibody
Z. Zhang, B. Ju, Q. Zheng…·N. Xia
A human antibody, VacW-209, broadly neutralizes SARS-CoV-2 variants including Omicron by targeting a conserved epitope, highlighting the importance of such antibodies in pandemic control.
DOI 10.1101/2022.01.19.476892 - BioengineeringbioRxiv
piggyBac-Mediated Genomic Integration of Linear dsDNA-Based Library for Deep Mutational Scanning in Mammalian Cells
Y. Wang, Y. Zhao, Y. Li…·S. Li
This paper develops two new strategies for constructing large variant DMS libraries in mammalian cells using piggyBac-mediated genomic integration and in-vitro ligation.
DOI 10.1007/s00018-023-04976-5 - Cancer BiologyCell Reports MedicinePeer-reviewed
A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data
E. F. Douglass, R. J. Allaway, B. Szalai…·A. Califano
The paper hosts a DREAM Challenge to evaluate computational models for predicting drug polypharmacology using perturbational profile data from 32 kinase inhibitors.
DOI 10.1016/j.xcrm.2021.100492 - MicrobiologybioRxivPreprint
Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant
N. Ikemura, S. Taminishi, T. Inaba…·A. Hoshino
This paper shows engineered ACE2 neutralizes Omicron and other sarbecoviruses effectively despite its high number of spike mutations.
DOI 10.1101/2021.12.22.473804 - ImmunologybioRxivPreprint
Waning immune responses against SARS-CoV-2 among vaccinees in Hong Kong
Q. Peng, R. Zhou, Y. Wang…·Z. Chen
This study compares immune responses between BioNTech and Sinovac vaccines in Hong Kong, finding Sinovac induces lower neutralizing antibodies and wanes faster against SARS-CoV-2 variants.
DOI 10.1101/2021.12.22.473934 - Cancer BiologybioRxiv
MicroRNA-like snoRNA-derived RNAs (sdRNAs) promote castration resistant prostate cancer
A. B. Coley, A. N. Stahly, M. V. Kasukurthi…·G. M. Borchert
This study identifies two snoRNA-derived fragments, sdRNA-D19b and sdRNA-A24, that promote castration-resistant prostate cancer by downregulating tumor suppressors and conferring drug resistance.
DOI 10.3390/cells11081302 - ImmunologybioRxivPreprint
RNA2Immune: A Manually Curated Database of Experimentally Supported Data Linking Noncoding RNA Regulation to the Immune System
J. Wang, S. Li, T. Wang…·L. Wang
RNA2Immune is a database linking noncoding RNAs to immune functions, diseases, and vaccines, containing 50,433 experimentally supported associations across 42 species.
- ImmunologybioRxivPreprint
Atypical B cells upregulate co-stimulatory molecules during malaria and secrete antibodies with T follicular helper cell support
C. S. Hopp, J. Skinner, S. L. Anzick…·P. D. Crompton
This study shows that atypical B cells actively respond to acute malaria and have the capacity to produce antibodies with T cell help.
DOI 10.1101/2021.12.07.471601 - Cancer BiologybioRxivPreprint
Dihydroartemisinin broke immune evasion through YAP1/JAK1/STAT1, 3 pathways to enhance anti-PD-1 therapy in hepatocellular carcinoma
Q. Peng, S. Li, X. Shi…·Y. Liu
This study shows dihydroartemisinin (DHA) enhances anti-PD-1 therapy in hepatocellular carcinoma by inhibiting YAP1 and disrupting immune evasion through PD-L1, JAK1/STAT1, and JAK3 pathways.
DOI 10.1101/2021.11.30.470572