Yan Li

Structure of a secreted lancelet carotenoid cleavage dioxygenase (CCD), from an ancestral CCD clade

The paper presents the structure and functional properties of a BCOL protein from the lancelet Branchiostoma floridae, revealing structural and sequence differences from other CCDs.

Integrated Spatial Metabolomics and Proteomics from the Same Tissue Section Using a Conductive ITO-PET Slide

This paper develops an ITO-PET slide that enables sequential MALDI-MSI and LCM-LC-MS analysis of the same tissue section, demonstrating comparable performance to conventional slides across multiple tissues.

Spatial proximity sequencing maps developmental dynamics in the germinal center

This paper introduces Sprox-seq, a multi-omic technique that maps protein interactions and mRNA in human germinal centers, revealing distinct B cell maturation pathways and spatially-enriched immune regulatory complexes.

Glutamine Metabolism Supports α cell Mass and Glucagon Secretion

This study identifies glutaminase as critical for α cell mass and glucagon secretion by linking glutamine metabolism to amino acid sensing and growth.

Decoupling CAR-T Expansion, Conversion, and Decay Timing: Physiologically Aligned Semi-Mechanistic Modeling with Smooth Gating and a Cauchy Likelihood Residual Model

This paper introduces a Cauchy likelihood residual model for CAR-T cellular kinetics, showing it improves robustness and physiological plausibility compared to Gaussian and Student's t models.

Visualization of the architecture of flexible chromatin and the binding of chromatin regulators

The paper visualizes chromatin structure and chromatin regulator binding using cryo-ET and subtomogram averaging, revealing nucleosome heterogeneity as a key factor in chromatin flexibility.

Delay Differential Equation (DDE) Modeling of CAR-T Cellular Kinetics: Application to BCMA-Targeted (Ide-cel, Orva-cel) and CD19-Targeted (Liso-cel) Therapies

This paper develops a delay differential equation model for CAR-T cell kinetics, showing it better fits longitudinal data and supports delayed conversion from effector to memory cells.

Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation

This study identifies intramolecular loops that regulate SARS-CoV-2 N-protein self-association and nucleic acid binding through phosphorylation-dependent conformational changes.

Survivin inhibition induces PD-L1 expression through cGAS stabilization and attenuates antitumor immunity

This study shows that Survivin inhibition increases PD-L1 expression via cGAS stabilization, leading to immune evasion and reduced antitumor immunity.

linearPOA: A parallel, memory-efficient framework for Partial Order Alignment with linear space complexity

linearPOA introduces a memory-efficient framework for Partial Order Alignment with linear space complexity, significantly reducing memory usage for long-read sequencing.

A class of deep intronic IGHMBP2 variants activate a shared cryptic splice donor, enabling correction of select variants with a single antisense oligonucleotide

This study identifies deep intronic IGHMBP2 variants causing SMARD1 and CMT2S, showing they activate a shared cryptic splice donor, enabling correction with a single antisense oligonucleotide in patient-derived motor neurons.

AAV-Delivered RNAi Targeting Mutant LDB3 Prevents and Reverses Myofibrillar Myopathy through Mechanosignaling Restoration

This study shows that AAV-delivered RNAi targeting mutant LDB3 can reverse or prevent myofibrillar myopathy by restoring mechanosignaling pathways in mice.

Establishment of a Long-Term Germ-Free Medaka Model Reveals Microbiota-Dependent Regulation of Growth, Immunity, and Metabolism

This study establishes a long-term germ-free medaka model to investigate microbiota-dependent effects on growth, immunity, and metabolism, finding that gut-derived metabolites partially restore developmental and immune deficits but not long-term survival.

Three Muscle-Specific DAF-16/FOXO Transcriptional Targets Activated by Reduced Insulin/IGF-1 Signaling

The paper identifies three muscle-specific DAF-16/FOXO targets activated by reduced insulin/IGF-1 signaling in C. elegans through transcriptomic and chromatin analyses.

Beyond Student's t: A Systematic Exploration of Heavy-Tailed Residual Densities for Outlier Handling in Population PK Modeling

This paper evaluates heavy-tailed residual distributions for outlier handling in population PK modeling, finding that the Student's t distribution provides more stable inference than exponential-tail alternatives under extreme contamination.

From Correlation to Causation: Cell-Type-Specific Gene Regulatory Networks in Alzheimer's Disease

This study constructs cell-type-specific gene regulatory networks in Alzheimer's disease using single-nucleus transcriptomics and genotype data, identifying both established and novel regulatory elements.

Machine learning-based image analysis of Parkinson's disease iPS-derived neurons predicts genotype and reveals mitochondria-lysosome abnormalities

The paper uses machine learning to analyze neuronal morphology in Parkinson's disease iPSC-derived neurons, identifying genotype-specific mitochondrial and lysosomal abnormalities.

Pp6-Pfkfb1 axis modulates intracellular bacterial proliferation by orchestrating host-pathogen metabolic crosstalk

This study identifies the Pp6-Pfkfb1 axis as a key regulator of host-pathogen metabolic crosstalk that modulates intracellular bacterial proliferation in Salmonella-infected macrophages.

Phosphoproteomic dysregulation drives tumor proliferation in Cushing's disease

This study identifies phosphoproteomic dysregulation as a driver of tumor proliferation in Cushing's disease and demonstrates reversibility using an FDA-approved PP2A agonist.

Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms

This study designs and tests dimeric RSV F-subunit vaccines in protein and mRNA forms, showing enhanced immunogenicity and protection against RSV infection in rodent models.

Myocyte Damage and Mass Loss Drives Increasing Water Content, Compliance, and Survival in Septic Cardiomyopathy

This paper investigates how myocyte damage and mass loss in septic cardiomyopathy affect left ventricular compliance, water content, and survival outcomes.

Dopamine and cortical iPSC-derived neurons with different Parkinsonian mutations show variation in lysosomal and mitochondrial dysfunction: implications for protein deposition versus selective cell loss

This study compares dopamine and cortical neurons with PD mutations to identify cellular dysfunctions linked to different pathological phenotypes.

Nervous system-wide single-cell morphology atlas of excitatory and inhibitory neurons in larval zebrafish

The paper creates a comprehensive atlas of larval zebrafish neuron morphology, including excitatory and inhibitory identities and connectivity patterns.

A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells

The paper develops EliteMHCII, a high-throughput platform to identify MHC II epitopes and assess peptide binding affinity, showing high-affinity peptides correlate with strong CD4+ T cell responses.

The Arabidopsis 14-3-3 proteins stabilize BRASSINOSTEROID INSENSITIVE1 at the plasma membrane

This study identifies 14-3-3 proteins as stabilizers of BRI1 by antagonizing its ubiquitination, enhancing BR signaling in Arabidopsis.

Qing-Luo-Yin eases angiogenesis in adjuvant-induced arthritis rats by activating PPARγ

This study shows Qing-Luo-Yin reduces angiogenesis in adjuvant-induced arthritis rats by activating PPARγ in T cells, impairing inflammatory responses and cytokine secretion.

Ca2+-driven PDIA6 phase separation to ensure proinsulin quality control

This study shows Ca2+ induces PDIA6 phase separation, enhancing proinsulin folding and preventing aggregation through recruitment of PDIA3.

Non-destructive in situ monitoring of structural changes of 3D tumor spheroids during the formation, migration, and fusion process

This study develops a side-view observation device to enable non-destructive, real-time in situ monitoring of 3D tumor spheroid formation, migration, and fusion dynamics.

Adipogenin Dictates Adipose Tissue Expansion by Facilitating the Assembly of a Dodecameric Seipin Complex

This study identifies Adig as a regulator of lipid droplet formation by stabilizing the dodecameric seipin complex, leading to increased fat mass and thermogenesis in mice.

The addition of antibiotics to embryo culture media caused altered expression of genes in pathways governing DNA integrity in mouse blastocysts

This study shows that adding antibiotics to mouse embryo culture media alters gene expression related to DNA integrity, potentially compromising genomic stability.