Yang Li

CHAIR an antigen-resolved antibody-reactome resource for healthy adult immune aging

CHAIR provides an antigen-resolved immune resource for healthy adult aging by integrating PhIP-seq, clinical data, and immune phenotyping across multiple age groups.

Conditional Deletion of All Neurexins Defines Diversity of Essential Synaptic Organizer Functions for Neurexins

The paper reanalyzes original data and conducts new experiments to show that neurexins have distinct functions in different synapse types.

Shared and idiosyncratic coding regimes coexist in macaque IT

The paper examines coding regimes in macaque inferotemporal cortex, finding both shared low-dimensional representations and sparse, feature-random single-neuron responses that contribute to object recognition.

SciCore-Omics: a tri-modal foundation model unifying histology, spatial transcriptomics and language for spatial biology

SciCore-Omics is a tri-modal foundation model that integrates histology, spatial transcriptomics, and language to improve spatial biology analysis and interpretation.

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

This study analyzes histone modifications H3K4me1 and H3K27ac during maternal-to-zygotic transition in mouse embryos, revealing dynamic reprogramming and enhancer type changes.

Hippocampal Glucuronyl C5-epimerase promotes stress resilience by directly engaging PI3K through a non-enzymatic mechanism

This study identifies Glce as a non-enzymatic regulator of hippocampal dendritic integrity and stress resilience through direct activation of PI3K, revealing a novel mechanism in depression pathophysiology.

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

The paper investigates cohesin-mediated chromatin loop extrusion in human cells, revealing two dynamic modes of extrusion and showing that CTCF depletion increases extrusion activity.

Risk assessment of zoonotic viruses in urban-adapted wildlife

The paper assesses zoonotic virus risks in urban-adapted wildlife by analyzing viral diversity and zoonotic potential across seven species in 115 countries.

Comprehensive profiling of N6-methyladnosine (m6A) readouts reveals novel m6A readers that regulate human embryonic stem cell differentiation

The paper identifies novel m6A readers that regulate human embryonic stem cell differentiation through comprehensive profiling of m6A readouts across multiple cell lines.

Targeting of CIP4-Calcineurin Signalosomes Improves Cardiac Structure and Function After Myocardial Infarction

This paper shows that targeting CIP4-CaNAβ2 signalosomes improves cardiac function and reduces remodeling after myocardial infarction in mice.

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.

Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching

This study identifies the intracellular signaling pathway of teneurins in synaptic partner matching using Drosophila models.

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

This paper introduces DRfold, a method that improves RNA tertiary structure prediction by integrating deep learning with geometric potentials, achieving significant performance gains over existing methods.

Why FIT and bHLH Ib interdependently regulate Fe-uptake

The paper investigates the interdependence between FIT and bHLH Ib transcription factors in regulating Fe uptake, showing they form a functional complex for target recognition and activation.

SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.

RBM45 associates with nuclear stress bodies and forms nuclear inclusions during chronic cellular stress and in neurodegenerative diseases

This study identifies RBM45's role in forming nuclear inclusions during stress and in neurodegenerative diseases, linking it to nuclear stress bodies and disease-specific pathology.

Reconstructing species evolutionary trees using the numerical features of microRNA

The paper reconstructs species evolutionary trees using microRNA numerical features, showing results consistent with known evolutionary timelines.

GeNets: A unified web platform for network-based analyses of genomic data

GeNets provides a platform to compare genomic networks using machine learning and allows analysis of genetic and RNA sequencing data.

Cycloserine for Treatment of Multidrug-Resistant Tuberculosis in China: A Retrospective Observational Study

This study evaluates cycloserine's efficacy and safety in treating MDR-TB in China, finding it improves outcomes for simple MDR-TB but not pre-XDR-TB or XDR-TB.

Epigenetic Reprogramming of Tissue-Specific Transcription Promotes Metastasis

This study shows that epigenetic reprogramming of tissue-specific transcription in cancer cells promotes metastasis, with FOXA2 playing a key role in liver colonization by metastatic colorectal cancer cells.

Hypothesis-free identification of modulators of genetic risk factors

The paper identifies context-dependent eQTLs in peripheral blood RNA-seq data from Dutch individuals using a hypothesis-free approach, revealing gene expression influenced by cell type and signaling pathways.

Allele-Specific Quantification of Structural Variations in Cancer Genomes

Weaver quantifies allele-specific structural variations and copy number alterations in aneuploid cancer genomes, showing high accuracy in simulation and real data.