G. Fan

Temporal-spatially metabolic reprogramming rewires the H3K27ac landscape to enable the initiation of liver regeneration

This study identifies metabolic reprogramming and its impact on the H3K27ac epigenetic landscape during liver regeneration.

Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease

The paper uses single-cell RNA sequencing to map zebrafish liver cell types and interactions, identifying macrophage subtypes and their role in nonalcoholic fatty liver disease.

Semantical and Geometrical Protein Encoding Toward Enhanced Bioactivity and Thermostability

This paper introduces a pre-training framework that combines sequential and geometric encoders to improve protein variant prediction for enhanced bioactivity and thermostability.

Protein Engineering with Lightweight Graph Denoising Neural Networks

This study introduces a lightweight graph neural network for protein engineering that predicts fitness and guides the design of effective mutants with improved physicochemical properties.

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria

This study analyzes sirenian genomes to identify genomic adaptations to aquatic life and conservation challenges.

Spatially-resolved single-cell atlas of ascidian endostyle provides insights into the origin of vertebrate pharyngeal organs

The paper constructs a spatially-resolved single-cell atlas of the ascidian endostyle, identifying new cell types and evolutionary insights into vertebrate pharyngeal organs.

Screening of genes related to the interaction between Listeria monocytogenes and host cells

The paper identifies co-expressed genes in host cells responding to Listeria monocytogenes infection and finds their involvement in immune and inflammatory pathways.

Structural dynamics underlying gating and regulation in IP3R channel

The paper determines 3D structures of IP3R1 in two ligand-bound states using cryo-EM and identifies dynamic properties of key domains involved in ligand binding and channel gating.

Functional Determination of Calcium Binding Sites Required for the Activation of Inositol 1,4,5-trisphosphate receptors.

This study identifies acidic residues in IP3Rs critical for Ca2+ binding and activation, showing their role in modulating channel activity and Ca2+ sensitivity.

Recent Reconfiguration Of An Ancient Developmental Gene Regulatory Network In Heliocidaris Sea Urchins

This study shows how natural selection rapidly reshapes developmental gene regulatory networks in sea urchins with divergent life histories, revealing evolutionary changes in gene regulation and chromatin status.

Single-cell RNA Sequencing Reveals the Temporal Diversity and Dynamics of Cardiac Immunity after Myocardial Infarction

This study uses single-cell RNA sequencing to analyze cardiac immune cell dynamics after myocardial infarction in mice, identifying key immune subsets and their roles in disease progression.

Natural variation in the control of flowering and shoot architecture in diploid Fragaria species

This study examines flowering and shoot architecture regulation in diploid Fragaria species, identifying genetic variation in TFL1 and GA20ox4 that influences flowering responses and plant morphology.

THEMIS is a priming substrate of non-receptor tyrosine phosphatase PTPN6/SHP1 and plays dual roles during T cell development

This study identifies THEMIS as a substrate of SHP1 and shows it has phosphorylation-dependent and -independent roles in T cell development.

Diversity, function and evolution of marine microbe genomes

The paper reviews marine microbiome studies, analyzes 17.59 Tb of sequencing data, and constructs genome and gene catalogues to explore marine prokaryotic diversity and function.

Integrated analysis of single-cell and transcriptome based RNA-seq multilayer network and WGCNA for construction and validation of an immune cell-related prognostic model in clear cell renal cell carcinoma

This paper constructs a prognostic model for clear cell renal cell carcinoma using immune cell-related genes from single-cell RNA-seq and transcriptome data, validated with clinical outcomes.

Addressing Enzymatic-Independent Tumor-Promoting Function of NAMPT via PROTAC-Mediated Degradation

This study develops two PROTACs targeting NAMPT, showing they degrade the protein more effectively than FK866 in tumor cells, highlighting PROTACs as a better strategy for dual-function proteins.

Complexin-1 regulated transition in the assembly of single neuronal SNARE complex

The paper investigates how complexin-1 regulates the assembly of SNARE complexes by stabilizing partially folded states and interacting with specific regions of SNARE proteins.

Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans

This study analyzes H7N9 virus genome mutations in human clinical samples to identify potential adaptations during infection.

Comparative analysis of clonal evolution among patients with right-sided colon cancer, left-sided colon cancer and rectal cancer

This study compares clonal evolution across right-sided colon cancer, left-sided colon cancer, and rectal cancer patients, finding differences in evolutionary patterns and identifying polyclonal origins of lymph node and extranodal tumor deposits.

In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution

The paper uses cryo-ET to determine the 7 Å structure of the AcrAB-TolC efflux pump in Escherichia coli, revealing its activation mechanism through interprotein interactions.

De novo synthesis and salvage pathway coordinately regulates polyamine homeostasis and determines T cell proliferation and function.

This study shows that polyamine homeostasis in T cells is regulated by de novo synthesis and salvage pathways, affecting proliferation and function, with implications for inflammatory and autoimmune diseases.

Potentiating the anti-tumor response of tumor infiltrated T cells by NAD+ supplementation

NAD+ supplementation enhances T cell activation and tumor-killing capacity in immunotherapies.

Loss of SHMT2 mediates 5-FU chemoresistance by inducing autophagy in colorectal cancer

This study shows that loss of SHMT2 promotes 5-FU resistance in CRC by inducing autophagy through p53 regulation.

Leptin deficient rats develop nonalcoholic steatohepatitis with unique disease progression

This study characterizes LepΔI14/ΔI14 rats as a NASH model through long-term transcriptomic analysis, revealing unique disease progression and gene expression patterns.

Single-Cell RNA Sequencing Reveals Regulatory Mechanism for Trophoblast Cell-Fate Divergence in Human Peri-Implantation Embryo

The paper uses single-cell RNA sequencing to identify TBX3 as a key regulator of trophoblast differentiation during human peri-implantation development.

Integrated multi-omics analysis to study the effects of simulated weightlessness on rhesus macaques (Macaca mulatta)

This study uses multi-omics analysis to examine the effects of simulated weightlessness on rhesus macaques, identifying molecular changes in blood, muscle, brain regions, and fecal samples.

Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

The paper resolves the sex-determination system in Ginkgo biloba, identifying XY chromosomes and five potential sex-determination genes originating ~14 million years ago.

Cryo-EM Reveals Ligand Induced Allostery Underlying InsP3R Channel Gating

The paper presents cryo-EM structures of InsP3R1 in activated and apo-states, revealing ligand-induced conformational changes that underlie channel gating.