Peng Zhang

Physics-informed neural network for predicting myocardial mechanics from in vivo physiological measurements

This paper introduces a physics-informed neural network to predict myocardial mechanics from physiological measurements, showing improved stress prediction and disease stratification in pulmonary hypertension.

A multimodal foundation model to integrate histology with spatial molecular programs

SQUALL integrates histology and spatial transcriptomics to enable virtual spatial gene expression profiling and clinical prediction across cancers and platforms.

Structural basis for phosphorylation-induced inactivation of the rice ammonium transporter AMT1;1

This study determines cryo-EM structures of the rice ammonium transporter OsAMT1;1 in wild-type and phosphomimetic states, revealing how phosphorylation induces inactivation by stabilizing a closed channel conformation.

A claim-centred atlas distinguishes biological corroboration from analytical depth in plant stress transcriptomes

The paper reanalyzes plant stress transcriptomes to distinguish biological corroboration from analytical depth using a claim-centred atlas called PLEASE.

Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma

This study introduces PreCSenM, a machine learning model that quantifies cellular senescence and identifies HDAC inhibitors as senescence inducers in lung adenocarcinoma.

The first chromosome-scale genome assembly of Blumeria graminis f. sp. avenae provides insights into genome evolution and host specialization

In situ Discovery of Immune Repertoire Reveals Antitumor Immunity and Therapeutic Antibodies

This paper introduces Archimap, a spatial transcriptomic platform that profiles immune repertoires and microbiota in FFPE tissues, revealing antitumor immunity and therapeutic antibodies.

The amplitude and latency of the earliest signal in V1 encode bottom-up saliency by feature conjunction

The paper shows that early V1 neural signals encode bottom-up saliency based on feature conjunction, with latency and amplitude predicting behavioral performance.

Myeloid HIF-1α Sustains Hypoxic Fibrotic Fronts and Drives Pulmonary Fibrosis

This study identifies myeloid HIF-1 as a driver of pulmonary fibrosis by sustaining hypoxic fronts and promoting fibroblast activation and matrix remodeling.

DeepSeMS: a large language model reveals hidden biosynthetic potential of the global ocean microbiome

DeepSeMS uses a large language model to predict chemical structures of secondary metabolites from microbial gene clusters, outperforming existing methods and discovering novel compounds in the ocean microbiome.

A genetically encoded GRAB sensor for measuring serotonin dynamics in vivo

This paper develops a genetically encoded sensor to measure serotonin dynamics in vivo, showing its effectiveness in both flies and mice across various conditions.

Spontaneous Axonal ER Ca2+ Waves Mediate a Shift From Action Potential-Dependent to Independent Glutamate Release in the YAC128 HD-Model

The paper shows that spontaneous axonal ER Ca2+ waves increase miniature glutamate release while reducing AP-dependent release in YAC128 HD-model neurons.

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq

The paper integrates RNA-Seq datasets to map RNA editing sites during mouse spermatogenesis, revealing their genomic distribution and functional impact.

A genetically encoded fluorescent sensor for rapid and specific in vivo detection ofnorepinephrine

The paper develops GRABNE sensors for rapid, specific in vivo detection of norepinephrine, demonstrating their use in various experimental contexts.

Fungal polysaccharopeptides reduce obesity by richness of specific microbiota and modulation of lipid metabolism

This study shows that fungal polysaccharopeptides reduce obesity through microbiota-dependent and -independent mechanisms, including increasing Akkermansia muciniphila abundance and modulating lipid metabolism.

UDP-glucose:anthocyanidin 3-O-glucoside-2”-O-glucosyltransferase catalyzes further glycosylation of anthocyanins in purple Ipomoea batatas

This study identifies Ib3GGT as a UDP-glucose-dependent anthocyanin 3-O-glucoside-2”-O-glucosyltransferase in purple sweetpotato, revealing its role in anthocyanin glycosylation and the importance of Thr-138 in UDP-glucose recognition.

The PTPRT pseudo-phosphatase domain is a denitrase

The study identifies the PTPRT pseudo-phosphatase domain as a denitrase that removes nitro-groups from tyrosine residues in paxillin, linking its dysfunction to tumor susceptibility.

The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history

This paper presents a half haplotype-resolved genome of hexaploid Ipomoea batatas, revealing two ancient whole genome duplication events and specialized compound biosynthesis gene clusters.

Omics Discovery Index - Discovering and Linking Public Omics Datasets

The paper introduces the Omics Discovery Index, a platform to search and link public omics datasets across different fields, addressing challenges in data organization and accessibility.

Choosing subsamples for sequencing studies by minimizing the average distance to the closest leaf

The paper introduces a method to select internal reference panels for imputation by minimizing average distance to the closest leaf, showing improved accuracy compared to maximizing phylogenetic diversity.