Nephrology

Structural similarities reveal an expansive conotoxin family with a two-finger toxin fold

Venomous animals have evolved a diverse repertoire of toxins with considerable pharmaceutical potential. The rapid evolution of peptide toxins, such as the conotoxins produced by venomous marine cone snails, often complicates efforts to infer their evolutionary relationships based solely on sequence information. Structural bioinformatics, however, can provide robust support. Here, we first solve t...

Mapping and reprogramming human tissue microenvironments with MintFlow

Tissue microenvironments reprogram local cellular states in disease, yet current computational spatial methods remain descriptive and do not simulate tissue perturbation. We present MintFlow, a generative AI algorithm that learns how the tissue microenvironment influences cell states and predicts how tissue perturbations can reprogram them. Applied to three human diseases, MintFlow uncovered disti...

A Deep Learning-based Method for Drug Molecule Representation and Property Prediction

Accurately and robustly representing drug molecule features, prediction of drug-target biomacromolecule interactions, and determining drug molecule ph...

Integrative network modeling of colorectal cancer reveals diagnostic signatures and therapeutic targets

Emerging evidence suggests that the interplay between multiple signaling pathways and the immune microenvironment influences tumorigenesis in cancers ...

Deep learning-based image quantification of epithelial cell shapes and its application to polycystic kidney disease

Cell shape is a fundamental determinant of tissue architecture and organ function. In epithelial tissues, cytoskeletal organization and tight junction...

Close-Up of vesicular ER Exit Sites by Volume Electron Imaging using FIB-SEM

Volume electron microscopy by high-pressure freeze substitution combined with block-face focused ion beam scanning electron microscopy (FIB-SEM) provi...

Deep Learning for Molecular and Genomic Characterization of Lung Cancer in Never-Smokers Using Hematoxylin and Eosin-Stained Images

Despite promising results in using deep learning to infer genetic features from histological whole-slide images (WSIs), no prior studies have specific...

An integrative machine learning approach identifies the centrality of ferroptosis, cuproptosis, and immune pathway crosstalk for breast cancer stratification and therapy guidance

Breast cancer (BRCA) is a leading cause of cancer-related mortality in women, characterized by marked heterogeneity in molecular subtypes, immune micr...

Lung Adenocarcinoma Just Desserts: An Expanding Pie of Activating Oncogenes or a Layer Cake of Integrated Alterations

The molecular landscape of lung adenocarcinoma (LUAD) is often summarized as a “pie chart” of driver oncogenes, suggesting identification and targetin...

Graph Autoencoder and StrNN based Causal Analysis of Mortality in Heart Failure Patients

Though analyzed for decades, dissecting and finding mechanisms of cardiovascular diseases, especially heart failures, are still an on-going task for m...

Advanced Deep Learning Enables Prediction of Allogeneic Stem Cell Mobilization Success

Hematopoietic stem and progenitor cell (HSPC) transplantation offers a potentially curative therapy for aggressive hematologic malignancies and bone m...

Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits

All cells in an animal collectively ensure, moment-to-moment, the survival of the whole organism in the face of environmental stressors1,2. Physiology...

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how comm...

Machine learning–driven decoding of maternal immune signatures in repeated pregnancy loss

Repeated pregnancy loss (RPL) is a multifactorial condition in which the underlying immunological mechanisms remain incompletely understood. Although ...

Non-Invasive Diagnostic Evaluation of Urinary Exosomal Let-7c Cluster Expression in Bladder Cancer Using Machine Learning Approaches

Bladder cancer (BCa) diagnosis typically relies on invasive cystoscopy, which is effective but costly and uncomfortable. Urinary microRNAs (miRNAs), e...

Multi-omics Integration of Microbiota Transplant Therapy in Children with Autism Spectrum Disorders

Microbiota transplant therapy (MTT) is a promising avenue for the substantial improvement of gastrointestinal and behavioral symptoms in children with...

Bioimage analysis for multiplexed FUCCI acquisitions powered by deep learning

The FUCCI sensor fluorescently labels cell cycle phases, which is essential to assess normal and abnormal cell-cycle progression in physiological and ...

Targeted Enzymatic Fragmentation of Lipoprotein(a) via Kringle IV Domains: A Clearance-Enhancing Therapeutic Strategy for Cardiovascular Disease

Elevated lipoprotein(a) [Lp(a)] is an independent, genetically determined risk factor for atherosclerotic cardiovascular disease (ASCVD). Its unique a...

The Liver is an Inflammatory Mediator of Pulmonary Arterial Hypertension

Inflammation is central to pulmonary arterial hypertension (PAH) pathogenesis. The liver regulates systemic immunity, yet its contribution to PAH rema...

Cancer target discovery enabled by transcriptome-based virtual CRISPR screening

Functional genetic screens have uncovered dependencies in many cancers, but experimentally screened models for most cancers are far outnumbered by mol...