Genetics

Multimodal AI Methods for Predicting Pathologic Complete Response in Breast Cancer.

Neoadjuvant chemotherapy (NAC) can eliminate all invasive cancer in some breast cancer patients, achieving a pathologic complete response (pCR) that is associated with a better prognosis. Prediction of pCR from pre-treatment radiology imaging is challenging but could provide immense value in the treatment planning. We propose a novel multimodal deep learning approach that combines pre-treatment dy...

De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of [NiFe]-Hydrogenase.

[NiFe]-Hydrogenases display remarkable catalytic efficiency for H2 production and oxidation but are sensitive to O2, which severely restricts their biotechnological applications. The identities and functional relevance of gas channels leading to the buried [NiFe] active site remain elusive, hindering rational enzyme engineering. Here, we introduce an artificial intelligence-guided de novo protein ...

Examine neural network models for protein sequencing based features prediction.

Protein functions are essential for understanding life at the molecular level. High-throughput sequencing generates vast amounts of raw protein sequen...

Integrated bulk and single-cell transcriptomic analyses identify senescence-related hub genes and microenvironmental remodeling in sarcopenia.

Increasing evidence indicates that cellular senescence, metabolic dysfunction, stromal remodeling, and immune perturbation collectively contribute to ...

Programmable Domestication: CRISPR, Pan-Genomics and System Level Engineering for Next-Generation Crops.

Global agriculture is increasingly challenged by climate instability, genetic erosion, emerging pathogens and rising food demands, exposing the limita...

Systems pharmacology reveals type I interferon and myeloid-like B cell reprogramming as candidate druggable axes in antiphospholipid syndrome.

Antiphospholipid syndrome (APS) lacks disease-modifying targeted therapies, and its molecular heterogeneity remains poorly characterized. We employed ...

Identification of Aging and Mitochondria-Related Hub Genes in Dilated Cardiomyopathy.

Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation and systolic dysfunction and is associated with mitochondrial dysfunction a...

Bioinformatics and Machine-Learning Identification of Pulmonary Hypertension Biomarkers and Candidate Therapeutic Compounds.

This study aimed to identify pulmonary hypertension (PH)-associated molecular biomarkers and candidate small-molecule compounds using public transcrip...

Deep learning differentiates myeloproliferative neoplasms and predicts JAK2 and CALR mutations from bone marrow smears.

Accurate differentiation of BCR::ABL1-negative myeloproliferative neoplasms (MPNs) based on bone marrow smear morphology remains challenging. While pr...

Tissue-Agnostic Cellular Morphometric Biomarkers for Risk-Adapted Management Across Gastrointestinal Precancerous Lesions and Cancers.

While precision oncology increasingly adopts tissue-agnostic paradigms, current strategies remain heavily reliant on molecular alterations, with limit...

Epigenetic markers expand genetic risk estimation in acute myeloid leukemia.

Gene mutations and chromosome abnormalities are important components of prognostication in acute myeloid leukemia (AML). Here we assessed whether DNA ...

Mirror Worlds: The Shared Regulatory Architecture of Cell Fate in Development and Cancer.

Lineage plasticity has emerged as a central mechanism through which cancer cells adapt to therapeutic pressure, evade immune surveillance, and acquire...

Microbiome-metabolome multi-omics biomarkers for infectious disease prognosis: Current evidence, AI-driven integration, and translational challenges.

Microbiome-metabolome interactions are emerging as promising predictors of infectious disease, beyond conventional pathogen detection. Growing evidenc...

Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.

Enhancers control tissue-specific gene expression across animals1. Although deep learning2,3 has enabled enhancer prediction and design in mammalian c...

Saliva Liquid Biopsy for Detection of Oral and Systemic Diseases.

Saliva has emerged as a compelling liquid biopsy for the non-invasive diagnosis and monitoring of both oral and systemic diseases. Secreted by major a...

Pathogenic Genetic Variants, Comorbid Autism and Adaptive Developmental Quotient as Independent Predictors of Intellectual Disability in Children With Global Developmental Delay: An Interpretable Machine Learning Model With Calibrated Risk Estimation.

BACKGROUND: Global developmental delay (GDD) frequently precedes intellectual disability (ID), but no validated multivariable prognostic tool exists t...

Limits of deep-learning-based RNA prediction methods.

In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions, but progress on RNA structure, ...

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.

Orphan genes - genes lacking detectable homologs outside a species - are widespread in microbial genomes and are thought to contribute to their adapta...

A Risk Prediction Model for Normal-Tension Glaucoma Progression Integrating Genetic Markers and Corneal Biomechanics.

OBJECTIVE: Normal-tension glaucoma (NTG) is characterized by progressive optic nerve damage despite intraocular pressure remaining consistently within...

NICE: A Two-Step Non-Invasive Framework for Embryo cfDNA Read Enrichment and Quality Assessment.

Non-invasive preimplantation genetic testing (niPGT) using cell-free DNA (cfDNA) extracted from spent embryo culture medium (SECM) has shown great pot...