Genetics

Video Generative Models as Geometry Learner

Recent generative approaches to geometry estimation adapt pretrained image diffusion models and treat the task as image-conditioned generation. Leveraging off-the-shelf image diffusion models, they either (i) train task-specific geometry models (for depth and surface normal estimation) independently, losing the opportunity of exploring the intrinsic correlation of these geometric targets, or (ii) ...

Functional profiling of spacecraft cleanroom microbiomes through genome-wide phenotype predictions

Current planetary protection approaches rely heavily on spore-based tests developed for Mars missions and may not adequately assess contamination risks for icy ocean worlds such as Europa. We developed a genome-based framework combining deep shotgun metagenomics and supervised machine learning to predict survival-relevant microbial traits in ESA JUICE launch-site cleanrooms. From 183 genome bins, ...

Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations

Negative selection on deleterious mutations plays a key role in shaping human genetic variation, yet the dominance effects of these mutations remain p...

Oligodendrocyte Enriched Brain Organoids Reveal Impaired Oligodendroglial Maturation and Altered Neural Network Activity in Down Syndrome

Individuals with Down syndrome (DS) display developmental delay, intellectual disability, premature brain ageing, and an increased risk of Alzheimer-l...

DISRUPTION OF A DNA REPAIR PROTEIN PROMOTES ANTIBIOTIC RESISTANCE IN ACINETOBACTER BAUMANNII

Acinetobacter baumannii is a high priority Gram negative opportunistic pathogen known for its high rates of multidrug resistance (MDR). Minocycline (M...

Evaluating the performance of splicing predictors on thousands of synthetic gene variants

Computational predictors of RNA splicing are increasingly used to interpret genetic variants and to design synthetic genes, yet they are almost always...

Scalable spatial DNA sequencing from archival tissue maps copy number subclones

Spatially resolved DNA sequencing holds promise due to its potential utility in understanding cancer intra-tumour heterogeneity and tumour evolution i...

PMPNN-DDG: an accurate machine learning-based {triangleup}{triangleup}G prediction pipeline trained on a novel interpretable feature set extracted from ProteinMPNN

An accurate and tractable approximation of the single-point mutation-induced change in protein thermodynamic stability, denoted by DDG, is critical fo...

Molecular Determinants of Functional Bacterial sRNA-mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning

Bacterial small RNAs (sRNAs) regulate gene expression by base pairing with target mRNAs, yet transcriptome-wide interactome mapping has shown that man...

Multimodal Machine Learning for Predicting Outcomes in the PASS-01 Trial of Systemic Therapy for Metastatic Pancreatic Cancer

Purpose Modified FOLFIRINOX (FFX) and gemcitabine plus nab-paclitaxel (GNP) are standard first-line treatments for metastatic pancreatic ductal adenoc...

CropCop: An Auditable 120-Class Plant-Health Model from Benchmark Reconstruction to a Quantised Runtime Artifact

A plant-health score can appear precise while resting on duplicated image families, a long-tailed label space, or a runtime file that was never evalua...

PANDA - Prototype-Anchored Alignment for Partially Unpaired Multimodal Learning, with Applications to Alzheimers MRI and TCGA Pathology

Multimodal medical prediction often faces incomplete pairing: auxiliary modalities with complementary signal are available for only a subset of subjec...

Cell type-resolved chromatin accessibility clocks for brain aging

Aging is a progressive decline in biological function that is proposed to be driven by the accumulation of epigenetic noise and the loss of epigenetic...

Detecting CYP2C19 deletions from genotyping array signals using neural networks

Since copy number variations (CNVs) in pharmacogenes can cause significant alterations in drug metabolism, their reliable detection is of high importa...

Bridging Morphology and Genomics: A rapid image-based assessment of genomic admixture in the endangered gayal (Bos frontalis)

Abstract The gayal (Bos frontalis) is an endangered semi-domesticated bovine species renowned for its high-quality beef. However, its semi-feral lifes...

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Modeling cellular behavior requires measurements that capture how cells evolve across time, environments, and interventions. Microscopy is uniquely su...

A Multimodal Foundation Model for Longitudinal Patient Representation and Scalable Insight Generation in Oncology

Precision oncology necessitates a longitudinal model of patient state that captures cancer evolution and treatment over time, integrating multimodal o...

Optimizing RNA yield using deep neural networks coupled to massively parallel screening

Messenger RNA (mRNA)-based therapeutics have emerged as a powerful platform for vaccines, protein replacement therapies, and cancer immunotherapy. A c...

Predicting Protein-RNA Binding Affinity Changes via Spatial Coupling-Aware State Space Modeling

Accurately predicting the effects of mutations on protein-RNA binding is crucial for elucidating disease mechanisms. Yet, exhaustively exploring the s...

Multiplexed Quantification of Variant Abundance in the Globin Gene Family: Integrating Saturation Mutagenesis with Cross-Paralog Prediction

Widespread genetic testing has expanded variant identification, yet functional characterization remains a bottleneck in genome guided medicine. Here, ...