Genetics

Deep learning representations of human Immune Health for precision immunology

The human immune system is composed of [~]30-50 distinct cell types, each of which can exist in different states of activation or differentiation. Indeed, the mammalian immune system has evolved to sense and respond to infections, cancers, injuries, and changes in tissue or host homeostasis (1). Moreover, an increasingly large fraction of approved drugs target the immune system directly, and/or ca...

FloREN: Decoding Immune Regulatory Networks through Interpretable Graph Transformer Patient Representations.

Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cellular heterogeneity, yet understanding the full cellular and regulatory environment of complex tissues remains challenging. In the era of large single-cell atlases, this technology has become increasingly accessible, and datasets have grown in scale and statistical power. As a result, sample representation methods have ...

Program Synthesis for Simulation-Based Inference: Joint Model Selection and Parameter Estimation

Neural simulation-based inference enables parameter estimation for complex models, but typically requires the user to specify a simulator encoding a f...

The energy landscape of DNA-binding proteins along the genome

Reconstructing the energy profile of DNA-binding proteins along the genome requires an algorithm that quantifies efficiently the binding free energy. ...

SGN: A Similarity-based Generative Network for Data Generation under Distribution Shift

Generative models trained on a source domain often produce samples that are poorly aligned with shifted target domains, limiting their effectiveness f...

Predicting phenotypes with one step genetic decision trees

Genomic prediction of complex traits is limited when phenotype records are restricted and when using linear models. Increasing the amount of phenotypi...

Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches

Progress has been made in identifying G-quadruplexes (G4s) and other non-canonical (non-B) DNA structures in live cells. However, these experiments ha...

Deep and Probabilistic Models for Gene Regulatory Network Inference

Gene regulatory networks (GRNs) link transcription factor (TF) proteins to their target genes, yet reconstructing these networks from genome-wide data...

A hybrid approach combining a phylogenetic method and Approximate Bayesian Computation Random Forest for phylogenetic network inference: application to the rice domestication process in Asia

Asian rice is one of the best documented crops in terms of genetic diversity. The domestication process, that probably started 9000 years ago in China...

Assessing the Role of Marker Density and Minor Allele Frequency on Machine Learning Driven Genomic Selection Accuracy in Grapevine

Although grapevine (Vitis spp.) is among the oldest and most economically significant fruit species globally, its genetic improvement faces major bott...

Coupled Cell-Intrinsic and Microenvironmental Heterogeneity Drives Divergent Trajectories in Castration-Resistant Prostate Cancer

Castration-resistant prostate cancer emerges from coupling between cell-intrinsic heterogeneity and microenvironmental constraints. Mechanistically di...

Shifu: an integrated framework for deep learning of RNA secondary structure

Deep learning has advanced RNA secondary-structure prediction by bypassing explicit energy rules to capture long-range dependencies, yet progress is l...

CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo

De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially...

Genomic foundation model embeddings encode higher-order viral genome architecture beyond sequence composition: a benchmark of Evo 2

Genomic foundation models such as Evo 2 are increasingly applied to microbial genomics, yet how well their representations capture viral genome organi...

Site-dependent transcriptomic signatures of endometriosis are conserved across hormonal states

Endometriosis, a chronic condition in which endometrial tissue grows at other sites in the body, produces lesions whose gene expression profiles vary ...

Machine Learning-Guided Engineering of High-Affinity Cross-Reactive Antibodies with Minimal Mutations

Antibodies raised against human targets often fail to recognize their animal orthologs, limiting preclinical evaluation in relevant models. We develop...

MeanFlowNFT: Bringing Forward-Process RL to Average-Velocity Generators

MeanFlow generators achieve fast few-step sampling by predicting average velocities over time intervals, making them attractive for efficient generati...

LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration

Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using sin...

The topology of adolescent mental health

The increased vulnerability to mental health problems in adolescence is frequently reported but poorly understood, hampered by a rigid diagnostic syst...

PRANA: A Deep Learning Method for Adapting Polygenic Risk Scores to Diverse Ethnic Groups

Polygenic risk scores (PRSs), which quantify inherited susceptibility to complex traits and diseases, have emerged as valuable tools for risk stratifi...