| 2025-12-06 |
Jamie Endicott |
scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling |
| 2025-11-14 |
Emily Chao |
Reference-informed evaluation of batch correction for single-cell omics data with overcorrection awareness |
| 2025-11-07 |
Cigdem Ak |
HALO: hierarchical causal modeling for single cell multi-omics data |
| 2025-10-31 |
John Cheeney |
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories |
| 2025-10-17 |
Julianna Hays |
Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions |
| 2025-10-10 |
Ian VanGordon |
Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression |
| 2025-10-03 |
Nikki Szczepanski |
Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles |
| 2025-09-17 |
Hugo Cros |
Thermodynamic computing system for AI applications |
| 2025-09-12 |
Aaron Doe |
ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images |
| 2025-08-10 |
Sam Kupp |
SuperGLUE: An interpretable multiomic integration method |
| 2025-08-29 |
Travis Moore |
Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data |
| 2025-08-21 |
Juyoung Lee |
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility |
| 2025-08-15 |
Connor Frankston |
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings |
| 2025-07-31 |
Kaoutar Ait-Ahmad |
Towards a general-purpose foundation model for computational pathology |
| 2025-07-24 |
Isfaq Ahmad |
Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies |
| 2025-07-17 |
Mustafa Akur |
A Foundation Model for Spatial Proteomics |
| 2025-07-12 |
Theresa Lusardi |
scEVE: a single-cell RNA-seq ensemble clustering algorithm |
| 2025-07-04 |
Sam Kupp |
Concerto: contrastive learning for multimodal single-cell atlas |
| 2025-06-27 |
John Cheney |
Identifying T cell antigen at the atomic level with graph convolutional network |
| 2025-06-21 |
Cigdem Ak |
Learning single-cell perturbation responses using neural optimal transport |
| 2025-05-30 |
Samantha Worme |
Dissecting regulatory syntax in human development with scalable multiomics and deep learning |
| 2025-05-23 |
Nikki Szczepanski |
Interpretable phenotype decoding from multi-condition sequencing data with ALPINE |
| 2025-05-23 |
Nikki Szczepanski |
Interpretable phenotype decoding from multi-condition sequencing data with ALPINE |
| 2025-05-09 |
Ian VanGordon |
SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data |
| 2025-03-21 |
Christopher Eddy |
Bridging equation learning and biological modeling with physics-informed neural networks |
| 2025-03-14 |
Travis Moore |
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data |
| 2025-02-28 |
Juyoung Lee |
Stripe asymmetry as a directionality signal for the genome |
| 2025-02-21 |
Mustafa Akur |
LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedical Applications |
| 2025-02-14 |
Connor Frankston |
scHiGex: predicting single-cell gene expression based on single-cell Hi-C data |
| 2025-01-24 |
Mustafa Akur |
BERT-style model paper (title not given) |
| 2025-01-17 |
Kaoutar Ait-Ahmad |
A foundation model of transcription across human cell types |
| 2024-12-13 |
Sydney Hamilton |
Machine Learning for Predicting Therapeutic Outcomes in Acute Myeloid Leukemia Patients |
| 2024-11-22 |
Layaa Sivakumar |
CelLink: Integrate single-cell multi-omics data with few linked features and imbalanced cell populations |
| 2024-11-15 |
Emily Chao |
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics |
| 2024-11-08 |
Cigdem Ak |
Multi-task learning from multimodal single-cell omics with Matilda |
| 2024-09-27 |
Samantha Worme |
Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements |
| 2024-09-20 |
Stephen Coleman |
scMaui: a widely applicable deep learning framework for single-cell multiomics integration |
| 2024-09-13 |
Ruben Lancaster |
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning |
| 2024-09-06 |
Ian VanGordon |
Analyzing single-cell bisulfite sequencing data with MethSCAn |
| 2024-08-30 |
Nikki Szczepanski |
Integration of Single-Cell RNA-Seq Datasets: A Review of Computational Methods |
| 2024-08-23 |
Hugo Cros |
SpaNorm: spatially-aware normalisation for spatial transcriptomics data |
| 2024-08-15 |
Aaron Doe |
Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology |
| 2024-08-09 |
Rosalyn Fey |
Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells |
| 2024-07-25 |
Garth Kong |
DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors |