Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining.
Proceedings of the Research in Computational Molecular Biology, 2025
AutoEval Done Right: Using Synthetic Data for Model Evaluation.
CoRR, 2024
Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level Data.
Proceedings of the Research in Computational Molecular Biology, 2022
Interpretable factor models of single-cell RNA-seq via variational autoencoders.
Bioinform., 2020
Decision-Making with Auto-Encoding Variational Bayes.
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements.
CoRR, 2019
Connectivity problems on heterogeneous graphs.
Algorithms Mol. Biol., 2019
A Deep Generative Model for Semi-Supervised Classification with Noisy Labels.
CoRR, 2018
Information Constraints on Auto-Encoding Variational Bayes.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018
A deep generative model for gene expression profiles from single-cell RNA sequencing.
CoRR, 2017
ImpulseDE: detection of differentially expressed genes in time series data using impulse models.
Bioinform., 2017
Offline Directed Steiner Network Problems on Dynamic Graphs.
CoRR, 2016
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data.
BMC Bioinform., 2016
Network-Free Inference of Knockout Effects in Yeast.
PLoS Comput. Biol., 2010
Prediction of Phenotype Information from Genotype Data.
Commun. Inf. Syst., 2010
Network models of cellular response to perturbation
PhD thesis, 2009
Improved network-based identification of protein orthologs.
Proceedings of the ECCB'08 Proceedings, 2008
Cross-Species Analysis of Protein-protein Interaction Networks.
Proceedings of the Protein-protein Interactions and Networks: Identification, 2008
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data.
Bioinform., 2007
Inferring Functional Pathways from Multi-Perturbation Data.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006