Lab Publications

Pre-prints

Jeremy Bigness, Xavi Loinaz, Shalin Patel, Erica Larschan, and R. Singh. “Integrating long-range regulatory interactions to predict gene expression using graph convolutional neural networks“.

Giancarlo Bonora, Vijay Ramani, R. Singh, He Fang, Dana Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William S. Noble, and Christine M. Disteche. “Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation“.

Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, R. Singh, Charles Lawrence, and Erica Larschan. “TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data“.

2020

Pinar Demetci*, Rebecca Santorella*, Björn Sandstede, William S. Noble, and R. Singh. “Gromov-Wasserstein optimal transport to align single-cell multi-omics data.” , ISMB Machine Learning in Computational and Systems Biology Workshop Track (ISMB MLCSB), ICML Workshop on Computational Biology (ICML WCB), and Machine Learning in Computational Biology (MLCB)
[Talk][Poster Presentation][Code]

R. Singh, Pinar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhijun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, and William S. Noble. “Unsupervised manifold alignment for single-cell multi-omics data“, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)
[Talk][Code]

Jacob Schreiber, R.Singh, Jeffrey Bilmes and William S. Noble. “A pitfall for machine learning methods aiming to predict across cell types“, Genome Biology

Derek Blakely, Eamon Collins, R. Singh, Andrew Norton, Jack Lanchantin, and Yanjun Qi. “FastSK: Fast Sequence Analysis with Gapped String Kernels“, European Conference on Computational Biology (ECCB) [Code]

* Equal Contribution