Nathan C. Sheffield

17 papers A* 1Journal 16

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation. Bioinform. Amir Hassan Shariatmadari, Alireza Jafari, Sikun Guo, Sneha Srinivasan, Nathan C. Sheffield, Aidong Zhang, Kishlay Jha
2025	J	`jnl`	Fast, memory-efficient genomic interval tokenizers for modern machine learning. CoRR Nathan J. LeRoy, Donald R. Campbell Jr, Seth Stadick, Oleksandr Khoroshevskyi, Sang-Hoon Park, Ziyang Hu, Nathan C. Sheffield
2025	A*	`conf`	HyHG: A Temporal Hypergraph Contrastive Learning Framework for Biomedical Hypothesis Generation. ICDM Amir Hassan Shariatmadari, Sikun Guo, Nathan C. Sheffield, Aidong Zhang, Kishlay Jha
2025	J	`jnl`	Standards in the Preparation of Biomedical Research Metadata: A Bridge2AI Perspective. CoRR J. Harry Caufield, Satrajit Ghosh, Sek Wong Kong, Jillian Parker, Nathan C. Sheffield, Bhavesh Patel, Andrew Williams, Timothy Clark, Monica C. Munoz-Torres
2024	J	`jnl`	DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. Bioinform. Guangzhi Xiong, Nathan Leroy, Stefan Bekiranov, Nathan C. Sheffield, Aidong Zhang
2023	J	`jnl`	GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA. Bioinform. Oleksandr Khoroshevskyi, Nathan Leroy, Vincent P. Reuter, Nathan C. Sheffield
2023	J	`jnl`	excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. Bioinform. Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael I. Love, Mikhail G. Dozmorov
2021	J	`jnl`	Embeddings of genomic region sets capture rich biological associations in lower dimensions. Bioinform. Erfaneh Gharavi, Aaron Gu, Guangtao Zheng, Jason P. Smith, Hyun Jae Cho, Aidong Zhang, Donald E. Brown, Nathan C. Sheffield
2021	J	`jnl`	IGD: high-performance search for large-scale genomic interval datasets. Bioinform. Jianglin Feng, Nathan C. Sheffield
2021	J	`jnl`	Refget: standardized access to reference sequences. Bioinform. Andrew D. Yates, Jeremy Adams, Somesh Chaturvedi, Robert Davies, Matthew R. Laird, Rasko Leinonen, Rishi Nag, Nathan C. Sheffield, Oliver Hofmann, Thomas M. Keane
2019	J	`jnl`	Augmented Interval List: a novel data structure for efficient genomic interval search. Bioinform. Jianglin Feng, Aakrosh Ratan, Nathan C. Sheffield
2018	J	`jnl`	BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinform. Zhenjia Wang, Mete Civelek, Clint L. Miller, Nathan C. Sheffield, Michael J. Guertin, Chongzhi Zang
2018	J	`jnl`	Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res. Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve
2018	J	`jnl`	LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. Nucleic Acids Res. V. P. Nagraj, Neal E. Magee, Nathan C. Sheffield
2018	J	`jnl`	MIRA: an R package for DNA methylation-based inference of regulatory activity. Bioinform. John T. Lawson, Eleni M. Tomazou, Christoph Bock, Nathan C. Sheffield
2018	J	`jnl`	simpleCache: R caching for reproducible, distributed, large-scale projects. J. Open Source Softw. Nathan C. Sheffield, V. P. Nagraj, Vincent P. Reuter
2016	J	`jnl`	LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinform. Nathan C. Sheffield, Christoph Bock