Author

Nathan Lewis

University of California San Diego

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Research Focus:host-pathogen & immune response· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Alyaa M. Abdel-Haleem Mohamed· 1 shared Annie N. CowelliD· 1 shared BAI Ding· 1 shared Bing Yu Zou· 1 shared Carlos Tong-Rios· 1 shared Danielle Ann GrotjahniD· 1 shared Digvijay SinghiD· 1 shared Elizabeth A. WinzeleriD· 1 shared

Activity by Year

2017-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperMicrobiology

Alyaa M. Abdel-Haleem Mohamed

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2 papers

Recent·Most cited

scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics

BAI Ding, Shentong Mo, Ruiyi Zhang, Yingtao Luo, Jiahao Gao, Jeremy Parker Yang, Qiuyang Wu, Digvijay Singh, Hamidreza Rahmani, Tiffany Amariuta, Danielle Ann Grotjahn, Sheng Zhong, Nathan Lewis, Wei Wang, Trey E. Ideker, , Eric Xing

scLong is a billion-parameter foundation model that captures long-range gene context in scRNA-seq by modeling all genes and integrating gene knowledge, outperforming existing models in various tasks.

Nature Communications · Feb 5, 2026Peer-reviewedBioinformatics

Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection

Gregory M. LaMonte, Pamela Orjuela-Sanchez, Lawrence Wang, Shangzhong Li, Justine Swann, Annie N. Cowell, Bing Yu Zou, Alyaa M. Abdel-Haleem Mohamed, Zaira Villa-Galarce, Marta Moreno, Carlos Tong-Rios, Joseph M. Vinetz, Nathan Lewis, Elizabeth A. Winzeler

The paper identifies MUC13 as upregulated in Plasmodium exoerythrocytic hepatic-stage infection and shows it can be used to identify anti-parasite compounds.

bioRxiv · Oct 2, 2017 · PreprintMicrobiology