Author

Navami Jain

Stanford University

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· 2 Genomics· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:metagenomics· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Aarushi Mehrotra· 1 shared Abigail Jackson· 1 shared Alexander L. JaffeiD· 1 shared Ami Siddharth BhattiD· 1 shared Annan Timon· 1 shared Anne E. DekasiD· 1 shared Arashdeep SinghiD· 1 shared Debora S. MarksiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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1 shared paperBioinformatics

Aarushi Mehrotra

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Evaluating variant effect prediction across viruses

Sarah F. Gurev, Noor Youssef, Navami Jain, Aarushi Mehrotra, Sarrah Rose Mikhail Leung, Abigail Jackson, Debora S. Marks

This paper evaluates variant effect prediction models on viruses, showing that state-of-the-art models underperform on viral proteins compared to alignment-based models, especially in low-sequence regimes.

bioRxiv · Aug 4, 2025 · PreprintBioinformatics

Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos

Alexander L. Jaffe, Kaitlin Harrison, Renée Z. Wang, Leah J. Taylor‐Kearney, Navami Jain, Noam Prywes, Patrick M. Shih, Jodi N. Young, Gabrielle Rocap, Anne E. Dekas

The paper identifies a Prochlorococcus lineage in oxygen deficient zones that expresses both form I and form II rubiscos, suggesting an adaptation to low oxygen environments.

Proceedings of the National Academy of Sciences · Nov 25, 2024Peer-reviewedMicrobiology

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer

Piyush Agrawal, Navami Jain, Vishaka Gopalan, Annan Timon, Arashdeep Singh, Padma Sheila Rajagopal, Sridhar S. Hannenhalli

This study applies a network-based method to identify key genes in BRCA subtypes and chemotherapy response in TNBC, revealing subtype-specific mediators and potential therapeutic targets.

iScience · Apr 16, 2024Peer-reviewedBioinformatics

Phanta: Phage-inclusive profiling of human gut metagenomes

Yishay Pinto, Meenakshi Chakraborty, Navami Jain, Ami Siddharth Bhatt

Phanta profiles human gut metagenomes to include viruses directly from short reads, identifying more viral species than assembly-based methods and revealing higher interindividual variability in the virome.

Nature Biotechnology · May 25, 2023Peer-reviewedGenomics