Author

Priya Ranjan

Oak Ridge National LaboratoryORCID 0000-0002-0357-1939Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Approach:statistical model· 4 Organism:bacteria (other)· 3 Research Focus:gene regulatory network inference· 3 Assay:metagenomics· 3 Organism:plant (other)· 3 Research Focus:software / tool· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Adam P. ArkiniD· 2 shared Christopher S. HenryiD· 2 shared Daniel JacobsoniD· 2 shared Gerald A. TuskaniD· 2 shared Janaka N. EdirisingheiD· 2 shared Jeremy SchmutziD· 2 shared José P. FariaiD· 2 shared Madhavi Z. MartiniD· 2 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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2 shared papersBioinformatics

Adam P. ArkinORCID

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Author profile →

5 papers

Recent·Most cited

RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2

B. G. Kapoor, Melissa A. Cregger, Jill Hamilton, Alayna Mead, Priya Ranjan

RAPID provides interactive R/Shiny tools for end-to-end 16S rRNA and ITS amplicon analysis using DADA2, simplifying workflow execution for non-computational researchers.

Bioinformatics · Aug 31, 2026Peer-reviewedBioinformatics

Data coherence over data volume drives generalisable genome-based prediction of microbial carbon utilisation

Dileep Kishore, Priya Ranjan, Christopher J. Neely, Mikaela Cashman, Zahmeeth Sakkaff, William J. Riehl, Marcin P. Joachimiak, Janaka N. Edirisinghe, José P. Faria, Pamela B. Weisenhorn, Myra B. Cohen, Dale A. Pelletier, Robert W. Cottingham, Christopher S. Henry, Mitchel J. Doktycz, , Paramvir Dehal

This study shows that filtering genomes based on coherent genotype-phenotype relationships improves cross-dataset prediction of microbial carbon utilisation, outperforming larger but less coherent datasets.

bioRxiv · Aug 12, 2026 · PreprintBioinformatics

Telomere-to-telomere assemblies reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by helitrons

David Kainer, Stanton Martin, Daniel Hopp, Sophie Mosher, Timothy James Tschaplinski, P. Doug Hyatt, Madhavi Z. Martin, Jared M. LeBoldus, Kelsey L. Søndreli, Posy E. Busby, Mengjun Shu, Kerrie Barry, Jeremy Schmutz, Anna Furches, Nan Zhao, , Michael R. Garvin

The paper uses long-read sequencing to analyze telomere-to-telomere assemblies in Populus trichocarpa, revealing complex KCS gene variation and its association with helitron transposons.

bioRxiv · Jul 10, 2025 · PreprintGenomics

The DOE Systems Biology Knowledgebase (KBase)

Adam P. Arkin, Robert W. Cottingham, Christopher S. Henry, Nomi L. Harris, Rick L. Stevens, Sergei Maslov, Paramvir Dehal, Doreen Ware, Fernando Pérez, Richard Shane Canon, Michael W. Sneddon, Matthew L Henderson, William J. Riehl, Dan Murphy-Olson, Stephen Y. Chan, , Dantong Yu

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

Nature Biotechnology · Jul 1, 2018Peer-reviewedBioinformatics✦ In-depth digest

Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery

Deborah A. Weighill, Piet C. Jones, Manesh B. Shah, Priya Ranjan, Wellington Muchero, Jeremy Schmutz, Avinash Sreedasyam, David Macaya‐Sanz, Robert W. Sykes, Nan Zhao, Madhavi Z. Martin, Stephen Paul DiFazio, Timothy James Tschaplinski, Gerald A. Tuskan, Daniel Jacobson

The paper integrates genomic, metabolomic, and network data to identify target genes involved in lignin biosynthesis/degradation in Populus trichocarpa.

Frontiers in Energy Research · May 11, 2018Peer-reviewedBioinformatics