Author

Shivani Upadhyaya

University of California, BerkeleyORCID 0000-0002-3330-4305Unclaimed ORCID profile · follow to get notified of new preprints

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Shivani Upadhyaya1 paper

Biology Disciplines

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Plant Biology· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:C. elegans· 2 Research Focus:cell type annotation· 2 Assay:metabolomics· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1

Frequent Co-Authors

Melissa RothiD· 3 shared Krishna NiyogiiD· 2 shared Alex Metcalf· 1 shared Athena SchepmoesiD· 1 shared Ian K. BlabyiD· 1 shared Kim K. HixsoniD· 1 shared Leo A. BaumgartiD· 1 shared Luca Cohen· 1 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersPlant Biology

Melissa RothORCID

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3 papers

Recent·Most cited

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

Shivani Upadhyaya, Suzanne M. Kosina, Kim K. Hixson, Athena Schepmoes, Ritesh Mewalal, Yu Zhang, Ronan C. O’Malley, Leo A. Baumgart, Ian K. Blaby, Mary S. Weir Lipton, Trent R. Northen, Krishna Niyogi, Melissa Roth

This study shows that TOR inhibition in algae increases amino acid levels through transcriptional activation of biosynthesis pathways and identifies a conserved transcription factor involved in nitrogen metabolism.

bioRxiv · Sep 29, 2025 · PreprintPlant Biology

An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation

Tim L. Jeffers, Ryan McCombs, Stefan Schmollinger, Srikanth Tirumani, Shivani Upadhyaya, Sabeeha Merchant, Krishna Niyogi, Melissa Roth

This paper designs a nutrient-replete medium for Chromochloris zofingiensis to support fast growth and high triacylglycerol accumulation by optimizing mineral concentrations based on cellular ionome data.

Plant Direct · Sep 1, 2025Peer-reviewedPlant Biology

Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by Chromochloris zofingiensis

Michelle Meagher, Alex Metcalf, Mark Vigliotti, S. Alex Ramsey, Walter Prentice, Luca Cohen, Shivani Upadhyaya, Melissa Roth, Nanette R. Boyle

The paper develops a genome-scale metabolic model for Chromochloris zofingiensis and demonstrates its ability to predict fermentation products and metabolic activity under different growth conditions.

Algal Research · Nov 23, 2024Peer-reviewedSystems Biology