Publications

You can also find my articles on my Google Scholar profile.

Single-cell RNA sequencing data analysis

• Epigenetic dysregulation in aged muscle stem cells drives mesenchymal progenitor expansion via IL-6 and Spp1 signaling. [contributing author]
  Accepted in Nature Aging (August 2025) Zenodo
  • Anaylsis of single cell datasets for various muscle celltypes in healthy and infected mice.
• Spatial organization of pulmonary type 2 inflammation by a macrophage-derived cholesterol metabolite. [contributing author]
  Under Review at Science (July 2025) Preprint
  • Analysis of macrophages from lung tissues in mice, along with HTO deconvolution.

Bulk RNA sequencing data analysis

• PI3Kd promotes T cell effector differentiation and plasticity during chronic infection. [contributing author]
  Under Review at Science Immunology (July 2025)
  • Mice RNA-seq
• Translocating bacteria in SIV infection are not stochastic and preferentially express cytosine methyltransferases. [contributing author]
  Published in Mucosal Immunology (2024) PDF, Weblink
  • Bacterial strains isolated from infected Rhesus macaques.
• Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides. [co-first author]
  Published in Microbial Cell Factories (2024) PDF, Weblink
  • Time course experiments for enhanced lipid production in R. toruloides by varying C:N ratio.

• Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift. [second author]
  Published in Frontiers in Microbiology (2023) PDF, Weblink, Github

• System analysis of Lipomyces starkeyi during growth on various plant-based sugars. [co-first author]
  Published in Genomics, Transcriptomics, Proteomics (2022) PDF, Weblink, Github
  
  • Analysis of transcriptomics and metabolomics data, and annotation of genes in the non-model yeast Lipomyces starkeyi.
    
• Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide. [contributing author]
  Published in FEMS Yeast Research (2022) PDF, Weblink
  • Analysis of transcriptomic data using carbon dioxide as a growth source for the yeast S. cerevisiae.
    
• Integrating transcriptomic and metabolomic analysis of the oleaginous yeast Rhodosporidium toruloides IFO0880 during growth under different carbon sources. [co-first author]
  Published in Applied Microbiology and Biotechnology (2021). PDF, Weblink, Github
  
  • Analysis of transcriptomics and metabolomics data, and annotation of genes in the non-model yeast Rhodospridium toruloides.
    

• Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach. [co-first author]
  Published in Applied Microbiology and Biotechnology (2021). PDF, Weblink, Github

• pH selectively regulates citric acid and lipid production in Yarrowia lipolytica W29 during nitrogen-limited growth on glucose. [contributing author]
  Published in Journal of Biotechnology (2019). PDF, Weblink
  

Genome assembly and phylogeny work

• Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates. [second author]
  Published in Bioresource Technology (2025) PDF, Weblink, Github
  
  • Whole Genome Assemby and Copy Number anaysis for evolved strains of the yeast Y. lipolytica.
    
• Identification and analysis of sugar transporters capable of co-transporting glucose and xylose simultaneously. [second author]
  Published in Biotechnology Journal (2021). PDF, Weblink, Patent
  
  • Identification of putative transporters using sequence alignment, phylogeny and orthology.
    

Experimental Work

• A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. [contributing author]
  Published in Metabolic Engineering Communications (2019 ). PDF, Weblink
  
  • Model validation by characterizing growth on various sugars and amino acids.