publications

2026

1. Cell

   

   The Temporal Architecture of the Seminiferous Epithelial Cycle Revealed by Spatial Transcriptomics

   Arun Chakravorty, J. Yun, H. Amrhein, K. Colon, T. Sato, Shosei Yoshida, Benjamin D. Simons, and Long Cai

   Cell, 2026

   Paper Bib

   Press

   @article{chakravorty2026cell,
     category = {basic},
     title = {The Temporal Architecture of the Seminiferous Epithelial Cycle Revealed by Spatial Transcriptomics},
     author = {Chakravorty, Arun and Yun, J. and Amrhein, H. and Colon, K. and Sato, T. and Yoshida, Shosei and Simons, Benjamin D. and Cai, Long},
     journal = {Cell},
     year = {2026},
     doi = {10.1016/j.cell.2026.04.036},
     press = {https://www.bbe.caltech.edu/news/single-tissue-snapshot-reveals-biological-processes-unfolding-over-time}
   }

2025

1. PhD Dissertation

   

   Bridging Space and Time: Resolving the Temporal Dynamics of the Seminiferous Epithelial Cycle Using Spatial Transcriptomics

   Arun Chakravorty

   2025

   Paper Bib

   @phdthesis{chakravorty2025bridging,
     category = {basic},
     title = {Bridging Space and Time: Resolving the Temporal Dynamics of the Seminiferous Epithelial Cycle Using Spatial Transcriptomics},
     author = {Chakravorty, Arun},
     school = {California Institute of Technology},
     year = {2025},
     type = {{Ph.D.} Thesis},
     url = {https://thesis.library.caltech.edu/17219/},
     doi = {10.7907/2rcd-0v79}
   }

2023

1. Nature

   

   A rise-to-threshold process for a relative-value decision

   Vikram Vijayan, Fei Wang, Kaiyu Wang, Arun Chakravorty, Atsuko Adachi, Hessameddin Akhlaghpour, Barry J. Dickson, and Gaby Maimon

   Nature, 2023

   Paper Bib

   Press

   @article{vijayan2023rise,
     category = {basic},
     title = {A rise-to-threshold process for a relative-value decision},
     author = {Vijayan, Vikram and Wang, Fei and Wang, Kaiyu and Chakravorty, Arun and Adachi, Atsuko and Akhlaghpour, Hessameddin and Dickson, Barry J. and Maimon, Gaby},
     journal = {Nature},
     volume = {619},
     number = {7970},
     pages = {563--571},
     year = {2023},
     publisher = {Nature Publishing Group},
     doi = {10.1038/s41586-023-06271-6},
     press = {https://www.rockefeller.edu/news/34303-researchers-discover-neuronal-mechanism-linked-to-a-minutes-long-decision-process-in-fruit-flies/}
   }

2022

1. Science Advances

   

   An internal expectation guides Drosophila egg-laying decisions

   Vikram Vijayan, Zikun Wang, Vikram Chandra, Arun Chakravorty, Rufei Li, Stephanie L. Sarbanes, Hessameddin Akhlaghpour, and Gaby Maimon

   Science Advances, 2022

   Paper Bib

   @article{vijayan2022internal,
     category = {basic},
     title = {An internal expectation guides {Drosophila} egg-laying decisions},
     author = {Vijayan, Vikram and Wang, Zikun and Chandra, Vikram and Chakravorty, Arun and Li, Rufei and Sarbanes, Stephanie L. and Akhlaghpour, Hessameddin and Maimon, Gaby},
     journal = {Science Advances},
     volume = {8},
     number = {43},
     pages = {eabn3852},
     year = {2022},
     doi = {10.1126/sciadv.abn3852}
   }

2014

1. ACS Synthetic Biology

   

   Standardization of functional reporter and antibiotic resistance cassettes to facilitate the genetic engineering of filamentous fungi

   Swati Sureka, Arun Chakravorty, Eric C. Holmes, Olga Spassibojko, Nupur Bhatt, Dongliang Wu, and B. Gillian Turgeon

   ACS Synthetic Biology, 2014

   Paper Bib

   @article{sureka2014standardization,
     category = {basic},
     title = {Standardization of functional reporter and antibiotic resistance cassettes to facilitate the genetic engineering of filamentous fungi},
     author = {Sureka, Swati and Chakravorty, Arun and Holmes, Eric C. and Spassibojko, Olga and Bhatt, Nupur and Wu, Dongliang and Turgeon, B. Gillian},
     journal = {ACS Synthetic Biology},
     volume = {3},
     number = {12},
     pages = {960--962},
     year = {2014},
     doi = {10.1021/sb5000143}
   }

2. Biosensors and Bioelectronics

   

   An arsenic-specific biosensor with genetically engineered Shewanella oneidensis in a bioelectrochemical system

   Dylan P. Webster, Michaela A. TerAvest, Devin F. R. Doud, Arun Chakravorty, Eric C. Holmes, Caleb M. Radens, Swati Sureka, Jeffrey A. Gralnick, and Largus T. Angenent

   Biosensors and Bioelectronics, 2014

   Paper Bib

   @article{webster2014arsenic,
     category = {basic},
     title = {An arsenic-specific biosensor with genetically engineered {Shewanella oneidensis} in a bioelectrochemical system},
     author = {Webster, Dylan P. and TerAvest, Michaela A. and Doud, Devin F. R. and Chakravorty, Arun and Holmes, Eric C. and Radens, Caleb M. and Sureka, Swati and Gralnick, Jeffrey A. and Angenent, Largus T.},
     journal = {Biosensors and Bioelectronics},
     volume = {62},
     pages = {320--324},
     year = {2014},
     doi = {10.1016/j.bios.2014.07.003}
   }