publications

2025

1. bioRxiv

   

   Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits

   D. D. Jatkar, M. A. Al-Radhawi, C. A. Voigt, and 1 more author

   bioRxiv, 2025

   DOI Bib

   @article{jatkar2025modeling,
     title = {Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits},
     author = {Jatkar, D. D. and Al-Radhawi, M. A. and Voigt, C. A. and Sontag, E. D.},
     journal = {bioRxiv},
     year = {2025},
     doi = {10.1101/2025.11.05.686856},
     url = {https://doi.org/10.1101/2025.11.05.686856},
   }

2. arXiv

   

   On the convergence of overparameterized problems: Inherent properties of the compositional structure of neural networks

   A. C. B. Oliveira, D. D. Jatkar, and E. D. Sontag

   arXiv preprint arXiv:2511.09810, 2025

   Submitted to Learning for Dynamics and Control (L4DC) 2026

   arXiv Bib

   @article{deoliveira2025convergence,
     title = {On the convergence of overparameterized problems: Inherent properties of the compositional structure of neural networks},
     author = {de Oliveira, A. C. B. and Jatkar, D. D. and Sontag, E. D.},
     journal = {arXiv preprint arXiv:2511.09810},
     year = {2025},
     url = {https://arxiv.org/abs/2511.09810},
     note = {Submitted to Learning for Dynamics and Control (L4DC) 2026},
   }

3. bioRxiv

   

   Paradoxical gene regulation explained by competition for genomic sites

   D. D. Jatkar, K. Manoj, E. D. Sontag, and 1 more author

   bioRxiv, 2025

   DOI Bib

   @article{jatkar2025paradoxical,
     title = {Paradoxical gene regulation explained by competition for genomic sites},
     author = {Jatkar, D. D. and Manoj, K. and Sontag, E. D. and Del Vecchio, D.},
     journal = {bioRxiv},
     year = {2025},
     doi = {10.1101/2025.11.27.691022},
     url = {https://doi.org/10.1101/2025.11.27.691022},
   }

4. bioRxiv

   Optimization of heuristic logic synthesis by iteratively reducing circuit substructures using a database of optimal implementations

   A. P. Tran, D. D. Jatkar, M. A. Al-Radhawi, and 2 more authors

   bioRxiv, 2025

   DOI Bib

   @article{tran2025optimization,
     title = {Optimization of heuristic logic synthesis by iteratively reducing circuit substructures using a database of optimal implementations},
     author = {Tran, A. P. and Jatkar, D. D. and Al-Radhawi, M. A. and Ernst, E. and Sontag, E. D.},
     journal = {bioRxiv},
     year = {2025},
     doi = {10.1101/2025.11.28.691216},
     url = {https://doi.org/10.1101/2025.11.28.691216},
   }

5. Optimal engineering of a symbiotic aerobe-anaerobe coculture

   D. D. Jatkar, A. C. B. Oliveira, A. Stohr, and 2 more authors

   2025

   Available upon request

   Bib

   @unpublished{jatkar2025optimal,
     title = {Optimal engineering of a symbiotic aerobe-anaerobe coculture},
     author = {Jatkar, D. D. and de Oliveira, A. C. B. and Stohr, A. and Woolston, B. M. and Sontag, E. D.},
     year = {2025},
     note = {Available upon request},
   }

6. Numerical methods for linearly constrained optimizations satisfying a weak form of the Polyak-Łojasiewicz inequality

   D. D. Jatkar, A. C. B. Oliveira, and E. D. Sontag

   2025

   Available upon request

   Bib

   @unpublished{jatkar2025numerical,
     title = {Numerical methods for linearly constrained optimizations satisfying a weak form of the Polyak-{\L}ojasiewicz inequality},
     author = {Jatkar, D. D. and de Oliveira, A. C. B. and Sontag, E. D.},
     year = {2025},
     note = {Available upon request},
   }

7. Permutation symmetry breaking enables fast and complete enumeration of logic circuits

   D. D. Jatkar, E. D. Sontag, and T. W. Grunberg

   2025

   Available upon request

   Bib

   @unpublished{jatkar2025permutation,
     title = {Permutation symmetry breaking enables fast and complete enumeration of logic circuits},
     author = {Jatkar, D. D. and Sontag, E. D. and Grunberg, T. W.},
     year = {2025},
     note = {Available upon request}
   }

8. A synthetic symbiotic co-culture of aerobes and anaerobes for bioproduction from \mathrmCO_2 and H_2

   G. Zhou, D. D. Jatkar, W. Gasparrini, and 2 more authors

   2025

   Available upon request

   Bib

   @unpublished{zhou2025synthetic,
     title = {A synthetic symbiotic co-culture of aerobes and anaerobes for bioproduction from $\mathrm{CO}_{2}$ and $H_{2}$},
     author = {Zhou, G. and Jatkar, D. D. and Gasparrini, W. and Stohr, A. and Woolston, B. M.},
     year = {2025},
     note = {Available upon request}
   }

9. Retroactivity and binding site competition leads to repression by an activator

   D. D. Jatkar, K. Manoj, E. D. Sontag, and 1 more author

   Jun 2025

   Poster presentation at Synthetic Biology: Engineering, Evolution & Design (SEED) 2025, Houston, TX, USA

   Bib

   @misc{jatkar2025retroactivity,
     title = {Retroactivity and binding site competition leads to repression by an activator},
     author = {Jatkar, D. D. and Manoj, K. and Sontag, E. D. and Del Vecchio, D.},
     year = {2025},
     month = jun,
     note = {Poster presentation at Synthetic Biology: Engineering, Evolution \& Design (SEED) 2025, Houston, TX, USA}
   }

2024

1. CDC

   

   Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action

   M. A. Al-Radhawi, K. Manoj, D. D. Jatkar, and 3 more authors

   In 2024 IEEE 63rd Conference on Decision and Control (CDC), Dec 2024

   Bib

   @inproceedings{alradhawi2024competition,
     title = {Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action},
     author = {Al-Radhawi, M. A. and Manoj, K. and Jatkar, D. D. and Duvall, A. and Del Vecchio, D. and Sontag, E. D.},
     booktitle = {2024 IEEE 63rd Conference on Decision and Control (CDC)},
     pages = {5579--5585},
     year = {2024},
     month = dec,
     organization = {IEEE},
   }

2. arXiv

   Interplay between contractivity and monotonicity for reaction networks

   A. Duvall, M. A. Al-Radhawi, D. D. Jatkar, and 1 more author

   arXiv preprint arXiv:2404.18734, Dec 2024

   Submitted with revisions to SIAM Journal on Applied Dynamical Systems

   arXiv Bib

   @article{duvall2024interplay,
     title = {Interplay between contractivity and monotonicity for reaction networks},
     author = {Duvall, A. and Al-Radhawi, M. A. and Jatkar, D. D. and Sontag, E. D.},
     journal = {arXiv preprint arXiv:2404.18734},
     year = {2024},
     url = {https://arxiv.org/abs/2404.18734},
     note = {Submitted with revisions to SIAM Journal on Applied Dynamical Systems}
   }

3. Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits

   D. D. Jatkar, M. A. Al-Radhawi, and E. D. Sontag

   Oct 2024

   Poster presentation at 7th International Conference on CRISPR Technologies, San Diego, CA, USA

   Bib

   @misc{jatkar2024modeling,
     title = {Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits},
     author = {Jatkar, D. D. and Al-Radhawi, M. A. and Sontag, E. D.},
     year = {2024},
     month = oct,
     note = {Poster presentation at 7th International Conference on CRISPR Technologies, San Diego, CA, USA}
   }

4. Engineering syntrophy in an anaerobe-aerobe co-culture for waste gas valorization

   D. D. Jatkar, G. Zhou, A. Stohr, and 3 more authors

   Aug 2024

   Poster presentation at Society for Industrial Microbiology & Biotechnology (SIMB) Annual Meeting 2024, Boston, MA, USA

   Bib

   @misc{jatkar2024engineering,
     title = {Engineering syntrophy in an anaerobe-aerobe co-culture for waste gas valorization},
     author = {Jatkar, D. D. and Zhou, G. and Stohr, A. and Gasparrini, W. and Sontag, E. D. and Woolston, B. M.},
     year = {2024},
     month = aug,
     note = {Poster presentation at Society for Industrial Microbiology \& Biotechnology (SIMB) Annual Meeting 2024, Boston, MA, USA}
   }

5. Competition for transcriptional resources in genetic circuits

   D. D. Jatkar, A. Duvall, E. Levine, and 2 more authors

   Jun 2024

   Poster presentation at Boston Bacterial Meeting (BBM) 2024, Boston University, Boston, MA, USA

   Bib

   @misc{jatkar2024competition,
     title = {Competition for transcriptional resources in genetic circuits},
     author = {Jatkar, D. D. and Duvall, A. and Levine, E. and Libby, E. A. and Sontag, E. D.},
     year = {2024},
     month = jun,
     note = {Poster presentation at Boston Bacterial Meeting (BBM) 2024, Boston University, Boston, MA, USA}
   }

2023

1. Elucidating interactions in engineered microbial communities towards renewable biofuel production

   D. D. Jatkar, G. Zhou, and B. M. Woolston

   Jun 2023

   Talk at American Chemical Society Northeast Regional Meeting (ACS NERM) 2023, Boston, MA, USA

   Bib

   @misc{jatkar2023elucidating,
     title = {Elucidating interactions in engineered microbial communities towards renewable biofuel production},
     author = {Jatkar, D. D. and Zhou, G. and Woolston, B. M.},
     year = {2023},
     month = jun,
     note = {Talk at American Chemical Society Northeast Regional Meeting (ACS NERM) 2023, Boston, MA, USA}
   }