Selected Publications

Google Scholar
Author order generally follows the convention in biology, where first author carried out majority of the work (joint first authorship is indicated by ‘∗’)

Journal papers

1. Palash Sashittal, Viola Chen, Amey Pasarkar, Benjamin Raphael
   Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data
   Bioinformatics, 2024.

2. Palash Sashittal, Hoachen Zhang, Christine Iacobuzio-Donahue and Benjamin Raphael
   ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model
   Genome Biology, 2023.

3. Palash Sashittal*, Henri Schmidt*, Michelle Chan and Benjamin Raphael
   Startle: a star homoplasy approach for CRISPR-Cas9 lineage tracing
   Cell Systems, 2023.

4. Henri Schmidt, Palash Sashittal and Benjamin Raphael
   A zero-agnostic model for copy number evolution in cancer
   PLOS Computational Biology, 2023.

5. Palash Sashittal, Robert Chiodi, Tim Morgan, Olivier Desjardins, Theodore Heindel and Daniel Bodony
   Modal analysis and interface tracking of multiphase flows using dynamic mode decomposition
   International Journal of Multiphase Flows, 2022.

6. Chuanyi Zhang*, Palash Sashittal*, Michael Xiang, Yichi Zhang, Ayesha Kazi and Mohammed El-Kebir
   Accurate identification of transcription regulatory sequences and genes in Coronaviruses
   Molecular Biology and Evolution, 2022.

7. Palash Sashittal, Simone Zaccaria and Mohammed El-Kebir
   Parsimonious clone tree integration in cancer
   Algorithms and Molecular Biology, 2022.

8. Chamtuet Oh*, Palash Sashittal*, Aijia Zhou, Leyi Wang, Mohammed El-Kebir and Thanh Nguyen
   Design of SARS-CoV-2 variant-specific PCR assays considering regional and temporal characteristics
   Applied and Environmental Microbiology, 2022.

9. Palash Sashittal, Chuanyi Zhang, Jian Peng and Mohammed El-Kebir
   Jumper enables discontinuous transcript assembly in Coronaviruses
   Nature Communications, 2021.

10. Palash Sashittal and Daniel Bodony
    Data driven sensor placement for fluid flows
    Theoretical and Computational Fluid Dynamics, 2021.

11. Leah Weber*, Palash Sashittal*, and Mohammed El-Kebir
    doubletD: detecting doublets in single-cell DNA sequencing data
    Bioinformatics, 2021.

12. Palash Sashittal and Mohammed El-Kebir
    Sampling and summarizing transmission trees with multi-strain infections
    Bioinformatics, 2020.

13. Palash Sashittal and Daniel Bodony
    Reduced-order control using low-rank dynamic mode decomposition
    Theoretical and Computational Fluid Dynamics, 2019.