*corresponding author, #co-first author

BioRxiv

18. Bibek Acharya, Sean Castillo, Rukhillo Kodirov, Anisha Shakya*, “Label-Free Fluorescence Microscopy Reveals Multiphase Organization in Biomolecular Condensates”, submitted bioRxiv doi: https://doi.org/10.1101/2025.07.13.663051

17. Neha Rana, Rukhillo Kodirov, John T. King*, Anisha Shakya*, “Protein Unfolding Thermodynamics Predict Multicomponent Phase Behavior”, submitted bioRxiv doi: https://doi.org/10.1101/2023.05.26.542380

Peer Reviewed Journals

16. John T. King*, Anisha Shakya*, “Modern Optical Microscopy Methods to Study Biomolecular Condensates”, Curr. Opin. Colloid Interface Sci. (2021), 52, 101421. (Invited Review)

15. John T. King*, Anisha Shakya*, “Phase Separation of DNA: From Past to Present”, Biophysical J. (2021), 120, 1139. (Invited Review)

14. Anisha Shakya, Martin Girard, John T. King, Monica Olvera de la Cruz, “Role of Chain Flexibility in Asymmetric Polyelectrolyte Complexation in Salt Solutions”, Macromolecules (2020), 53, 1258.

13. Anisha Shakya*#, Seonyoung Park#, Neha Rana, John T. King*, “Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization”, Biophysical J. (2020), 118, 753. (Front Cover)

12. Martin Girard, Annaliese Ehlen, Anisha Shakya, Monica Olvera de la Cruz, Tristan Bereau, “Hoobas: Highly Object-Oriented Molecular Builder”, Computational Mat. Sci. (2019), 167, 25.

11. Seong Jun Park, Anisha Shakya, John T. King, “Depletion Layer Dynamics of Polyelectrolyte Solutions in Poiseuille Flow”, Proc. Natl. Acad. Sci. U.S.A (direct submission, 2019), 116, 16256.

10. Anisha Shakya, John T. King, “DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets”, Biophysical J. (2018), 115, 1840. (Featured in New and Notable and Spotlight for Early Career Investigators)

9. Anisha Shakya, John T. King, “Non-Fickian Molecular Transport in Protein-DNA droplets”, ACS Macro Lett. (2018), 7, 1220. (Supplementary Cover)

    Graduate Publications

8. Isaac J. Kimsey, Eric S. Szymanski, Walter J. Zahurancik, Anisha Shakya, Yi Xue, Chia-Chieh Chu, Bharathwaj Sathyamoorthy, Zucai Suo, Hashim M. Al-Hashimi, “Dynamic Basis for dG•dT Misincorporation via Tautomerization and Ionization”, Nature (2018), 554, 195.

7. Anisha Shakya, Hashim M. Al-Hashimi, Mark M. Banaszak Holl, “Three RNA-Microenvironments Detected in Fluxional Gene Delivery Polyplexes”, ACS Macro Lett. (2016), 5, 1104.

6. Dawn K. Merriman, Yi Xue, Shan Yang, Isaac J. Kimsey, Anisha Shakya, Mary Clay, Hashim M. Al-Hashimi, “Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes Over a Broad Range of Timescales”, Biochemistry (2016), 55, 4445.

5. Anisha Shakya, Casey A. Dougherty, Yi Xue, Hashim M. Al-Hashimi, Mark M. Banaszak Holl, “Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release”, Biomacromolecules (2015), 17, 154.

4. Rahul Rattan, Sriram Vaidyanathan, Gordon S.-H Wu, Anisha Shakya, Bradford G. Orr, Mark M. Banaszak Holl, “Polyplex-Induced Cytosolic Nuclease Activation leads to Differential Transgene Expression”, Mol. Pharm. (2013), 10, 3013.

3. Anisha Shakya#, Zhijie Wang#, Junsi Gu, Shichen Lian, Stephen Maldonado, “Sensitization of p-GaP with CdSe Quantum dots: Light Stimulated Hole Injection”, J. Am. Chem. Soc. (2013), 135, 9275.

    Undergraduate Publications

2. Yeon Jae Ko, Anisha Shakya, Haopeng Wang, Andrej Grubisic, Weijun Zheng, Matthias Götz, Gerd Ganteför, Kit H. Bowen, Puru Jena, Boggavarapu Kiran, “Electronic Structure and Properties of Isoelectronic Magic Clusters: Al13X (X = H, Au, Li, Na, K, Rb, Cs)”, J. Chem. Phys. (2010), 133, 124308.

1. Valerie J. Carabetta, Tuo Li, Anisha Shakya, Todd M. Greco, Ileana M. Cristea, “Integrating Lys-N Proteolysis and N-Terminal Guanidination for Improved Fragmentation and Relative Quantification of Singly-Charged Ions”, J. Am. Soc. Mass Spec. (2010), 21, 1050.