Anushree publications full

Full publication and patent list, Dr. Anushree Chatterjee

2019

45. Antoni E. Bordoy#, Nolan O'Connor#, and Anushree Chatterjee* (2019). Construction of two-input logic gates using Transcriptional Interference. ACS Synthetic Biology 8(10), 2428-2441. bioRxiv.
doi: https://doi.org/10.1021/acssynbio.9b00321
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‍44. Thomas R. Aunins, Kristen A. Eller, Colleen M. Courtney, Max Levy, Samuel M. Goodman, Prashant Nagpal, and, Anushree Chatterjee* (2019). Isolating the Escherichia coli transcriptomic response to superoxide generation from cadmium chalcogenide quantum dots. ACS Biomaterials Science and Engineering 5(9), 4206-4218.
doi: 10.1021/acsbiomaterials.9b01087
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‍43. Max Levy, John R. Bertram , Kristen A. Eller,, Anushree Chatterjee, Prashant Nagpal* (2019). Near-infrared light triggered antimicrobial indium phosphide quantum dots. Angewandte Chemie 58(33), 11414-11418. https://doi.org/10.1002/anie.201906501
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‍42. Max Levy, Partha P. Chowdhary, Kristen A. Eller, Anushree Chatterjee, and Prashant Nagpal* (2019). Tuning ternary Zn1-xCdxTe quantum dot composition: Engineering electronic states for light-activated superoxide generation as a therapeutic against multidrug-resistant bacteria. ACS Biomaterials Science and Engineering 5(6) 3111-3118.
doi:10.1021/acsbiomaterials.9b00524
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‍2018

41. Logan T. Collins, Peter B. Otoupal, Jocelyn K. Campos, Colleen M. Courtney, and Anushree Chatterjee* (2018). Design of a de novo aggregating antimicrobial peptide and a bacterial conjugation based delivery system. Biochemistry 58 (11), pp 1521–1526. bioRxiv 325621.
doi : 10.1021/acs.biochem.8b00888.Biochemistry special issue invitation for "The Chemistry of Synthetic Biology."

40. Gary R. Abel, Lee E. Korshoj, Peter B. Otoupal, Sajida A. Khan, Anushree Chatterjee, and Prashant Nagpal* (2019). Nucleotide and Structural Label Identification in Single RNA Molecules with Quantum Tunneling Spectroscopy. Chemical Sciences- Royal Society of Chemistry 10, 1052-1063.
doi: 10.1039/C8SC03354D

‍39. Peter B. Otoupal and Anushree Chatterjee* (2018). CRISPR gene expression perturbations for enhancing bacterial tolerance to biofuels. Frontiers in Biotechnology and Bioengineering 6:122. doi: 10.3389/fbioe.2018.00122.Invited Research Article.

38. Max Levy, Colleen M. Courtney, Partha P. Choudhary, Yuchen Ding, Emerson Grey, Samuel M. Goodman, Anushree Chatterjee, and Prashant Nagpal* (2018). Assessing Different Reactive Oxygen Species as Potential Antibiotics: Selectivity of Intracellular Superoxide Generation Using Quantum Dots. ACS Applied Bio Materials 1 (2), pp 529–537.
doi: 10.1021/acsabm.8b00292.

37. Peter B. Otoupal, William T. Cordell, Vismaya Bachu, Madeleine J. Sitton and Anushree Chatterjee* (2018). Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis. Nature Communications Biology 1:129.
doi: 10.1038/s42003-018-0135-2

36. Thomas R. Aunins, Katherine A. Marsh, Gitanjali Subramanya, Susan L. Uprichard, Alan S. Perelson, and Anushree Chatterjee* (2018). Intracellular hepatitis C modeling predicts infection dynamics and viral protein mechanisms. Journal of Virology 92(11) e02098-17.
doi:10.1128/JVI.02098-17

‍35. Samuel M. Goodman, Max Levy, Fei-Fei Li, Yuchen Ding, Colleen M. Courtney, Partha P. Chowdhury, Annette Erbse, Anushree Chatterjee, Prashant Nagpal* (2018). Designing Superoxide-Generating Quantum Dots for Selective Light-Activated Nanotherapy. Frontiers in Chemistry 6:46.
doi: 10.3389/fchem.2018.00046

‍34. Thomas R. Aunins, Keesha E. Erickson, Nripesh Prasad, Shawn E. Levy, Angela Jones, Shristi Shrestha, Rick Mastracchio, Louis Stodieck, David Klaus, Luis Zea*, Anushree Chatterjee* (2018). Spaceflight modifies Escherichia coli gene expression in response to antibiotic exposure and reveals role of oxidative stress. Frontiers in Microbiology 9:310.
doi: 10.3389/fmicb.2018.00310

‍2017

33. Dodaveri M. Sagar, Lee E. Korshoj, Katrina B. Hanson, Partha P. Choudhary, Peter B. Otoupal, Anushree Chatterjee, and Prashant Nagpal* (2018). High-Throughput Block Optical DNA Sequence Identification. Small 14 (4), 1703165.
DOI: 10.1002/smll.201703165.
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32. Colleen M. Courtney, Samuel Goodman, Toni Nagy, Max Levy, Pallavi Bhusal, Nancy E. Madinger, Corrella Detweiler, Prashant Nagpal*, and Anushree Chatterjee* (2017). Potentiating clinical drug resistant bacteria via stimuli-activated superoxide generation. Science Advances 3:e1701776.
‍DOI: 10.1126/sciadv.1701776
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31. Lee E. Korshoj, Sepideh Afsari, Anushree Chatterjee, Prashant Nagpal* (2017). Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition. The Journal of American Chemical Society 139 (43), pp 15420–15428.
DOI: 10.1021/jacs.7b08246

30. Sepideh Afsari, Lee E. Korshoj, Gary R. Abel, Sajida A. Khan, Anushree Chatterjee, Prashant Nagpal* (2017). Quantum Point Contact Single-Nucleotide Conductance for DNA and RNA Sequence Identification. ACS Nano 11 (11), pp 11169–11181.
DOI: 10.1021/acsnano.7b05500

29. Keesha E. Erickson, James D. Winkler, Danh T. Nguyen, Ryan T. Gill, and Anushree Chatterjee* (2017). The Tolerome: A database of transcriptome-level contributions to diverse Escherichia coli resistance and tolerance phenotypes. ACS Synthetic Biology 6 (12), pp 2302–2315.
DOI: 10.1021/acssynbio.7b00235. Link to database.

28. Steele Reynolds, Colleen M. Courtney, Keesha E. Erickson, Lisa Wolfe, Anushree Chatterjee, Prashant Nagpal, Ryan T. Gill* (2017). ROS Mediated Selection for Increased NADPH Availability in Escherichia coli. Biotechnology and Bioengineering 114(11) pp 2685–2689.
DOI: 10.1002/bit.26385

‍27. Keesha E. Erickson, Nancy E. Madinger, and Anushree Chatterjee* (2017). Draft genome sequences of clinical isolates of multidrug-resistant Acinetobacter baumannii.Genome Announcements 5:e01547-16. https://doi.org/10.1128/genomeA.01547-16.

26. Lee E. Korshoj, Sepideh Afsari, Sajida Khan, Anushree Chatterjee*, Prashant Nagpal* (2017). Single nucleotide DNA sequence identification using biophysical signatures from nanoelectronic quantum tunneling. Small 13(11):1603033.
DOI: 10.1002/smll.201603033

‍25. Keesha E. Erickson, Peter B. Otoupal, and Anushree Chatterjee* (2017). Transcriptome level signatures in gene expression and gene expression variability during bacterial adaptive evolution. mSphere 2:e00009-17. DOI: 10.1128/mSphere.00009-17

‍24. Peter B. Otoupal, Keesha E. Erickson, Antoni E. Bordoy, and Anushree Chatterjee* (2017). "CRISPR perturbation of gene expression alters bacterial fitness under stress and reveals underlying epistatic constraints." ACS Synthetic Biology 6 (1), pp 94–107.
DOI: 10.1021/acssynbio.6b00050. Published online August 2016.

2016

23. Antoni E. Bordoy, Usha S.Varanasi, Colleen M. Courtney and Anushree Chatterjee* (2016). "Transcriptional Interference in convergent promoters as a means for Tunable Gene Expression." ACS Synthetic Biology 5(12), 1331-1341.
DOI: 10.1021/acssynbio.5b00223.

22. Keesha E. Erickson, Nancy E. Madinger, and Anushree Chatterjee* (2016). "Draft Genome sequence for a Clinical isolate of Vancomycin resistant Enterococcus faecalis." Genome Announcements 4(3): e00584-16. doi:10.1128/genomeA.00584-16.

21. Colleen M. Courtney#, Samuel Goodman#, Jessica Mc Daniel, Nancy Madinder, Anushree Chatterjee*, and Prashant Nagpal* (2016). "Photoexcited Quantum Dots for Killing Multi-Drug Resistant Bacteria." Nature Materials 15, 529-534.
‍DOI: 10.1038/nmat4542 (Link)
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2015

20. Laetitia Canini, Jeremie Guedj, Anushree Chatterjee, Annabelle Lemenuel-Diot, Patrick F. Smith, and Alan S. Perelson* (2015), "Modeling the interaction between danoprevir and mericitabine in the treatment of chronic HCV infection." Antiviral Therapy (Advance article).
‍DOI: 10.3851/IMP3006 (Link)

19. Keesha E. Erickson, Peter B. Otoupal, and Anushree Chatterjee* (2015). "Gene expression variability underlies adaptive resistance in phenotypically heterogenous bacterial populations." ACS Infectious Diseases 1(11), pp 555-567.
‍doi:10.1021/acsinfecdis.5b00095 (Link)
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18. Antoni E. Bordoy, and Anushree Chatterjee* (2015), "cis-Antisense Transcription Gives Rise to a Tunable Genetic Switch Behavior: A Mathematical Modeling Approach." PLoS ONE 10(7): e0133873. doi:10.1371/ journal.pone.0133873. (Link)

17. Colleen M. Courtney, and Anushree Chatterjee* (2015), "Sequence-specific peptide nucleic acid based antisense inhibitors of TEM-1 beta-lactamase and mechanism of adaptive resistance." ACS Infectious Diseases 1 (6), pp 253–263.
‍doi: 10.1021/acsinfecdis.5b00042. (Link)

16. Josep Casamada Ribot, Anushree Chatterjee*, and Prashant Nagpal* (2015), "Measurements of Single nucleotide Electronic states as Nanoelectronic fingerprints for Identification of DNA Nucleobases, their Protonated and Unprotonated states, Isomers and Tautomers." The Journal of Physical Chemistry Letters B 119 (15), pp 4968–4974.
‍doi: 10.1021/acs.jpcb.5b01403. (Link)

15. Laetitia Canini#, Anushree Chatterjee#, Jeremie Guedj, Annabelle Lemenuel-Diot, Patrick F. Smith and Alan S. Perelson* (2015), “A pharmacokinetic/viral kinetic model to evaluate treatment of chronic hepatitis C virus with danoprevir.” Antiviral Therapy, 20(5):469-77.
‍doi: 10.3851/IMP2879. (Link)

2014

14. Keesha E Erickson, Ryan T Gill, and Anushree Chatterjee* (2014), "CONSTRICTOR: Constraint modification provides insight into design of biochemical networks." PLoS ONE 9(11):e113820. doi:10.1371/journal.pone.0113820. (Link)

13. Samuel Goodman, Vivek Singh, Josep C. Ribot, Anushree Chatterjee, and Prashant Nagpal* (2014). "Multiple Energy Exciton shelves in Quantum Dot-DNA Nano-bioelectronics." The Journal of Physical Chemistry Letters (5) 5, pp 3909–3913.
‍doi:10.1021/jz502058y. (Link)

12. Colleen M. Courtney and Anushree Chatterjee* (2014), “cis-Antisense RNA and Transcriptional interference: coupled layers of gene regulation.” Journal of Gene Therapy 2(1):9. (Link) (Invited Review).
‍doi: 10.13188/2381-3326.1000004

‍2013

11. Che-Chi Shu, Anushree Chatterjee, Wei-Shou Hu, and Doraiswami Ramkrishna* (2013), “Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling.” PLoS ONE 8(11): e79196. doi:10.1371/journal.pone.0079196. (Link)

10. Anushree Chatterjee#, Laura C. Cook#, Che-Chi Shu, Yuching Chen, Dawn Manias, Doraiswami Ramkrishna, Gary M. Dunny and Wei-Shou Hu* (2013), “Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer.” Proceedings of National Academy of Sciences, 110(17), 7086-7090. (Link).

9. Anushree Chatterjee, Patrick F. Smith and Alan S. Perelson* (2013), “Hepatitis C viral kinetics: the past, present and future.” Clinics in Liver Disease, 17 (1): 13-26. (Link)

8. Anushree Chatterjee#, Jeremie Guedj# and Alan S. Perelson* (2012), “Mathematical modeling of HCV infection: what can it teach us in the Direct Antiviral Agents era?” Antiviral Therapy, 17 (6 Pt B): 1171-1182. (Link).

2011

7. Anushree Chatterjee, Christopher M. Johnson, Che-Chi Shu, Yiannis N. Kaznessis, Doraiswami Ramkrishna, Gary M. Dunny and Wei-Shou Hu* (2011).“Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation.”Proceedings of the National Academy of Sciences, 108: 9721-9726. (Link)

‍6. Anushree Chatterjee, Laurie Drews, Sarika Mehra, Eriko Takano, Yiannis N. Kaznessis and Wei-Shou Hu* (2011),“Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis.” PLoS ONE, 6:e21974. (Link)

5. Christopher M Johnson, Heather Haeming, Anushree Chatterjee, Wei-Shou Hu, Keith E. Weaver, and Gary M. Dunny* (2011), “RNA-mediated reciprocal regulation between two bacterial operons is RNAse III dependent.” mBio, 2(5): e00189-11. (Link)

4. Che-Chi Shu, Anushree Chatterjee, Gary M. Dunny, Wei-Shou Hu and Doraiswami Ramkrishna* (2011), “Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance Model.” PLoS Computational Biology, 7(8):e1002140. (Link)

3. Laura CC Cook, Anushree Chatterjee, Aaron Barnes, Jeremy Yarwood, Wei-Shou Hu and GaryM. Dunny*(2011), “Biofilm growth alters regulation of conjugation by a bacterial pheromone.” Molecular Microbiology, 81(6), 1499-1510. (Link)

2008

1. Anushree Chatterjee, Yiannis N. Kaznessis and Wei-Shou Hu* (2008): “Tweaking biological switches through a better understanding of bistability behavior.” Current Opinion in Biotechnology, Tissue, cell and pathway engineering, 19:475-481. (Link)

13. Chatterjee A., Eller K.A., Campos J. Provisional Patent Application No. 62/660,130. “Bacterial Secretion System Combined with Probiotics to Deliver Antisense Therapies.” Filing date: 04/20/2018.

12. Nagpal, P., Chatterjee A., Courtney C.M., Goodman, S. New U.S. Patent Application No. 15/559,577, “Novel Light-Activated Compositions and Methods of Using the Same.” Filing date: 09/19/2017.

11. Chatterjee A., Otoupal P.B. International Patent Application No. PCT/US2017/032298. “Compositions and Methods for Altering Bacterial Fitness.” Filing date: 05/11/2017.

10. Chatterjee A., Otoupal P.B. U.S. Provisional Patent Application No. 62/334,967. “Compositions and Methods for Altering Bacterial Fitness.”

9. Nagpal, P., Chatterjee A., Courtney C.M., Goodman, S. U.S. PCT/US2016/023191 “Novel Light-Activated Compositions and Methods of Using the Same.”

‍8. Chatterjee A., Courtney C.M., U.S. PCT CU3751B-PPA1. “Sequence specific and organism specific antimicrobials and related materials and methods.”

7. Nagpal, P., Chatterjee A., Courtney C.M., Goodman, S. U.S. Provisional Patent Application No. 62/136,128. “Novel Light-Activated Compositions and Methods of Using the Same.”

6. Nagpal P., Chatterjee, A., Gold, L.. U.S. Provisional Patent Application No. 62/135,059. “Quantum Molecular Sequencing (QM-Seq): Identification of unique nanoelectronic tunneling spectroscopy fingerprints for DNA, RNA, and single nucleotide modifications.”

‍5. Chatterjee A., Courtney C.M., U.S. Provisional Patent Application No. 62/109,799. “Sequence specific and organism specific antimicrobials and related materials and methods.”

4. Nagpal P., Chatterjee A., Ribot J.C., U.S. Provisional Patent Application No. 62/089,063. “Quantum Molecular Sequencing (QM-Seq): Identification of unique nanoelectronic tunneling spectroscopy fingerprints for DNA, RNA, and single nucleotide modifications.”

3. Nagpal P., Chatterjee A., Ribot J.C. PCT/US2014/055512 “Quantum Molecular Sequencing (QM-Seq): Identification of unique nanoelectronic tunneling spectroscopy fingerprints for DNA, RNA, and single nucleotide modifications.”

2. Nagpal P., Chatterjee A., Ribot J.C., Provisional Patent Application Number: 61/877,634, “Third generation sequencing using STM-STS for fast detection of single DNA molecules and single nucleotide modifications.”

1. Chatterjee A. and Bhaskarwar, A.N., Patent no. 2427/DEL/2007, “A process of preparation of pollution preventing temperature sensitive lithographic ink composition and product thereof.”

Patents