*Corresponding author(s), #Equal contribution

48. Thomas R. Aunins#, Keesha E. Erickson#, Anushree Chatterjee* (2019). Transcriptome-based design of antisense inhibitors re-sensitizes CRE E. coli to carbapenems. (Submitted). bioRxiv

47. Kristen A. Eller#, Thomas R. Aunins#, Colleen M. Courtney, Jocelyn K. Campos, Peter B. Otoupal, Keesha E. Erickson, Nancy E. Madinger, and Anushree Chatterjee* (2019). Facile Accelerated Specific Therapeutic (FAST) Platform to Counter Multidrug-Resistance Bacteria. (Submitted). bioRxiv

46. Peter B. Otoupal, Keesha E. Erickson, Kristen A. Eller, Jocelyn K. Campos, Thomas R. Aunins, Anushree Chatterjee* (2019). Potentiating antibiotic treatment using fitness-neutral gene expression perturbations. (Submitted). bioRxiv

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

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

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

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

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 epistasisNature Communications Biology 1:129. doi: 10.1038/s42003-018-0135-2

See press coverage: University of Colorado press release- How to stop an antibiotic-resistant superbug, Phys.Org, Scicasts, Science Daily, Todaychan.com, Australia Remonews.com, EurekAlert, News Medical, Tech Explorist, Naava.org, Daily World News, Nature Antimicrobial Resistance, FirstPost, Drug Target Review, Wakajobs, News Archive UK, UK Remo News, R&D Magazine, NM News Magazine, Exponential Technology, Udaipur KiranInnovation NewsQuartz, Patch.com, Daily Camera, Denver Post, BioNews.

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

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.

See press coverage: University of Colorado Press Release (Link), Phys.Org (Link), Health Unlocked (Link), Global News Connect (Link)Buffzone (Link), NewsWise (Link), Health & Medicine News (Link), Science Daily (Link).

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

See press coverage: BBC News, Newsweek, Science NewsCenter for Infectious Disease Research and Policy (CIDRAP)University of Colorado Boulder press release,ResearchGate News, IEEE SpectrumNanotechWebEurekAlert!Nanowerk,Phys.orgScience DailyFuturism, Drug Discovery and Development,CourthousenewsLavanguardia,El Pais,Azo NanoteckcrispyEl observerUltimahoraGears of BizLaboratory talkChemEuropeBionity,Science Alert,CEmagNewswiseNews Medical LifesciencesTechnology.org., International Business TimesmsnZapScience SpringsOptics and PhotonicsScience TrendsTrue viral NewsScience SpringsThe Surg.

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

See press coverage: University of Colorado Press Release (Link), Phys.Org (Link), Health Unlocked (Link), Global News Connect (Link)Buffzone (Link), NewsWise (Link), Health & Medicine News (Link), Science Daily (Link).

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

See press coverage: University of Colorado Press Release (Link), Phys.Org (Link), Health Unlocked (Link), Global News Connect (Link)Buffzone (Link), NewsWise (Link), Health & Medicine News (Link), Science Daily (Link).

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.7b00235Link 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.

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

See press coverage: Voice of America (Link), ABC's Denver Channel 7 News (Link), National Science Foundation News Highlight (Link), University of Colorado press release (Link), Material Research Society (Link), Infectious Disease New (Link), Boston Global Media (Link), Huffington Post (Link), ChBE Highlight (Link), TImes of India (Link), Zee News (Link), Yahoo News (Link), Popular Mechanics (Link), Big News Network (Link), Sciencedaily (Link), Phy.Org (Link), Eurekalert (Link), Tech News Now (Link), Jersey Tribune (Link), Bioportfolio (Link), Wn.com (Link), Science Alert (Link), Science Newsline, News Wise (Link), News Headline Spot (Link), Science News (Link), Quantum Times (Link), Bristish Society of Nanomedicine (Link), Nanowerk (Link), Innivation Toronto (Link), ZME Science (Link), Inverse (Link), ScienMag (Link), News Medical (Link), Tech Times (Link), Business Standard (Link), IndiaNewEngland (Link), GizMag (Link), BGR  (Link), RT (Link), Medical Daily (Link), International News Coverage: Indain Media (TImes of India (Link), Frontier Mail (Link)), British Media (Daily Mail (Link)), Spanish Media (Lainformacion (Link), elEconomista.es (Link)Quo.es (Link)) , Russian Media (ACLP.ru (Link))), Australian Media (Big News Network(Link)) Armenian Media (NEWS.am (Link)), German Media (Trendsderzukunft (Link))

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)
Selected for Gram negative issue of ACS Infectious Disease
Featured in Gram negative issue of ACS Infectious Disease (Link)

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 4968–4974doi: 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)

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

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).7. 

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)

Article press

  1. Selected and evaluated the Faculty of 1000 (F1000) as top 2% of published articles in biology and medicine (http://f1000.com/11331957)
  2. Featured in “University of Minnesota News.”http://www1.umn.edu/news/features/2011/UR_CONTENT_343890.html
  3. Featured in Hutchinson Leader, Minnesota, http://www.hutchinsonleader.com/view/full_story/14491407/article-U-of-M-researchers-to-pathogenic-bacteria--Resistance-is-futile

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 Microbiology81(6), 1499-1510. (Link)

2. Che-Chi Shu, Anushree Chatterjee, Wei-Shou Hu and Doraiswami Ramkrishna* (2012), “Modeling of Gene regulatory processes by Population mediated Signaling. New applications of Population balances.” Chemical Engineering Science, 70: 188-199. (Link)

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)

Patents

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.”