Research Highlights

We report a novel Light-Activated Nanotherapy that kills Clinically isolated Multi Drug Resistant Bacteria in manuscript led by Colleen and Sam, "Photoexcited Quantum Dots for Killing Multi-Drug Resistant Bacteria" in Nature Materials!

See media coverage

We present a novel application of CRISPR-Cas9 technology for investigating how gene expression governs the adaptive pathways available to bacteria during the evolution of resistance in Peter's paper titled, "CRISPR perturbation of gene expression alters bacterial fitness under stress and reveals underlying epistatic constraints" in ACS Synthetic biology!

We report a novel tool for synthetic biology and metabolic engineering by investigating transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters, in paper led by Toni, "Transcriptional Interference in convergent promoters as a means for Tunable Gene Expression" in ACS Synthetic biology!


We report a novel gene expression variability based approach to identify important genes involved in bacterial adaptive resistance, in paper led by Keesha, "Gene expression variability underlies adaptive resistance in phenotypically heterogenous bacterial populations" in ACS Infectious Diseases!

We report a new mathematical model that describes tunabilty of genetic switch behavior during antisense transcription, in a paper led by Toni, "cis-Antisense Transcription Gives Rise to a Tunable Genetic Switch Behavior: A Mathematical Modeling Approach" in PLoS ONE!

We report a bet-hedging based mechanism of adaptive resistance to PNA based antimicrobials in a paper led by Colleen, "Sequence-specific peptide nucleic acid based antisense inhibitors of TEM-1 beta-lactamase and mechanism of adaptive resistance" in ACS Infectious Diseases!

We reveal novel nanoelectronic fingerprints for DNA in paper led by Josep, "Measurements of Single nucleotide Electronic states as Nanoelectronic fingerprints for Identification of DNA Nucleobases, their Protonated and Unprotonated states, Isomers and Tautomers," in Journal of Physical Chemistry Letters B!

New Metabolic Flux Analysis tool CONSTRICTOR is available on Opensource

Our lab designs and reports a new FBA tool called CONSTRICTOR, in a paper led by Keesha, "CONSTRICTOR: Constraint modification provides insight into design of biochemical networks" in PLoS ONE!

Sam's paper "Multiple Energy Exciton shelves in Quantum Dot-DNA Nano-bioelectronics" is published in The Journal of Physical Chemistry Letters!

Our mathematical modeling paper on "A pharmacokinetic/viral kinetic model to evaluate treatment of chronic hepatitis C virus with danoprevir" accepted in Antiviral Therapy!

Anushree's paper on "Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer" is published in PNAS!



Our research group uses a combination of interdisciplinary approaches including chemical engineering, synthetic biology, systems biology, molecular biology, microbiology, metabolic engineering and computational biology to address key global challenges including medical and energy needs. We are interested in adopting an integrated mathematical modeling and experimental approach to investigate fundamental and medically relevant issues such as understanding the molecular mechanisms responsible for antibiotic and antiviral resistance, and for developing “next-generation smart antimicrobials” by rationally engineering novel therapeutics that target essential bacterial/viral genes in a potentially resistance-free manner. We study genetic regulatory networks that control propagation of infectious diseases, with the goal of discovering novel drug targets for therapy. Using synthetic biology tools we design, construct and engineer modular synthetic genetic devices that can achieve higher-order biological computation, for variety of biotechnological and bioenergy applications. To this end, we engineer biological parts such as transcription factors, promoter sequences, receptors, feedback loops, and regulatory RNA to build complex genetic networks that can be used to optimize cellular machinery for production of bio-fuels and pharmaceuticals, and for gene therapy applications. Using these genetic devices, we apply systems biology approaches to understand functioning of complex genetic networks and to build rules to manipulate such networks.

ABC Channel News Features our Light-activated nanotherapy against antibiotic-resistant “superbugs”!

Link to video

In the ever-escalating evolutionary battle with drug-resistant bacteria, humans may soon have a leg up thanks to adaptive, light-activated nanotherapy developed by researchers at the University of Colorado Boulder.

Antibiotic-resistant bacteria such as Salmonella, E. Coli and Staphylococcus infect some 2 million people and kill at least 23,000 people in the United States each year. Efforts to thwart these so-called “superbugs” have consistently fallen short due to the bacteria’s ability to rapidly adapt and develop immunity to common antibiotics such as penicillin.  

New research from CU-Boulder, however, suggests that the solution to this big global problem might be to think small—very small.

In findings published today in the journal Nature Materials, researchers at the Department of Chemical and Biological Engineering and the BioFrontiers Institute describe new light-activated therapeutic nanoparticles known as “quantum dots.” The dots, which are about 20,000 times smaller than a human hair and resemble the tiny semiconductors used in consumer electronics, successfully killed 92 percent of drug-resistant bacterial cells in a lab-grown culture.....

- See more at:

Lab launches start up company PRAAN Biosciences based on novel Quantum Molecular Sequencing technology


Nagpal and Chatterjee labs are the co-founders of PRAAN Biosciences, Inc., a Boulder, Colorado-based startup based on a novel sequencing technology called "Quantum Molecular Sequencing" that can sequence genetic profiles using just a single molecule, technology that may aid in the diagnosis and treatment of superbug strains as well as genetic disorders and cancer. The authors have filed number of patents on the new technology. PRAAN in Sankrit means "river of life." CU Technology Transfer Office also has recongnized Quantum Molecular Sequencing technology developed by our and Nagpal lab with the New Inventor of the Year award. We are developing a platform technology for fast, reliable, high-throughput and cost effective single molecule sequencing of nulciec acids.This kind of sequencing is an important step in the developement of new diagnostic tools for personalized medicine and infectious disease diagnostics.



Peter's paper on "CRISPR perturbation of gene expression alters bacterial fitness under stress and reveals underlying epistatic constraints" is published in ACS Synthetic Biology. Congrats!

Lab's Quantum dot antibiotic research featured by reporter Shelley Schlender on 88.5 FM KGNU Science Show "How on Earth." See KGNU Link

Hear The Podcast

Toni's paper on "Transcriptional Interference in convergent promoters as a means for Tunable Gene Expression" is published in ACS Synthetic Biology. Congrats!

Quantum dot antibiotic work highlighted in MRS Bulletin!

See MRS Bulletin Link

Quantum dot antibiotic work featured in France's Tech 24 TV show!

See Tech24 Link

Vismaya and Pallavi recieve UROP awards to pursue research. Congrats!

Keesha recieves NSF-EAPSI Fellowship to conduct collaborative research. Congrats!

Lee recieves GAANN fellowship. Congrats!

Our Light Activated Nanotherapy featured in ABC's Denver Channel 7 News! Link to video

Sepideh and Sajida join lab as postdoctoral fellows. Welcome!

New graduate students Lee, Partha join Chatterjee Lab. Welcome!

Keesha wins Dean's Graduate Student Research Grant for discovery of novel drug targets for treating MDR infections. Congrats!

Anushree presents five talks on synthetic biology, antimicrobial adaptive resistance, and strategies for novel therapeutics for MDR bacterial infections at AIChE 2015 conference.

Our paper featured in the Gram Negative Issue of ACS Infectious Disease! See Link

Anushree gives an invited talk at the Department of Integrative Biology at University of Colorado Denver

Our lab recieves funding from Agilent Technologies!

Anushree gives an invited talk at the Q-Bio 2015 Summer School

Keesha wins Graduate School Domestic Travel grant. Congrats!

Group bids farewell to Usha. Usha joins BASF as a research scientist! Congratulations and best wishes!

Peter wins National Science Foundation Graduate Fellowship. Congratulations!

Upcoming talks of the Chatterjee Lab in ACS Spring 2015 Meeting. AE, CMCa, CMCb, JCR, KEEa, KEEb, POa, POb, SGa, SGb.

Our lab recieves prestigious William M. Keck Foundation research award! Keck Foundation | ChBE News | CU Engineering News

Chatterjee and Nagpal labs co-found start-up company PRAAN Biosciences. An exciting journey begins!

Chatterjee lab High School student gives TEDx Mile High Talk

Shakira and Emma recieve UROP fellowship. Congrats!

Dr. Chatterjee and Dr. Nagpal are named New Inventors of the Year for developing the Quantum Molecular Sequencing platform technology...... Read more

Chatterjee Lab high school student Logan Collins wins numerous awards .... Read more


Read more


William M. Keck Foundation

Agilent Technologies

National Science Foundation

National Insitute of Health

University of Colorado


Department of Chemical and Biological Engineering

BioFrontiers Insititute

PRAAN Biosciences

Get in Touch

  • Phone/Fax:
    (303)7356586/ (303)4928425
  • Email:
  • Address:
    3415 Colorado Avenue
    596 UCB, Boulder
  • CO 80303, USA