Chatterjee Lab

Research Highlights

We report using Quantum dot antibiotics to potentiate antibiotics in highly drug-resistant clinical isolates in paper "Potentiating clinical drug resistant bacteria via stimuli-activated superoxide generation" published in Science Advances.

See media coverage

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 report the first database that can mine gene expression data sets to identify key players of adaptive resistance in bacteria. "The Tolerome: A database of transcriptome-level contributions to diverse Escherichia coli resistance and tolerance phenotypes." published in ACS Synthetic Biology.

Link to database

We are pleased to report a new systems bology approach to mine and identify key gene signatures in complex gene expression data sets in our publication "Transcriptome level signatures in gene expression and gene expression variability during bacterial adaptive evolution," in mSphere.

We are pleased to report four publications on novel single-molecule sequencing methods in 2017! These publications can be found in ACS Nano, JACS, and Small.

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 synthetic biology, systems biology, microbiology, and nanoengineering to address the key global challenge involving antimicrobial resistance. We aim at developing strategies for rationally engineering next-generation smart antimicrobials that can eliminate multi-drug resistant superbugs, with the ultimate goal of creating therapies that can evade evolution of drug-resistance in microbes. To this end, we are also interested in investigating the non-genetic mechanisms responsible for antimicrobial tolerance/resistance to devise strategies that can one day prevent evolution of drug resistance. Using synthetic biology tools we are also interested in designing, constructing and engineering modular synthetic genetic devices based on less-explored naturally occurring mechanisms, for both understanding fundamentally how nature works as well as built devices for potential biotechnological applications.

Anushree speaks at Institute of Systems Biology's Future of Health Symposium


SESSION 3: PREVENTION AND THERAPY Anushree Chatterjee, PhD | University of Colorado at Boulder "From Synthetic Biology to Nanobiotechnology: Rational Antimicrobial Engineering Approaches for Combating Multidrug-Resistant Pathogens"

BBC features our Quantum dot antibiotic research!

CGTN America features our lab's research

MSN, Newsweek, Science News, CIDRAP features our work on potentiating drug-resistant clinical bacteria to antibiotics

BOULDER, COLORADO —Light-activated nanoparticles, also known as quantum dots, can provide a crucial boost in effectiveness for antibiotic treatments used to combat drug-resistant superbugs such as Ecoli and Salmonella, new CU Boulder research shows......Read article

UC Health features our research on combating antibiotic resistance

Todd Neff for UC Health- DENVER, CO. Science can border on science fiction. Designing swarms of infinitesimal semiconductors that, shined with green light, turn standard oxygen into a superoxide that makes life hell for drug-resistant bacteria – that qualifies..... Link to article

Voice of America features our Quantum dot based Antibiotic research

BOULDER, COLORADO — Scientists have been creating antibiotics to kill deadly bacteria for nearly 80 years. Unfortunately, the bacteria that cause disease can adapt so quickly, some have evolved into superbugs that are resistant to all antibiotics, and making new drugs is a long, expensive, involved process.... Read article

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 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 Sanskrit 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 nucleic acids.This kind of sequencing is an important step in the developement of new diagnostic tools for personalized medicine and infectious disease diagnostics.



Peter successfully defends his Ph. D. and becomes Dr. Peter Otoupal! Peter will move on to his new post-doc position at Sandia National Lab starting August. Many congratulations Peter!

Peter's paper "CHAOS: Deterring Bacterial Adaptation via Epistatic Gene Expression Perturbations"is accepted in Nature Communications Biology! Congrats!

Anushree nominated as "Rising Stars" by the journal Frontiers of Chemistry!

Peter wins Excellence in Graduate student research award from ChBE department. Congrats!

Will Cordell wins Marilyn and Howard L. Anseth Outstanding Undergraduate Research Award and Outstanding Undergraduate Research Awards ‐Gold medal. Congrats!

Kristen and Tom recieve NSF GRFP Honorable mentions. Congrats!

Anushree receives ACS Infectious Diseases Young Investigator Award!

Anushree becomes Associate Editor of Frontiers in Bioengineering and Biotechnology.

BBC features our Quantum dot antibiotic research! Link to article

Tom's paper "Intracellular hepatitis C modeling predicts infection dynamics and viral protein mechanisms" published in Journal of Virology. Congrats Tom!

Tom's paper "Spaceflight modifies Escherichia coli gene expression in response to antibiotic exposure and reveals role of oxidative stress" is published in Frontiers in Microbiology. Congrats Tom!

University of Colorado Health features our research to combat antibiotic resistance! Link to article.

Peter wins third place in Stars symposium. Congrats!

Lee's paper on "Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition" published in JACS. Congratulations!

Keesha's paper on "The Tolerome: A database of transcriptome-level contributions to diverse Escherichia coli resistance and tolerance phenotypes" published in ACS Syn Bio. Congratulations!

Our potentiating antibiotics paper in Science Advances receives press coverage including Center for Infectious Disease Research and Policy (CIDRAP), University of Colorado Boulder press release, ResearchGate News, IEEE Spectrum, NanotechWeb, EurekAlert!, Nanowerk, Newsweek. See additional press coverage.

Colleen's paper on "Potentiating clinical drug resistant bacteria via stimuli-activated superoxide generation" published in Science Advances. Congratulations!

Sepideh's paper "Quantum Point Contact Single-Nucleotide Conductance for DNA and RNA Sequence Identification" published in ACS Nano. Congratulations!

Colleen moves on to her new post-doc position at Sandia National Lab at Livermore. Congratulations and all the best!

Anushree receives grant funding from National Science Foundation!

Colleen successfully defends her Ph.D., and becomes Dr. Courtney!! Congratulations!!

Colleen recieves Max Peters Outstanding Graduate Student Award. Congratulations!

Keesha successfully defends her Ph.D. and becomes Dr. Erickson! Keesha moves on to pursue postdoctoral research at Los Alamos National Laboratory. Congratulations and all the best!!

Anushree recieves DARPA Young Faculty Award! Link

Lee wins NSF Graduate Fellowship. Congratulations! Link

Keesha's paper on "Transcriptome level signatures in gene expression and gene expression variability during bacterial adaptive evolutionpublished in mSphere. Congrats!

Voice of America features our Quantum Dot Antibiotic work in article, "Tiny Robots May Someday Fight Superbugs Inside Our Bodies"


Colleen won 2nd place at the 9th Annual Bionanotechnology Graduate Student Award Session at AIChE. Her award talk was titled “Photoexcited Quantum Dots Potentiate Antibiotic Activity in Multidrug-Resistant Bacteria”. Congrats Colleen! Link

Lee's paper titled "Single nucleotide DNA sequence identification using biophysical signatures from nanoelectronic quantum tunneling" published in Small. Congrats Lee!

Colleen wins Best Poster Award from the Biochemical Engineering Journal and the AIChE Food, Pharmaceutical and Bioengineering Division for her work titled, "Sequence Specific Antisense Inhibitors of Non-Traditional Antibiotic Pathways." Congrats Colleen! Link

Anushree recognized as one of the most highly prolific authors for ACS Infectious Diseases! Link

Sam Goodman defends his Ph.D. and moves on to a postdoctoral fellow position at the National Academy of Sciences. Congrats Sam!

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 Peter!

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 Toni!

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 Keesha!

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



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W. M. Keck Foundation

Defense Advanced Research Program Agency

National Science Foundation

University of Colorado


Department of Chemical and Biological Engineering

BioFrontiers Insititute

Get in Touch

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