First name: Alaksh
  Last name: Choudhury
  Function: Postdoc
  Email: alaksh.choudhury

Research interest

I am interested in developing molecular biology tools for high-throughput genome manipulation. Subsequently, I want to apply these tools for understanding protein fitness landscapes for complex regulatory proteins, and population dynamics of evolving bacteria in different genetic backgrounds and environments.



2019: Ph.D. in Chemical Engineering, University of Colorado, Boulder
2014: M.S. in Biotechnology, Northwestern University, Chicago
2011: B.E. in Industrial Biotechnology, Manipal Institute of Technology

Exhaustive list of publications


Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O
Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs.
Nature Communications 2023, 14, 6319.


Hobson CA, Cointe A, Jacquier H, Choudhury A, Magnan M, Courroux C, Tenaillon O, Bonacorsi S, Birgy A
Cross-resistance to cefiderocol and ceftazidime-avibactam in KPC β-lactamase mutants and the inoculum effect.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2021, 27, 1172.e7-1172.e10.


Choudhury A, Fankhauser RG, Freed EF, Oh EJ, Morgenthaler AB, Bassalo MC, Copley SD, Kaar JL, Gill RT
Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli.
ACS synthetic biology 2020, 9, 1083-1099.

Iwasaki RS, Ozdilek BA, Garst AD, Choudhury A, Batey RT
Small molecule regulated sgRNAs enable control of genome editing in E. coli by Cas9.
Nature Communications 2020, 11, 1394.

Liu R, Liang L, Freed EF, Choudhury A, Eckert CA, Gill RT
Engineering regulatory networks for complex phenotypes in E. coli.
Nature Communications 2020, 11, 4050.

Hobson CA, Bonacorsi S, Jacquier H, Choudhury A, Magnan M, Cointe A, Bercot B, Tenaillon O, Birgy A
KPC Beta-Lactamases Are Permissive to Insertions and Deletions Conferring Substrate Spectrum Modifications and Resistance to Ceftazidime-Avibactam.
Antimicrobial Agents and Chemotherapy 2020, 64, e01175-20.

Chen C, Choudhury A, Zhang S, Garst AD, Song X, Liu X, Chen T, Gill RT, Wang Z
Integrating CRISPR-Enabled Trackable Genome Engineering and Transcriptomic Analysis of Global Regulators for Antibiotic Resistance Selection and Identification in Escherichia coli.
mSystems 2020, 5, e00232-20.

Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT
CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli.
Molecular Systems Biology 2020, 16, e9265.