1. Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides
    Amir Pandi, David Adam, Amir Zare, Van Tuan Trinh, Stefan L Schaefer, Marie Burt, Björn Klabunde, Elizaveta Bobkova, Manish Kushwaha, Yeganeh Foroughijabbari, and  others
    Nature Communications, 2023


  1. Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts
    Angelo Cardoso Batista, Antoine Levrier, Paul Soudier, Peter L Voyvodic, Tatjana Achmedov, Tristan Reif-Trauttmansdorff, Angelique DeVisch, Martin Cohen-Gonsaud, Jean-Loup Faulon, Chase L Beisel, and  others
    ACS synthetic biology, 2022
  2. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering
    Joan Hérisson, Thomas Duigou, Melchior Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El Moubayed, Pablo Carbonell, Neil Swainston, and  others
    Nature Communications, 2022
  3. Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates
    Mahnaz Sabeti Azad, Angelo Cardoso Batista, Jean-Loup Faulon, Chase L Beisel, Jerome Bonnet, and Manish Kushwaha
    Journal of visualized experiments: JoVE, 2022
  4. PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H 2 O 2 as Signal Integrator
    Paul Soudier, Ana Zúñiga, Thomas Duigou, Peter L Voyvodic, Kenza Bazi-Kabbaj, Manish Kushwaha, Julie A Vendrell, Jerome Solassol, Jerome Bonnet, and Jean-Loup Faulon
    ACS synthetic biology, 2022
  5. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima
    Paul Soudier, Daniel Rodriguez Pinzon, Tristan Reif-Trauttmansdorff, Hassan Hijazi, Maëva Cherrière, Cátia Goncalves Pereira, Doriane Blaise, Maxime Pispisa, Angelyne Saint-Julien, William Hamlet, and  others
    Synthetic and systems biotechnology, 2022
  6. Cell-Free Biosensors and AI Integration
    Paul Soudier, Léon Faure, Manish Kushwaha, and Jean-Loup Faulon
    Methods in molecular biology (Clifton, NJ), 2022
  7. A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission
    Amit Pathania, Corbin Hopper, Amir Pandi, Matthias Függer, Thomas Nowak, and Manish Kushwaha
    bioRxiv, 2022


  1. Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs
    Jacob Beal, Geoff S Baldwin, Natalie G Farny, Markus Gershater, Traci Haddock-Angelli, Russell Buckley-Taylor, Ari Dwijayanti, Daisuke Kiga, Meagan Lizarazo, John Marken, and  others
    PloS one, 2021
  2. Optimising protein synthesis in cell-free systems, a review
    Angelo C Batista, Paul Soudier, Manish Kushwaha, and Jean-Loup Faulon
    Engineering Biology, 2021
  3. Reaching Agreement in Competitive Microbial Systems
    Victoria Andaur, Janna Burman, Matthias Függer, Manish Kushwaha, Bilal Manssouri, Thomas Nowak, and Joel Rybicki


  1. Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics
    Roberto Galizi, John N Duncan, William Rostain, Charlotte M Quinn, Marko Storch, Manish Kushwaha, and Alfonso Jaramillo
    The CRISPR journal, 2020
  2. Digital circuit design for biological and silicon computers
    Matthias Függer, Manish Kushwaha, and Thomas Nowak
    Advances in Synthetic Biology, 2020


  1. Metabolic perceptrons for neural computing in biological systems
    Amir Pandi, Mathilde Koch, Peter L Voyvodic, Paul Soudier, Jerome Bonnet, Manish Kushwaha, and Jean-Loup Faulon
    Nature communications, 2019
  2. Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in Trypanosoma brucei
    James Budzak, Louise E Kerry, Aris Aristodemou, Belinda S Hall, Kathrin Witmer, Manish Kushwaha, Carys Davies, Megan L Povelones, Jacquelyn R McDonald, Aakash Sur, and  others
    Proceedings of the National Academy of Sciences of the United States of America, 2019


  1. Quantification of bacterial fluorescence using independent calibrants
    Jacob Beal, Traci Haddock-Angelli, Geoff Baldwin, Markus Gershater, Ari Dwijayanti, Marko Storch, Kim Mora, Meagan Lizarazo, Randy Rettberg, and  others
    PloS one, 2018


  1. Using RNA as Molecular Code for Programming Cellular Function
    Manish Kushwaha, William Rostain, Satya Prakash, John N Duncan, and Alfonso Jaramillo
    ACS synthetic biology, 2016
  2. Functionalization of an Antisense Small RNA
    Guillermo Rodrigo, Satya Prakash, Teresa Cordero, Manish Kushwaha, and Alfonso Jaramillo
    Journal of molecular biology, 2016


  1. A portable expression resource for engineering cross-species genetic circuits and pathways
    Manish Kushwaha, and Howard M Salis
    Nature communications, 2015
  2. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei
    Tara Stanne, Mani Shankar Narayanan, Sophie Ridewood, Alexandra Ling, Kathrin Witmer, Manish Kushwaha, Simone Wiesler, Bill Wickstead, Jennifer Wood, and Gloria Rudenko
    The Journal of biological chemistry, 2015


  1. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
    Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard M Salis
    Molecular systems biology, 2014


  1. TbISWI regulates multiple polymerase I (Pol I)-transcribed loci and is present at Pol II transcription boundaries in Trypanosoma brucei
    Tara M Stanne, Manish Kushwaha, Matthew Wand, Jesse E Taylor, and Gloria Rudenko
    Eukaryotic cell, 2011
  2. NLP is a novel transcription regulator involved in VSG expression site control in Trypanosoma brucei
    Mani Shankar Narayanan, Manish Kushwaha, Klaus Ersfeld, Alexander Fullbrook, Tara M Stanne, and Gloria Rudenko
    Nucleic acids research, 2011


  1. TbISWI and its role in transcriptional control in Trypanosoma brucei
    Manish Kushwaha
    Oxford University, UK, 2010


  1. Computational analysis of Entamoeba histolytica genome-Exploring junk DNA for hidden messages