Manish Kushwaha

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Publications

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Intercellular DNA Communication for Bio-Computation in Synthetic Bacterial Consortia

Manish Kushwaha

Synthetic Biology: Engineering, Evolution, & Design Meeting (SEED 2025), Society for Biological Engineering (SBE), American Institute of Chemical Engineers (AIChE), Jun 2025, Houston, TX, United States

Communication dans un congrès hal-05139381v1

Bacterial multi-cellular computing using intercellular DNA communication

Manish Kushwaha

FEMS MICRO Milan 2025, Federation of European Microbiological Societies, Jul 2025, Milan, Italy

Communication dans un congrès hal-05165090v1

Building multicellular bacterial circuits using phages for communication

Manish Kushwaha

Global Open Genetic Engineering Competition 2024, Feb 2024, Online, United States

Communication dans un congrès hal-04699392v1

Synthetic Multi-cellular Circuits in Bacteria Using Engineered Phages for Cell-to-Cell Communication

Manish Kushwaha

Synthetic Biology Young Speaker Series (SynBYSS), Sep 2024, Online, United States

Communication dans un congrès hal-04699423v1

Multi-cellular Circuits in Bacteria Using Engineered Phages for Synthetic Cell-to-Cell Communication

Abhinav Pujar , Amit Pathania , Manish Kushwaha

Symposium on Synthetic and Systems Biology 2024 (BioSynSys), Jun 2024, Montpellier, France

Communication dans un congrès hal-04699415v1
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Information processing circuits in cell-free systems: beyond gene expression regulation

Manish Kushwaha , Amir Pandi , Mathilde Koch , Paul Soudier , Angelo Cardoso Batista et al.

International Conference on Engineering Synthetic Cells and Organelles, May 2023, Minneapolis, MN, USA, United States

Communication dans un congrès hal-04563028v1

Synthetic Multi-cellular Circuits in Bacteria Using Engineered Phages for Cell-to-Cell Communication

Manish Kushwaha , Abhinav Pujar , Amit Pathania , Corbin Hopper , Roman Luchko et al.

Synthetic Biology UK 2023, Biochemical Society, Nov 2023, Bristol, United Kingdom

Communication dans un congrès hal-04699371v1
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Exonuclease-deficient cellular extracts for cell-free expression from linear DNA templates

Manish Kushwaha

Build-a-Cell seminar series (online), Aug 2022, online, United States

Communication dans un congrès hal-04563088v1

Designing synthetic intercellular communication in bacterial cultures

Manish Kushwaha

Assises du département MICA, May 2022, Biarritz, France

Communication dans un congrès hal-04563478v1
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The Thinking Dead: using cell-free systems for decision-making circuits

Manish Kushwaha

International Genetic Engineering Machine (iGEM) French Meetup 2021, 9 French iGEM teams 2021, Sep 2021, Paris (online), France

Communication dans un congrès hal-04563148v1
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Bacteriophages for intercellular communication in bacterial cultures

Manish Kushwaha

Séminaire Bioss, Dec 2021, Online, France

Communication dans un congrès hal-04563183v1

The Galaxy-SynBioCAD portal: tools and workflows for synthetic biology and metabolic engineering

Thomas Duigou , Joan Hérisson , Jean-Loup Faulon , Guillaume Gricourt , Kenza Bazi Kabbaj et al.

Journées du PEPI IBIS 2021, Nov 2021, Toulouse, France

Communication dans un congrès hal-04355490v1

Biological Design and Engineering By and For machine Learning

Léon Faure , Manish Kushwaha , Thomas Duigou , Jean-Loup Faulon

Engineering, Evolution & Design (SEED), AICHE, Jun 2021, Vitual, United States

Communication dans un congrès hal-04275493v1
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Distributed Computation with Continual Population Growth

Da-Jung Cho , Matthias Függer , Corbin Hopper , Manish Kushwaha , Thomas Nowak et al.

DISC 2020 - 34th International Symposium on DIStributed Computing, 2020, virtual, Germany. p. 1-17, ⟨10.4230/LIPIcs.DISC.2020.6⟩

Communication dans un congrès hal-02946883v1
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Tutorial On Computing In Synthetic Biology

Manish Kushwaha

CELLS: Workshop on Computing among Cells 2019, International Symposium on DIStributed Computing (DISC), Oct 2019, Budapast, Hungary

Communication dans un congrès hal-04563112v1
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Metabolic Perceptrons for Neural Computing in Cell Free Systems

Amir Pandi , Mathilde Koch , Peter Voyvodic , Paul Soudier , Jerome Bonnet et al.

AIChE Cell Free Systems Conference, American Institute of Chemical Engineers (AIChE), Dec 2019, Boston (MA), United States

Communication dans un congrès hal-04563371v1

Exploiting bacteriophage-derived signals as external wires for biological computing

Manish Kushwaha

Highly Constrained Discrete Agents for Modeling Natural Systems, Working Group HicDiesMeus, Nov 2018, Paris, France

Communication dans un congrès hal-04563263v1
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Reconstituting alternative life using the test-bed of cell-free systems

Maud Hofmann , Farouk Abdo , Olivier Borkowski , Manish Kushwaha

Philosophical Transactions of the Royal Society B: Biological Sciences, In press, 380 (1936), pp.20240293. ⟨10.1098/rstb.2024.0293⟩

Article dans une revue (article de synthèse) hal-05027262v1
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Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia

Abhinav Pujar , Amit Pathania , Corbin Hopper , Amir Pandi , Cristian Ruiz Calderón et al.

Nucleic Acids Research, In press, pp.gkae1256. ⟨10.1093/nar/gkae1256⟩

Article dans une revue hal-04857279v1
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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 et al.

Nature Communications, 2023, 14 (1), pp. 7197. ⟨10.1038/s41467-023-42434-9⟩

Article dans une revue hal-04278003v1
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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 , Jérôme Bonnet et al.

Journal of visualized experiments : JoVE, In press, ⟨10.3791/64236⟩

Article dans une revue hal-03748754v1
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Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

Paul Soudier , Daniel Rodriguez Pinzon , Tristan Reif-Trauttmansdorff , Hassan Hijazi , Maëva Cherrière et al.

Synthetic and Systems Biotechnology, 2022, 7 (2), pp.791-801. ⟨10.1016/j.synbio.2022.03.003⟩

Article dans une revue hal-03626102v1
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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Joan Hérisson , Thomas Duigou , Melchior Du Lac , Kenza Bazi-Kabbaj , Mahnaz Sabeti Azad et al.

Nature Communications, 2022, 13 (1), pp.5082. ⟨10.1038/s41467-022-32661-x⟩

Article dans une revue hal-03649340v2
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PeroxiHUB : a modular cell-free biosensing platform using H2O2 as signal integrator

Paul Soudier , Ana Zúñiga , Thomas Duigou , Peter Voyvodic , Kenza Bazi-Kabbaj et al.

ACS Synthetic Biology, 2022, 11 (8), pp 2578-2588. ⟨10.1021/acssynbio.2c00138⟩

Article dans une revue hal-03649349v2
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Distributed computation with continual population growth

Da-Jung Cho , Matthias Függer , Corbin Hopper , Manish Kushwaha , Thomas Nowak et al.

Distributed Computing, 2021, ⟨10.1007/s00446-021-00404-8⟩

Article dans une revue hal-03519002v1
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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 et al.

PLoS ONE, 2021, 16 (6), pp.e0252263. ⟨10.1371/journal.pone.0252263⟩

Article dans une revue hal-03545776v1
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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 et al.

ACS Synthetic Biology, 2021, pp.acssynbio.1c00448. ⟨10.1101/2021.09.07.459228⟩

Article dans une revue hal-03545788v1
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Optimising protein synthesis in cell‐free systems, a review

Angelo C Batista , Paul Soudier , Manish Kushwaha , Jean‐loup Faulon

Engineering Biology, 2021, 5 (1), pp.10-19. ⟨10.1049/enb2.12004⟩

Article dans une revue (article de synthèse) hal-03545761v1
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Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics

Roberto Galizi , John N Duncan , William Rostain , Charlotte M Quinn , Marko Storch et al.

The Crispr Journal, 2020, 3 (5), pp.398-408. ⟨10.1089/crispr.2020.0029⟩

Article dans une revue hal-03545565v1
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Metabolic perceptrons for neural computing in biological systems

Amir Pandi , Mathilde Koch , Peter L. Voyvodic , Paul Soudier , Jérôme Bonnet et al.

Nature Communications, 2019, 10 (1), pp.1-13. ⟨10.1038/s41467-019-11889-0⟩

Article dans une revue hal-02275517v1
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Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in <em>Trypanosoma brucei</em>

James Budzak , Louise E. Kerry , Aris Aristodemou , Belinda S. Hall , Kathrin Witmer et al.

Proceedings of the National Academy of Sciences of the United States of America, 2019, ⟨10.1073/pnas.1905552116⟩

Article dans une revue hal-02627270v1

Quantification of bacterial fluorescence using independent calibrants

Jacob Beal , Traci Haddock-Angelli , Geoff Baldwin , Markus Gershater , Ari Dwijayanti et al.

PLoS ONE, 2018, 13 (6), pp.e0199432. ⟨10.1371/journal.pone.0199432⟩

Article dans une revue hal-04415924v1
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Functionalization of an antisense small RNA

Guillermo Rodrigo , Satya Prakash , Teresa Cordero , Manish Kushwaha , Alfonso Jaramillo

Journal of Molecular Biology, 2016, 428 (5, Part B), pp.889-892. ⟨10.1016/j.jmb.2015.12.022⟩

Article dans une revue hal-02633553v1
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Using RNA as molecular code for programming cellular function

Manish Kushwaha , William Rostain , Satya Prakash , John N. Duncan , Alfonso Jaramillo

ACS Synthetic Biology, 2016, 5 (8), pp.795-809. ⟨10.1021/acssynbio.5b00297⟩

Article dans une revue (article de synthèse) hal-02637711v1
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A portable expression resource for engineering cross-species genetic circuits and pathways

Manish Kushwaha , Howard M. Salis

Nature Communications, 2015, 6, pp.1-11. ⟨10.1038/ncomms8832⟩

Article dans une revue hal-01860861v1
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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 et al.

Journal of Biological Chemistry, 2015, 290 (45), pp.26954-26967. ⟨10.1074/jbc.M115.679019⟩

Article dans une revue hal-04559158v1
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Identification of the ISWI chromatin remodeling complex of the early branching eukaryote Trypanosoma brucei

Tara M. Stanne , Mani Shankar Narayanan , Sophie Ridewood , Alexandra Ling , Kathrin Witmer et al.

Journal of Biological Chemistry, 2015, 290 (45), pp.26954-26967. ⟨10.1074/jbc.M115.679019⟩

Article dans une revue hal-01860866v1
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Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

Iman Farasat , Manish Kushwaha , Jason Collens , Michael Easterbrook , Matthew Guido et al.

Molecular Systems Biology, 2014, 10 (6), pp.1-18. ⟨10.15252/msb.20134955⟩

Article dans une revue hal-01860867v1
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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 et al.

Nucleic Acids Research, 2011, 39 (6), pp.2018-2031. ⟨10.1093/nar/gkq950⟩

Article dans une revue hal-01860869v1
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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 , Gloria Rudenko

Eukaryotic Cell, 2011, 10 (7), pp.964-976. ⟨10.1128/EC.05048-11⟩

Article dans une revue hal-01860860v1
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Cell-Free Biosensors and AI integration

Paul Soudier , Léon Faure , Manish Kushwaha , Jean-Loup Faulon

Cell-Free Gene Expression, 2433, Springer US, pp.303-323, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1998-8_19⟩

Chapitre d'ouvrage hal-03545753v1
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Digital Circuit Design for Biological and Silicon Computers

Matthias Függer , Manish Kushwaha , Thomas Nowak

Advances in Synthetic Biology, Springer Singapore, pp.153-171, 2020, ⟨10.1007/978-981-15-0081-7_9⟩

Chapitre d'ouvrage hal-02549707v1