Manish Kushwaha

Publications

Chapitre d'ouvrage (3)

Benefit and cost of a protein Manish Kushwaha,Wolfram Liebermeister,Elad Noor,Kirill Sechkar,Diana Széliová Economic Principles in Cell Biology, Zenodo, 2026, ⟨10.5281/zenodo.17955349⟩ Chapitre d'ouvrage hal-05570055v1
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
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

Communication dans un congrès (17)

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
Information processing circuits in cell-free systems: beyond gene expression regulation Manish Kushwaha,Amir Pandi,Mathilde Koch,Paul Soudier,Angelo Cardoso Batistaet 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 Luchkoet al. Synthetic Biology UK 2023, Biochemical Society, Nov 2023, Bristol, United Kingdom Communication dans un congrès hal-04699371v1
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
Bacteriophages for intercellular communication in bacterial cultures Manish Kushwaha Séminaire Bioss, Dec 2021, Online, France Communication dans un congrès hal-04563183v1
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
The Galaxy-SynBioCAD portal: tools and workflows for synthetic biology and metabolic engineering Thomas Duigou,Joan Hérisson,Jean-Loup Faulon,Guillaume Gricourt,Kenza Bazi Kabbajet 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
Distributed Computation with Continual Population Growth Da-Jung Cho,Matthias Függer,Corbin Hopper,Manish Kushwaha,Thomas Nowaket 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
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
Metabolic Perceptrons for Neural Computing in Cell Free Systems Amir Pandi,Mathilde Koch,Peter Voyvodic,Paul Soudier,Jerome Bonnetet 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

Article dans une revue (23)

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
Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia Abhinav Pujar,Amit Pathania,Corbin Hopper,Amir Pandi,Cristian Ruiz Calderónet al. Nucleic Acids Research, In press, pp.gkae1256. ⟨10.1093/nar/gkae1256⟩ Article dans une revue hal-04857279v1
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 Schaeferet al. Nature Communications, 2023, 14 (1), pp. 7197. ⟨10.1038/s41467-023-42434-9⟩ Article dans une revue hal-04278003v1
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 Bonnetet al. Journal of visualized experiments : JoVE, In press, ⟨10.3791/64236⟩ Article dans une revue hal-03748754v1
Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima Paul Soudier,Daniel Rodriguez Pinzon,Tristan Reif-Trauttmansdorff,Hassan Hijazi,Maëva Cherrièreet al. Synthetic and Systems Biotechnology, 2022, 7 (2), pp.791-801. ⟨10.1016/j.synbio.2022.03.003⟩ Article dans une revue hal-03626102v1
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering Joan Hérisson,Thomas Duigou,Melchior Du Lac,Kenza Bazi-Kabbaj,Mahnaz Sabeti Azadet al. Nature Communications, 2022, 13 (1), pp.5082. ⟨10.1038/s41467-022-32661-x⟩ Article dans une revue hal-03649340v2
PeroxiHUB : a modular cell-free biosensing platform using H2O2 as signal integrator Paul Soudier,Ana Zúñiga,Thomas Duigou,Peter Voyvodic,Kenza Bazi-Kabbajet al. ACS Synthetic Biology, 2022, 11 (8), pp 2578-2588. ⟨10.1021/acssynbio.2c00138⟩ Article dans une revue hal-03649349v2
Distributed computation with continual population growth Da-Jung Cho,Matthias Függer,Corbin Hopper,Manish Kushwaha,Thomas Nowaket al. Distributed Computing, 2021, ⟨10.1007/s00446-021-00404-8⟩ Article dans une revue hal-03519002v1
Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs Jacob Beal,Geoff S Baldwin,Natalie G Farny,Markus Gershater,Traci Haddock-Angelliet al. PLoS ONE, 2021, 16 (6), pp.e0252263. ⟨10.1371/journal.pone.0252263⟩ Article dans une revue hal-03545776v1
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
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 Achmedovet al. ACS Synthetic Biology, 2021, pp.acssynbio.1c00448. ⟨10.1101/2021.09.07.459228⟩ Article dans une revue hal-03545788v1
Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics Roberto Galizi,John N Duncan,William Rostain,Charlotte M Quinn,Marko Storchet al. The Crispr Journal, 2020, 3 (5), pp.398-408. ⟨10.1089/crispr.2020.0029⟩ Article dans une revue hal-03545565v1
Metabolic perceptrons for neural computing in biological systems Amir Pandi,Mathilde Koch,Peter L. Voyvodic,Paul Soudier,Jérôme Bonnetet al. Nature Communications, 2019, 10 (1), pp.1-13. ⟨10.1038/s41467-019-11889-0⟩ Article dans une revue hal-02275517v1
Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in &lt;em&gt;Trypanosoma brucei&lt;/em&gt; James Budzak,Louise E. Kerry,Aris Aristodemou,Belinda S. Hall,Kathrin Witmeret 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 Dwijayantiet al. PLoS ONE, 2018, 13 (6), pp.e0199432. ⟨10.1371/journal.pone.0199432⟩ Article dans une revue hal-04415924v1
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
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
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
Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei Tara Stanne,Mani Shankar Narayanan,Sophie Ridewood,Alexandra Ling,Kathrin Witmeret al. Journal of Biological Chemistry, 2015, 290 (45), pp.26954-26967. ⟨10.1074/jbc.M115.679019⟩ Article dans une revue hal-04559158v1
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 Witmeret al. Journal of Biological Chemistry, 2015, 290 (45), pp.26954-26967. ⟨10.1074/jbc.M115.679019⟩ Article dans une revue hal-01860866v1
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria Iman Farasat,Manish Kushwaha,Jason Collens,Michael Easterbrook,Matthew Guidoet al. Molecular Systems Biology, 2014, 10 (6), pp.1-18. ⟨10.15252/msb.20134955⟩ Article dans une revue hal-01860867v1
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. Stanneet al. Nucleic Acids Research, 2011, 39 (6), pp.2018-2031. ⟨10.1093/nar/gkq950⟩ Article dans une revue hal-01860869v1
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

Pré-publication, Document de travail (5)

An M13 phagemid toolbox for engineering tuneable DNA communication in bacterial consortia Abhinav Pujar,Anchita Sharma,Hadi Jbara,Manish Kushwaha 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05134741v1
Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia Abhinav Pujar,Amit Pathania,Corbin Hopper,Amir Pandi,Matthias Fuggeret al. 2024 Pré-publication, Document de travail hal-04699429v1
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 Schaeferet al. 2023 Pré-publication, Document de travail hal-04009404v1
Reaching Agreement in Competitive Microbial Systems Victoria Andaur,Janna Burman,Matthias Függer,Manish Kushwaha,Bilal Manssouriet al. 2022 Pré-publication, Document de travail (preprint/prepublication) hal-03545888v1
A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission Amit Pathania,Corbin Hopper,Amir Pandi,Matthias Függer,Thomas Nowaket al. 2022 Pré-publication, Document de travail hal-03670575v2

Poster de conférence (4)

Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering Thomas Duigou,Joan Hérisson,Melchior Du Lac,Kenza Bazi-Kabbaj,Mahnaz Sabeti Azadet al. JOBIM 2022, Jul 2022, Rennes, France. Poster de conférence hal-04302811v1
Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering Joan Hérisson,Thomas Duigou,Melchior Du Lac,Kenza Bazi Kabbaj,Mahnaz Sabeti Azadet al. Global BioFoundries Alliance Meeting 2022 (GBA2022), Oct 2022, Montréal, Canada Poster de conférence hal-04351669v1
Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering Thomas Duigou,Joan Hérisson,Melchior Du Lac,Kenza Bazi-Kabbaj,Mahnaz Sabeti Azadet al. BioSynSys 2022, Sep 2022, Paris, France. Poster de conférence hal-04302912v1
Metabolic Perceptrons for Neural Computing in Biological Systems. Paul Soudier,Amir Pandi,Mathilde Koch,Peter Voyvodic,Manish Kushwahaet al. EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heildelberg, Germany Poster de conférence hal-04275677v1

Thèse (1)

TbISWI and its role in transcriptional control in &lt;em&gt;Trypanosoma brucei&lt;/em&gt; Manish Kushwaha Life Sciences [q-bio]. University of Oxford, 2010. English. ⟨NNT : ⟩ Thèse tel-02818155v1

Mémoire d'étudiant (1)

Computational analysis of &lt;em&gt;Entamoeba histolytica&lt;/em&gt; genome- Exploring junk DNA for hidden messages Manish Kushwaha Life Sciences [q-bio]. 2006 Mémoire d'étudiant hal-02824521v1