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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.
2023
Pré-publication, Document de travail hal-04009404v1
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Reaching Agreement in Competitive Microbial Systems

 Victoria Andaur , Janna Burman , Matthias Függer , Manish Kushwaha , Bilal Manssouri , et al.
2022
Pré-publication, Document de travail hal-03545888v1
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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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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

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

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
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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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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 hal-02637711v1
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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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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

Metabolic Perceptrons for Neural Computing in Biological Systems.

 Paul Soudier , Amir Pandi , Mathilde Koch , Peter Voyvodic , Manish Kushwaha , et al.
EMBO workshop “Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heildelberg, Germany
Poster de conférence hal-04275677v1
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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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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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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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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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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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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 Azad , et al.
JOBIM 2022, Jul 2022, Rennes, France.
Poster de conférence hal-04302811v1
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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 Azad , et al.
BioSynSys 2022, Sep 2022, Paris, France.
Poster de conférence hal-04302912v1
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TbISWI and its role in transcriptional control in Trypanosoma brucei

 Manish Kushwaha
Life Sciences [q-bio]. University of Oxford, 2010. English. ⟨NNT : ⟩
Thèse tel-02818155v1
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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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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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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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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 hal-03545761v1
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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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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

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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A synthetic communication system uncovers extracellular immunity that self-limits bacteriophage transmission

 Amit Pathania , Corbin Hopper , Amir Pandi , Matthias Függer , Thomas Nowak , et al.
2022
Pré-publication, Document de travail hal-03670575v2
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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 , 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
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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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