Publications

Publications PEPR MoleculArXiv


50 documents

Articles dans une revue21 document

  • Rémi Sieskind, Sophia Missoury, Frédéric Bonhomme, Pauline Nogaret, Soizick Lucas-Staat, et al.. Exploitation of phage Carin-5’s own DNA polymerase to sequence its T-hypermodified genome. Scientific Reports, 2025, 15 (1), pp.43299. ⟨10.1038/s41598-025-26930-0⟩. ⟨hal-05409778⟩
  • Marie Flamme, Germain Niogret, Luke Mckenzie, Usman Akhtar, Fabienne Levi-Acobas, et al.. Selection of Ruthenium Polypyridyl Complex-Modified Aptamers for Photodynamic Therapy against Streptococcus Pneumonia. Journal of the American Chemical Society, In press, ⟨10.1021/jacs.5c13224⟩. ⟨hal-05357414⟩
  • Florestan de Moor, Olivier Boullé, Dominique Lavenier. De-Bruijn graph partitioning for scalable and accurate DNA storage processing. Bioinformatics, 2025, 41 (11), pp.1-9. ⟨10.1093/bioinformatics/btaf618⟩. ⟨hal-05375444⟩
  • Greta Charlotte Dahm, Usman Akhtar, Alix Bouvier-Müller, Laura Lim, Fabienne Levi-Acobas, et al.. Probing three-dimensional cyclooctatetraene for nucleobase modification in aptamer selection. Communications Chemistry, 2025, 8 (1), pp.276. ⟨10.1038/s42004-025-01629-5⟩. ⟨pasteur-05262586⟩
  • Jakub Ossowski, Cyril Antheaume, Jean‐françois Lutz, Maria Nerantzaki. Selective and Precise Editing of Digital Polymers Through Parallel or Series Toehold‐Mediated Strand Displacement. Advanced Functional Materials, 2025, pp.e11868. ⟨10.1002/adfm.202511868⟩. ⟨hal-05406191⟩
  • Pierre Nicolas Bizat, Nazarii Sabat, Marcel Hollenstein. Recent advances in biocatalytic and chemoenzymatic synthesis of oligonucleotides. ChemBioChem, 2025, 26 (9), pp.e202400987. ⟨10.1002/cbic.202400987⟩. ⟨pasteur-05119218⟩
  • Luca Iesu, Mariam Sai, Vladimir Torbeev, Bruno Kieffer, Juan Pelta, et al.. Single-molecule nanopore sensing of proline cis / trans amide isomers. Chemical Science, 2025, 232, pp.113948. ⟨10.1039/d5sc01156f⟩. ⟨hal-05089004⟩
  • Rémi Sieskind, Sophia Missoury, Clément Madru, Isciane Commenge, Germain Niogret, et al.. Crystal structures of monomeric BsmI restriction endonuclease reveal coordinated sequential cleavage of two DNA strands. Communications Biology, 2025, 8 (1), pp.387. ⟨10.1038/S42003-025-07612-Z⟩. ⟨pasteur-04986492⟩
  • Maria Nerantzaki, Claire Husser, Isaure Sergent, Laurence Charles, Jean-François Lutz, et al.. Chemical Synthesis and Poly(ethylene glycol)-Like Conjugation of the Mango-II Fluorogenic RNA Aptamer. Bioconjugate Chemistry, 2025, 36 (3), pp.449-456. ⟨10.1021/acs.bioconjchem.4c00540⟩. ⟨hal-05078762⟩
  • Benoit Pousse, Abdelaziz Al Ouahabi, Paul Baxter, Laurence Charles, Jean‐françois Lutz. Conception and Synthesis of Sequence‐Coded Morpholinos. Chemistry - A European Journal, 2025, 31 (29), pp.e202501161. ⟨10.1002/chem.202501161⟩. ⟨hal-05406167⟩
  • Chloé Berton, Gouenou Coatrieux, Héléne Gasnier, Sahar Haddad, Reda Bellafqira, et al.. A Dynamic Sliding Window Encoding for Secured DNA Data Storage Compliant With Biological and Indexing Constraints. IEEE Access, 2025, 13, pp.66009-66030. ⟨10.1109/ACCESS.2025.3560387⟩. ⟨hal-05067257⟩
  • Alexandros Petropoulos, Laurence Charles, Jean‐michel Becht, Michael Schmitt, Jacques Lalevée, et al.. Photo‐Accelerated Synthesis of Oligo(triazole amide)s. Macromolecular Rapid Communications, In press, Online ahead of print. ⟨10.1002/marc.202400759⟩. ⟨hal-04798416⟩
  • Sotaro Takiguchi, Nanami Takeuchi, Vasily Shenshin, Guillaume Gines, Anthony J Genot, et al.. Harnessing DNA computing and nanopore decoding for practical applications: from informatics to microRNA-targeting diagnostics. Chemical Society Reviews, 2024, 54, pp.8 - 32. ⟨10.1039/d3cs00396e⟩. ⟨hal-05391044⟩
  • Nazarii Sabat, Andreas Stämpfli, Steven Hanlon, Serena Bisagni, Filippo Sladojevich, et al.. Template-dependent DNA ligation for the synthesis of modified oligonucleotides. Nature Communications, 2024, 15 (1), pp.8009. ⟨10.1038/s41467-024-52141-8⟩. ⟨pasteur-04956998v2⟩
  • Germain Niogret, Camille Chériaux, Frédéric Bonhomme, Fabienne Levi-Acobas, Carlotta Figliola, et al.. A toolbox for enzymatic modification of nucleic acids with photosensitizers for photodynamic therapy. RSC Chemical Biology, 2024, 5, pp.841-852. ⟨10.1039/d4cb00103f⟩. ⟨hal-04653532v2⟩
  • Julien Leblanc, Olivier Boulle, Emeline Roux, Jacques Nicolas, Dominique Lavenier, et al.. Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information. Biotechniques, 2024, 76 (5), pp.203-215. ⟨10.2144/btn-2023-0109⟩. ⟨hal-04567229⟩
  • Nazarii Sabat, Andreas Stämpfli, Marie Flamme, Steven Hanlon, Serena Bisagni, et al.. Artificial nucleotide codons for enzymatic DNA synthesis. Chemical Communications, 2023, 59 (98), pp.14547-14550. ⟨10.1039/d3cc04933g⟩. ⟨pasteur-04452276⟩
  • Germain Niogret, Pascal Röthlisberger, Fabienne Levi-Acobas, Frédéric Bonhomme, Gilles Gasser, et al.. Facilitated Synthetic Access to Boronic Acid-Modified Nucleoside Triphosphates and Compatibility with Enzymatic DNA Synthesis. SYNLETT, 2023, 35 (06), pp.677-683. ⟨10.1055/a-2212-7704⟩. ⟨pasteur-04614013⟩
  • Germain Niogret, Alix Bouvier-Müller, Chiara Figazzolo, Jack M Joyce, Frédéric Bonhomme, et al.. Interrogating aptamer chemical space through modified nucleotide substitution facilitated by enzymatic DNA synthesis. ChemBioChem, 2023, 25 (1), pp.e202300539. ⟨10.1002/cbic.202300539⟩. ⟨hal-04248298⟩
  • Dominique Lavenier, Marc Antonini, Yannick Rondelez, A.J. Genot. Stocker les données : la piste prometteuse de l’ADN. Interstices, 2023. ⟨hal-04073357⟩
  • Belaid Hamoum, Elsa Dupraz. Channel Model and Decoder With Memory for DNA Data Storage With Nanopore Sequencing. IEEE Access, 2023, 11, pp.52075-52087. ⟨10.1109/ACCESS.2023.3278975⟩. ⟨hal-04184188v2⟩

Communications dans un congrès20 document

  • Sara Al Sayyed, Aline Roumy, Thomas Maugey, Nicolas Lobato-Dauzier, Anthony J Genot. Compact image representation for content-based image retrieval in DNA data storage. PCS 2025 - Picture Coding Symposium, Dec 2025, Aachen, Germany. pp.1-5. ⟨hal-05322329⟩
  • Guilhem Larrieu. Large-Scale DNA Synthesis. International MoleculArXiv Autumn School on DNA Data Storage, Nov 2025, Cargese (Corse), France. ⟨hal-05399905⟩
  • Sara Al Sayyed, Aline Roumy, Thomas Maugey. Efficient Constraining of Transcoding in DNA-Based Image Storage. ICIP 2025 - IEEE International Conference on Image Processing, Sep 2025, Anchorage (AK), USA, United States. pp.1-6. ⟨hal-05300068⟩
  • Claire Couvreur, Michela Testolina, Théo Ladune, Pierrick Philippe, Marc Antonini. Comparaison de différents codecs pour la compression d'image sur ADN synthétique. GRETSI’25 - XXXe Colloque Francophone de Traitement du Signal et des Images, Aug 2025, Strasbourg, France. ⟨hal-05269745⟩
  • Ramy Khabbaz, Marc Antonini, Serge Kas Hanna. Marker Guess and Check Plus (MGC+): An Efficient Short Blocklength Code for Random Edit Errors. 13th International Symposium on Topics in Coding (ISTC 2025), Aug 2025, Los Angeles, CA, United States. ⟨10.1109/ISTC65386.2025.11154528⟩. ⟨hal-05330323⟩
  • Davi Nachtigall Lazzarotto, Michela Testolina, Serge Kas Hanna, Osamu Watanabe, Eva Gil San Antonio, et al.. Overview of JPEG DNA coding system for image storage on synthetic DNA. Applications of Digital Image Processing XLVIII, Aug 2025, San Diego, France. pp.27, ⟨10.1117/12.3068093⟩. ⟨hal-05330969⟩
  • Xavier Pic, Raja Appuswamy. COMBINING PROGRESSIVE IMAGE COMPRESSION AND RANDOM ACCESS IN DNA DATA STORAGE. DSP 2025, 25th International Conference on Digital Signal Processing, IEEE, Jun 2025, Costa Navarino, Greece. ⟨hal-05066885⟩
  • Ramy Khabbaz, Marc Antonini, Serge Kas Hanna. Novel Efficient Codes for Correcting Random Edit Errors in DNA Storage. Storage and Computing with DNA, 2025, Paris, France. ⟨hal-05331841⟩
  • Ramy Khabbaz, Marc Antonini, Serge Kas Hanna. Novel Efficient Codes for Correcting Random Edit Errors in DNA Storage. New Trends in DNA-based Data Storage, 2025, Prague, Czech Republic. ⟨hal-05331842⟩
  • Jeremy Mateos, Dominique Lavenier, Melpomeni Dimopoulou, Anthony Genot, Marc Antonini. Primer design for DNA storage random access. CORESA 2024 - 23ème conférence sur COmpression et REprésentation des Signaux Audiovisuels, Nov 2024, Rennes, France. pp.1-3. ⟨hal-04739300⟩
  • Serge Kas Hanna. Short Systematic Codes for Correcting Random Edit Errors in DNA Storage. 2024 IEEE International Symposium on Information Theory (ISIT), Jul 2024, Athène, Greece. pp.663-668, ⟨10.1109/ISIT57864.2024.10619614⟩. ⟨hal-05330328⟩
  • Trung Hieu Le, Xavier Pic, Jeremy Mateos, Marc Antonini. Implicit neural multiple description for DNA-based data storage. 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2024), IEEE, Apr 2024, Seoul, South Korea. ⟨hal-04381574v2⟩
  • Xavier Pic, Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini. MQ-Coder inspired arithmetic coder for synthetic DNA data storage. ICIP 2023 (IEEE 30th International Conference on Image Processing), Oct 2023, Kuala Lumpur, Malaysia. ⟨10.1109/ICIP49359.2023.10223113⟩. ⟨hal-04186223⟩
  • Xavier Pic, Eva Gil San Antonio, Melpomeni Dimopoulou, Marc Antonini. Image storage on synthetic DNA using compressive autoencoders and DNA-adapted entropy coders. IEEE 25th International Workshop on Multimedia Signal Processing, Sep 2023, Poitiers, France. ⟨hal-04186220⟩
  • Belaïd Hamoum, Aref Ezzeddine, Elsa Dupraz. Synchronization Algorithms from High-Rate LDPC Codes for DNA Data Storage. DSP 2023: 24th International Conference on Digital Signal Processing, Jun 2023, Rhodes, Greece. pp.1-5, ⟨10.1109/DSP58604.2023.10167916⟩. ⟨hal-04183975⟩
  • Xavier Pic, Eva Gil San Antonio, Melpomeni Dimopoulou, Marc Antonini. Rotating labeling of entropy coders for synthetic DNA data storage. 2023 24th International Conference on Digital Signal Processing (DSP), Jun 2023, Rhodes (Rodos), Greece. pp.1-5, ⟨10.1109/DSP58604.2023.10167907⟩. ⟨hal-04186229⟩
  • Dominique Lavenier. DNA Storage: Synthesis and Sequencing Semiconductor Technologies. IEDM 2022 - 68th Annual IEEE International Electron Devices Meeting, Dec 2022, San Francisco, United States. pp.1-4. ⟨hal-03902786⟩
  • Olivier Boullé, Dominique Lavenier. Experimental DNA storage platform. DSMM 2022 - 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France. pp.1-1. ⟨hal-03817374⟩
  • Elsa Dupraz, Belaid Hamoum. A DNA Data Storage Channel Model Trained on Genomics Data with Nanopore Sequencing. DSMM 2022: 1st International Conference on Data Storage in Molecular Media, Mar 2022, Marburg (virtual), Germany. ⟨hal-03767162⟩
  • Belaid Hamoum, Elsa Dupraz, Laura Conde-Canencia, Dominique Lavenier. Channel Model with Memory for DNA Data Storage with Nanopore Sequencing. ISTC 2021: 11th International Symposium on Topics in Coding, Aug 2021, Montreal, Canada. pp.1-5, ⟨10.1109/ISTC49272.2021.9594243⟩. ⟨hal-03337117⟩

Ouvrages (y compris édition critique et traduction)1 document

  • Dominique Lavenier. Stocker nos données sur ADN. Editions Apogée. , https://www.editions-apogee.com/espace-des-sciences/719-stocker-nos-dones-sur-adn.html, 2025, Espace de sciences, Rennes, 978-2-84398-876-9. ⟨hal-05375812⟩

Chapitres d'ouvrage2 document

  • Dominique Lavenier, Marc Antonini. Stockage d'information sur ADN. Le calcul à découvert, CNRS Editions, 2025, 978-2-271-15373-9. ⟨hal-05376118⟩
  • Guillaume Gines, Anthony J Genot, Yannick Rondelez. Parallel Computations with DNA-Encoded Chemical Reaction Networks. Visions of DNA Nanotechnology at 40 for the Next 40, Springer Nature Singapore, pp.349-369, 2023, Natural Computing Series, ⟨10.1007/978-981-19-9891-1_19⟩. ⟨hal-04287184⟩

Pré-publications, Documents de travail6 document

  • Rémi Sieskind, Sophia Missoury, Frédéric Bonhomme, Pauline Nogaret, Marc Monot, et al.. From Demodification to Sequencing: the Genome of Bacteriophage Carin-5. 2025. ⟨hal-05351923⟩
  • Serge Kas Hanna. GC+ Code: A Systematic Short Blocklength Code for Correcting Random Edit Errors in DNA Storage. 2025. ⟨hal-05331839⟩
  • Serge Kas Hanna. On the Reliability of Information Retrieval From MDS Coded Data in DNA Storage. 2025. ⟨hal-05331837⟩
  • Sophia Missoury, Soizick Lucas-Staat, Rémi Sieskind, Marc Delarue. Structural Basis for DNA Replication and Uracil Repair in Phage A-Family DNA Polymerases. 2025. ⟨pasteur-05016154⟩
  • Julien Leblanc, Olivier Boulle, Emeline Roux, Nicolas Jacques, Dominique Lavenier, et al.. In vitro construction and long read sequencing analysis of a 24 kb long artificial DNA sequence encoding the Universal Declaration of the Rights of Man and of the Citizen. 2023. ⟨hal-04357386⟩
  • Trung Hieu Le, Xavier Pic, Marc Antonini. INR-MDSQC: Implicit Neural Representation Multiple Description Scalar Quantization for robust image Coding. 2023. ⟨hal-04148808⟩

Documents récupérés de l'archive ouverte HAL logo