Publications

Publications / communications (en cours) …

En complément de la liste ci-dessous, voici le lien vers les publications de l’équipe dans Hal : Lien Hal Tibs.

2022

• S. Faro, T. Lecroq, K. Park, and S. Scafiti, « On the longest common cartesian substring problem, » The computer journal, 2022.
  [Bibtex]

  @article( FLPS2022,
  author = "S. Faro and T. Lecroq and K. Park and S. Scafiti",
  title = "On the Longest Common Cartesian Substring Problem",
  journal = "The Computer Journal",
  note = "bxab204",
  year = 2022,
  )

• T. Lecroq and M. Salson, « Sequence indexing, » in From sequences to graphs: discrete methods and structures for bioinformatics, A. Chateau and M. Salson, Eds., Iste wiley, 2022, p. 49–86.
  [Bibtex]

  @incollection( LS2022,
  author = "T. Lecroq and M. Salson",
  title = "Sequence indexing",
  booktitle = "From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics",
  editor = "A. Chateau and M. Salson",
  publisher = "ISTE Wiley",
  chapter = 2,
  year = 2022,
  pages = "49--86",
  )

• V. Sater, P. -J. Viailly, T. Lecroq, É. Prieur-Gaston, É. Bohers, M. Viennot, P. Ruminy, H. Dauchel, P. Vera, and F. Jardin, « Umi-varcal: a low-frequency variant caller for umi-tagged paired-end sequencing data, » in Variant calling – methods and protocols, C. Ng and S. Piscuoglio, Eds., Springer, 2022, p. 235–245.
  [Bibtex]

  @incollection{Sater2021,
  author = "V. Sater and P.-J. Viailly and T. Lecroq and \'E. Prieur-Gaston and \'E. Bohers and M. Viennot and P. Ruminy and H. Dauchel and P. Vera and F. Jardin",
  editor="Ng, Charlotte and Piscuoglio, Salvatore",
  title="UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data",
  booktitle = "Variant Calling - Methods and Protocols",
  series = "Methods in Molecular Biology",
  publisher = "Springer",
  year = 2022,
  pages = "235--245",
  }

2021

• S. Song, G. Gu, C. Ryu, S. Faro, T. Lecroq, and K. Park, « Fast algorithms for single and multiple pattern cartesian tree matching, » Theor. comput. sci., vol. 849, p. 47–63, 2021.
  [Bibtex]

  @article{DBLP:journals/tcs/SongGRFLP21,
  author = {Siwoo Song and
  Geonmo Gu and
  Cheol Ryu and
  Simone Faro and
  Thierry Lecroq and
  Kunsoo Park},
  title = {Fast algorithms for single and multiple pattern Cartesian tree matching},
  journal = {Theor. Comput. Sci.},
  volume = {849},
  pages = {47--63},
  year = {2021},
  url = {https://doi.org/10.1016/j.tcs.2020.10.009},
  doi = {10.1016/j.tcs.2020.10.009},
  timestamp = {Thu, 10 Dec 2020 13:12:57 +0100},
  biburl = {https://dblp.org/rec/journals/tcs/SongGRFLP21.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

• M. Crochemore, T. Lecroq, and W. Rytter, 125 problems in text algorithms, Cambrige university press, 2021.
  [Bibtex]

  @book( CLR2021,
  title = "125 Problems in Text Algorithms",
  author = "Maxime Crochemore and Thierry Lecroq and Wojciech Rytter",
  publisher = "Cambrige University Press",
  year = 2021,
  )

• M. Crochemore, T. Lecroq, and W. Rytter, 125 problems in text algorithms, Acorn publishing co, 2021.
  [Bibtex]

  @book( CLR2021b,
  title = "125 Problems in Text Algorithms",
  author = "Maxime Crochemore and Thierry Lecroq and Wojciech Rytter",
  publisher = "Acorn Publishing Co",
  year = 2021,
  note = "In Korean",
  )

• P. Morisse, C. Marchet, A. Limasset, T. Lecroq, and A. Lefebvre, « Scalable long read self-correction and assembly polishing with multiple sequence alignment, » Scientific reports, vol. 11, iss. 1, p. 1–13, 2021.
  [Bibtex]

  @article( CONSENT2021,
  author = "P. Morisse and C. Marchet and A. Limasset and T. Lecroq and A. Lefebvre",
  title = "Scalable long read self-correction and assembly polishing with multiple sequence alignment",
  journal = "Scientific Reports",
  year = 2021,
  volume = 11,
  number = 1,
  pages = "1--13",
  )

• T. Lecroq and M. Salson, « Indexation de séquences, » in Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, A. Chateau and M. Salson, Eds., Iste sciences, 2021, pp. 47-83.
  [Bibtex]

  @incollection( LS2021,
  author = "T. Lecroq and M. Salson",
  title = "Indexation de séquences",
  booktitle = "Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique",
  editor = "A. Chateau and M. Salson",
  publisher = "ISTE Sciences",
  chapter = 2,
  year = 2021,
  pages = "47-83",
  )

• P. -J. Viailly, V. Sater, M. Viennot, E. Bohers, N. Vergne, C. Berard, H. Dauchel, T. Lecroq, A. Celebi, P. Ruminy, V. Marchand, M. -D. Lanic, S. Dubois, D. Penther, H. Tilly, S. Mareschal, and F. Jardin, « Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers, » Bmc bioinformatics, vol. 22, iss. 120, 2021.
  [Bibtex]

  @article( Viailly2021,
  author = "P.-J. Viailly and V. Sater and M. Viennot and E. Bohers and N. Vergne and C. Berard and H. Dauchel and T. Lecroq and A. Celebi and P. Ruminy and V. Marchand and M.-D. Lanic and S. Dubois and D. Penther and H. Tilly and S. Mareschal and F. Jardin",
  title = "Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers",
  journal = "BMC Bioinformatics",
  volume = 22,
  year = 2021,
  number = 120,
  )

• V. Sater, P. -J. Viailly, T. Lecroq, P. Ruminy, É. Prieur-Gaston, C. Bérard, and F. Jardin, « Umi-gen: a umi-based read simulator for variant calling evaluation, » in Journées ouvertes biologie informatique mathématiques (jobim 2021), Paris, France, 2021.
  [Bibtex]

  @inproceedings(Sater2021,
  author = "V. Sater and P.-J. Viailly and T. Lecroq and P. Ruminy and É. Prieur-Gaston and C. Bérard and F. Jardin",
  title = "UMI-Gen: a UMI-based read simulator for variant calling evaluation",
  booktitle = "Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2021)",
  address = "Paris, France",
  year = 2021,
  note = "accepted",
  )

• M. Koptelov, A. Zimmermann, B. Crémilleux, and L. F. Soualmia, « Lpbycd: a new scalable and interpretable approach for link prediction via community detection in bipartite networks, » Appl. netw. sci., vol. 6, iss. 1, p. 72, 2021.
  [Bibtex]

  @article{DBLP:journals/ans/KoptelovZCS21,
  author = {Maksim Koptelov and
  Albrecht Zimmermann and
  Bruno Cr{\'{e}}milleux and
  Lina Fatima Soualmia},
  title = {LPbyCD: a new scalable and interpretable approach for Link Prediction
  via Community Detection in bipartite networks},
  journal = {Appl. Netw. Sci.},
  volume = {6},
  number = {1},
  pages = {72},
  year = {2021},
  url = {https://doi.org/10.1007/s41109-021-00415-1},
  doi = {10.1007/s41109-021-00415-1},
  timestamp = {Tue, 12 Oct 2021 01:00:00 +0200},
  biburl = {https://dblp.org/rec/journals/ans/KoptelovZCS21.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

• L. F. Soualmia, V. Lafon, and S. J. Darmoni, « Patient and graph embeddings for predictive diagnosis of drug iatrogenesis, » in Public health and informatics – proceedings of MIE 2021, medical informatics europe, virtual event, may 29-31, 2021, 2021, p. 482–483.
  [Bibtex]

  @inproceedings{DBLP:conf/mie/SoualmiaLD21,
  author = {Lina Fatima Soualmia and
  Vincent Lafon and
  St{\'{e}}fan Jacques Darmoni},
  editor = {John Mantas and
  Lacramioara Stoicu{-}Tivadar and
  Catherine E. Chronaki and
  Arie Hasman and
  Patrick Weber and
  Parisis Gallos and
  Mihaela Marcella Vida and
  Emmanouil Zoulias and
  Oana Sorina Chirila},
  title = {Patient and Graph Embeddings for Predictive Diagnosis of Drug Iatrogenesis},
  booktitle = {Public Health and Informatics - Proceedings of {MIE} 2021, Medical
  Informatics Europe, Virtual Event, May 29-31, 2021},
  series = {Studies in Health Technology and Informatics},
  volume = {281},
  pages = {482--483},
  publisher = {{IOS} Press},
  year = {2021},
  url = {https://doi.org/10.3233/SHTI210205},
  doi = {10.3233/SHTI210205},
  timestamp = {Fri, 30 Jul 2021 13:59:35 +0200},
  biburl = {https://dblp.org/rec/conf/mie/SoualmiaLD21.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

• T. P. Laffouilhère, J. Grosjean, J. Benichou, S. J. Darmoni, and L. F. Soualmia, « Ontological models supporting covariates selection in observational studies, » in Public health and informatics – proceedings of MIE 2021, medical informatics europe, virtual event, may 29-31, 2021, 2021, p. 1095–1096.
  [Bibtex]

  @inproceedings{DBLP:conf/mie/LaffouilhereGBD21,
  author = {Thibaut Pressat Laffouilh{\`{e}}re and
  Julien Grosjean and
  Jacques Benichou and
  St{\'{e}}fan Jacques Darmoni and
  Lina Fatima Soualmia},
  editor = {John Mantas and
  Lacramioara Stoicu{-}Tivadar and
  Catherine E. Chronaki and
  Arie Hasman and
  Patrick Weber and
  Parisis Gallos and
  Mihaela Marcella Vida and
  Emmanouil Zoulias and
  Oana Sorina Chirila},
  title = {Ontological Models Supporting Covariates Selection in Observational
  Studies},
  booktitle = {Public Health and Informatics - Proceedings of {MIE} 2021, Medical
  Informatics Europe, Virtual Event, May 29-31, 2021},
  series = {Studies in Health Technology and Informatics},
  volume = {281},
  pages = {1095--1096},
  publisher = {{IOS} Press},
  year = {2021},
  url = {https://doi.org/10.3233/SHTI210361},
  doi = {10.3233/SHTI210361},
  timestamp = {Fri, 30 Jul 2021 01:00:00 +0200},
  biburl = {https://dblp.org/rec/conf/mie/LaffouilhereGBD21.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

2020

• G. Gu, S. Song, S. Faro, T. Lecroq, and K. Park, « Fast multiple pattern cartesian tree matching, » in The 14th international conference and workshops on algorithms and computation (walcom 2020), singapore, 2020, 2020.
  [Bibtex]

  @inproceedings{walcom2020,
  author = "G. Gu and S. Song and S. Faro and T. Lecroq and K. Park",
  title = "Fast Multiple Pattern Cartesian Tree Matching",
  booktitle = "The 14th International Conference and Workshops on Algorithms and Computation (WALCOM 2020), Singapore, 2020",
  year = 2020,
  note = "accepted",
  }

• M. Koptelov, A. Zimmermann, B. Crémilleux, and L. F. Soualmia, « Link Prediction via Community Detection in Bipartite Multi-Layer Graphs, » in 35th ACM/SIGAPP Symposium On Applied Computing, Brno, Czech Republic, 2020.
  [Bibtex]

  @inproceedings{koptelov:hal-02474290,
  TITLE = {{Link Prediction via Community Detection in Bipartite Multi-Layer Graphs}},
  AUTHOR = {Koptelov, Maksim and Zimmermann, Albrecht and Cr{\'e}milleux, Bruno and Soualmia, Lina F.},
  URL = {https://hal.archives-ouvertes.fr/hal-02474290},
  BOOKTITLE = {{35th ACM/SIGAPP Symposium On Applied Computing}},
  ADDRESS = {Brno, Czech Republic},
  YEAR = {2020},
  MONTH = Mar,
  DOI = {10.1145/3341105.3373874},
  KEYWORDS = {best},
  PDF = {https://hal.archives-ouvertes.fr/hal-02474290/file/SAC2020.pdf},
  HAL_ID = {hal-02474290},
  HAL_VERSION = {v1},
  }

• A. Quillet, C. Saad, G. Ferry, Y. Anouar, N. Vergne, T. Lecroq, and C. Dubessy, « Improving bioinformatics prediction of microRNA targets by ranks aggregation, » Frontiers in genetics, vol. 10, iss. 20, p. 1330, 2020.
  [Bibtex]

  @ARTICLE( QSFAVLD2019,
  author = "A. Quillet and C. Saad and G. Ferry and Y. Anouar and N. Vergne and T. Lecroq and C. Dubessy",
  title = "Improving bioinformatics prediction of {microRNA} targets by ranks aggregation",
  journal = "Frontiers in Genetics",
  year = 2020,
  volume = 10,
  number = 20,
  pages = "1330",
  comment = {Q1},
  )

• V. Sater, P. -J. Viailly, T. Lecroq, É. Prieur-Gaston, É. Bohers, M. Viennot, P. Ruminy, H. Dauchel, P. Vera, and F. Jardin, « UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries, » Bioinformatics, vol. 36, iss. 9, p. 2718–2724, 2020.
  [Bibtex]

  @article( Sater2020,
  author = "V. Sater and P.-J. Viailly and T. Lecroq and \'E. Prieur-Gaston and \'E. Bohers and M. Viennot and P. Ruminy and H. Dauchel and P. Vera and F. Jardin",
  title = "{UMI-VarCal}: a new {UMI}-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing {NGS} libraries",
  journal = "Bioinformatics",
  year = 2020,
  volume = 36,
  number = 9,
  pages = "2718--2724",
  comment = {Q1?},
  )

• N. Adam, G. Coutance, P. Viailly, F. Drieux, P. Ruminy, A. A. Sater, C. Toquet, P. Rouvier, A. François, M. Chenard, E. Epailly, R. Guillemain, S. Pattier, A. Gay, S. Varnous, J. Taupin, M. Rabant, A. Loupy, P. Bruneval, and J. P. Duong Van Huyen, « Reverse transcriptase multiplex ligation-dependent probe amplification in endomyocardial biopsies for the diagnosis of cardiac allograft rejection, » Journal of Heart and Lung Transplantation, vol. 39, iss. 2, p. 115–124, 2020.
  [Bibtex]

  @article{adam:hal-02468295,
  TITLE = {{Reverse transcriptase multiplex ligation-dependent probe amplification in endomyocardial biopsies for the diagnosis of cardiac allograft rejection}},
  AUTHOR = {Adam, Nicolas and Coutance, Guillaume and Viailly, Pierre-Julien and Drieux, Fanny and Ruminy, Philippe and Sater, Ahmad Abdel and Toquet, Claire and Rouvier, Philippe and Fran{\c c}ois, Arnaud and Chenard, Marie-Pierre and Epailly, Eric and Guillemain, Romain and Pattier, Sabine and Gay, Arnaud and Varnous, Shaida and Taupin, Jean-Luc and Rabant, Marion and Loupy, Alexandre and Bruneval, Patrick and Duong Van Huyen, Jean Paul},
  URL = {https://hal.archives-ouvertes.fr/hal-02468295},
  JOURNAL = {{Journal of Heart and Lung Transplantation}},
  PUBLISHER = {{Elsevier}},
  VOLUME = {39},
  NUMBER = {2},
  PAGES = {115--124},
  YEAR = {2020},
  MONTH = Feb,
  DOI = {10.1016/j.healun.2019.11.010},
  HAL_ID = {hal-02468295},
  HAL_VERSION = {v1},
  comment = {Q1?},
  }

• V. Bobée, F. Drieux, V. Marchand, V. Sater, L. Veresezan, J. Picquenot, P. Viailly, M. Lanic, M. Viennot, E. Bohers, L. Oberic, C. Copie-Bergman, T. J. Molina, P. Gaulard, C. Haioun, G. Salles, H. Tilly, F. Jardin, and P. Ruminy, « Combining gene expression profiling and machine learning to diagnose b-cell non-hodgkin lymphoma, » Blood cancer journal, vol. 10, iss. 59, 2020.
  [Bibtex]

  @article{blood2020,
  author = "Bobée, Victor and Drieux, Fanny and Marchand, Vinciane and Sater, Vincent and Veresezan, Liana and Picquenot, Jean-Michel and Viailly, Pierre-Julien and Lanic, Marie-Delphine and Viennot, Mathieu and Bohers, Elodie and Oberic, Lucie and Copie-Bergman, Christiane and Molina, Thierry Jo and Gaulard, Philippe and Haioun, Corinne and Salles, Gilles and Tilly, Hervé and Jardin, Fabrice and Ruminy, Philippe",
  year = 2020,
  title = "Combining gene expression profiling and machine learning to diagnose B-cell non-Hodgkin lymphoma",
  journal = "Blood Cancer Journal",
  number = 59,
  volume = 10,
  DOI = "10.1038/s41408-020-0322-5",
  comment = {Q1?},
  }

• H. Tubeuf, C. Charbonnier, O. Soukarieh, A. Blavier, A. Lefebvre, H. Dauchel, T. Frebourg, P. Gaildrat, and A. Martins, , » Human mutation, vol. 41, iss. 10, p. 1811–1829, 2020.
  [Bibtex]

  @article( HM2020,
  tittle = "Large‐scale comparative evaluation of user‐friendly tools for predicting variant‐induced alterations of splicing regulatory elements",
  author = "Hélène Tubeuf and Camille Charbonnier and Omar Soukarieh and André Blavier and Arnaud Lefebvre and Hélène Dauchel and Thierry Frebourg and Pascaline Gaildrat and Alexandra Martins",
  year = 2020,
  journal = "Human Mutation",
  volume = 41,
  number = 10,
  pages = "1811--1829",
  )

• S. Faro, T. Lecroq, and K. Park, « Fast practical computation of the longest common cartesian substrings of two strings, » in Proceedings of the prague stringology conference 2020, Czech Technical University in Prague, Czech Republic, 2020, p. 48–60.
  [Bibtex]

  @INPROCEEDINGS( PSC2020-5,
  author = "Simone Faro and Thierry Lecroq and Kunsoo Park",
  title = "Fast Practical Computation of the Longest Common Cartesian Substrings of Two Strings",
  booktitle = "Proceedings of the Prague Stringology Conference 2020",
  address = "Czech Technical University in Prague, Czech Republic",
  editor = "Jan Holub and Jan {\v{Z}}{\v{d}}{\'{a}}rek",
  isbn = "978-80-01-06749-9",
  year = 2020,
  pages = "48--60",
  )

• V. Sater, P. Viailly, T. Lecroq, P. Ruminy, C. Bérard, É. Prieur-Gaston, and F. Jardin, « Umi-gen: a umi-based read simulator for variant calling evaluation in paired-end sequencing ngs libraries, » Computational and structural biotechnology journal, vol. 18, p. 2270–2280, 2020.
  [Bibtex]

  @article( umigene2020,
  journal = "Computational and Structural Biotechnology Journal",
  volume = 18,
  year = 2020,
  pages = "2270--2280",
  title = "UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries",
  author = "Vincent Sater and Pierre-Julien Viailly and Thierry Lecroq and Philippe Ruminy and Caroline Bérard and Élise Prieur-Gaston and Fabrice Jardin",
  )

• B. Séroussi, K. F. Hollis, and L. F. Soualmia, « Transparency of health informatics processes as the condition of healthcare professionals’ and patients’ trust and adoption: the rise of ethical requirements, » Yearbook of medical informatics, vol. 29, iss. 1, p. 7–10, 2020.
  [Bibtex]

  @article( SHS2021,
  title = "Transparency of Health Informatics Processes as the Condition of Healthcare Professionals' and Patients' Trust and Adoption: the Rise of Ethical Requirements",
  author = "B. Séroussi and K.F. Hollis and L.F. Soualmia",
  journal = "Yearbook of Medical Informatics",
  volume = "29",
  number = 1,
  pages = "7--10",
  year = 2020,
  )

• V. Sater, P. Viailly, T. Lecroq, P. Ruminy, É. Prieur-Gaston, C. Bérard, and F. Jardin, Umi-gen: a new umi-based read simulator for variant calling evaluation in paired-end sequencing, 2020.
  [Bibtex]

  @misc{seqbim2020,
  author = "Vincent Sater and Pierre-Julien Viailly and Thierry Lecroq and Philippe Ruminy and Élise Prieur-Gaston and Caroline Bérard and Fabrice Jardin",
  title = "UMI-Gen: a new UMI-based read simulator for variant calling evaluation in paired-end sequencing",
  howpublished = "SeqBIM",
  note = "Toulouse, France",
  year = "2020",
  }

• M. Koptelov, A. Zimmermann, B. Crémilleux, and L. Soualmia, « Link prediction via community detection in bipartite multi-layer graphs, » in SAC ’20: the 35th ACM/SIGAPP symposium on applied computing, online event, [brno, czech republic], march 30 – april 3, 2020, 2020, p. 430–439.
  [Bibtex]

  @inproceedings{DBLP:conf/sac/KoptelovZCS20,
  author = {Maksim Koptelov and
  Albrecht Zimmermann and
  Bruno Cr{\'{e}}milleux and
  Lina Soualmia},
  editor = {Chih{-}Cheng Hung and
  Tom{\'{a}}s Cern{\'{y}} and
  Dongwan Shin and
  Alessio Bechini},
  title = {Link prediction via community detection in bipartite multi-layer graphs},
  booktitle = {{SAC} '20: The 35th {ACM/SIGAPP} Symposium on Applied Computing, online
  event, [Brno, Czech Republic], March 30 - April 3, 2020},
  pages = {430--439},
  publisher = {{ACM}},
  year = {2020},
  url = {https://doi.org/10.1145/3341105.3373874},
  doi = {10.1145/3341105.3373874},
  timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
  biburl = {https://dblp.org/rec/conf/sac/KoptelovZCS20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

2019

• C. Marchet, P. Morisse, L. Lecompte, A. Limasset, A. Lefebvre, T. Lecroq, and P. Peterlongo, « Elector: evaluator for long reads correction methods, » Biorxiv, vol. 512889, 2019.
  [Bibtex]

  @article {elector,
  title = {ELECTOR: Evaluator for long reads correction methods},
  author = {Marchet, Camille and Morisse, Pierre and Lecompte, Lolita and Limasset, Antoine and Lefebvre, Arnaud and Lecroq, Thierry and Peterlongo, Pierre},
  volume = {512889},
  journal = {bioRxiv},
  year = {2019},
  }

• P. Morisse, C. Marchet, A. Limasset, T. Lecroq, and A. Lefebvre, « CONSENT: scalable self-correction of long reads with multiple sequence alignment, » Biorxiv, vol. 546630, 2019.
  [Bibtex]

  @article {consent,
  title = "{CONSENT}: Scalable self-correction of long reads with multiple sequence alignment",
  author = "Pierre Morisse and Camille Marchet and Antoine Limasset and Thierry Lecroq and Arnaud Lefebvre",
  volume = {546630},
  journal = {bioRxiv},
  year = {2019},
  }

• S. Song, C. Ryu, S. Faro, T. Lecroq, and K. Park, « Fast cartesian tree matching, » Corr, vol. abs/1908.04937, 2019.
  [Bibtex]

  @article{fctm,
  author = "S. Song and C. Ryu and S. Faro and T. Lecroq and K. Park",
  title = "Fast Cartesian Tree Matching",
  year = 2019,
  journal = {CoRR},
  volume = "abs/1908.04937",
  }

• G. Gu, S. Song, S. Faro, T. Lecroq, and K. Park, « Fast multiple pattern cartesian tree matching, » Corr, vol. abs/1911.01644, 2019.
  [Bibtex]

  @article{fmctm,
  title = "Fast Multiple Pattern Cartesian Tree Matching",
  author = "G. Gu and S. Song and S. Faro and T. Lecroq and K. Park",
  year = 2019,
  journal = {CoRR},
  volume = "abs/1911.01644",
  }

• V. Sater, P. Viailly, T. Lecroq, É. Prieur-Gaston, E. Bohers, M. Viennot, P. Ruminy, H. Dauchel, P. Vera, and F. Jardin, « UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries, » Biorxiv, vol. 775817, 2019.
  [Bibtex]

  @article {umivarcal,
  title = "{UMI-VarCal}: a new {UMI}-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing {NGS} libraries",
  author = "Vincent Sater and Pierre-Julien Viailly and Thierry Lecroq and {\'E}lise Prieur-Gaston and Elodie Bohers and Mathieu Viennot and Philippe Ruminy and Helene Dauchel and Pierre Vera and Fabrice Jardin",
  volume = 775817,
  journal = {bioRxiv},
  year = {2019},
  }

• A. Quillet, Y. Anouar, T. Lecroq, and C. Dubessy, « Prediction tools for miRNA targets: toward a better comprehension for biologists, » , 2019.
  [Bibtex]

  @article{quillet_anouar_lecroq_dubessy_2019,
  title={Prediction tools for {miRNA} targets: toward a better comprehension for Biologists},
  url={osf.io/4gjyn},
  DOI={10.31219/osf.io/4gjyn},
  publisher={OSF Preprints},
  author={Quillet, Aurélien and Anouar, Youssef and Lecroq, Thierry and Dubessy, Christophe},
  year={2019},
  month= Dec
  }

• K. F. Hollis, L. F. Soualmia, and B. Séroussi, « Artificial intelligence in health informatics: hype or reality?, » Imia yearbook of medical informatics, vol. 28, iss. 1, p. 3–4, 2019.
  [Bibtex]

  @article{hollis,
  title = "Artificial Intelligence in Health Informatics: Hype or Reality?",
  author = "Hollis, Kate Fultz and Soualmia, Lina F. and Séroussi, Brigitte",
  journal = {IMIA Yearbook of Medical Informatics},
  volume = 28,
  number = 1,
  year = {2019},
  pages = {3--4},
  keywords = {best},
  }

• P. -J. Viailly, A. A. Sater, H. Dauchel, A. Celebi, C. Bérard, N. Vergne, M. Viennot, E. Bohers, P. Ruminy, T. Lecroq, H. Tilly, P. Vera, and F. Jardin, « mCNA: a new methodology to improve high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers, » in Jobim, Nantes, France, 2019.
  [Bibtex]

  @INPROCEEDINGS( Viailly2019,
  author = "P.-J. Viailly and A. Abdel Sater and H. Dauchel and A. Celebi and C. Bérard and N. Vergne and M. Viennot and E. Bohers and P. Ruminy and T. Lecroq and H. Tilly and P. Vera and F. Jardin",
  title = "{mCNA}: a new methodology to improve high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers",
  booktitle = "JOBIM",
  address = "Nantes, France",
  year = 2019,
  )

• P. Morisse, C. Marchet, A. Limasset, T. Lecroq, and A. Lefebvre, « CONSENT: scalable self-correction of long reads with multiple sequence alignment, » in Jobim, Nantes, France, 2019.
  [Bibtex]

  @INPROCEEDINGS( Morisse2019,
  author = "P. Morisse and C. Marchet and A. Limasset and T. Lecroq and A. Lefebvre",
  title = "{CONSENT}: Scalable self-correction of long reads with multiple sequence alignment",
  booktitle = "JOBIM",
  address = "Nantes, France",
  year = 2019,
  )

• C. Ryu, T. Lecroq, and K. Park, « Fast string matching in scan speed, » in 12th annual meeting of the asian association for algorithms and computation (aaac), Seoul, South Korea, 2019.
  [Bibtex]

  @inproceedings{ryu2019,
  author = "C. Ryu and T. Lecroq and K. Park",
  title = "Fast String Matching in Scan Speed",
  booktitle = "12th Annual Meeting of the Asian Association for Algorithms and Computation (AAAC)",
  address = "Seoul, South Korea",
  year = 2019,
  }

• P. Morisse, C. Marchet, A. Limasset, T. Lecroq, and A. Lefebvre, « CONSENT: scalable self-correction of long reads with multiple sequence alignment, » in Recomb-seq, Washington DC, USA, 2019.
  [Bibtex]

  @inproceedings{morisse2019b,
  author = "P. Morisse and C. Marchet and A. Limasset and T. Lecroq and A. Lefebvre",
  title = "{CONSENT}: Scalable self-correction of long reads with multiple sequence alignment",
  booktitle = "RECOMB-seq",
  address = "Washington DC, USA",
  year = 2019,
  }

• R. Lelong, L. Soualmia, J. Grosjean, M. Taalba, and S. Darmoni, « Building a Semantic Health Data Warehouse: Evaluation of a search tool in Clinical trials (Preprint), » JMIR Medical Informatics, 2019.
  [Bibtex]

  @article{lelong:hal-02407129,
  TITLE = {{Building a Semantic Health Data Warehouse: Evaluation of a search tool in Clinical trials (Preprint)}},
  AUTHOR = {Lelong, Romain and Soualmia, Lina and Grosjean, Julien and Taalba, Mehdi and Darmoni, Stefan},
  URL = {https://hal.archives-ouvertes.fr/hal-02407129},
  JOURNAL = {{JMIR Medical Informatics}},
  PUBLISHER = {{JMIR Publications}},
  YEAR = {2019},
  MONTH = Aug,
  DOI = {10.2196/13917},
  HAL_ID = {hal-02407129},
  HAL_VERSION = {v1},
  comment = {pas dans scimago},
  }

• C. Cabot, S. J. Darmoni, and L. F. Soualmia, « Cimind: A phonetic-based tool for multilingual named entity recognition in biomedical texts, » J. biomed. informatics, vol. 94, 2019.
  [Bibtex]

  @article{DBLP:journals/jbi/CabotDS19,
  author = {Chlo{\'{e}} Cabot and
  St{\'{e}}fan Jacques Darmoni and
  Lina Fatima Soualmia},
  title = {Cimind: {A} phonetic-based tool for multilingual named entity recognition
  in biomedical texts},
  journal = {J. Biomed. Informatics},
  volume = {94},
  year = {2019},
  url = {https://doi.org/10.1016/j.jbi.2019.103176},
  doi = {10.1016/j.jbi.2019.103176},
  timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
  biburl = {https://dblp.org/rec/journals/jbi/CabotDS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

• S. Abdeddaïm, S. Vimard, and L. F. Soualmia, « The mesh-gram neural network model: extending word embedding vectors with mesh concepts for semantic similarity, » in MEDINFO 2019: health and wellbeing e-networks for all – proceedings of the 17th world congress on medical and health informatics, lyon, france, 25-30 august 2019, 2019, p. 5–9.
  [Bibtex]

  @inproceedings{DBLP:conf/medinfo/AbdeddaimVS19,
  author = {Sa{\"{\i}}d Abdedda{\"{\i}}m and
  Sylvestre Vimard and
  Lina Fatima Soualmia},
  editor = {Lucila Ohno{-}Machado and
  Brigitte S{\'{e}}roussi},
  title = {The MeSH-Gram Neural Network Model: Extending Word Embedding Vectors
  with MeSH Concepts for Semantic Similarity},
  booktitle = {{MEDINFO} 2019: Health and Wellbeing e-Networks for All - Proceedings
  of the 17th World Congress on Medical and Health Informatics, Lyon,
  France, 25-30 August 2019},
  series = {Studies in Health Technology and Informatics},
  volume = {264},
  pages = {5--9},
  publisher = {{IOS} Press},
  year = {2019},
  url = {https://doi.org/10.3233/SHTI190172},
  doi = {10.3233/SHTI190172},
  timestamp = {Wed, 03 Feb 2021 08:34:29 +0100},
  biburl = {https://dblp.org/rec/conf/medinfo/AbdeddaimVS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
  }

2018

• J. Holmes, L. Soualmia, and B. Séroussi, « A 21st century embarrassment of riches: the balance between health data access, usage, and sharing, » Imia yearbook of medical informatics, vol. 27, iss. 1, p. 5–6, 2018.
  [Bibtex]

  @article{seroussi2,
  title = "A 21st Century Embarrassment of Riches: The Balance Between Health Data Access, Usage, and Sharing",
  author = "JH Holmes and LF Soualmia and B S\'eroussi",
  journal = {IMIA Yearbook of Medical Informatics},
  volume = 27,
  number = 1,
  year = {2018},
  pages = {5--6},
  keywords = {best},
  }

• P. -J. Viailly, E. Bohers, M. Viennot, A. A. Sater, H. Dauchel, T. Lecroq, P. Vera, and F. Jardin, « I-LowVarFreq: improving low-frequency variant detection using a new UMI-based variant calling approach for paired-end sequencing NGS libraries, » in Jobim, Marseilles, France, 2018.
  [Bibtex]

  @INPROCEEDINGS( Viailly2018,
  author = "P.-J. Viailly and E. Bohers and M. Viennot and A. Abdel Sater and H. Dauchel and T. Lecroq and P. Vera and F. Jardin",
  title = "{I-LowVarFreq}: improving low-frequency variant detection using a new {UMI}-based variant calling approach for paired-end sequencing {NGS} libraries",
  booktitle = "JOBIM",
  address = "Marseilles, France",
  year = 2018,
  )

• W. Chebil, L. F. Soualmia, and M. N. Omri, « Possibilistic information retrieval model based on a multi-terminology, » in Advanced data mining and applications – 14th international conference, ADMA 2018, nanjing, china, november 16-18, 2018, proceedings, 2018, p. 66–79.
  [Bibtex]

  @inproceedings{DBLP:conf/adma/ChebilSO18,
  author = {Wiem Chebil and
  Lina Fatima Soualmia and
  Mohamed Nazih Omri},
  title = {Possibilistic Information Retrieval Model Based on a Multi-terminology},
  booktitle = {Advanced Data Mining and Applications - 14th International Conference,
  {ADMA} 2018, Nanjing, China, November 16-18, 2018, Proceedings},
  pages = {66--79},
  year = {2018},
  editor = {Guojun Gan and
  Bohan Li and
  Xue Li and
  Shuliang Wang},
  series = {Lecture Notes in Computer Science},
  volume = {11323},
  publisher = {Springer},
  }