Research Laboratories

Research Team EA 4108
Data Processing in Biology & Health (LITIS)

TIBS


Head


Pr Lecroq


Contact


TIBS - LITIS EA 4108
CURIB
UFR Sciences & Techniques
University of Rouen Normandy
76821 Mont-Saint-Aignan Cedex, France
Phone: +33 235 1460 13

thierry.lecroq@univ-rouen.fr

https://www.litislab.fr/equipe/index/tibs


Research Topics


Indexing and information retrieval in two main areas: biology and health:
- sequence algorithmics
- biostatistics
- analysis of NGS data in genomics, transcriptomics and proteomics
- knowledge management in health: semantic annotation and systems interoperability

Composition


11 staffs (teacher-researchers)
1 PhD student
1 Engineer

Facilities


Computings facilities of the Computer Science Laboratory LITIS located in the data
center of the University of Rouen Normandy

Activity


TIBS group is one of 7 teams of the LITIS laboratory (Director: Laurent Heutte).
The group aims at indexing and searching for information in biology and health data.
It collaborates with different labs of the University of Rouen Normandy (Inserm U1239, Inserm U1245,
Inserm U1234, GlycoMev EA 4358, ...) and
also with other bioinformatics and health informatics groups in France (LIRMM, IRISA, CRIStAL, LIMICS, ...)
and has strong connections with computer science groups troughout the world (Catania, Seoul, ...)

Main Contributions


- miRabel: A simple and efficient miRNA target prediction tool
 (http://bioinfo.univ-rouen.fr/mirabel/index.php)
- Package R SMM: Simulation and Estimation of Multi-State Discrete-Time Semi-Markov and Markov Models
 (https://cran.r-project.org/web/packages/SMM/index.html)
- HG-CoLoR: hybrid correction of third generation sequencing data
 (https://github.com/morispi/HG-CoLoR)
- ELECTOR: evaluation tool of third generation sequencing data methods
 (https://github.com/kamimrcht/ELECTOR)
- CONSENT: self-correction of third generation sequencing data
 (https://github.com/morispi/ CONSENT)
- analysis of gene expression profiles of tumors by RT-MLPA (reverse transcriptase multiplex ligation
dependant probe amplification)
 (https://bioinfo.calym.org/RTMLPA)
- UMI-VarCal: low frequency variang calling using UMI
 (https://gitlab.com/vincent-sater/umi-varcal-master)
- UMI-Gen: a UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries
 (https://gitlab.com/vincent-sater/umigen)

Main Publications


2020

  • C. Marchet, P. Morisse, L. Lecompte, A. Limasset, A. Lefebvre, T. Lecroq and P. Peterlongo. ELECTOR: Evaluator for long reads correction methods. NAR Genomics and Bioinformatics 2020, 2: 1.
    101
  • Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME and Zhang W. Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation. Front Genet 2020, 10: 1330.
    32047509
  • V. Sater, P.-J. Viailly, T. Lecroq, P. Ruminy, C. Bérard, É. Prieur-Gaston and F. Jardin. UMI-Gen: a UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries. Computational and Structural Biotechnology Journal 2020
    103
  • Xu C, Gu X, Padmanabhan R, Wu Z, Peng Q, DiCarlo J and Wang Y. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. Bioinformatics 2020, 36: 2718-2724.
    31985795

2019

  • Anapindi KDB, Romanova EV, Southey BR and Sweedler JV. Strategies for the Identification of Bioactive Neuropeptides in Vertebrates. Front Neurosci 2019, 13: 948.
    31619945
  • B. Cazaux, T. Lecroq and E. Rivals. Linking indexing data structures to de Bruijn Graphs: construction and update. Journal of Computer and System Sciences 2019, 104: 165-183.
    105
  • Cabot C, Soualmia LF, Grosjean J, Griffon N and Darmoni SJ. Cimind: A phonetic-based tool for multilingual named entity recognition in biomedical texts. J Biomed Inform 2019, 94: 103176.
    30980962
  • Gazzarata R, Giannini B and Giacomini M. Semantic data interoperability, digital medicine, and e-health in infectious disease management: a review. Eur J Clin Microbiol Infect Dis 2019, 38: 1023-1034.
    30771124
  • V.S. Barbu, C. Bérard, D. Cellier, M. Sautreuil and N. Vergne. SMM : An R Package for Estimation and Simulation of Discrete-time semi-Markov Models. The R Journal 2019, 10: 226.
    104

2018

  • De Martino A, Bartual A, Willis A, Meichenin A, Villazán B, Maheswari U and Bowler C. Comparative in depth RNA sequencing of P. tricornutum's morphotypes reveals specific features of the oval morphotype. Sci Rep 2018, 8: 14340.
    30254372
  • Morisse P, Lecroq T and Lefebvre A. Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph. Bioinformatics 2018, 34: 4213-4222.
    29955770