Team

Permanent Staff

  • Marie-Dominique Devignes (CNRS researcher ; Team Leader since September 2019) — complex network analysis; biological data mining; knowledge discovery in biological databases. marie-dominique.devignes AT loria.fr  |  +33 3 83 59 20 65
  • Malika Smail-Tabbone (MC, HDR, Université de Lorraine) — Data integration and analysis; knowledge discovery from biomedical data; graph and relational data mining.         malika.smail AT loria.fr
  • Bernard Maigret (Emeritus CNRS researcher) — molecular dynamics simulation; virtual drug screening. bernard.maigret AT loria.fr
  • Sabeur Aridhi (MC, TELECOM Nancy) — big data; artificial intelligence; cloud computing; bioinformatics. sabeur.aridhi AT loria.fr
  • Isaure Chauvot de Beauchêne (CNRS researcher) — modeling proteins and their complexes, especially with nucleic acids. isaure.chauvot-de-beauchene AT loria.fr
  • Hamed Khakzad (Inria Junior Professor Chair). hamed.khakzad AT inria.fr
  • Yasaman Karami (Inria researcher). yasaman.karami AT inria.fr

Postdocs

  • Sneha Bheemireddy (Inria) — Predicting communication networks in protein-nucleic acid complexes. Supervisor: Yasaman Karami; sneha.bheemireddy AT inria.fr

PhD Students

  • Omid Mokhtari —  Predicting biomolecular interactions via deep learning. Supervisor: Hamed Khakzad; omid.mokhtari AT inria.fr
  • Victor Pryakhin — Elucidating conformational dynamics of protein-RNA complexes. Supervisors: Yasaman Karami and Malika Smail; victor.pryakhin AT inria.fr
  • Mohammed Khatbane — Machine learning and graph-based techniques to predict long-term bacterial community structure. Supervisors: Sabeur Aridhi, Yannick Toussaint, Cécile Mangavel (LIBio) ; mohammed.khatbane AT loria.fr
  • Diego Amaya Ramirez — 3D-modeling of HLA antigens – Structure-based study of donor-receptor compatibility. Supervisor: Marie-Dominique Devignes; diego.amaya-ramirez AT inria.fr

Assistants

  • Sophie Drouot (Inria Team Assistant)
    sophie.drouot AT inria.fr  |  +33 3 83 59 30 52
  • Antoinette Courrier (CNRS Team Assistant)
    antoinette.courrier AT loria.fr  |  +33 3 83 59 20 09

Alumni

  • Anna Kravchenko (RNAct PhD student) — Improving methods to dock RNA with proteins. Thesis defended on 20 December 2023.
  • Hrishikesh Dhondge (RNAct PhD student) — Data analysis on RNA recognition motifs (RRMs). Thesis defended on 11 July 2023.
  • Athénaïs Vaginay (PhD student) — Model Construction and Analysis of Biological Networks: Application to Perturbed Networks in Diseases. Thesis defended on 7 July 2023.
  • Kamrul Islam (PhD student) — Distributed link prediction in large complex graphs: application to biomolecule interactions. Thesis defended on 16 December 2022.
    kamrul.islam AT loria.fr
  • Antoine Moniot (PhD student) — Modeling protein / nucleic acid complexes by combinatorial structural fragment assembly. Thesis defended on December 12, 2022.
    antoine.moniot AT loria.fr
  • Dominique Mias-Lucquin (Post-Doc Fellow) — Modelling ICE St3 relaxase-ssDNA interactions  2019-2022. dominique.mias-lucquin AT loria.fr
  • Kevin Dalleau (PhD student) « Une approche stochastique à base d’arbres aléatoires pour le calcul de dissimilarités: application au clustering pour diverses structures de données ». Thesis defended on November 23, 2021
  • Camille Besançon (Post-Doc Fellow) — Modelling long non coding RNA (ANRIL) interaction with regulatory proteins    2020-2021
  • Amina Ahmed Nacer (Post-Doc, Région Lorraine-CHRU de Nancy) – GraphScore project. 2019-2020
  • Bishnu Sarker (PhD student) — Developing distributed graph-based approaches for large-scale protein function annotation and knowledge discovery. Thesis defended on April 24, 2021.
  • Wissem Inoubli (PhD student, Tunis University) — Graph mining of distributed and dynamic graphs. Thesis defended on January 7, 2021.
  • Karina Mayumi Sakita (PhD student, State University of Maringá) – Virtual screening for identifying inhibitors.
  • Maria Elisa Ruiz-Echartea (PhD student) — Pairwise and Multi-Component Protein-Protein Docking Using Exhaustive Branch-and-Bound Tri-Dimensional Rotational Searches. Thesis defended on December 18, 2019.
  • Gabin Personeni (PhD student) — exploration of linked open data in view of knowledge discovery. Thesis defended on November 9, 2018.
  • Seyed Ziaeddin Alborzi (PhD student) — automatic protein domain function annotation. Thesis defended on February 23, 2018

Former Team Members

  • Louane Sigrist (Engineer Bioinformatics) – HLA-3D-Diff project
    louane.sigrist AT loria.fr
  • Amal Stiti (M2 student, University of Tunis) – Distributed graph computing for protein function annotation
    amal.stiti AT loria.fr
  • Emmanuel Bresso (Research Engineer) — Fight Heart Failure ANR project
  • Philippe Noel (Bioinformatics Master-2 Inria Apprentice) — Design of Inhibitors of the Transfer of Antimicrobial Resistance – (LUE project « CITRAM »)
  • Claire Lacomblez (Engineer) — Design and Development of a Database System to Study the Effects of Epleronone on Heart Failure and Obesity (ANR project « FIGHT-HF »)
  • Dave Ritchie (Inria researcher; Capsid team founder) — protein docking; protein interactions; protein structure alignment. Dave Ritchie passed away on September, 15, 2019 (Obituary)
  • Antoine Chemardin (Development Engineer) — Galaxy structural bioinformatics platform