Blerina Sinaimeri

Teacher photo


Databases & Big Data


I am  an Associate Professor of Computer Science at LUISS Guido Carli University. Before joining LUISS, I was a permanent researcher
 (Chargeè de rechercher) at the  French National Institute for Research in Digital Science and Technology (INRIA).  I got my Ph.D. in Computer Science at Sapienza University of Rome in 2010.  My research interests lie mostly in algorithmic and computational aspects of graph theory. This includes applications  in areas as wide ranging as computational biology and social sciences. Within this framework I study the reciprocal evolution of interacting systems.  My papers have appeared in journals such as Algorithmica,  Theoretical Computer Science, Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 

During my career I have taught a number of courses including: Network Algorithms, Advanced Algorithms, Programming, Discrete Mathematics, Algorithms and Data Structures, Combinatorics.  I have taught both at the undergraduate (bachelor) and graduate (master) level both in Italy and in France  Universit_é Lyon 1, _École Normale Sup_érieure de Lyon (ENS), Institut National des Sciences Appliquées de Lyon (INSA)). 

I am also very interested in public dissemination of science and I have been involved in a range of educational activities for different audiences. 

  • Acuña, Vicente; Soares de Lima, Leandro Ishi; Italiano, Giuseppe Francesco; Pepè Sciarria, Luca; Sagot, Marie-France; Sinaimeri, Blerina (2021). A family of tree-based generators for bubbles in directed graphs. JOURNAL OF GRAPH ALGORITHMS AND APPLICATIONS, p. 563-580. ISSN 1526-1719.
  • Acuña, V.; Grossi, R.; Italiano, G. F.; Lima, L.; Rizzi, R.; Sacomoto, G.; Sagot, M. -F.; Sinaimeri, B. (2020). On Bubble Generators in Directed Graphs. ALGORITHMICA, p. 898-914. ISSN 0178-4617.
  • Calamoneri, T.; Gastaldello, M.; Mary, A.; Sagot, M. -F.; Sinaimeri, Blerina (2020). Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility. ALGORITHMS FOR MOLECULAR BIOLOGY, p. 14-29. ISSN 1748-7188.
  • Monti, A.; Sinaimeri, Blerina (2020). String factorisations with maximum or minimum dimension. THEORETICAL COMPUTER SCIENCE, p. 65-73. ISSN 0304-3975.
  • Wang, Y.; Mary, A.; Sagot, M. -F.; Sinaimeri, Blerina (2020). Capybara: Equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions. BIOINFORMATICS, p. 4197-4199. ISSN 1367-4803.
  • Urbini, L.; Sinaimeri, Blerina; Matias, C.; Sagot, M. -F. (2019). Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, p. 738-748. ISSN 1545-5963.
  • Huber, K. T.; Moulton, V.; Sagot, M. -F.; Sinaimeri, Blerina (2019). Exploring and visualizing spaces of tree reconciliations. SYSTEMATIC BIOLOGY, p. 607-618. ISSN 1063-5157.
  • Calamoneri, T.; Monti, A.; Sinaimeri, Blerina (2019). Co-divergence and tree topology. JOURNAL OF MATHEMATICAL BIOLOGY, p. 1149-1167. ISSN 0303-6812.
  • Huber, K. T.; Moulton, V.; Sagot, M. -F.; Sinaimeri, Blerina (2018). Geometric medians in reconciliation spaces of phylogenetic trees. INFORMATION PROCESSING LETTERS, p. 96-101. ISSN 0020-0190.
  • Monti, A.; Sinaimeri, Blerina (2018). On variants of Vertex Geography on undirected graphs. DISCRETE APPLIED MATHEMATICS, p. 268-275. ISSN 0166-218X.
  • Lima, L.; Sinaimeri, Blerina; Sacomoto, G.; Lopez-Maestre, H.; Marchet, C.; Miele, V.; Sagot, M. -F.; Lacroix, V. (2017). Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. ALGORITHMS FOR MOLECULAR BIOLOGY, p. 2-19. ISSN 1748-7188.
  • Calamoneri, T.; Sinaimeri, Blerina (2016). Pairwise compatibility graphs: A survey. SIAM REVIEW, p. 445-460. ISSN 0036-1445.
  • Donati, B.; Baudet, C.; Sinaimeri, Blerina; Crescenzi, P.; Sagot, M. -F. (2015). EUCALYPT: Efficient tree reconciliation enumerator. ALGORITHMS FOR MOLECULAR BIOLOGY, p. 3-13. ISSN 1748-7188.
  • Baudet, C.; Donati, B.; Sinaimeri, Blerina; Crescenzi, P.; Gautier, C.; Matias, C.; Sagot, M. -F. (2015). Cophylogeny reconstruction via an approximate bayesian computation. SYSTEMATIC BIOLOGY, p. 416-431. ISSN 1063-5157.
  • Calamoneri, Tiziana; Frangioni, A.; Sinaimeri, Blerina (2014). Pairwise Compatibility Graphs of Caterpillars. COMPUTER JOURNAL, p. 1616-1623. ISSN 0010-4620.
  • Calamoneri, Tiziana; Sinaimeri, Blerina (2013). L(2,1)-labeling of oriented planar graphs. DISCRETE APPLIED MATHEMATICS, p. 1719-1725. ISSN 0166-218X.
  • Calamoneri, Tiziana; D., Frascaria; Sinaimeri, Blerina (2013). All graphs with at most seven vertices are Pairwise compatibility graphs. COMPUTER JOURNAL, p. 882-886. ISSN 0010-4620.
  • Calamoneri, Tiziana; Montefusco, Eugenio; Petreschi, Rossella; Sinaimeri, Blerina (2013). Exploring pairwise compatibility graphs. THEORETICAL COMPUTER SCIENCE, p. 23-36. ISSN 0304-3975.
  • Monti, Angelo; Sinaimeri, Blerina (2011). Rainbow graph splitting. THEORETICAL COMPUTER SCIENCE, p. 5315-5324. ISSN 0304-3975.
  • Furedi, Zoltan; Kantor, Ida; Monti, Angelo; Sinaimeri, Blerina (2010). On reverse-free codes and permutations. SIAM JOURNAL ON DISCRETE MATHEMATICS, p. 964-978. ISSN 0895-4801.