Lafond, Manuel

Professeur, Faculté des sciences
FAC. SCIENCES Informatique

Coordonnées

Courriel


819-821-8000, poste 62034

Diplômes

(2016) Algorithmes de construction et correction d'arbres de gènes par la réconciliation. Doctorat. Université de Montréal.

(2010) Baccalauréat. Université du Québec à Montréal.

Expérience académique

(2018) Assistant Professor. Université de Sherbrooke.

Présentation

Sujets de recherche

Bioinformatique.

Disciplines de recherche

Informatique.

Mots-clés

Bioinformatique, Algorithmique, Évolution (des espèces, des gènes, des tumeurs), Théorie des graphes, Clustering.

Langues parlées et écrites

Anglais, Français

Prix et distinctions

  • (2018) NSERC postdoctoral fellowship. Conseil de recherches en sciences naturelles et en génie (CRSNG). (Prix / Récompense).
  • (2016) Dean's Honor List. Université de Montréal. (Distinction).
  • (2016) Mitacs Globalink award - Campus France. Mitacs. (Prix / Récompense).
  • (2016) FRQNT Doctoral Scholarship. Fonds de recherche du Québec - Nature et technologies (FRQNT). (Prix / Récompense).
  • (2013) FRQNT Masters Scholarship. Fonds de recherche du Québec - Nature et technologies (FRQNT). (Prix / Récompense).
  • DIRO Excellence award. Université de Montréal. (Prix / Récompense).
  • Hydro-Québec Excellence award. Hydro-Québec. (Prix / Récompense).

Financement

Subvention. (Obtenu). Chercheur principal. NSERC Discovery Grant. (2019-2024).

Subvention. (En cours d’évaluation). FRQNT - Établissement de nouveaux chercheurs universitaires ($30,000/an) [demande en cours d'évaluation]. (2020-2022).

Publications

Articles de revue

  • S Briand, C Dessimoz, N El-Mabrouk, M Lafond, G Lobinska. (2020). A Generalized Robinson-Foulds Distance for Labeled Trees. BMC Genomics [Q1], (Article accepté).
  • M Lafond, G Cordonnier. (2020). Comparing copy-number profiles under multi-copy amplifications and deletions. BMC Genomics [Q1], (Article accepté).
  • M Lafond, M Hellmuth. (2020). Reconstruction of time-consistent species trees (submitted). Journal of Mathematical Biology [Q1], (Article soumis).
  • A Mane, M Lafond, P Feijao, C Chauve. (2020). The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications. Algorithms for Molecular Biology [Q1], (Article accepté).
  • S Dobrev, E Kranakis, D Krizanc, M Lafond, J Maňuch, L Narayanan, J Opatrny, L Stacho. (2020). Weak coverage of a rectangular barrier. Algorithmica [Q1], (Article publié).
  • M Delabre, N El-Mabrouk, K Huber, M Lafond, V Moulton, ENoutahi, M S Castellanos. (2019). Evolution through segmental duplications and losses: A Super-Reconciliation approach. Algorithms for Molecular Biology [Q1], (Article publié).
  • Lafond M, Scornavacca C. (2019). On the Weighted Quartet Consensus Problem. Theoretical Computer Science [Q1], (Article publié).
  • R Dondi, M Lafond, C Scornavacca. (2019). Reconciling multiple genes trees via segmental duplications and losses. Algorithms for Molecular Biology [Q1], (Article publié).
  • Lafond M, El-Mabrouk N, Huber KT, Moulton V. (2019). The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics. Theoretical Computer Science [Q1], (Article publié).
  • Lafond M, Miardan M*, Sankoff D. (2018). Accurate prediction of orthologs in the presence of divergence after duplication. Bioinformatics [Q1] (work presented by Lafond M at the ISMB 2018 conference), (Article publié).
  • Cordasco G, Gargano L, Lafond M, Narayanan L, Rescigno AA, Vaccaro U, Wu K. (2018). Whom to Befriend to Influence People. Theoretical Computer Science [Q1] (paper selected for the special issue of the SIROCCO 2016 conference), (Article publié).
  • Dondi R, Lafond M, El-Mabrouk N. (2017). Approximating the Correction of Weighted and Unweighted Orthology and Paralogy Relations. Algorithms for Molecular Biology [Q1] (paper selected for the special issue of the WABI 2016 conference), 12(1), (Article publié).
  • Lafond M, Chauve C, El-Mabrouk N, Ouangraoua A. (2017). Gene tree construction and correction using supertree and reconciliation. IEEE/ACM Transactions on Computational Biology and Bioinformatics [Q2], (Article publié).
  • Gambette P, Van Iersel L, Jones M, Lafond M, Pardi F, Scornavacca C. (2017). Rearrangement Moves on Phylogenetic Networks. PLoS Computational Biology [Q1], 13(8), (Article publié).
  • Kuitche E, Lafond M, Ouangraoua A. (2017). Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. Journal of Bioinformatics and Computational Biology [Q3] (paper selected for the special issue of the BICOB 2017 conference), 15(06), (Article publié).
  • Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C. (2017). The SCJ small parsimony problem for weighted gene adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics [Q2] (paper selected for the special issue of the ISBRA 2016 conference), (Article publié).
  • Noutahi E*, Semeria M, Lafond M, Seguin J*, Boussau B, Guéguen L, El-Mabrouk N, Tannier E. (2016). Efficient Gene Tree Correction Guided by Genome Evolution. PLoS One [Q1], 11(8), (Article publié).
  • Lafond M, Dondi R, El-Mabrouk N. (2016). The link between orthology relations and gene trees: a correction perspective. Algorithms for Molecular Biology [Q1] (paper selected for the special issue of the WABI 2015 conference), 11(1), (Article publié).
  • Lafond M, Seamone B. (2015). Hamiltonian chordal graphs are not cycle extendible. SIAM Journal on Discrete Mathematics [Q1], 29(2), 877-887. (Article publié).
  • Lafond M, Ouangraoua A, El-Mabrouk N. (2015). Reconstructing a SuperGeneTree minimizing reconciliation. BMC Bioinformatics [Q1] (work presented by Lafond M at the RECOMB-CG 2016 conference), (Article publié).
  • Lafond M, El-Mabrouk N. (2014). Orthology and paralogy constraints: satisfiability and consistency. BMC Genomics [Q1] (work presented by Lafond M a tthe RECOMB-CG 2014 conference), 15(6), (Article publié).
  • Lafond M, Chauve C, Dondi R, El-Mabrouk N. (2014). Polytomy refinement for the correction of dubious duplications in gene trees. Bioinformatics [Q1] (work presented by Lafond M at the ECCB 2014 conference), 30(17), 519-526. (Article publié).
  • Lafond M, Semeria M, Swenson K M, Tannier E, El-Mabrouk N. (2013). Gene tree correction guided by orthology. BMC Bioinformatics [Q1] (work presented by Lafond M at the RECOMB-CG 2013 conference), 14(15), (Article publié).

Chapitres de livre

  • Lafond M, Swenson K M, El-Mabrouk N. (2013). Error Detection and Correction of Gene Trees. Models and Algorithms for Genome Evolution (261-285). Springer. (Article publié).

Articles de conférence

  • M Lafond. (2020). Even better fixed-parameter algorithms for bicluster editing (submitted). 46th International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2020).
  • M Lafond, B Zhu, P Zou. (2020). Genomic Problems Involving Copy Number Profiles: Complexity and Algorithms (submitted). 31th Annual Symposium on Combinatorial Pattern Matching (CPM 2020). (Article soumis).
  • M Lafond, B Zhu, P Zou. (2020). The Tandem Duplication Distance is NP-hard. 37 th Symposium on Theoretical Aspects of Computer Science (STACS 2020). (Article publié).
  • M Lafond, G Cordonnier. (2019). Comparing copy-number profiles under multi-copy amplifications and deletions. RECOMB-CG 2019.
  • A Ehresmann, M Lafond, L Narayanan, J Opatrny. (2019). Distributed Pattern Formation in a Ring. 26th International Colloquium on Structural Information and Communication Complexity (SIROCCO 2019). (Article publié).
  • J Czyzowicz, K Georgiou, R Killick, E Kranakis, D Krizanc, M Lafond, L Narayanan, J Opatrny, S Shende. (2019). Energy consumption of group search on a line. 46th International Colloquium on Automata, Languages and Programming (ICALP 2019). (Article publié).
  • R Dondi, M Lafond. (2019). On the Tractability of Covering a Graph with 2-Clubs. International Symposium on Fundamentals of Computation Theory (FCT 2019).
  • J Czyzowicz, K Georgiou, R Killick, E Kranakis, D Krizanc, M Lafond, L Narayanan, J Opatrny, S Shende. (2019). Time-energy tradeoffs for evacuation by two robots in the wireless model. 26th International Colloquium on Structural Information and Communication Complexity (SIROCCO 2019). (Article publié).
  • Chuangpishit H, Lafond M, Narayanan L. (2018). Editing graphs to satisfy diversity requirements. 12th Annual International Conference on Combinatorial Optimization and Applications (COCOA'18, to be presented by Lafond M). (Article accepté).
  • Dondi R, Lafond M, Scornavacca C. (2018). Reconciling Multiple Genes Trees via Segmental Duplications and Losses. 18th Workshop on Algorithms in Bioinformatics (WABI 2018, presented by Lafond M). (Article publié).
  • Delabre M, El-Mabrouk N, Huber K, Lafond M, Moulton V, Noutahi E, Castellanos MS. (2018). Reconstructing the history of syntenies through Super-Reconciliation. 16th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2018). (Article accepté).
  • Krizanc D, Lafond M, Narayanan L, Opatrny J, Shende S. (2018). Satisfying Neighbor Preferences on a Circle. Lecture Notes in Computer Science, 727-740. (Article publié).
  • Lafond M. (2018). The complexity of speedrunning video games. Leibniz International Proceedings in Informatics (LIPIcs), (Article publié).
  • Mane A, Lafond M, Feijao P, Chauve C. (2018). The rooted SCJ median with single gene duplications. 16th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2018). (Article accepté).
  • Chauve C, Jones M, Lafond M, Scornavacca C, Weller M. (2017). Constructing a consensus phylogeny from a leaf-removal distance. Lecture Notes in Computer Science, 129-143. (Article publié).
  • Lafond M. (2017). On strongly chordal graphs that are not leaf powers. Lecture Notes in Computer Science, (Article publié).
  • Lafond M, Scornavacca C. (2017). On the weighted quartet consensus problem. 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017, presented by Lafond M). DOI. (Article publié).
  • Dobrev S, Lafond M, Narayanan L, Opatrny J. (2017). Optimal Local Buffer Management for Information Gathering with Adversarial Traffic. 29th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2017, presented by Lafond M). 265-274. DOI. (Article publié).
  • Kuitche E, Lafond M, Ouangraoua A. (2017). Reconstructing Protein and Gene Phylogenies by Extending the Framework of Reconciliation. 9th International Conference on Bioinformatics and Computational Biology (BICOB 2017). (Article publié).
  • Dobrev S, Kranakis E, Krizanc D, Lafond M, Manuch J, Narayanan L, Opatrny J, Stacho L. (2017). Weak Coverage of a Rectangular Barrier. Lecture Notes in Computer Science, (Article publié).
  • Dondi R, Lafond M, El-Mabrouk N. (2016). Correction of weighted orthology and paralogy relations-complexity and algorithmic results. Lecture Notes in Bioinformatics, (Article publié).
  • Lafond M, Noutahi E, El-Mabrouk N. (2016). Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. Leibniz International Proceedings in Informatics (LIPIcs), DOI. (Article publié).
  • Lafond M, Narayanan L, Wu K. (2016). Whom to befriend to influence people. Lecture Notes in Computer Science, 340-357. (Article publié).
  • Lafond M, El-Mabrouk N. (2015). Orthology relation and gene tree correction: complexity results. Lecture Notes in Bioinformatics, 66-79. (Article publié).
  • Lafond M, Aimeur E. (2013). The Scourge of Internet Personal Data Collection. 8th International Conference on Availability, Reliability and Security (ARES 2013). 821-828. DOI. (Article publié).
  • Lafond M*, Swenson KM, El-Mabrouk N. (2012). An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. Lecture Notes in Bioinformatics, 102-122. (Article publié).
  • Lafond M, Brosseau P-O, Aimeur E. (2012). Privacy invasion in business environments. 10th Annual Conference on Privacy, Security and Trust (PST 2012). DOI. (Article publié).

Autres contributions

Activités de collaboration internationale

  • Organisateur. (2019). Groupe de travail en bioinformatique - dans le cadre des rencontres Sherbrooke-Montpellier 2019.

Présentations

  • (2020). Algorithmic Challenges in Reconstructing Cancer Evolution from Copy-Numbers. Séminaires d'algorithmes pour la bioinformatique du LIRMM. France.
  • (2020). Algorithmic Challenges in Reconstructing Cancer Evolution from Copy-Numbers. 8th European Congress of Mathematics, discrete biomathematics special session (upcoming). Slovénie.
  • (2019). Théorie des graphes et évolution : les puissances de feuilles. Séminaires mathématiques de l'Université de Sherbrooke.
  • (2019). Will we ever find a forbidden subgraph characterization of leaf powers?. 9th Slovenian International Conference on Graph Theory (bioinformatics special session). Slovénie.
  • (2018). Algorithmic problems for the reconstruction of cancer tumor evolution. Université de Sherbrooke Research Seminars in Computer Science. Canada.
  • (2017). Algorithms for the validation and correction of orthology relations. Meetings of the Montreal Bioinformatics Users Group (MonBUG). Montreal, Canada.
  • (2017). The graph classes of gene orthology. Colloquium of the Math Department of UOttawa. Ottawa, Canada.
  • (2016). Algorithms for the validation and correction of gene relations. Colloques des Méthodes et Algorithmes pour la Bioinformatique (MAB) de l'Université de Montpellier. Montpellier, France.
  • (2014). Inférence d’histoires évolutives de gènes par spéciation et duplication. Conférence MiDIRO de l’Université de Montréal. Montreal, Canada.
  • (2013). Error Detection and Correction of Gene Trees. Montreal-Toronto Computational Molecular and Systems Biology Retreat. Montreal, Canada.
  • (2013). Gene Tree Correction guided by Orthology. Workshop on Mathematics in Sequence Evolution: Biological Models and Applications. Montreal, Canada.
  • (2012). An optimal reconciliation algorithm for gene trees with polytomies. Montreal-Toronto Computational Molecular and Systems Biology Retreat. Toronto, Canada.