Vladimir Makarenkov
Professeur
Professeur
Unité : Département d'informatique
Courriel : makarenkov.vladimir@uqam.ca
Téléphone : (514) 987-3000 poste 3870
Local : PK-4815
Langues :
Français, Anglais, Russe
Directions de thèses et mémoires
Publications
- Lord, E., Leclercq, M., Boc, A., Diallo, A.B. et Makarenkov, V. (2012). Armadillo 1.1: An original workflow platform for designing and conducting phylogenetic analysis and simulations. PLoS ONE, 7(1). http://dx.doi.org/10.1371/journal.pone.0029903.
- Dragiev, P., Nadon, R. et Makarenkov, V. (2012). Two effective methods for correcting experimental high-throughput screening data. Bioinformatics, 28(13), 1775–1782. http://dx.doi.org/10.1093/bioinformatics/bts262.
- Layeghifard, M., Peres-Neto, P.R. et Makarenkov, V. (2012). Using directed phylogenetic networks to retrace species dispersal history. Molecular Phylogenetics and Evolution, 64(1), 190–197. http://dx.doi.org/10.1016/j.ympev.2012.03.016.
- Badescu, D., Boc, A., Diallo, A.B. et Makarenkov, V. (2011). Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index. BMC Bioinformatics, 12(9). http://dx.doi.org/10.1186/1471-2105-12-S9-S9.
- Dragiev, P., Nadon, R. et Makarenkov, V. (2011). Systematic error detection in experimental high-throughput screening. BMC Bioinformatics, 12. http://dx.doi.org/10.1186/1471-2105-12-25.
- Boc, A. et Makarenkov, V. (2011). Towards an accurate identification of mosaic genes and partial horizontal gene transfers. Nucleic Acids Research, 39(21). http://dx.doi.org/10.1093/nar/gkr735.
- Diallo, A.B., Makarenkov, V. et Blanchette, M. (2010). Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics (Oxford, England), 26(1), 130–131.
Obtenir "Ancestors 1.0: a web server for ancestral sequence reconstruction" aux bibliothèques de l'UQAM
- Boc, A., Philippe, H. et Makarenkov, V. (2010). Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Systematic Biology, 59(2), 195–211. http://dx.doi.org/10.1093/sysbio/syp103.
- Mballo, C. et Makarenkov, V. (2010). Using machine learning methods to predict experimental high throughput screening data. Combinatorial Chemistry and High Throughput Screening, 13(5), 430–441. http://dx.doi.org/10.2174/138620710791292958.
- Makarenkov, V., Boc, A., Xie, J., Peres-Neto, P., Lapointe, F.-J. et Legendre, P. (2010). Weighted bootstrapping: A correction method for assessing the robustness of phylogenetic trees. BMC Evolutionary Biology, 10(1). http://dx.doi.org/10.1186/1471-2148-10-250.
- Diallo, A.B., Badescu, D., Blanchette, M. et Makarenkov, V. (2009). A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses. Journal of Computational Biology, 16(10), 1461–1473. http://dx.doi.org/10.1089/cmb.2009.0091.
- Badescu, D., Diallo, A.B., Blanchette, M. et Makarenkov, V. (2008). An evolutionary study of the human papillomavirus genomes. Lecture Notes in Computer Science, 5267 LNBI, 128–142. http://dx.doi.org/10.1007/978-3-540-87989-3_10.
- Makarenkov, V., Zentilli, P., Kevorkov, D., Gagarin, A., Malo, N. et Nadon, R. (2007). An efficient method for the detection and elimination of systematic error in high-throughput screening. Bioinformatics, 23(13), 1648–1657. http://dx.doi.org/10.1093/bioinformatics/btm145.
- Diallo, A.B., Makarenkov, V. et Blanchette, M. (2007). Exact and heuristic algorithms for the indel maximum likelihood problem. Journal of Computational Biology, 14(4), 446–461. Obtenir "Exact and heuristic algorithms for the indel maximum likelihood problem" aux bibliothèques de l'UQAM
- Diallo, A.B., Makarenkov, V. et Blanchette, M. (2006). Finding maximum likelihood indel scenarios. Lecture Notes in Computer Science, 4205 LNBI, 171–185. Obtenir "Finding maximum likelihood indel scenarios" aux bibliothèques de l'UQAM
- Makarenkov, V., Kevorkov, D., Zentilli, P., Gagarin, A., Malo, N. et Nadon, R. (2006). HTS-Corrector: Software for the statistical analysis and correction of experimental high-throughput screening data. Bioinformatics, 22(11), 1408–1409. http://dx.doi.org/10.1093/bioinformatics/btl126.
- Gagarin, A., Makarenkov, V. et Zentilli, P. (2006). Using clustering techniques to improve hit selection in high-throughput screening. Journal of Biomolecular Screening, 11(8), 903–914. http://dx.doi.org/10.1177/1087057106293590.
- Kevorkov, D. et Makarenkov, V. (2005). Statistical analysis of systematic errors in high-throughput screening. Journal of Biomolecular Screening, 10(6), 557–567. http://dx.doi.org/10.1177/1087057105276989.
- Makarenkov, V. et Lapointe, F.-J. (2004). A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. Bioinformatics, 20(13), 2113–2121. http://dx.doi.org/10.1093/bioinformatics/bth211.
- Makarenkov, V. et Legendre, P. (2004). From a phylogenetic tree to a reticulated network. Journal of Computational Biology, 11(1), 195–212. http://dx.doi.org/10.1089/106652704773416966.
- Makarenkov, V., Legendre, P. et Desdevises, Y. (2004). Modelling phylogenetic relationships using reticulated networks. Zoologica Scripta, 33(1), 89–96. http://dx.doi.org/10.1111/j.1463-6409.2004.00141.x.
- Guénoche, A., Leclerc, B. et Makarenkov, V. (2004). On the extension of a partial metric to a tree metric. Discrete Mathematics, 276(1-3), 229–248. http://dx.doi.org/10.1016/S0012-365X(03)00294-2.
- Levasseur, C., Landry, P.-A., Makarenkov, V., Kirsch, J.A.W. et Lapointe, F.-J. (2003). Incomplete distance matrices, supertrees and bat phylogeny. Molecular Phylogenetics and Evolution, 27(2), 239–246. http://dx.doi.org/10.1016/S1055-7903(02)00415-3.
- Boc, A. et Makarenkov, V. (2003). New efficient algorithm for detection of horizontal gene transfer events. Lecture Notes in Computer Science, 2812, 190–201. Obtenir "New efficient algorithm for detection of horizontal gene transfer events" aux bibliothèques de l'UQAM
- Makarenkov, V. et Legendre, P. (2002). Nonlinear redundancy analysis and canonical correspondence analysis based on polynomial regression. Ecology, 83(4), 1146–1161. Obtenir "Nonlinear redundancy analysis and canonical correspondence analysis based on polynomial regression" aux bibliothèques de l'UQAM
- Legendre, P. et Makarenkov, V. (2002). Reconstruction of biogeographic and evolutionary networks using reticulograms. Systematic Biology, 51(2), 199–216. http://dx.doi.org/10.1080/10635150252899725.
- Makarenkov, V. et Legendre, P. (2001). Optimal variable weighting for ultrametric and additive trees and K-means partitioning: Methods and software. Journal of Classification, 18(2), 245–271. Obtenir "Optimal variable weighting for ultrametric and additive trees and K-means partitioning: Methods and software" aux bibliothèques de l'UQAM
- Makarenkov, V. (2001). T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics, 17(7), 664–668. Obtenir "T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks" aux bibliothèques de l'UQAM
- Makarenkov, V. et Leclerc, B. (2000). Comparison of additive trees using circular orders. Journal of Computational Biology, 7(5), 731–744. http://dx.doi.org/10.1089/106652701446170.
- Guénoche, A., Leclerc, B. et Makarenkov, V. (2000). Generalized trees related with tree metrics. Electronic Notes in Discrete Mathematics, 5, 1–3. Obtenir "Generalized trees related with tree metrics" aux bibliothèques de l'UQAM
- Makarenkov, V. et Leclerc, B. (1999). An algorithm for the fitting of a tree metric according to a weighted least-squares criterion. Journal of Classification, 16(1), 3–26. Obtenir "An algorithm for the fitting of a tree metric according to a weighted least-squares criterion" aux bibliothèques de l'UQAM
- Leclerc, B. et Makarenkov, V. (1998). On some relations between 2-trees and tree metrics. Discrete Mathematics, 192(1-3), 223–249. Obtenir "On some relations between 2-trees and tree metrics" aux bibliothèques de l'UQAM