Circular orders of tree metrics, and their uses for the reconstruction and fitting of phylogenetic trees. - Vladimir Makarenkov; Bruno Leclerc (Mathematical Hierarchies and Biology, 1996)

On some relations between 2-trees and tree metrics. - Bruno Leclerc; Vladimir Makarenkov (Discret. Math., 1998)

Generalized trees related with tree metrics. - Alain Guénoche; Bruno Leclerc; Vladimir Makarenkov (Electron. Notes Discret. Math., 2000)

Comparison of Additive Trees Using Circular Orders. - Vladimir Makarenkov; Bruno Leclerc (J. Comput. Biol., 2000)

T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. - Vladimir Makarenkov (Bioinform., 2001)

Optimal Variable Weighting for Ultrametric and Additive Trees and K -means Partitioning: Methods and Software. - Vladimir Makarenkov; Pierre Legendre (J. Classif., 2001)

New Efficient Algorithm for Detection of Horizontal Gene Transfer Events. - Alix Boc; Vladimir Makarenkov (WABI, 2003)

A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. - Vladimir Makarenkov; François-Joseph Lapointe (Bioinform., 2004)

On the extension of a partial metric to a tree metric. - Alain Guénoche; Bruno Leclerc; Vladimir Makarenkov (Discret. Math., 2004)

From a Phylogenetic Tree to a Reticulated Network. - Vladimir Makarenkov; Pierre Legendre (J. Comput. Biol., 2004)

Finding Maximum Likelihood Indel Scenarios. - Abdoulaye Baniré Diallo; Vladimir Makarenkov; Mathieu Blanchette (Comparative Genomics, 2006)

HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data. - Vladimir Makarenkov; Dmytro Kevorkov; Pablo Zentilli; Andrei V. Gagarin; Nathalie Malo; Robert Nadon (Bioinform., 2006)

A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model. - Abdoulaye Baniré Diallo; Vladimir Makarenkov; Mathieu Blanchette; François-Joseph Lapointe (Data Science and Classification, 2006)

Comparison of Two Methods for Detecting and Correcting Systematic Error in High-throughput Screening Data. - Andrei Gagarin; Dmytro Kevorkov; Vladimir Makarenkov; Pablo Zentilli (Data Science and Classification, 2006)

New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios. - Vladimir Makarenkov; Alix Boc; Charles F. Delwiche; Alpha Boubacar Diallo; Hervé Philippe (Data Science and Classification, 2006)

An efficient method for the detection and elimination of systematic error in high-throughput screening. - Vladimir Makarenkov; Pablo Zentilli; Dmytro Kevorkov; Andrei V. Gagarin; Nathalie Malo; Robert Nadon (Bioinform., 2007)

Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. - Abdoulaye Baniré Diallo; Vladimir Makarenkov; Mathieu Blanchette (J. Comput. Biol., 2007)

An Evolutionary Study of the Human Papillomavirus Genomes. - Dunarel Badescu; Abdoulaye Baniré Diallo; Mathieu Blanchette; Vladimir Makarenkov (RECOMB-CG, 2008)

A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. - Abdoulaye Baniré Diallo; Dunarel Badescu; Mathieu Blanchette; Vladimir Makarenkov (J. Comput. Biol., 2009)

Using Unsupervised Machine Learning Methods in High-Throughput Screening. - Chérif Mballo; Vladimir Makarenkov (DMIN, 2010)

Ancestors 1.0: a web server for ancestral sequence reconstruction. - Abdoulaye Baniré Diallo; Vladimir Makarenkov; Mathieu Blanchette (Bioinform., 2010)

Fast Mining of Iceberg Lattices: A Modular Approach Using Generators. - Laszlo Szathmary; Petko Valtchev; Amedeo Napoli; Robert Godin; Alix Boc; Vladimir Makarenkov (CLA, 2011)

Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index. - Dunarel Badescu; Alix Boc; Abdoulaye Baniré Diallo; Vladimir Makarenkov (BMC Bioinform., 2011)

Systematic error detection in experimental high-throughput screening. - Plamen Dragiev; Robert Nadon; Vladimir Makarenkov (BMC Bioinform., 2011)

Two effective methods for correcting experimental high-throughput screening data. - Plamen Dragiev; Robert Nadon; Vladimir Makarenkov (Bioinform., 2012)

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. - Alix Boc; Alpha Boubacar Diallo; Vladimir Makarenkov (Nucleic Acids Res., 2012)

Effect of Hundreds Sequenced Genomes on the Classification of Human Papillomaviruses. - Bruno Daigle; Vladimir Makarenkov; Abdoulaye Baniré Diallo (ECDA, 2013)

An Efficient Algorithm for the Detection and Classification of Horizontal Gene Transfer Events and Identification of Mosaic Genes. - Alix Boc; Pierre Legendre; Vladimir Makarenkov (Algorithms from and for Nature and Life, 2013)

A New Effective Method for Elimination of Systematic Error in Experimental High-Throughput Screening. - Vladimir Makarenkov; Plamen Dragiev; Robert Nadon (Algorithms from and for Nature and Life, 2013)

A fast compound algorithm for mining generators, closed itemsets, and computing links between equivalence classes. - Laszlo Szathmary; Petko Valtchev; Amedeo Napoli; Robert Godin; Alix Boc; Vladimir Makarenkov (Ann. Math. Artif. Intell., 2014)

A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. - Matthieu Willems; Nadia Tahiri; Vladimir Makarenkov (J. Bioinform. Comput. Biol., 2014)

Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions. - Iurie Caraus; Abdulaziz A. Alsuwailem; Robert Nadon; Vladimir Makarenkov (Briefings Bioinform., 2015)

Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms. - Etienne Lord; Abdoulaye Baniré Diallo; Vladimir Makarenkov (BMC Bioinform., 2015)

Applying subclustering and Lp distance in Weighted K-Means with distributed centroids. - Renato Cordeiro de Amorim; Vladimir Makarenkov (Neurocomputing, 2016)

A-Wardpβ: Effective hierarchical clustering using the Minkowski metric and a fast k-means initialisation. - Renato Cordeiro de Amorim; Vladimir Makarenkov; Boris G. Mirkin (Inf. Sci., 2016)

Detecting and removing multiplicative spatial bias in high-throughput screening technologies. - Iurie Caraus; Bogdan Mazoure; Robert Nadon; Vladimir Makarenkov (Bioinform., 2017)

Using the stability of objects to determine the number of clusters in datasets. - Etienne Lord; Matthieu Willems; François-Joseph Lapointe; Vladimir Makarenkov (Inf. Sci., 2017)

The Minkowski central partition as a pointer to a suitable distance exponent and consensus partitioning. - Renato Cordeiro de Amorim; Andrei Shestakov; Boris G. Mirkin; Vladimir Makarenkov (Pattern Recognit., 2017)

An Efficient Electric Vehicle Path-Planner That Considers the Waiting Time. - Jaël Champagne Gareau; Éric Beaudry; Vladimir Makarenkov (SIGSPATIAL/GIS, 2019)

An intelligent shopping list based on the application of partitioning and machine learning algorithms. - Nadia Tahiri; Bogdan Mazoure; Vladimir Makarenkov (SciPy, 2019)

NE-nu-SVC: A New Nested Ensemble Clinical Decision Support System for Effective Diagnosis of Coronary Artery Disease. - Moloud Abdar; U. Rajendra Acharya; Nizal Sarrafzadegan; Vladimir Makarenkov (IEEE Access, 2019)

A Hybrid Latent Space Data Fusion Method for Multimodal Emotion Recognition. - Shahla Nemati; Reza Rohani; Mohammad Ehsan Basiri; Moloud Abdar; Neil Y. Yen; Vladimir Makarenkov (IEEE Access, 2019)

A new machine learning technique for an accurate diagnosis of coronary artery disease. - Moloud Abdar; Wojciech Ksiazek; U. Rajendra Acharya; Ru-San Tan; Vladimir Makarenkov; Pawel Plawiak (Comput. Methods Programs Biomed., 2019)

IAPSO-AIRS: A novel improved machine learning-based system for wart disease treatment. - Moloud Abdar; Vivi Nur Wijayaningrum; Sadiq Hussain; Roohallah Alizadehsani; Pawel Plawiak; U. Rajendra Acharya; Vladimir Makarenkov (J. Medical Syst., 2019)

VecHGrad for Solving Accurately Tensor Decomposition. - Jérémy Charlier; Vladimir Makarenkov (Canadian AI, 2020)

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks. - Henry Xing; Steven W. Kembel; Vladimir Makarenkov (Bioinform., 2020)

Core Clustering as a Tool for Tackling Noise in Cluster Labels. - Renato Cordeiro de Amorim; Vladimir Makarenkov; Boris G. Mirkin (J. Classif., 2020)

Provably efficient reconstruction of policy networks. - Bogdan Mazoure; Thang Doan; Tianyu Li; Vladimir Makarenkov; Joelle Pineau; Doina Precup; Guillaume Rabusseau (CoRR, 2020)

XtracTree for Regulator Validation of Bagging Methods Used in Retail Banking. - Jérémy Charlier; Vladimir Makarenkov (CoRR, 2020)

DGHNL: A new deep genetic hierarchical network of learners for prediction of credit scoring. - Pawel Plawiak; Moloud Abdar; Joanna Plawiak; Vladimir Makarenkov; U. Rajendra Acharya (Inf. Sci., 2020)

Fast and Optimal Planner for the Discrete Grid-Based Coverage Path-Planning Problem. - Jaël Champagne Gareau; Éric Beaudry; Vladimir Makarenkov (IDEAL, 2021)

Improving cluster recovery with feature rescaling factors. - Renato Cordeiro de Amorim; Vladimir Makarenkov (Appl. Intell., 2021)

Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing. - Jérémy Charlier; Robert Nadon; Vladimir Makarenkov (Bioinform., 2021)

Uncertainty quantification in skin cancer classification using three-way decision-based Bayesian deep learning. - Moloud Abdar; Maryam Samami; Sajjad Dehghani Mahmoodabad; Thang Doan; Bogdan Mazoure; Reza Hashemifesharaki; Li Liu 002; Abbas Khosravi; U. Rajendra Acharya; Vladimir Makarenkov; Saeid Nahavandi (Comput. Biol. Medicine, 2021)

A review of uncertainty quantification in deep learning: Techniques, applications and challenges. - Moloud Abdar; Farhad Pourpanah; Sadiq Hussain; Dana Rezazadegan; Li Liu 002; Mohammad Ghavamzadeh; Paul W. Fieguth; Xiaochun Cao; Abbas Khosravi; U. Rajendra Acharya; Vladimir Makarenkov; Saeid Nahavandi (Inf. Fusion, 2021)

Automated detection of shockable ECG signals: A review. - Mohamed Hammad; Kandala N. V. P. S. Rajesh; Amira Abdelatey; Moloud Abdar; Mariam Zomorodi Moghadam; Ru-San Tan; U. Rajendra Acharya; Joanna Plawiak; Ryszard Tadeusiewicz; Vladimir Makarenkov; Nizal Sarrafzadegan; Abbas Khosravi; et al. (Inf. Sci., 2021)

Object Weighting: A New Clustering Approach to Deal with Outliers and Cluster Overlap in Computational Biology. - Alexandre Gondeau; Zahia Aouabed; Mohamed Hijri; Pedro R. Peres-Neto; Vladimir Makarenkov (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Cache-Efficient Memory Representation of Markov Decision Processes. - Jaël Champagne Gareau; Éric Beaudry; Vladimir Makarenkov (Canadian AI, 2022)

SimPlot++: a Python application for representing sequence similarity and detecting recombination. - Stéphane Samson; Etienne Lord; Vladimir Makarenkov (Bioinform., 2022)

Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance. - Nadia Tahiri; Bernard Fichet; Vladimir Makarenkov (Bioinform., 2022)

Fast and optimal branch-and-bound planner for the grid-based coverage path planning problem based on an admissible heuristic function. - Jaël Champagne Gareau; Éric Beaudry; Vladimir Makarenkov (Frontiers Robotics AI, 2022)

Low-Rank Representation of Reinforcement Learning Policies. - Bogdan Mazoure; Thang Doan; Tianyu Li; Vladimir Makarenkov; Joelle Pineau; Doina Precup; Guillaume Rabusseau (J. Artif. Intell. Res., 2022)

Cache-Efficient Dynamic Programming MDP Solver. - Jaël Champagne Gareau; Guillaume Gosset; Éric Beaudry; Vladimir Makarenkov (ECAI, 2023)

Inferring multiple consensus trees and supertrees using clustering: a review. - Vladimir Makarenkov; Gayane S. Barseghyan; Nadia Tahiri (CoRR, 2023)

UncertaintyFuseNet: Robust uncertainty-aware hierarchical feature fusion model with Ensemble Monte Carlo Dropout for COVID-19 detection. - Moloud Abdar; Soorena Salari; Sina Qahremani; Hak-Keung Lam; Fakhri Karray; Sadiq Hussain; Abbas Khosravi; U. Rajendra Acharya; Vladimir Makarenkov; Saeid Nahavandi (Inf. Fusion, 2023)

Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review. - Zeinab Sherkatghanad; Moloud Abdar; Jérémy Charlier; Vladimir Makarenkov (Briefings Bioinform., 2023)

Binarized multi-gate mixture of Bayesian experts for cardiac syndrome X diagnosis: A clinician-in-the-loop scenario with a belief-uncertainty fusion paradigm. - Moloud Abdar; Arash Mehrzadi; Milad Goudarzi; Farzad Masoudkabir; Leonardo Rundo; Mohammad Mamouei; Evis Sala; Abbas Khosravi; Vladimir Makarenkov; U. Rajendra Acharya; Seyedmohammad Saadatagah; Mohammadreza Naderian; et al. (Inf. Fusion, 2023)

On k-means iterations and Gaussian clusters. - Renato Cordeiro de Amorim; Vladimir Makarenkov (Neurocomputing, 2023)

Inertia-Based Indices to Determine the Number of Clusters in K-Means: An Experimental Evaluation. - Andrei Rykov; Renato Cordeiro de Amorim; Vladimir Makarenkov; Boris G. Mirkin (IEEE Access, 2024)

BayTTA: Uncertainty-aware medical image classification with optimized test-time augmentation using Bayesian model averaging. - Zeinab Sherkatghanad; Moloud Abdar; Mohammadreza Bakhtyari; Vladimir Makarenkov (CoRR, 2024)

BayTTA: Uncertainty-aware medical image classification with optimized test-time augmentation using Bayesian model averaging. - Zeinab Sherkatghanad; Moloud Abdar; Mohammadreza Bakhtyari; Pawel Plawiak; Vladimir Makarenkov (Knowl. Based Syst., 2025)

Improving clustering quality evaluation in noisy Gaussian mixtures. - Renato Cordeiro de Amorim; Vladimir Makarenkov (CoRR, 2025)