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Publications

2017

  • Ahmed Halioui, Petko Valtchev and Abdoulaye Banire Diallo. Ontology-based workflow extraction from texts using word sense disambiguation. Accepted at International Workshop on Data Mining in Bioinformatics (BIOKDD'17)

  • Ahmed Halioui, Petko Valtchev and Abdoulaye Banire Diallo. T-GOWler: Discovering Generalized Process Models within Texts. Accepted at Journal of Computational Biology.

  • Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Banire Diallo. A machine learning approach for viral genome classification. BMC Bioinformatics 18:208 [article]

  • Ahmed Halioui, Tomas Martin, Petko Valtchev and Abdoulaye Banire Diallo. Ontology-powered pattern mining : discovery of frequent abstract workflows in phylogeny. At The 32nd ACM Symposium on Applied Computing, Marrakesh, Morocco. 2017 [article]

2016

  • Dhifli Wajdi and Abdoulaye Baniré Diallo. Face Recognition in the Wild. Procedia Computer Science 96:1571-1580 (Proceeding of 20th International Conferenceon Knowledge Based and Intelligent Information and EngineeringSystems, KES2016, 5-7 September 2016, York, United Kingdom) [article]

  • Mickael Leclercq, Abdoulaye Baniré Diallo and Mathieu Blanchette. Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences. Nucleic Acids Research, gkw1085. [article]

  • Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A. Badawi, Fathey Sarhan and Abdoulaye Baniré Diallo. A novel comprehensive wheat miRNA database, including related bioinformatics software. Current Plant Biology. [http://dx.doi.org/10.1016/j.cpb.2016.10.003]

  • Ahmed Halioui, Petko Valtchev and Abdoulaye Banire Diallo. Ontology-based workflow extraction from texts using word sense disambiguation. bioRxiv [article]

  • Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Banire Diallo. CASTOR: A machine learning platform for reproducible viral genome classification. bioRxiv. [https://doi.org/10.1101/082768]

  • Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Banire Diallo. CASTOR: A machine learning approach for generic viral genome classification. Poster at the 14th RECOMB Comparative Genomics Satellite Workshop, Montreal 2016. [https://doi.org/10.13140/RG.2.2.15979.34080]

  • Golrokh Kiani, Mohamed Amine Remita and Abdoulaye Banire Diallo. In silico approach to identify evolutionary breakpoints and their associations with cancer rearrangements on human genome. Poster at the 14th RECOMB Comparative Genomics Satellite Workshop, Montreal 2016.

  • Dhifli Wajdi and Abdoulaye Baniré Diallo. ProtNN: Fast and accurate protein 3D-structure classification in structural and topological space. BioData Mining, 9(1), 30. [article]

  • Dhifli Wajdi and Abdoulaye Baniré Diallo. Toward an Efficient Multi-class Classification in an Open Universe at the 12th International Conference on Machine Learning and Data Mining (MLDM 2016), At NY city, NY, USA [article]

2015

  • Ahmed Halioui, Petko Valtchev and Abdoulaye Banire Diallo. Acquisition of generic problem solving knowledge through information extraction and pattern mining. in ICTAI 27th IEEE International Conference on Tools with Artificial Intelligence, November 9-11, 2015, Vietri Sul mare, Italy. [article]

  • Dhifli Wajdi and Abdoulaye Baniré Diallo. PGR: A Novel Graph Repository of Protein 3D-Structures. J Data Mining Genomics Proteomics 6: 172. doi:10.4172/2153-0602.1000172 [article]

  • Ahmed Halioui, Petko Valtchev and Abdoulaye Banire Diallo. Workflow Mining : Discovering Generalized Process Models from Texts. in IJCAI Workshop BAI: Advances in Bioinformatics and Artificial Intelligence: Bridging the gap, 27 July, 2015, Buenos Aires, Argentina. [article]

  • Bruno Daigle, Vladimir Makarenkov and Abdoulaye Baniré Diallo. Effect of Hundreds Sequenced Genomes on the Classification of Human Papillomaviruses. In Data Science, Learning by Latent Structures, and Knowledge Discovery (pp. 309-318). Springer Berlin Heidelberg.  [article]

  • Agharbaoui Z., Leclercq M., Remita M.A., Badawi M., Lord E., Houde M., Danyluk J., Diallo AB. and Sarhan, F. An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. BMC genomics 16.1): 339.  [article]

  • Etienne Lord, Abdoulaye Baniré Diallo and Vladimir Makarenkov. Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms. BMC Bioinformatics, 16(1), 68. [pdf]

  • Wajdi Dhifli and Abdoulaye Baniré Diallo. Galaxy-X: A Novel Approach for Multi-class Classification in an Open Universe arXiv. [article]

  • Bruno Daigle, Mohamed Amine Remita and Abdoulaye Baniré Diallo. Une approche de discrimination des virus du papillome humain selon le pouvoir pathogène à partir de l’analyse des caractéristiques protéiques At XXII èmes rencontres de la Société Francophone de Classification, At Nantes, France. [article]

  • Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A. Badawi, Vladimir Makarenkov, Fathey Sarhan and Abdoulaye Baniré Diallo. WMP: A novel comprehensive wheat miRNA database, including related bioinformatics software. bioRxiv. [article]

  • Mohamed Amine Remita, Ahmed Halioui and Abdoulaye Baniré Diallo. Automated Classification of Viral Genomes based on Restriction Site Distribution. ISCB Africa ASBCB Conference on Bioinformatics 2015 Dar es Salaam

2014

  • Remita M.A., Halioui A. and Diallo A.B. Supervised Classification of Viral Genomes based on Restriction Site Distribution. 2014. European Conference on Data Analysis (ECDA) Bremen, Germany

2013

  • Leclercq, M., Diallo, A. B., and Blanchette, M. Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic acids research, 41(15), 7200-7211. [pdf]

  • Remita M.A., Halioui A. and Diallo A.B. Automatic annotation and classification of new papillomavirus genomes. International Federation of Classification Societies (IFCS) Tilburg, Netherlands

  • Lord E., Diallo A.B., and Makarenkov V. Workflow Classification Based On The K-Means Partitioning. International Federation of Classification Societies (IFCS) Tilburg, Netherlands

2012

  • Lord, E., Leclercq, M., Boc, A., Diallo, A.B., & Makarenkov, V. Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations. PLoS ONE 7(1): e29903. doi: 10.1371/journal.pone.0029903 [article]

  • Diallo, A.B., Agharbaoui, Z., Leclercq, M., Remita, M.A., Fahimiya, S., Badawi, M., Houde, M. et Sarhan, F. Large scale identification of microRNAs associated with stress responses and development in hexaploid wheat ESTs, RECOMB SB/RG/DREAM 2012. [poster]

  • Leclercq, M. et Diallo, A.B. Évaluation et sélection d'attributs utilisés pour la classification des microARNs chez les organismes vivants. Actes de la Société Francophone de Classification, Marseilles France. 5 pages.

  • Agharbaoui, Z., Leclercq, M., Remita, M.A., Houde, M., Sarhan, F. et Diallo, A.B. Large scale identification of diffentially expressed microARNs in abiotic stress response. BIOCOMP 2012, Varna, Bulgaria.

  • Ransy, D.G., Lord, E., Motorina, A., Merindol, N., Akouamba, B.S., Samson, J., Lapointe, N., Boucher, M., Diallo, A.B. et Hugo Soudeyns. Analysis of selective pressures exerted on the envelope gene in pregnant women infected with HIV-1. Canadian Conference on HIV/AIDS Research 2012, Montreal, Canada.

  • Halioui, A., Valtchev, V. et Diallo, A.B. Un systàme de recommandation phylogénétique basé sur un modàle de le flux de données. Colloque d'Informatique Cognitive IC2012, Montréal, Québec, Canada.


2011

  • Horvath, J., Sheedy, C. Merrett, S, Diallo, A.B., Swofford, D., NISC, Green, E.D. et Willard, H (2011): Comparative analysis of the primate X inactivation Center Region and Reconstruction of the Ancestral Primate XIST Locus. Genome Research, 21(6):850-862. [article]

  • Sadri, J., Diallo, A.B. et Blanchette, M. (2011) : Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics, 27(13):i266-i274.[article]

  • 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) doi:10.1186/1471-2105-12-S9-S9. [article]

  • Boc, A., Badescu, D., Diallo, A.B. et Makarenkov, V. (2011) : An efficient algorithm for the detection and classification of horizontal gene transfer events and identification of mosaic genes. Actes de la rencontre de l’International Federation of Classification Societies 2011. Francfurt, Allemagne.


2010

  • Diallo, A.B., Blanchette, M. et Makarenkov, V. (2010): Ancestors 1.0: A web server for ancestral Genome reconstruction. Bioinformatics, 26(1), 130-131.

  • Badescu, D., Diallo, A.B., Makarenkov, V. et Blanchette, M. (2010) Identification of specific genomic regions responsible of the invasivity of Neisseria meningitidis. Actes de l’International Federation of Classification Societies 2009, Dresden, Germany, Springer-verlag, 491–507.

  • Diallo, A.B., Valtchev, P. et Makarenkov, V. (2010) Une approche efficace d'identification et de catégorisation de nouveaux motifs d’évolution dans la famille de mammifàre. Actes de la Société Francophone de classification, Réunion, 2010, 30-33.

  • Agharbaoui, Z., Leclercq, M., Houde, M., Diallo, A.B. et Sarhan, F. (2010) : Genomic scale identification of microRNAs associated with stress responses and development in wheat. Plant Biology 2010, Montréal, Canada.

  • Lord, E., Leclercq, M., Boc, A. Makarenkov, V. et Diallo, A.B. (2010) : Armadillo, a simple approach of automating comparative genomics tasks using workflows. Research in Computational Biology-Comparative Genomics 2010, Ottawa, Canada.

  • Leclercq, M., Agharbaoui, Z., Houde, M., Sarhan, F. et Diallo, A.B. (2010): Large scale identification of microRNAs associated with stress response and development in wheat. Research in Computational Biology-Comparative Genomics 2010, Ottawa, Canada.

  • Diallo, A.B. (2010): A Generalized Hidden Markov Model for Ancestral Sequence Estimation and Multiple sequence alignment Refinement Research in Comptutational Biology 2010, Lisboa, Portugal.

  • Diallo, A.B., David, L., Rasmussen, M., Kellis, M. et Alm, E.J. (2010): Maximum Likelihood method for gene tree reconstruction and recon- ciliation to a known species tree in the presence of duplication, loss and Horizontal gene transfer. Research in Comptutational Biology 2010, Lisboa, Portugal.


2009

  • Diallo, A.B., Makarenkov, V. et Blanchette, M. (2009): A web server for ancestral sequence reconstruction. Research in Comptutational Biology 2009, Tucson, Arizona.

  • 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), 1461-73.


2008

  • Diallo, A.B., Badescu, D., Makarenkov, V. et Blanchette, M. (2008): An Evolutionary study of the Human Papilloma Viruses. Research in Computational Biology-Comparative Genomics (Recomb-CG). LNBI 5267, 128–140.

  • Diallo, A.B., Badescu, D., Makarenkov, V. et Blanchette, M. (2008) : Phylogeny of the Human Papilloma Viruses and Carcinome classification. Actes du premier meeting conjoint du Classification and Data analysis Group et de la Société Francophone de Classification, Caserta, Italie, 285-288.

  • Makarenkov, V., Boc, A., Diallo Al. Bo. et Diallo Ab. Ba∗. (2008): Algorithms for detecting complete and partial horizontal gene transfers: Theory and practice, dans Data Mining and Math. Program. ,P.M. Pardalos and P. Hansen eds., CRM Proc. and AMS Lecture Notes, 45, 159-179.


2007

  • Blanchette, M., Diallo, A. B., Green, E. D., Miller, W. et Haussler, D. (2007): Computational reconstruction of ancestral DNA sequences. Chapter 11 of the book : Methods in Molecular Biology: Phylogenomics. Edited by W.J. Murphy, Humana Press Inc. Totowa, NJ, 171-184.

  • Nguyen, D., Boc, A., Diallo, A. B. et Makarenkov, V. (2007): Étude de la classification des bactériophages. Actes de la 13àme rencontre de la Société Francophone de Classification. 161-165.

  • DIALLO, A. B., BLANCHETTE, M. and MAKARENKOV, V. (2007) : Exact and Heuristic Method to the Indels Maximum Likelihood Problem. Journal of Computational Biology. Accepted for publication. [pdf]

  • MAKARENKOV, V., BOC, A., DIALLO, Al. Bo., DIALLO, Ab. Ba. (2007): Complete and partial horizontal gene transfer: theory and practice. Proceeding of the workshop of: "Exploration de données et programmation mathématique". Centre de Recherche en Mathématiques de Montréal.

2006


  • DIALLO, A. B., MAKARENKOV, V. and LAPOINTE, F.-J. (2006): A new effective method for estimation of missing values in the sequence data prior to phylogenetic analysis. Evolutionary Bioinformatics Online. 2, 127-135.[pdf]

  • DIALLO, A. B., BLANCHETTE, M. and MAKARENKOV, V. (2006) : Finding Maximum Likelihood Indel Scenarios. Comparative Genomics, Lecture Notes in Computer Science, 4205, Springer, 171-185.[pdf]

  • BLANCHETTE, M., DIALLO, A. B., GREEN, E. D., MILLER, W. and HAUSSLER, D. (2006): Computational reconstruction of ancestral DNA sequences. Chapitre 11 of the book Phylogenomics and comparative genomics. Humana Press. 36 pages.

  • DIALLO, A. B., MAKARENKOV, V., BLANCHETTE, M. and LAPOINTE, F.-J. (2006): A new efficient method for assessing missing nucleotides in DNA sequences in the framework of a generic evolutionary model. proceedings of the meeting of the International Federation of Classification Societies 2006. eds Batagelj, V., Bock, H.H., Ferligoj, A., Ziberna, A., Springer-Verlag, Data Science and Classification, Ljublijana, 333-340. [pdf]

  • DIALLO, A. B., BLANCHETTE, M. and MAKARENKOV, V. (2006) : Problems of the representation of ancestral genome reconstruction. First Barbados workshop in paleogenomics. Barbados 2006.

  • DIALLO, A. B., BLANCHETTE, M. and MAKARENKOV, V. (2006) : Inferring the most likely indel evolutionary scenarios. Phylogenomics conference, Montréal 2006.

  • MONGIN, E., DIALLO, A.B., DEWAR, K., BLANCHETTE, M. (2006): Transcription factor binding site co-occurrence within mammalian regulatory modules. Cold Spring Harbor meeting, Genome Informatics, september 2006.

  • DIALLO, A. B., MAKARENKOV, V., BLANCHETTE, M. and LAPOINTE, F.-J. (2006): A new efficient method for the estimation of missing values in sequence data prior to phylogenetic analysis. Phylogenomics Conference, Saint Adèle, march 2006

2005


  • DIALLO, Ab. Ba., DIALLO, Al. Bo. and MAKARENKOV, V. (2005): Une nouvelle méthode efficace pour l'estimation des donné manquantes en vue de l'infé phylogénétique. Proceeding of the 12th meeting of Société Francophone de Classification. Montréal 2006. [pdf]

2004


  • MAKARENKOV, V., BOC, A. and DIALLO, A. B. (2004): Representing Lateral gene transfer in species classification. Unique scenario, proceedings of the meeting of the International Federation of Classification Societies 2004, eds Banks, D., House, L., McMorris, F.R., Arabie, P., Gaul, W., Springer-Verlag, Classification, Clustering, and Data Mining Applications, Chicago, 439-447. [pdf]

  • DIALLO, A. B., MAKARENKOV, V., BOC, A. et LAPOINTE, F.J. (2004) : Une nouvelle méthode efficace pour l'estimation des données manquantes dans les séquences de nucléotides avant la reconstruction phylogénétique. Actes du colloque des 5ème Journées Ouvertes de Bioinformatique et Mathématiques, Montréal, Canada, 2004. [pdf]

  • BOC, A., MAKARENKOV, V. and DIALLO, A. B. (2004) : Une nouvelle méthode pour la détection de transferts horizontaux de gène: la réconciliation topologique d'arbres de gène et d'espèces. Actes du colloque des 5ème Journées Ouvertes de Bioinformatique et Mathématiques, Montréal, Canada, 2004. [pdf]


2003


  • BOC, A., DIALLO, A. B. and MAKARENKOV, V. (2003) : Comment détecter le transfert latéral de gènes dans la classification d'espèces. proceeding of the 12th meeting of la Société Francophone de Classification. Neuchatel Switzerland, 75-78.


  • BOC, A., DIALLO, A. B. and MAKARENKOV, V. (2003): New algorithm for improving reticulated networks. Currents in Computational Molecular Biology, eds. Spang R., Béziat P., Vingron M., Poster, Research in Computational Molecular Biology, Berlin, Germany, 143-144. [pdf]

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